diff --git a/.gitignore b/.gitignore index cb914e644..7d12e1766 100644 --- a/.gitignore +++ b/.gitignore @@ -87,6 +87,7 @@ ipython_config.py # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839 # User-specific stuff +.idea/**/*.iml .idea/**/workspace.xml .idea/**/tasks.xml .idea/**/usage.statistics.xml @@ -114,14 +115,15 @@ ipython_config.py # When using Gradle or Maven with auto-import, you should exclude module files, # since they will be recreated, and may cause churn. Uncomment if using # auto-import. -# .idea/artifacts -# .idea/compiler.xml -# .idea/jarRepositories.xml -# .idea/modules.xml -# .idea/*.iml -# .idea/modules -# *.iml -# *.ipr + .idea/artifacts + .idea/compiler.xml + .idea/jarRepositories.xml + .idea/modules.xml + .idea/*.iml + .idea/*.xml + .idea/modules + *.iml + *.ipr # CMake cmake-build-*/ @@ -303,3 +305,5 @@ gurobi.log /documentation_builder/test*\.* /.benchmarks /.testmondata +/.idea/sonarlint/ +/.idea/sonarlint/issuestore/ diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml new file mode 100644 index 000000000..74459b697 --- /dev/null +++ b/.idea/inspectionProfiles/Project_Default.xml @@ -0,0 +1,13 @@ + + + + \ No newline at end of file diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml new file mode 100644 index 000000000..105ce2da2 --- /dev/null +++ b/.idea/inspectionProfiles/profiles_settings.xml @@ -0,0 +1,6 @@ + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 000000000..60adcbf46 --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,10 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 000000000..c8e807676 --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 000000000..94a25f7f4 --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/documentation_builder/getting_started.ipynb b/documentation_builder/getting_started.ipynb index 9f2be895b..6663a80cf 100644 --- a/documentation_builder/getting_started.ipynb +++ b/documentation_builder/getting_started.ipynb @@ -40,7 +40,7 @@ "import cobra\n", "from cobra.io import load_model\n", "\n", - "# \"iJO1366\" and \"salmonella\" are also valid arguments\n", + "# \"iJO1366\" and \"iYS1720\" are also valid arguments\n", "model = load_model(\"textbook\")" ] }, diff --git a/documentation_builder/loopless.ipynb b/documentation_builder/loopless.ipynb index 98af41600..86b82b432 100644 --- a/documentation_builder/loopless.ipynb +++ b/documentation_builder/loopless.ipynb @@ -13014,7 +13014,7 @@ } ], "source": [ - "salmonella = load_model('salmonella')\n", + "salmonella = load_model('iYS1720')\n", "nominal = salmonella.optimize()\n", "loopless = loopless_solution(salmonella)" ] diff --git a/documentation_builder/metadata.ipynb b/documentation_builder/metadata.ipynb new file mode 100644 index 000000000..2889f41c4 --- /dev/null +++ b/documentation_builder/metadata.ipynb @@ -0,0 +1,548 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.0" + }, + "colab": { + "name": "metadata.ipynb", + "provenance": [] + } + }, + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "bVgYSbcPLbwU", + "colab_type": "text" + }, + "source": [ + "# Metadata\n", + "\n", + "Metadata in the form of annotations, provenance or additional key:value pairs is an important asset for a model.\n", + "Such data can be handled via the `annotation` field on cobra objects" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "Rv-QKmAPM8PY", + "colab_type": "text", + "pycharm": { + "name": "#%% md\n" + } + }, + "source": [ + "# History\n", + "\n", + "History attribute, present in the `annotation` attribute of a COBRA component, stores the history of the component like creators, created date and modified date of that component." + ] + }, + { + "cell_type": "code", + "metadata": { + "pycharm": { + "name": "#%%\n" + }, + "id": "EsBAtYeHLbwc", + "colab_type": "code", + "colab": {} + }, + "source": [ + "from cobra.core import Metabolite\n", + "from cobra.core.metadata import History, Creator, HistoryDatetime\n", + "\n", + "metabolite = Metabolite(id=\"glc\", name=\"D-glucose\")\n" + ], + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "The dates have to be objects of `HistoryDateTime` class and creators that of `Creator` class. We can add then directly via constructor." + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "history = History(\n", + " creators=[\n", + " Creator(\n", + " first_name=\"Matthias\",\n", + " last_name=\"Koenig\",\n", + " organization_name=\"HU\",\n", + " email=\"test@test.com\",\n", + " ),\n", + " ],\n", + " created_date=HistoryDatetime(\"2020-06-26T02:34:30+05:30\"),\n", + " modified_dates=[\n", + " HistoryDatetime(\"2020-06-26T12:34:11+00:00\"),\n", + " HistoryDatetime(\"2020-06-26T00:34:11+05:30\"),\n", + " ],\n", + " )\n", + "\n", + "metabolite.annotation.history = history" + ], + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + } + }, + { + "cell_type": "markdown", + "source": [ + "Or we can also add them by making object separtely and then adding in the history object." + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "new_creator = Creator(\n", + " first_name=\"Andreas\",\n", + " last_name=\"Draeger\",\n", + " organization_name=\"University of Tübingen\",\n", + " email=\"test2@test2.com\",\n", + " )\n", + "\n", + "metabolite.annotation.history.creators.append(new_creator)\n", + "modified_hdtime = HistoryDatetime()\n", + "modified_hdtime.utcnow()\n", + "metabolite.annotation.history.modified_dates.append(modified_hdtime)" + ], + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + } + }, + { + "cell_type": "markdown", + "source": [ + "# CVTerms\n", + "\n", + "CVTerms stands for Controlled Vocabulary Terms, are is used to store the external resources which are linked with the given COBRA component. We can make CVTerm's object either by passing the data directly from the constructor. We can also define the nested data for linked resources." + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "annotation_dict = {\n", + " \"bqb_hasTaxon\": [{\"resources\": [\"http://identifiers.org/taxonomy/511145\"]}],\n", + " \"bqm_is\": [\n", + " {\n", + " \"nested_data\": {\n", + " \"bqb_isDescribedBy\": [\n", + " {\"resources\": [\"https://identifiers.org/pubmed/1111111\"]},\n", + " {\"resources\": [\"https://identifiers.org/eco/ECO:0000004\"]},\n", + " ]\n", + " },\n", + " \"resources\": [\"http://identifiers.org/bigg.model/e_coli_core\"],\n", + " }\n", + " ],\n", + "}\n", + "\n", + "cvterms = CVTerms(annotation_dict)\n", + "metabolite.annotation.cvterms = cvterms\n", + "\n" + ], + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + } + }, + { + "cell_type": "markdown", + "source": [ + "Or we can also add data by making separate `CVTerm` objects and then adding them at a particular index (indexing is done for a single qualifier for adding alternative annotation)." + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "cvterm1 = CVTerm(Qualifier.bqb_isDescribedBy, \"http://identifiers.org/doi/10.1128/ecosalplus.10.2.1\")\n", + "cvterm2 = CVTerm(Qualifier.bqb_isDescribedBy, \"http://identifiers.org/ncbigi/gi:16128336\")\n", + "\n", + "metabolite.annotation.cvterms.add_cvterm(cvterm1, 0)\n", + "metabolite.annotation.cvterms.add_cvterm(cvterm1, 1)" + ], + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + } + }, + { + "cell_type": "markdown", + "source": [ + "# KeyValuePairs\n", + "\n", + "The KeyValuePair class is used for storing any type of key-value pair data, which is not suitable to store anywhere else in the model" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + " entry1 = {\n", + " \"id\": \"id1\",\n", + " \"name\": \"abc_xyz\",\n", + " \"key\": \"key1\",\n", + " \"value\": \"45\",\n", + " \"uri\": \"https://tinyurl.com/ybyr7b62\",\n", + " }\n", + " entry2 = KeyValueEntry.from_data({\n", + " \"id\": \"id2\",\n", + " \"name\": \"abc_xyz2\",\n", + " \"key\": \"key2\",\n", + " \"value\": \"48\",\n", + " \"uri\": \"https://tinyurl2.com/ybyr7b62\",\n", + " })\n", + "\n", + " kvp = KeyValuePairs(entries=[entry1, entry2])\n", + " metabolite.annotation.keyvaluepairs = kvp" + ], + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + } + }, + { + "cell_type": "markdown", + "source": [ + "# Notes\n", + "The `notes` field under a COBRA component is used to store the notes data. Though it is not a right place to store key-value pairs, but earlier implementation has left many models where notes field have key-value pairs inside it. The current implementation contains a notes string as well as a notes dictionary, both synchronized with each other. One can only update values inside the notes dictioanry, adding new key-value pairs is restricted. Updating the dictionary will update the notes string also (only the key-value pair part). String manipulation, if required, will have to be done manually." + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "notes_str = (\n", + " '\\\n", + "\\n\\\n", + " \\n\\\n", + "
\\n\\\n", + "

Key1 : Value 1

\\n\\\n", + "

Key2 : Value2

\\n\\\n", + "
\\n\\\n", + "

A Heading

\\n\\\n", + "
e_coli_core - Escherichia coli '\n", + " \"str. K-12 substr. MG1655
\\n\\\n", + "
\\n\\\n", + "

Key3 : Value 3

\\n\\\n", + "
\\n\\\n", + " \\n\\\n", + "\"\n", + ")\n", + "\n", + "metabolite.notes = Notes(notes_str)\n", + "metabolite.notes[\"Key1\"] = \"New Value1\"" + ], + "metadata": { + "collapsed": false, + "pycharm": { + "name": "#%%\n" + } + } + }, + { + "cell_type": "markdown", + "metadata": { + "id": "11wwIBGHWM66", + "colab_type": "text" + }, + "source": [ + "notes_str = (\n", + " '\\\n", + "\\n\\\n", + " \\n\\\n", + "
\\n\\\n", + "

Key1 : Value 1

\\n\\\n", + "

Key2 : Value2

\\n\\\n", + "
\\n\\\n", + "

A Heading

\\n\\\n", + "
e_coli_core - Escherichia coli '\n", + " \"str. K-12 substr. MG1655
\\n\\\n", + "
\\n\\\n", + "

Key3 : Value 3

\\n\\\n", + "
\\n\\\n", + " \\n\\\n", + "\"\n", + ")\n", + "\n", + "metabolite.notes = Notes(notes_str)\n", + "metabolite.notes[\"Key1\"] = \"New Value1\"" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "Tmo3MUtpWn8K", + "colab_type": "code", + "colab": {} + }, + "source": [ + "history = History(\n", + " creators=[\n", + " Creator(\n", + " first_name=\"Matthias\",\n", + " last_name=\"Koenig\",\n", + " organization_name=\"HU\",\n", + " email=\"test@test.com\",\n", + " ),\n", + " ],\n", + " created_date=HistoryDatetime(\"2020-06-26T02:34:30+05:30\"),\n", + " modified_dates=[\n", + " HistoryDatetime(\"2020-06-26T12:34:11+00:00\"),\n", + " HistoryDatetime(\"2020-06-26T00:34:11+05:30\"),\n", + " ],\n", + " )\n", + "\n", + "metabolite.annotation.history = history" + ], + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "6EtjXs5FWsB2", + "colab_type": "text" + }, + "source": [ + "Or we can also add them by making object separtely and then adding in the history object." + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "9tiNKucaW1nT", + "colab_type": "code", + "colab": {} + }, + "source": [ + "new_creator = Creator(\n", + " first_name=\"Andreas\",\n", + " last_name=\"Draeger\",\n", + " organization_name=\"University of Tübingen\",\n", + " email=\"test2@test2.com\",\n", + " )\n", + "\n", + "metabolite.annotation.history.creators.append(new_creator)\n", + "modified_hdtime = HistoryDatetime()\n", + "modified_hdtime.utcnow()\n", + "metabolite.annotation.history.modified_dates.append(modified_hdtime)" + ], + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "wXst9A76PuoJ", + "colab_type": "text" + }, + "source": [ + "# CVTerms\n", + "\n", + "CVTerms stands for Controlled Vocabulary Terms, are is used to store the external resources which are linked with the given COBRA component. We can make CVTerm's object either by passing the data directly from the constructor. We can also define the nested data for linked resources." + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "whC9AASSQKnn", + "colab_type": "code", + "colab": {} + }, + "source": [ + "annotation_dict = {\n", + " \"bqb_hasTaxon\": [{\"resources\": [\"http://identifiers.org/taxonomy/511145\"]}],\n", + " \"bqm_is\": [\n", + " {\n", + " \"nested_data\": {\n", + " \"bqb_isDescribedBy\": [\n", + " {\"resources\": [\"https://identifiers.org/pubmed/1111111\"]},\n", + " {\"resources\": [\"https://identifiers.org/eco/ECO:0000004\"]},\n", + " ]\n", + " },\n", + " \"resources\": [\"http://identifiers.org/bigg.model/e_coli_core\"],\n", + " }\n", + " ],\n", + "}\n", + "\n", + "cvterms = CVTerms(annotation_dict)\n", + "metabolite.annotation.cvterms = cvterms\n", + "\n" + ], + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "-BP4wL2JXUlK", + "colab_type": "text" + }, + "source": [ + "Or we can also add data by making separate `CVTerm` objects and then adding them at a particular index (indexing is done for a single qualifier for adding alternative annotation)." + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "DEyuH1cqXoar", + "colab_type": "code", + "colab": {} + }, + "source": [ + "cvterm1 = CVTerm(Qualifier.bqb_isDescribedBy, \"http://identifiers.org/doi/10.1128/ecosalplus.10.2.1\")\n", + "cvterm2 = CVTerm(Qualifier.bqb_isDescribedBy, \"http://identifiers.org/ncbigi/gi:16128336\")\n", + "\n", + "metabolite.annotation.cvterms.add_cvterm(cvterm1, 0)\n", + "metabolite.annotation.cvterms.add_cvterm(cvterm1, 1)" + ], + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "olUCYEdwSw6k", + "colab_type": "text" + }, + "source": [ + "# KeyValuePairs\n", + "\n", + "The KeyValuePair class is used for storing any type of key-value pair data, which is not suitable to store anywhere else in the model" + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "ENKACjXES9k1", + "colab_type": "code", + "colab": {} + }, + "source": [ + " entry1 = {\n", + " \"id\": \"id1\",\n", + " \"name\": \"abc_xyz\",\n", + " \"key\": \"key1\",\n", + " \"value\": \"45\",\n", + " \"uri\": \"https://tinyurl.com/ybyr7b62\",\n", + " }\n", + " entry2 = KeyValueEntry.from_data({\n", + " \"id\": \"id2\",\n", + " \"name\": \"abc_xyz2\",\n", + " \"key\": \"key2\",\n", + " \"value\": \"48\",\n", + " \"uri\": \"https://tinyurl2.com/ybyr7b62\",\n", + " })\n", + "\n", + " kvp = KeyValuePairs(entries=[entry1, entry2])\n", + " metabolite.annotation.keyvaluepairs = kvp" + ], + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "Rl3UV44OTe4Q", + "colab_type": "text" + }, + "source": [ + "# Notes\n", + "The `notes` field under a COBRA component is used to store the notes data. Though it is not a right place to store key-value pairs, but earlier implementation has left many models where notes field have key-value pairs inside it. The current implementation contains a notes string as well as a notes dictionary, both synchronized with each other. One can only update values inside the notes dictioanry, adding new key-value pairs is restricted. Updating the dictionary will update the notes string also (only the key-value pair part). String manipulation, if required, will have to be done manually." + ] + }, + { + "cell_type": "code", + "metadata": { + "id": "psrA4ROmU4X6", + "colab_type": "code", + "colab": {} + }, + "source": [ + "notes_str = (\n", + " '\\\n", + "\\n\\\n", + " \\n\\\n", + "
\\n\\\n", + "

Key1 : Value 1

\\n\\\n", + "

Key2 : Value2

\\n\\\n", + "
\\n\\\n", + "

A Heading

\\n\\\n", + "
e_coli_core - Escherichia coli '\n", + " \"str. K-12 substr. MG1655
\\n\\\n", + "
\\n\\\n", + "

Key3 : Value 3

\\n\\\n", + "
\\n\\\n", + " \\n\\\n", + "\"\n", + ")\n", + "\n", + "metabolite.notes = Notes(notes_str)\n", + "metabolite.notes[\"Key1\"] = \"New Value1\"" + ], + "execution_count": null, + "outputs": [] + } + ] +} \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index d8268a0e3..51e840892 100644 --- a/setup.cfg +++ b/setup.cfg @@ -6,7 +6,7 @@ parse = (?P\d+) \.(?P\d+) \.(?P\d+) (?P[a]*)(?P\d*) -serialize = +serialize = {major}.{minor}.{patch}{release}{num} {major}.{minor}.{patch} tag_name = {new_version} @@ -15,7 +15,7 @@ tag_name = {new_version} name = cobra url = https://opencobra.github.io/cobrapy download_url = https://pypi.org/project/cobra -project_urls = +project_urls = Source Code = https://github.com/opencobra/cobrapy Documentation = https://cobrapy.readthedocs.io Bug Tracker = https://github.com/opencobra/cobrapy/issues @@ -23,7 +23,7 @@ author = The cobrapy core development team. author_email = cobra-pie@googlegroups.com maintainer = Moritz E. Beber maintainer_email = moritz.beber@gmail.com -classifiers = +classifiers = Development Status :: 5 - Production/Stable Intended Audience :: Science/Research License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) @@ -41,7 +41,7 @@ license = LGPL-2.0-or-later OR GPL-2.0-or-later description = COBRApy is a package for constraint-based modeling of metabolic networks. long_description = file: README.rst, INSTALL.rst long_description_content_type = text/x-rst -keywords = +keywords = metabolism biology constraint-based @@ -53,7 +53,7 @@ keywords = [options] zip_safe = True -install_requires = +install_requires = appdirs ~=1.4 depinfo ~=1.7 diskcache ~=5.0 @@ -68,24 +68,25 @@ install_requires = rich >=8.0 ruamel.yaml ~=0.16 swiglpk -tests_require = + jsonschema +tests_require = tox packages = find: -package_dir = +package_dir = = src [options.packages.find] where = src [options.package_data] -cobra = +cobra = data/* io/*.json [options.extras_require] -array = +array = scipy -development = +development = black bumpversion isort @@ -97,7 +98,7 @@ universal = 1 [bumpversion:part:release] optional_value = placeholder first_value = placeholder -values = +values = placeholder a diff --git a/src/cobra/core/__init__.py b/src/cobra/core/__init__.py index 12e082517..5dff2a3fb 100644 --- a/src/cobra/core/__init__.py +++ b/src/cobra/core/__init__.py @@ -2,6 +2,7 @@ from cobra.core.dictlist import DictList from cobra.core.gene import Gene, GPR from cobra.core.metabolite import Metabolite +from cobra.core.metadata import * from cobra.core.model import Model from cobra.core.object import Object from cobra.core.reaction import Reaction diff --git a/src/cobra/core/gene.py b/src/cobra/core/gene.py index 0d1f86f29..a9911431a 100644 --- a/src/cobra/core/gene.py +++ b/src/cobra/core/gene.py @@ -751,7 +751,7 @@ def eval_gpr(expr: Union[Expression, GPR], knockouts: Union[DictList, set]) -> b otherwise false """ warn( - "eval_gpr() will be removed soon." "Use GPR().eval(knockouts) in the future", + "eval_gpr() will be removed soon. Use GPR().eval(knockouts) in the future", DeprecationWarning, ) if isinstance(expr, GPR): diff --git a/src/cobra/core/metadata/__init__.py b/src/cobra/core/metadata/__init__.py new file mode 100644 index 000000000..a103c4db2 --- /dev/null +++ b/src/cobra/core/metadata/__init__.py @@ -0,0 +1,13 @@ +"""Provide functions for loading, saving and modifying metadata annotations.""" + +from cobra.core.metadata.cvterm import ( + Qualifier, + CVTerms, + ExternalResources, + CVTerm, +) +from cobra.core.metadata.history import Creator, History, HistoryDatetime +from cobra.core.metadata.keyvaluepairs import KeyValuePairs +from cobra.core.metadata.metadata import MetaData +from cobra.core.metadata.notes import Notes +from cobra.core.metadata.helper import * diff --git a/src/cobra/core/metadata/cvterm.py b/src/cobra/core/metadata/cvterm.py new file mode 100644 index 000000000..81274d2c2 --- /dev/null +++ b/src/cobra/core/metadata/cvterm.py @@ -0,0 +1,625 @@ +"""Define the Controlled Vocabulary term class.""" + +import logging +import re +from collections import OrderedDict, UserList +from enum import Enum +from typing import Callable, Dict, FrozenSet, Iterable, List, Optional, Pattern, Union + +from .helper import URL_IDENTIFIERS_PATTERN, parse_identifiers_uri + + +logger = logging.getLogger(__name__) + + +class Qualifier(Enum): + """The possible qualifiers inside a CVTerm""" + + bqb_is = 0 + bqb_hasPart = 1 + bqb_isPartOf = 2 + bqb_isVersionOf = 3 + bqb_hasVersion = 4 + bqb_isHomologTo = 5 + bqb_isDescribedBy = 6 + bqb_isEncodedBy = 7 + bqb_encodes = 8 + bqb_occursIn = 9 + bqb_hasProperty = 10 + bqb_isPropertyOf = 11 + bqb_hasTaxon = 12 + bqb_unknown = 13 + bqm_is = 14 + bqm_isDescribedBy = 15 + bqm_isDerivedFrom = 16 + bqm_isInstanceOf = 17 + bqm_hasInstance = 18 + bqm_unknown = 19 + + +class CVTerm: + """ + Representation of one CVTerm of an object in their + dependency structure. It is a ???? + + + named tuple where the first named field is a qualifier and the second named field + is ExternalResources. + + UserList keeps the data in the property data, which is a real list. + + This is how a CVTerm looks : + CVTerm.qualifier = "bqb_is" + CVTerm.ex_res = + {"resources": [ + "resource_uri", + ... + ], + "nested_data": CVTerms Object + } + + + The internal dictionary is an ExternalResources + + 1. The only way to add annotation data via old format is by + using the method "add_simple_annotations()". + 2. Single CVTerm data can be added by using "add_cvterm()". + 3. Multiple CVTerm data can be added by using "add_cvterms()". + """ + + def __init__( + self, + ex_res: "ExternalResources" = None, + qualifier: Union[Qualifier, str] = Qualifier.bqb_is, + ): + self._ex_res = None + self._qualifier = None + self._ex_res = self.check_ex_res_type(ex_res) + self._qualifier = self.check_qualifier_type(qualifier) + + @property + def qualifier(self) -> Qualifier: + return self._qualifier + + @qualifier.setter + def qualifier(self, qualifier: Union[str, int, Qualifier]) -> None: + self._qualifier = self.check_qualifier_type(qualifier) + + @property + def external_resources(self) -> "ExternalResources": + return self._ex_res + + @external_resources.setter + def external_resources( + self, external_resources: Union[dict, "ExternalResources"] + ) -> None: + self._ex_res = self.check_ex_res_type(external_resources) + + @staticmethod + def check_ex_res_type( + ex_res: Union["ExternalResources", Dict] + ) -> "ExternalResources": + if ex_res is None: + return ExternalResources() + elif isinstance(ex_res, ExternalResources): + return ex_res + elif isinstance(ex_res, dict): + return ExternalResources.from_dict(ex_res) + else: + raise TypeError( + f"Allowed types for CVTerms ex_ress are ExternalResources " + f"or dict, not {type(ex_res)}: {ex_res}" + ) + + @staticmethod + def check_qualifier_type(qual: Union[int, str, Qualifier]) -> Qualifier: + if ( + isinstance(qual, str) + and qual not in Qualifier.__members__ + or (isinstance(qual, int) and not 0 <= qual < Qualifier.__len__()) + ): + raise TypeError(f"{qual} is not a supported enum Qualifier") + elif isinstance(qual, Qualifier): + return qual + elif isinstance(qual, str): + return Qualifier[qual] + elif isinstance(qual, int): + return Qualifier(qual) + else: + raise TypeError( + f"Allowed types for CVTerm qualifier must be Qualifier," + f"str member of the Qualifier enum " + f"or an int between 0 and the Qualifier enum length " + f"{type(qual)}, {qual}" + ) + + def to_ordered_dict(self) -> dict: + """Represent a CVTerms object in python dict. + + Returns: + ------- + dict: + a dict where each key has is a qualifier and has a list of all external + resources in the original self._cvterms dictionary for that key + + """ + return OrderedDict({self.qualifier: self.external_resources.to_dict()}) + + @classmethod + def from_dict(cls, data_dict: Dict): + return cls( + ex_res=data_dict.get("external_resources", None), + qualifier=data_dict.get("qualifier", Qualifier["bqb_is"]), + ) + + def __eq__(self, other: "CVTerm") -> bool: + if not isinstance(other, CVTerm): + return False + if self.qualifier != other.qualifier: + return False + if self.external_resources != other.external_resources: + return False + return True + + +class CVTerms(UserList): + """ + Representation of all CVTerms of an object in their + dependency structure. It is list that contains qualifiers and external resouces + for each CVTerm. + + Parameters + ---------- + data : list + a list containing qualifier and external resources in CVTerm forma + + This is how a CVTerms looks : + [ + "bqb_is": [ + { + "resources": [ + "resource_uri", + ... + ], + "nested_data": CVTerms Object + }, + ... + ], + ... + ] + + 1. The only way to add annotation data via old format is by + using the method "add_simple_annotations()". + 2. Single CVTerm data can be added by using "add_cvterm()". + 3. Multiple CVTerm data can be added by using "add_cvterms()". + """ + + def __init__(self, data=None): + + # storing data in new annotation format + # as described above + if data is None: + data = [] + data = [self._check_CVTerm(datum) for datum in data] + super().__init__(data) + + @staticmethod + def _check_CVTerm(cvterm: Union["CVTerm", Dict]) -> Optional["CVTerm"]: + if cvterm is None: + return + if isinstance(cvterm, CVTerm): + return cvterm + elif isinstance(cvterm, dict): + return CVTerm.from_dict(cvterm) + else: + raise TypeError( + f"Allowed types for CVTerms ex_ress are CVTerm " + f"or dict, not {type(cvterm)}: {cvterm}" + ) + + @staticmethod + def from_data(data: Union[List, Dict, "CVTerm"]) -> "CVTerms": + """Parses a CVTerms object from given data""" + if data is None: + return CVTerms() + if isinstance(data, dict): + # TODO - need to check dict.py + return CVTerms.from_dict(data) + elif isinstance(data, list): + return CVTerms(data) + elif isinstance(data, CVTerm): + return CVTerms([data]) + else: + raise TypeError(f"Invalid format for CVTerms: '{data}'") + + def to_dict(self) -> dict: + """Represent a CVTerms object in python dict. + + Returns: + ------- + dict: + a dict where each key has is a qualifier and has a list of all external + resources in the original self.data list that match that qualifier + + """ + qualifier_set = set() + for cvterm in self.data: + qualifier_set.add(cvterm.qualifier.name) + empty_lists = [[] for _ in qualifier_set] + qualifier_dict = dict(zip(qualifier_set, empty_lists)) + for cvterm in self.data: + qualifier_dict[cvterm.qualifier.name].append( + cvterm.external_resources.to_dict() + ) + return OrderedDict(qualifier_dict) + + @classmethod + def from_dict(cls, data_dict): + cvterms_list = [] + for qual, ex_resources in data_dict.items(): + cvterms = [ + CVTerm( + ex_res=ExternalResources.from_dict(ex_res), + qualifier=Qualifier[qual], + ) + for ex_res in ex_resources + ] + cvterms_list.extend(cvterms) + return cls(cvterms_list) + + def add_cvterms(self, cvterms: Iterable[Union[Dict, "CVTerm"]]) -> None: + """ + Adds multiple CVTerm to CVTerms. + + Parameters + ---------- + cvterms : CVTerms list of CVTerm or dict (to be added in CVTerms dict) + the cvterms to be added + """ + self.extend(cvterms) + + def add_simple_annotations(self, data: Union[Dict, List] = None) -> None: + """ + Adds cvterms via old annotation format. If no qualifier + is linked to the identifier, default qualifier i.e "bqb_is" + will be used. + This function will add identifiers.org to as the URI. + If the annotation does not match the identifier format, you should XXXXX????? + + Parameters + ---------- + data : dict + the data in old annotation format + """ + if data is None: + data = {} + + if not isinstance(data, (dict, list)): + raise TypeError(f"The data passed must be of type dict or list: {data}") + + cvterm_list = [] + for key, value in data.items(): + + # if single identifiers are put directly as string, + # put them inside a list. For eg: + # { "chebi": "CHEBI:17234"} -> { "chebi": ["CHEBI:17234"]} + if isinstance(value, str): + data[key] = [value] + value = [value] + if not isinstance(value, (list, str)): + raise TypeError( + f"The value passed must be of type list or str: {value}" + ) + + # adding data one by one + for identifier in value: + qual = Qualifier["bqb_is"] + # if no qualifier is linked to identifier i.e. annotation + # of the form { "chebi": "CHEBI:17234"} + if isinstance(identifier, str): + uri = "https://identifiers.org/" + key + "/" + identifier + # if some qualifier is linked to the identifier i.e. annotation + # of the form { "chebi": ["bqb_is", "CHEBI:17234"]} + elif isinstance(identifier, list): + uri = "https://identifiers.org/" + key + "/" + identifier[1] + qual = Qualifier[identifier[0]] + else: + raise TypeError( + f"The identifier passed must be of type string " + f"or list: {identifier}" + ) + cvterm_list.append( + CVTerm(ex_res=ExternalResources([uri]), qualifier=qual) + ) + self.add_cvterms(cvterm_list) + + @property + def annotations(self) -> Dict: + annotation_dict = {} + resources = self.resources + for res in resources: + if re.match(URL_IDENTIFIERS_PATTERN, res): + provider, identifier = parse_identifiers_uri(res) + if provider in annotation_dict.keys(): + annotation_dict[provider].append(identifier) + else: + annotation_dict[provider] = [identifier] + return {k: sorted(annotation_dict[k]) for k in sorted(annotation_dict.keys())} + + @property + def resources(self) -> FrozenSet: + """Get all resources. + + Returns: + ------- + FrozenSet: + a set of all external resources in the original self._cvterms dictionary + including external resources of nested data + """ + resources = set() + for datum in self.data: + if ( + datum.external_resources.resources + or datum.external_resources.nested_data + ): + resources.update(datum.external_resources.resource_set) + return frozenset(resources) + + @property + def qualifiers(self) -> FrozenSet: + qualifier_set = set() + for datum in self.data: + qualifier_set.add(datum.qualifier) + return frozenset(qualifier_set) + + def query_qualifier( + self, + search_function: Union[str, Pattern, Callable, Qualifier], + ) -> "CVTerms": + """Query the CV terms by Qualifier. + + Parameters + ---------- + search_function : a string, regular expression, function or Qualifier + Used to find the matching elements in the list. + - a regular expression (possibly compiled), in which case the + given attribute of the object should match the regular expression. + - a function which takes one argument and returns True for + desired values + + Returns + ------- + CVTerms + a new list of CVTerm objects which match the query + + """ + if isinstance(search_function, Pattern): + # if the search_function is a regular expression + regex_searcher = re.compile(search_function) + + matches = [ + cvterm + for cvterm in self.data + if regex_searcher.findall(cvterm.qualifier) != [] + ] + elif isinstance(search_function, (Qualifier, int, str)): + search_function = CVTerm.check_qualifier_type(search_function) + + matches = [cvterm for cvterm in self if cvterm.qualifier == search_function] + + else: + matches = [cvterm for cvterm in self if search_function(cvterm)] + + results = self.__class__(matches) + return results + + def query_resources( + self, + search_function: Union[str, Pattern, Callable, "ExternalResources"], + search_nested_data=False, + ) -> "CVTerms": + """Query the CV terms by External Resources. + + Parameters + ---------- + search_function : a string, regular expression, function or External Resources + Used to find the matching elements in the list. + - a regular expression (possibly compiled), in which case the + given attribute of the object should match the regular expression. + - a function which takes one argument and returns True for + desired values + + search_nested_data: bool + Should the nested_data of each resource be searched as well. Default False. + + Returns + ------- + CVTerms + a new list of CVTerm objects which match the query + + """ + if isinstance(search_function, (Pattern, str)): + # if the search_function is a regular expression + regex_searcher = re.compile(search_function) + + if search_nested_data: + + def _match_resources(x): + return [regex_searcher.findall(res) != [] for res in x.resource_set] + + else: + + def _match_resources(x): + return [regex_searcher.findall(res) != [] for res in x.resources] + + matches = [cvterm for cvterm in self.data if any(_match_resources(cvterm))] + elif isinstance(search_function, ExternalResources): + search_function = CVTerm.check_ex_res_type(search_function) + + if search_nested_data: + matches = [ + cvterm + for cvterm in self.data + if search_function in cvterm.resource_set + ] + else: + matches = [ + cvterm + for cvterm in self.data + if search_function in cvterm.external_resources + ] + + else: + matches = [cvterm for cvterm in self if search_function(cvterm)] + + results = self.__class__(matches) + return results + + def __setitem__(self, key: int, value: CVTerm) -> None: + UserList.__setitem__(self, key, self._check_CVTerm(value)) + + def append(self, item: CVTerm) -> None: + """Append CVTerm to end.""" + self._check_CVTerm(item) + UserList.append(self, item) + + def extend(self, iterable: Union["CVTerms", Iterable[Union[CVTerm, Dict]]]) -> None: + """Extend data list by appending elements from the iterable. + + Parameters + ---------- + iterable : Iterable + """ + if isinstance(iterable, CVTerms): + self.data.extend(iterable.data) + elif isinstance(iterable, Iterable): + self.data.extend([self._check_CVTerm(i) for i in iterable]) + + def __eq__(self, other: "CVTerms") -> bool: + """Compare two CVTerms objects to find out whether they + are same (have same data) or not + """ + if not isinstance(other, CVTerms): + return False + if len(self.data) != len(other.data): + return False + for self_i, other_i in zip(self.data, other.data): + if self_i != other_i: + return False + return True + + +class ExternalResources: + """ + Class representation of a single set of resources and its nested + annotation. + + Parameters + ---------- + resources: list + A list of URLs (resources) + nested_data : CVTerms + Nested annotation, in CVTerms format + + Can also be created from dictionary, see ExternalResources.from_dict() + """ + + def __init__(self, resources: List = None, nested_data=None): + self._resources = None + self._nested_data = None + self.resources = resources + if resources: + self.nested_data = nested_data + + @property + def resources(self) -> List: + return self._resources + + @resources.setter + def resources(self, value: List) -> None: + if value is None or isinstance(value, list): + self._resources = value + elif not isinstance(value, list): + raise TypeError(f"The resources must be wrapped inside a list: {value}") + + @property + def resource_set(self) -> FrozenSet: + resources = set() + resources.update(self.resources) + if self.nested_data: + resources.update(self.nested_data.resources) + return frozenset(resources) + + @property + def nested_data(self) -> CVTerms: + return self._nested_data + + @nested_data.setter + def nested_data(self, value: Union[Dict, CVTerm, CVTerms]): + if value is None: + self._nested_data = CVTerms() + elif isinstance(value, CVTerm): + self._nested_data = CVTerms([value]) + elif isinstance(value, CVTerms): + self._nested_data = value + elif isinstance(value, dict): + self._nested_data = CVTerms.from_dict(value) + else: + raise TypeError( + f"The nested data structure does not have valid CVTerm format: {value}" + ) + + def to_dict(self): + """Represents a ExternalResource object as python dict""" + ex_dic = {"resources": list(self._resources)} + if self.nested_data is not None and len(self.nested_data): + ex_dic["nested_data"] = self.nested_data.to_dict() + return ex_dic + + @classmethod + def from_dict(cls, input_data: Dict) -> "ExternalResources": + """ + + Parameters + ---------- + input_data: dict + + Returns + ------- + ExternalResources2: ExternalResources + + """ + ex_res = cls( + resources=input_data.get("resources", None), + nested_data=input_data.get("nested_data", None), + ) + return ex_res + + def __eq__(self, other: "ExternalResources") -> bool: + """ + Compare two ExternalResources objects to find out whether + they are same (have same data) or not + """ + if self.resources != other.resources: + return False + if self.nested_data is None and other.nested_data is None: + return True + elif self.nested_data is None or other.nested_data is None: + return False + elif self.nested_data != other.nested_data: + return False + return True + + def __str__(self) -> str: + return str(self.to_dict()) + + def __repr__(self) -> str: + return self.__str__() + + def _repr_html_(self): + return f""" +

+ Resources{"

".join(self.resources)}

+ Nested Data{self.nested_data}

+ Memory address{id(self):#x} +

""" diff --git a/src/cobra/core/metadata/helper.py b/src/cobra/core/metadata/helper.py new file mode 100644 index 000000000..0420f30b3 --- /dev/null +++ b/src/cobra/core/metadata/helper.py @@ -0,0 +1,45 @@ +"""Helper functions and properties for dealing with annotation data. + +This is a unification of helper functions from sbml.py and cvterm.py. + +""" +import logging +import re +from typing import Tuple, Union + + +LOGGER = logging.getLogger(__name__) + +__all__ = ["URL_IDENTIFIERS_PATTERN", "parse_identifiers_uri"] + +# the URL pattern to parse provider and identifier +URL_IDENTIFIERS_PATTERN = re.compile(r"^https?://identifiers.org/(.+?)[:/](.+)") + + +def parse_identifiers_uri(uri: str) -> Union[None, Tuple[str, str]]: + """Parse provider and term from given identifiers annotation uri. + + Parameters + ---------- + uri : str + uri (identifiers.org url) + + Returns + ------- + (provider, identifier) if resolvable, None otherwise + """ + match = URL_IDENTIFIERS_PATTERN.match(uri) + if match: + provider, identifier = match.group(1), match.group(2) + if provider.isupper(): + identifier = f"{provider}:{identifier}" + provider = provider.lower() + else: + LOGGER.warning( + f"{uri} does not conform to " + f"'http(s)://identifiers.org/collection/id' or" + f"'http(s)://identifiers.org/COLLECTION:id" + ) + return None + + return provider, identifier diff --git a/src/cobra/core/metadata/history.py b/src/cobra/core/metadata/history.py new file mode 100644 index 000000000..465c2511b --- /dev/null +++ b/src/cobra/core/metadata/history.py @@ -0,0 +1,286 @@ +"""Encodes History and Creator. + +The history allows to encode provenance meta-data about +model objects. The history allows to encode who created or modified +objects in a model with respective time stamps. +""" +from datetime import datetime +from typing import Dict, Iterable, List, Optional, Union + + +STRTIME_FORMAT = "%Y-%m-%dT%H:%M:%S%z" + + +class History: + """History object encoding object provenance. + + Parameters + ---------- + creators : list + A list of Creators + created_date : HistoryDatetime + The datetime of creation in W3CDTF ISO 8601 format + modified_dates : list + A list of datetimes when the object was modified. + """ + + def __init__( + self, + creators: List["Creator"] = None, + created_date: "HistoryDatetime" = None, + modified_dates: List["HistoryDatetime"] = None, + ): + if modified_dates is None: + modified_dates = [] + if creators is None: + creators = [] + self._creators = [] + self._created_date = None + self._modified_dates = [] + + # use properties to set fields + self.creators = creators + self.created_date = created_date + self.modified_dates = modified_dates + + @property + def creators(self) -> List: + return self._creators + + @creators.setter + def creators(self, values: Iterable["Creator"]) -> None: + self._creators = [Creator.from_data(v) for v in values] + + @property + def created_date(self) -> "HistoryDatetime": + return self._created_date + + @created_date.setter + def created_date(self, date: Union[str, "HistoryDateTime"]) -> None: + self._created_date = HistoryDatetime(date) + + @property + def modified_dates(self) -> List: + return self._modified_dates + + @modified_dates.setter + def modified_dates(self, dates: Iterable[Union[str, "HistoryDateTime"]]) -> None: + self._modified_dates = [HistoryDatetime(d) for d in dates] + + @staticmethod + def from_data(data: Union[Dict, "History"]) -> "History": + """Parse history from data.""" + if data is None: + return History() + elif isinstance(data, History): + return data + elif isinstance(data, dict): + return History(**data) + else: + raise TypeError(f"Unsupported type for History: '{data}'") + + def is_empty(self) -> bool: + """Checks if history is empty. + + Returns False if at least one history attribute is set, else True. + """ + if self.creators: + return False + if self.created_date.datetime: + return False + if self.modified_dates: + return False + return True + + def __eq__(self, history: "History") -> bool: + """Checking equality of two history objects. + + A history is equal if all attributes are equal. + """ + # check equality of creators + if len(self.creators) != len(history.creators): + return False + for k, creator in enumerate(self.creators): + if creator != history.creators[k]: + return False + + # checking equality of created_date + if self.created_date != history.created_date: + return False + + # checking equality of modified_dates + if len(self.modified_dates) != len(history.modified_dates): + return False + for k, modified_date in enumerate(self.modified_dates): + if modified_date != history.modified_dates[k]: + return False + + return True + + def to_dict(self): + """Returns dictionary representation.""" + modified_dates = [] + for modified_date in self._modified_dates: + modified_dates.append(modified_date.datetime) + return { + "creators": [c.to_dict() for c in self.creators], + "created_date": self.created_date.datetime, + "modified_dates": modified_dates, + } + + def __str__(self) -> str: + return str(self.to_dict()) + + def __repr__(self): + return f"<{self.__class__.__name__} {self.creators}>" + + +class Creator: + """Metadata for person who created an object. + + Parameters + ---------- + given_name : str, + family_name : str, + email : str, + organisation : str + """ + + def __init__( + self, + given_name: str = None, + family_name: str = None, + email: str = None, + organisation: str = None, + ): + self.given_name = given_name # type: str + self.family_name = family_name # type: str + self.email = email # type: str + self.organisation = organisation # type: str + + @staticmethod + def from_data(data: Union[Dict, "Creator"]) -> "Creator": + """Parse creator from data.""" + if not data: + return Creator() + elif isinstance(data, Creator): + return data + elif isinstance(data, dict): + return Creator(**data) + else: + raise TypeError(f"Invalid format for Creator: {data}") + + def __eq__(self, creator_obj: "Creator") -> bool: + """Compare creator objects for equality + + Two creators are equal if all fields are equal. + """ + if ( + self.given_name != creator_obj.given_name + or self.family_name != creator_obj.family_name + or self.email != creator_obj.email + or self.organisation != creator_obj.organisation + ): + return False + + return True + + def to_dict(self): + return { + "given_name": self.given_name, + "family_name": self.family_name, + "email": self.email, + "organisation": self.organisation, + } + + def __str__(self) -> str: + return str(self.to_dict()) + + def __repr__(self): + return f"<{self.__class__.__name__} {self.given_name} {self.family_name}>" + + +class HistoryDatetime: + """Datetime allowed in a model history. + + This class make sure that datetimes are of the form: + %Y-%m-%dT%H:%M:%S%z + + Parameter + --------- + datetime: str, datetime + date in the form of a string + """ + + def __init__(self, history_datetime: str = None): + self._datetime: Optional[str] = None + self.datetime = history_datetime + + @property + def datetime(self) -> str: + return self._datetime + + @datetime.setter + def datetime(self, value: str) -> None: + self._datetime = self.parse_datetime(value) + + def parse_datetime(self, value: str) -> Optional[str]: + if value is None: + return None + if isinstance(value, HistoryDatetime): + return value.datetime + elif isinstance(value, str): + self.validate_datetime(value) + return value + elif isinstance(value, datetime): + return value.strftime(STRTIME_FORMAT) + else: + raise TypeError( + f"Invalid type passed for datetime. " + f"Accepted types are 'str' or " + f"'datetime' objects: {value}" + ) + + @staticmethod + def utcnow() -> "HistoryDatetime": + """HistoryDatetime with current UTC time.""" + return HistoryDatetime(datetime.utcnow().strftime(STRTIME_FORMAT)) + + @staticmethod + def validate_datetime(datetime_str: str) -> None: + """Validate if the date format is of type w3cdtf ISO 8601. + + Raises ValueError if not valid. + """ + if not isinstance(datetime_str, str): + raise TypeError(f"The date passed must be of type string: {datetime_str}") + + # python 3.6 doesn't allow : (colon) in the utc offset. + try: + datetime.strptime(datetime_str, STRTIME_FORMAT) + except ValueError as e: + # checking for python 3.6 + if "Z" in datetime_str: + try: + datetime.strptime( + datetime_str.replace("Z", ""), "%Y-%m-%dT%H:%M:%S" + ) + except ValueError as e1: + raise ValueError(str(e1)) + else: + utcoff = datetime_str[20:25] + utcoff_p36 = utcoff.replace(":", "") + date_p36 = datetime_str.replace(utcoff, utcoff_p36) + try: + datetime.strptime(date_p36, STRTIME_FORMAT) + except ValueError: + raise ValueError(str(e)) + + def __eq__(self, history_datetime: "HistoryDatetime") -> bool: + return self.datetime == history_datetime.datetime + + def __str__(self) -> str: + return self.datetime + + def __repr__(self): + return f"<{self.__class__.__name__} {self.datetime}>" diff --git a/src/cobra/core/metadata/keyvaluepairs.py b/src/cobra/core/metadata/keyvaluepairs.py new file mode 100644 index 000000000..5a2e6ad87 --- /dev/null +++ b/src/cobra/core/metadata/keyvaluepairs.py @@ -0,0 +1,109 @@ +from collections import UserDict +from typing import Dict, Iterable, Union + +from ...util import format_long_string + + +class KeyValueEntry: + """Single key-value entry. + + The key is an attribute on the entry. + + Parameters + ---------- + id : str + name : str + key : str + value : str + uri : str + """ + + def __init__( + self, + id: str = None, + name: str = None, + key: str = None, + value: str = None, + uri: str = None, + ): + self.id = id + self.name = name + self.key = key + self.value = value + self.uri = uri + + @staticmethod + def from_data(data: Union[Dict, "KeyValueEntry"]) -> "KeyValueEntry": + """Makes a KeyValueDict object using the data passed.""" + if data is None: + return KeyValueEntry() + elif isinstance(data, KeyValueEntry): + return data + elif isinstance(data, dict): + return KeyValueEntry(**data) + else: + raise TypeError(f"Invalid format for KeyValueEntry: '{data}'") + + def to_dict(self) -> dict: + return { + "id": self.id, + "name": self.name, + "key": self.key, + "value": self.value, + "uri": self.uri, + } + + def __str__(self) -> str: + return str(self.to_dict()) + + def __repr__(self) -> str: + return f"<{self.__class__.__name__} ({self.key}, {self.value}, {self.uri})>" + + +class KeyValuePairs(UserDict): + """An UserDict to store KeyValueEntries. + + Parameters + ---------- + entries : Iterable + an iterable containing entry information + """ + + def __init__(self, entries: Iterable[Union[Dict, KeyValueEntry]] = None): + super().__init__() + if entries: + for item in entries: + entry = KeyValueEntry.from_data(item) + self.data[entry.key] = entry + + def __setitem__(self, key: str, item: Union[Dict, KeyValueEntry]) -> None: + entry = KeyValueEntry.from_data(item) + self.data[key] = entry + + def __str__(self) -> str: + """Convert KeyValuePairs to str. + + Parameters + ---------- + self : KeyValuePairs + UserDict defining key value pairs + + Returns + ------ + string + a string representation of a dictionary + """ + return str(self.to_dict()) + + def __repr__(self) -> str: + return ( + f"{self.__class__.__module__}.{self.__class__.__qualname__}" + f"({self.to_dict()!r})" + ) + + def _repr_html_(self) -> str: + return f"""

KeyValuePairs

{format_long_string( + self.__str__(), 100)}

""" + + def to_dict(self) -> dict: + return {k: v.to_dict() for k, v in self.data.items()} diff --git a/src/cobra/core/metadata/metadata.py b/src/cobra/core/metadata/metadata.py new file mode 100644 index 000000000..37b81b1de --- /dev/null +++ b/src/cobra/core/metadata/metadata.py @@ -0,0 +1,213 @@ +"""Define the cobra MetaData class.""" + +from collections import OrderedDict +from collections.abc import MutableMapping +from typing import Dict, Iterable, Iterator, List, Union + +from ..metadata.cvterm import CVTerm, CVTerms +from ..metadata.history import Creator, History +from ..metadata.keyvaluepairs import KeyValuePairs + + +class MetaData(MutableMapping): + """Meta-data of a cobrapy object. + + Meta-data encodes additional information on an object such as annotations + or notes. Such information is currently stored in SBML on the notes and + annotation fields. + + Meta-data consists of three components: + - CVTerms: storing resource:identifier annotation information. The annotation + information is exposed via the dict interface for full backwards compatibility + to the earlier object.annotation field. + - History: storing the object history consisting of creators, created date, and + modified dates. + - KeyValuePairs, a list of key-value pairs to store additional information + + Parameters + ---------- + cvterms : dict or CVTerms object + The cvterms store annotations to external resources + history : dict, History + The history stores information about the creator, + created and modified dates. + sbo: str + The sbo term to use for the entity. If you want to use more than one SBO term + (not recommended), use SBO in identifers.org format and put it in cvterms. + keyvaluepairs : list + Key-value pairs which are not suitable to be + represented anywhere else in the model. + Data is represented as an OrderedDict. + """ + + def __init__( + self, + cvterms: Union[Dict, CVTerms] = None, + history: Union[Dict, History] = None, + sbo: str = "", + keyvaluepairs: List = None, + ): + """Initialize the MetaData class. + + Parameters + --------- + cvterms : dict or CVTerms, optional + Which controlled vocabulary terms does the metadata have. Default None. + history: dict or History, optional + History of annotation, including creation data, creators, and optional + modificiation date. Default None. + sbo: str + SBO term, if relevant. Default "". + If there are + keyvaluepairs: KeyValuePairs + For annotations that don't match the identifiers.org format. + + """ + self._cvterms = CVTerms.from_data(cvterms) + self._history = History.from_data(history) + self._keyvaluepairs = KeyValuePairs(keyvaluepairs) + self._sbo = sbo + + # use setters + self.sbo = sbo + self.cvterms = cvterms + self.history = history + self.keyvaluepairs = keyvaluepairs + + @property + def annotations(self) -> Dict: + """Backwards compatible annotations.""" + anno_dict = self.cvterms.annotations + if self.sbo: + anno_dict["sbo"] = self.sbo + return anno_dict + + @property + def sbo(self) -> str: + """Return the SBO term of the MetaData. + + Returns + ------- + str: SBO as string + """ + return self._sbo + + @sbo.setter + def sbo(self, value: str) -> None: + """Set the SBO term.""" + self._sbo = value + + def __setitem__(self, key: str, value: List) -> None: + """Set the item for accessing metadata as dict (the old style annotation). + + Parameters + ---------- + key: str + provider key word. + value: List + A list that will contain either term(s) or qualifier and term(s). + + If the key is sbo, sets the self.sbo term to the first item in the list. If + you'd like to add multiple SBO terms, use the CVTerms() and add sbo as + identifiers.org formatted links. + + See Also + -------- + CVTerms().add_simple_annotations() + + """ + if key == "sbo": + if isinstance(value, list): + value = value[0] + self.sbo = value + else: + self._cvterms.add_simple_annotations(dict({key: value})) + + def __getitem__(self, key: str) -> Union[str, List]: + if key == "sbo": + return [self.sbo] + else: + return self.annotations[key] + + def __delitem__(self, key: str) -> None: + if key == "sbo": + self.sbo = "" + else: + del self.annotations[key] + + def __iter__(self) -> Iterator: + return iter(self.annotations) + + def __len__(self) -> int: + return len(self.annotations) + + def __str__(self) -> str: + return str(dict(self.annotations)) + + def __repr__(self) -> str: + return str(dict(self.annotations)) + + @property + def cvterms(self) -> "CVTerms": + return self._cvterms + + @cvterms.setter + def cvterms(self, cvterms: Union[Dict, CVTerms]) -> None: + self._cvterms = CVTerms.from_data(cvterms) + + def add_cvterms(self, cvterms: Iterable[Union[Dict, CVTerm]]) -> None: + self._cvterms.add_cvterms(cvterms) + + @property + def history(self) -> History: + return self._history + + @history.setter + def history(self, history: Union[Dict, History]) -> None: + self._history = History.from_data(history) + + def add_creator(self, creator: Creator): + self.history.creators.append(creator) + + @property + def keyvaluepairs(self) -> KeyValuePairs: + return self._keyvaluepairs + + @keyvaluepairs.setter + def keyvaluepairs(self, keyvaluepairs: Union[Dict, KeyValuePairs]) -> None: + self._keyvaluepairs = KeyValuePairs(keyvaluepairs) + + def to_dict(self) -> Dict: + """Creates string dictionary for serialization""" + d = OrderedDict() + if self.sbo: + # set first SBO term as sbo + d["sbo"] = self.sbo + + if self.cvterms: + d["cvterms"] = self.cvterms.to_dict() + + if self.history and not self.history.is_empty(): + d["history"] = self.history.to_dict() + + if self.keyvaluepairs: + d["keyvaluepairs"] = self.keyvaluepairs.to_dict() + + return d + + @staticmethod + def from_dict(data: Dict) -> "MetaData": + cvterms = data["cvterms"] if "cvterms" in data else None + history = data["history"] if "history" in data else None + keyValuepairs = data["keyvaluepairs"] if "keyvaluepairs" in data else None + + if cvterms or history or keyValuepairs: + annotation = MetaData(cvterms, history, keyValuepairs) + else: + annotation = MetaData() + annotation.cvterms.add_simple_annotations(data) + + if "sbo" in data: + annotation["sbo"] = data["sbo"] + + return annotation diff --git a/src/cobra/core/metadata/notes.py b/src/cobra/core/metadata/notes.py new file mode 100644 index 000000000..bdaf27b1e --- /dev/null +++ b/src/cobra/core/metadata/notes.py @@ -0,0 +1,206 @@ +import logging +import re +from collections.abc import MutableMapping +from typing import Dict, Iterator + + +logger = logging.getLogger(__name__) + + +class Notes(MutableMapping): + """Class representation of 'notes' of an object. + + The previous version of COBRApy was parsing entries of + the form '

key : value

' and making + a dict out of it. All other information was simply + left out. When writing the model back to SBML, this + dict was converted in the string: + + " +

key1: value1

" +

key2: value2

" + ... + " + + The 'notes' attribute on an object stored this key: value + dictionary. + + The current version of 'notes' has a dedicated class + that behaves like a dict storing the key-value pairs + present inside the notes string (making it backward + compatible). In addition the the complete notes + information is stored. + + The dict and the string of 'notes' are both synchronized + with each other. + Importantly, the 'notes' attribute is not meant to to + store any machine-readable information. To enforce this + behavior the addition of new key-values inside the + 'notes' dict is not permitted. Trying to do so + will throw an ValueError. The KeyValuePairs should be used + to store key:value information for objects. + + The complete 'notes' string is + directly written to formats like "JSON", "YAML" etc when + COBRA model is written in these format. And when writing + SBML, 'notes' is initialized using the method: + + SBase.getNotesString() + + which makes the xhtml content of the notes using the string. + + Parameters + ---------- + notes_xhtml : string + The complete notes (xhtml) data in the form of a string. + """ + + # pattern checking for "

key : value

" type string + PATTERN_PTAG = re.compile( + r"<(?P(\w+:)?)p[^>]*>(?P.*?)", + re.IGNORECASE | re.DOTALL, + ) + + def __init__(self, notes_xhtml: str = None): + self._data = {} + self._notes_xhtml = None + self.notes_xhtml = notes_xhtml + + @property + def notes_xhtml(self) -> str: + """Return the html content of notes in the form of a string.""" + return self._notes_xhtml + + @notes_xhtml.setter + def notes_xhtml(self, value: str) -> None: + """Set the notes_xhtml string""" + if value is None: + self._notes_xhtml = value + self._data = {} + elif isinstance(value, str): + self._notes_xhtml = value + self._data = {} + self.update_notes_dict() + else: + raise TypeError(f"notes data must be of type string: {value}") + + def __eq__(self, other: "Notes") -> bool: + if not isinstance(other, Notes): + return False + return self._notes_xhtml == other._notes_xhtml + + def __getitem__(self, key: str) -> str: + return self._data[key] + + def __setitem__(self, key: str, value: str) -> None: + if key not in self._data: + raise ValueError( + "Notes string is not a right place " + "to store key value pairs. Store them " + "at appropriate place in the document." + ) + else: + self._data[key] = value + self.update_notes_str(key, value) + + def __delitem__(self, key: str) -> None: + del self._data[key] + + def __iter__(self) -> Iterator: + return iter(self._data) + + def __len__(self) -> int: + return len(self._data) + + def __str__(self) -> str: + if self._notes_xhtml is None: + return "" + return self.notes_xhtml + + def __repr__(self) -> str: + return self.__str__() + + def update_notes_dict(self) -> None: + """Update notes dictionary according to key-value stored in notes string.""" + if self._notes_xhtml: + for match in Notes.PATTERN_PTAG.finditer(self._notes_xhtml): + try: + key, value = match.group("content").split(":", 1) + except ValueError: + continue + self._data[key.strip()] = value.strip() + + def update_notes_str(self, key: str, value: str) -> None: + """Updates the notes string according to key-value pairs passed. + + If any such 'key' is present inside notes string having format + '

key : oldvalue

', then it will be updated to store the new value. + But if that 'key' is not present, an ValueError will be thrown. + """ + # if notes string is empty + if self._notes_xhtml is None: + raise ValueError( + "Notes string is not a right place to store key value pairs. " + "Store them at appropriate place in the document." + ) + + if not isinstance(value, str): + logger.warning( + f"The value must be of type string. \n" + f"Converting value {value} to 'string' type and " + f"then putting in notes string...." + ) + value = str(value) + + # pattern to search for inside notes string + pattern = re.compile( + rf"<(?P(\w+:)?)p[^>]*>(\s*)" + rf"{key}(\s*):(\s*)(?P.*?)(\s*)", + re.IGNORECASE | re.DOTALL, + ) + match = re.search(pattern, self._notes_xhtml) + + # if no such key-value substring is + # already present inside notes string + if match is None: + del self._data[key] + raise ValueError( + "Notes string is not the right place to store key value pairs." + "Store them at appropriate place in the document." + ) + # otherwise update the content + else: + start = match.start("content") + end = match.end("content") + modified_str = self._notes_xhtml[:start] + value + self._notes_xhtml[end:] + self._notes_xhtml = modified_str + + @classmethod + def notes_from_dict(cls, data_dict: Dict) -> "Notes": + """Creates a new note based on a dictionary. + + This method can be used to create a completely new Notes object from a + dictionary. It should be used when creating notes from scratch (such as import + if the function already sets up a dict). + + Parameters + ---------- + data_dict: dict + A dictionary that will be transformed to string. + + Returns + ------- + Notes + A new Notes object. + """ + # TODO - make it warn about annotion terms and/or use a local version of + # identifiers for that. See slamonella.xml for an example, since metabolites + # have PUBCHEM, KEGG. Also, some KEGG values are 0, which is invalid. + # TODO - Some metabolites in salmonella.xml have CHARGE in notes that disagrees + # with charge in the object (I think). Should warn/log. + str_list = [''] + str_suffix = "" + for k, v in data_dict.items(): + str_list.append(f"

{k}: {v}

") + str_list.append(str_suffix) + return cls("\n".join(str_list)) diff --git a/src/cobra/core/model.py b/src/cobra/core/model.py index 5abf5acaf..2efc8d0e9 100644 --- a/src/cobra/core/model.py +++ b/src/cobra/core/model.py @@ -97,6 +97,7 @@ def __init__(self, id_or_model=None, name=None): self.reactions = DictList() # A list of cobra.Reactions self.metabolites = DictList() # A list of cobra.Metabolites self.groups = DictList() # A list of cobra.Groups + self._const_ids = set() # genes based on their ids {Gene.id: Gene} self._compartments = {} self._contexts = [] @@ -324,7 +325,7 @@ def copy(self): "reactions", "genes", "notes", - "annotation", + "_annotation", "groups", } for attr in self.__dict__: @@ -334,13 +335,14 @@ def copy(self): new.annotation = deepcopy(self.annotation) new.metabolites = DictList() - do_not_copy_by_ref = {"_reaction", "_model"} + do_not_copy_by_ref = {"_reaction", "_model", "_annotation"} for metabolite in self.metabolites: new_met = metabolite.__class__() for attr, value in metabolite.__dict__.items(): if attr not in do_not_copy_by_ref: new_met.__dict__[attr] = copy(value) if attr == "formula" else value new_met._model = new + new_met.annotation = deepcopy(metabolite.annotation) new.metabolites.append(new_met) new.genes = DictList() @@ -352,16 +354,18 @@ def copy(self): copy(value) if attr == "formula" else value ) new_gene._model = new + new_gene.annotation = deepcopy(gene.annotation) new.genes.append(new_gene) new.reactions = DictList() - do_not_copy_by_ref = {"_model", "_metabolites", "_genes"} + do_not_copy_by_ref = {"_model", "_metabolites", "_genes", "_annotation"} for reaction in self.reactions: new_reaction = reaction.__class__() for attr, value in reaction.__dict__.items(): if attr not in do_not_copy_by_ref: new_reaction.__dict__[attr] = copy(value) new_reaction._model = new + new_reaction._annotation = deepcopy(reaction.annotation) new.reactions.append(new_reaction) # update awareness for metabolite, stoic in reaction._metabolites.items(): @@ -371,7 +375,7 @@ def copy(self): new_reaction.update_genes_from_gpr() new.groups = DictList() - do_not_copy_by_ref = {"_model", "_members"} + do_not_copy_by_ref = {"_model", "_members", "_annotation"} # Groups can be members of other groups. We initialize them first and # then update their members. for group in self.groups: @@ -380,6 +384,7 @@ def copy(self): if attr not in do_not_copy_by_ref: new_group.__dict__[attr] = copy(value) new_group._model = new + new_group.annotation = deepcopy(group.annotation) new.groups.append(new_group) for group in self.groups: new_group = new.groups.get_by_id(group.id) @@ -393,7 +398,7 @@ def copy(self): elif isinstance(member, Gene): new_object = new.genes.get_by_id(member.id) elif isinstance(member, Group): - new_object = new.genes.get_by_id(member.id) + new_object = new.groups.get_by_id(member.id) else: raise TypeError( "The group member {!r} is unexpectedly not a " diff --git a/src/cobra/core/object.py b/src/cobra/core/object.py index 78d092d05..acc2751e2 100644 --- a/src/cobra/core/object.py +++ b/src/cobra/core/object.py @@ -2,6 +2,8 @@ from typing import Optional +from cobra.core.metadata import MetaData, Notes + class Object: """Defines common behavior of object in cobra.core.""" @@ -22,8 +24,8 @@ def __init__(self, id: Optional[str] = None, name: str = "") -> None: self._id = id self.name = name - self.notes = {} - self._annotation = {} + self._notes = Notes() + self._annotation = MetaData() @property def id(self) -> str: @@ -70,7 +72,7 @@ def _set_id_with_model(self, value) -> None: self._id = value @property - def annotation(self) -> dict: + def annotation(self) -> MetaData: """Get annotation dictionary. Returns @@ -93,10 +95,26 @@ def annotation(self, annotation): ------ TypeError if annotation not a dict. """ - if not isinstance(annotation, dict): - raise TypeError("Annotation must be a dict") - else: + if isinstance(annotation, MetaData): self._annotation = annotation + elif isinstance(annotation, dict): + self._annotation = MetaData().from_dict(annotation) + else: + raise TypeError( + f"The data passed for annotation must be inside " + f"a dictionary or MetaData: {annotation}" + ) + + @property + def notes(self): + return getattr(self, "_notes", None) + + @notes.setter + def notes(self, data): + if isinstance(data, Notes): + self._notes = data + return + self._notes.notes_xhtml = data def __getstate__(self) -> dict: """Get state of annotation. diff --git a/src/cobra/data/mini.json b/src/cobra/data/mini.json index 658bd26c1..e4f3da62c 100644 --- a/src/cobra/data/mini.json +++ b/src/cobra/data/mini.json @@ -5,1120 +5,1224 @@ }, "genes": [ { - "id": "b0755", + "id": "G_b0755", "name": "gpmA" }, { - "id": "b0875", + "id": "G_b0875", "name": "aqpZ" }, { - "id": "b1101", + "id": "G_b1101", "name": "ptsG" }, { - "id": "b1380", + "id": "G_b1380", "name": "ldhA" }, { - "id": "b1621", + "id": "G_b1621", "name": "malX" }, { "annotation": { - "ncbigi": [ - "GI:1208453", - "GI:1652654" - ] + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/ncbiprotein/1208453", + "http://identifiers.org/ncbiprotein/1652654" + ] + } + ] + } }, - "id": "b1676", + "id": "G_b1676", "name": "pykF" }, { - "id": "b1723", + "id": "G_b1723", "name": "pfkB" }, { - "id": "b1773", + "id": "G_b1773", "name": "ydjI" }, { - "id": "b1779", + "id": "G_b1779", "name": "gapA" }, { - "id": "b1817", + "id": "G_b1817", "name": "manX" }, { - "id": "b1818", + "id": "G_b1818", "name": "manY" }, { - "id": "b1819", + "id": "G_b1819", "name": "manZ" }, { - "id": "b1854", + "id": "G_b1854", "name": "pykA" }, { - "id": "b2097", + "id": "G_b2097", "name": "fbaB" }, { - "id": "b2133", + "id": "G_b2133", "name": "dld" }, { - "id": "b2415", + "id": "G_b2415", "name": "ptsH" }, { - "id": "b2416", + "id": "G_b2416", "name": "ptsI" }, { - "id": "b2417", + "id": "G_b2417", "name": "crr" }, { "annotation": { - "ncbigi": "GI:1653839" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/ncbiprotein/1653839" + ] + } + ] + } }, - "id": "b2779", + "id": "G_b2779", "name": "eno" }, { - "id": "b2925", + "id": "G_b2925", "name": "fbaA" }, { "annotation": { - "ncbigi": "GI:1653609" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/ncbiprotein/1653609" + ] + } + ] + } }, - "id": "b2926", + "id": "G_b2926", "name": "pgk" }, { - "id": "b2987", + "id": "G_b2987", "name": "pitB" }, { - "id": "b3493", + "id": "G_b3493", "name": "pitA" }, { - "id": "b3612", + "id": "G_b3612", "name": "gpmM" }, { "annotation": { - "ncbigi": [ - "GI:1006614", - "GI:1651919" - ] + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/ncbiprotein/1006614", + "http://identifiers.org/ncbiprotein/1651919" + ] + } + ] + } }, - "id": "b3916", + "id": "G_b3916", "name": "pfkA" }, { - "id": "b3919", + "id": "G_b3919", "name": "tpiA" }, { "annotation": { - "ncbigi": "GI:1653253" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/ncbiprotein/1653253" + ] + } + ] + } }, - "id": "b4025", + "id": "G_b4025", "name": "pgi" }, { - "id": "b4395", + "id": "G_b4395", "name": "ytjC" }, { - "id": "s0001", + "id": "G_s0001", "name": "G_s0001" } ], + "groups": [], "id": "mini_textbook", "metabolites": [ { "annotation": { - "bigg.metabolite": "13dpg", - "biocyc": "DPG", - "chebi": [ - "CHEBI:16001", - "CHEBI:1658", - "CHEBI:20189", - "CHEBI:57604", - "CHEBI:11881" - ], - "hmdb": "HMDB01270", - "kegg.compound": "C00236", - "pubchem.substance": "3535", - "reactome": "REACT_29800", - "seed.compound": "cpd00203", - "unipathway.compound": "UPC00236" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.metabolite/13dpg", + "http://identifiers.org/biocyc/DPG", + "http://identifiers.org/chebi/CHEBI:16001", + "http://identifiers.org/chebi/CHEBI:1658", + "http://identifiers.org/chebi/CHEBI:20189", + "http://identifiers.org/chebi/CHEBI:57604", + "http://identifiers.org/chebi/CHEBI:11881", + "http://identifiers.org/hmdb/HMDB01270", + "http://identifiers.org/kegg.compound/C00236", + "http://identifiers.org/pubchem.substance/3535", + "http://identifiers.org/reactome/REACT_29800", + "http://identifiers.org/seed.compound/cpd00203", + "http://identifiers.org/unipathway.compound/UPC00236" + ] + } + ] + } }, "charge": -4, "compartment": "c", "formula": "C3H4O10P2", - "id": "13dpg_c", + "id": "M_13dpg_c", "name": "3-Phospho-D-glyceroyl phosphate" }, { "annotation": { - "bigg.metabolite": "2pg", - "biocyc": "2-PG", - "chebi": [ - "CHEBI:1267", - "CHEBI:58289", - "CHEBI:17835", - "CHEBI:21028", - "CHEBI:11651", - "CHEBI:12986", - "CHEBI:24344", - "CHEBI:39868" - ], - "hmdb": [ - "HMDB03391", - "HMDB00362" - ], - "kegg.compound": "C00631", - "pubchem.substance": "3904", - "reactome": "REACT_30485", - "seed.compound": "cpd00482", - "unipathway.compound": "UPC00631" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.metabolite/2pg", + "http://identifiers.org/biocyc/2-PG", + "http://identifiers.org/chebi/CHEBI:1267", + "http://identifiers.org/chebi/CHEBI:58289", + "http://identifiers.org/chebi/CHEBI:17835", + "http://identifiers.org/chebi/CHEBI:21028", + "http://identifiers.org/chebi/CHEBI:11651", + "http://identifiers.org/chebi/CHEBI:12986", + "http://identifiers.org/chebi/CHEBI:24344", + "http://identifiers.org/chebi/CHEBI:39868", + "http://identifiers.org/hmdb/HMDB03391", + "http://identifiers.org/hmdb/HMDB00362", + "http://identifiers.org/kegg.compound/C00631", + "http://identifiers.org/pubchem.substance/3904", + "http://identifiers.org/reactome/REACT_30485", + "http://identifiers.org/seed.compound/cpd00482", + "http://identifiers.org/unipathway.compound/UPC00631" + ] + } + ] + } }, "charge": -3, "compartment": "c", "formula": "C3H4O7P", - "id": "2pg_c", + "id": "M_2pg_c", "name": "D-Glycerate 2-phosphate" }, { "annotation": { - "bigg.metabolite": "3pg", - "biocyc": "G3P", - "chebi": [ - "CHEBI:40016", - "CHEBI:58272", - "CHEBI:57998", - "CHEBI:11879", - "CHEBI:1657", - "CHEBI:1659", - "CHEBI:17050", - "CHEBI:21029", - "CHEBI:11882", - "CHEBI:11880", - "CHEBI:12987", - "CHEBI:17794", - "CHEBI:24345" - ], - "hmdb": "HMDB00807", - "kegg.compound": [ - "C00197", - "C00597" - ], - "pubchem.substance": "3497", - "reactome": "REACT_29728", - "seed.compound": "cpd00169", - "unipathway.compound": [ - "UPC00597", - "UPC00197" - ] + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.metabolite/3pg", + "http://identifiers.org/biocyc/G3P", + "http://identifiers.org/chebi/CHEBI:40016", + "http://identifiers.org/chebi/CHEBI:58272", + "http://identifiers.org/chebi/CHEBI:57998", + "http://identifiers.org/chebi/CHEBI:11879", + "http://identifiers.org/chebi/CHEBI:1657", + "http://identifiers.org/chebi/CHEBI:1659", + "http://identifiers.org/chebi/CHEBI:17050", + "http://identifiers.org/chebi/CHEBI:21029", + "http://identifiers.org/chebi/CHEBI:11882", + "http://identifiers.org/chebi/CHEBI:11880", + "http://identifiers.org/chebi/CHEBI:12987", + "http://identifiers.org/chebi/CHEBI:17794", + "http://identifiers.org/chebi/CHEBI:24345", + "http://identifiers.org/hmdb/HMDB00807", + "http://identifiers.org/kegg.compound/C00197", + "http://identifiers.org/kegg.compound/C00597", + "http://identifiers.org/pubchem.substance/3497", + "http://identifiers.org/reactome/REACT_29728", + "http://identifiers.org/seed.compound/cpd00169", + "http://identifiers.org/unipathway.compound/UPC00597", + "http://identifiers.org/unipathway.compound/UPC00197" + ] + } + ] + } }, "charge": -3, "compartment": "c", "formula": "C3H4O7P", - "id": "3pg_c", + "id": "M_3pg_c", "name": "3-Phospho-D-glycerate" }, { "annotation": { - "bigg.metabolite": "adp", - "biocyc": [ - "ADP", - "ADP-GROUP" - ], - "cas": [ - "58-64-0" - ], - "chebi": [ - "CHEBI:13222", - "CHEBI:16761", - "CHEBI:2342", - "CHEBI:22244", - "CHEBI:40553", - "CHEBI:456216" - ], - "hmdb": "HMDB01341", - "kegg.compound": "C00008", - "kegg.glycan": "G11113", - "pubchem.substance": "3310", - "reactome": [ - "REACT_190072", - "REACT_481002", - "REACT_211606", - "REACT_429160", - "REACT_29370", - "REACT_196180", - "REACT_113581", - "REACT_113582", - "REACT_114564", - "REACT_114565", - "REACT_429153" - ], - "seed.compound": "cpd00008", - "unipathway.compound": "UPC00008" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.metabolite/adp", + "http://identifiers.org/biocyc/ADP", + "http://identifiers.org/biocyc/ADP-GROUP", + "http://identifiers.org/cas/58-64-0", + "http://identifiers.org/cas/58-64-0", + "http://identifiers.org/chebi/CHEBI:13222", + "http://identifiers.org/chebi/CHEBI:16761", + "http://identifiers.org/chebi/CHEBI:2342", + "http://identifiers.org/chebi/CHEBI:22244", + "http://identifiers.org/chebi/CHEBI:40553", + "http://identifiers.org/chebi/CHEBI:456216", + "http://identifiers.org/hmdb/HMDB01341", + "http://identifiers.org/kegg.compound/C00008", + "http://identifiers.org/kegg.glycan/G11113", + "http://identifiers.org/pubchem.substance/3310", + "http://identifiers.org/reactome/REACT_190072", + "http://identifiers.org/reactome/REACT_481002", + "http://identifiers.org/reactome/REACT_211606", + "http://identifiers.org/reactome/REACT_429160", + "http://identifiers.org/reactome/REACT_29370", + "http://identifiers.org/reactome/REACT_196180", + "http://identifiers.org/reactome/REACT_113581", + "http://identifiers.org/reactome/REACT_113582", + "http://identifiers.org/reactome/REACT_114564", + "http://identifiers.org/reactome/REACT_114565", + "http://identifiers.org/reactome/REACT_429153", + "http://identifiers.org/seed.compound/cpd00008", + "http://identifiers.org/unipathway.compound/UPC00008" + ] + } + ] + } }, "charge": -3, "compartment": "c", "formula": "C10H12N5O10P2", - 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"id": "atp_c", + "id": "M_atp_c", "name": "ATP" }, { "annotation": { - "bigg.metabolite": "dhap", - "biocyc": "DIHYDROXY-ACETONE-PHOSPHATE", - "cas": [ - "57-04-5" - ], - "chebi": [ - "CHEBI:14341", - "CHEBI:57642", - "CHEBI:14342", - "CHEBI:16108", - "CHEBI:5454", - "CHEBI:24355", - "CHEBI:39571" - ], - "hmdb": [ - "HMDB01473", - "HMDB11735" - ], - "kegg.compound": "C00111", - "pubchem.substance": "3411", - "reactome": [ - "REACT_188451", - "REACT_75970", - "REACT_390404" - ], - "seed.compound": "cpd00095", - "unipathway.compound": "UPC00111" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.metabolite/dhap", + "http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE", + "http://identifiers.org/cas/57-04-5", + "http://identifiers.org/cas/57-04-5", + "http://identifiers.org/chebi/CHEBI:14341", + "http://identifiers.org/chebi/CHEBI:57642", + "http://identifiers.org/chebi/CHEBI:14342", + "http://identifiers.org/chebi/CHEBI:16108", + "http://identifiers.org/chebi/CHEBI:5454", + "http://identifiers.org/chebi/CHEBI:24355", + "http://identifiers.org/chebi/CHEBI:39571", + "http://identifiers.org/hmdb/HMDB01473", + "http://identifiers.org/hmdb/HMDB11735", + "http://identifiers.org/kegg.compound/C00111", + "http://identifiers.org/pubchem.substance/3411", + "http://identifiers.org/reactome/REACT_188451", + "http://identifiers.org/reactome/REACT_75970", + "http://identifiers.org/reactome/REACT_390404", + "http://identifiers.org/seed.compound/cpd00095", + "http://identifiers.org/unipathway.compound/UPC00111" + ] + } + ] + } }, "charge": -2, "compartment": "c", "formula": "C3H5O6P", - "id": "dhap_c", + "id": "M_dhap_c", "name": "Dihydroxyacetone phosphate" }, { "annotation": { - "bigg.metabolite": "f6p", - "biocyc": "FRUCTOSE-6P", - "cas": [ - "643-13-0" - ], - "chebi": [ - "CHEBI:57634", - "CHEBI:12352", - "CHEBI:45804", - "CHEBI:61527", - "CHEBI:61553", - "CHEBI:10375", - "CHEBI:16084", - "CHEBI:42378", - "CHEBI:22768" - ], - "hmdb": "HMDB03971", - "kegg.compound": [ - "C05345", - "C00085" - ], - "pubchem.substance": "3385", - "seed.compound": "cpd00072", - "unipathway.compound": [ - "UPC05345", - "UPC00085" - ] + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.metabolite/f6p", + "http://identifiers.org/biocyc/FRUCTOSE-6P", + "http://identifiers.org/cas/643-13-0", + "http://identifiers.org/cas/643-13-0", + "http://identifiers.org/chebi/CHEBI:57634", + "http://identifiers.org/chebi/CHEBI:12352", + "http://identifiers.org/chebi/CHEBI:45804", + "http://identifiers.org/chebi/CHEBI:61527", + "http://identifiers.org/chebi/CHEBI:61553", + "http://identifiers.org/chebi/CHEBI:10375", + "http://identifiers.org/chebi/CHEBI:16084", + "http://identifiers.org/chebi/CHEBI:42378", + "http://identifiers.org/chebi/CHEBI:22768", + "http://identifiers.org/hmdb/HMDB03971", + "http://identifiers.org/kegg.compound/C05345", + "http://identifiers.org/kegg.compound/C00085", + "http://identifiers.org/pubchem.substance/3385", + "http://identifiers.org/seed.compound/cpd00072", + "http://identifiers.org/unipathway.compound/UPC05345", + "http://identifiers.org/unipathway.compound/UPC00085" + ] + } + ] + } }, "charge": -2, "compartment": "c", "formula": "C6H11O9P", - 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"bigg.reaction": "TPI" + "cvterms": { + "bqb_is": [ + { + "nested_data": {}, + "resources": [ + "http://identifiers.org/bigg.reaction/TPI" + ] + } + ] + } }, "gene_reaction_rule": "b3919", - "id": "TPI", + "id": "R_TPI", "lower_bound": -1000.0, "metabolites": { - "dhap_c": -1.0, - "g3p_c": 1.0 + "M_dhap_c": -1.0, + "M_g3p_c": 1.0 }, "name": "triose-phosphate isomerase", "upper_bound": 1000.0 diff --git a/src/cobra/data/mini.mat b/src/cobra/data/mini.mat index a470f0f50..27d43ce08 100644 Binary files a/src/cobra/data/mini.mat and b/src/cobra/data/mini.mat differ diff --git a/src/cobra/data/mini.pickle b/src/cobra/data/mini.pickle index 135ce225e..9c591745b 100644 Binary files a/src/cobra/data/mini.pickle and b/src/cobra/data/mini.pickle differ diff --git a/src/cobra/data/mini.yml b/src/cobra/data/mini.yml index e5e9e3b05..36dc27232 100644 --- a/src/cobra/data/mini.yml +++ b/src/cobra/data/mini.yml @@ -1,1167 +1,1278 @@ !!omap - metabolites: - !!omap - - id: 13dpg_c + - id: M_13dpg_c - name: 3-Phospho-D-glyceroyl phosphate - compartment: c - charge: -4 - formula: C3H4O10P2 - annotation: !!omap - - bigg.metabolite: 13dpg - - biocyc: DPG - - chebi: - - CHEBI:16001 - - CHEBI:1658 - - CHEBI:20189 - - CHEBI:57604 - - CHEBI:11881 - - hmdb: HMDB01270 - - kegg.compound: C00236 - - pubchem.substance: '3535' - - reactome: REACT_29800 - - seed.compound: cpd00203 - - unipathway.compound: UPC00236 - - !!omap - - id: 2pg_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/13dpg + - http://identifiers.org/biocyc/DPG + - http://identifiers.org/chebi/CHEBI:16001 + - http://identifiers.org/chebi/CHEBI:1658 + - http://identifiers.org/chebi/CHEBI:20189 + - http://identifiers.org/chebi/CHEBI:57604 + - http://identifiers.org/chebi/CHEBI:11881 + - http://identifiers.org/hmdb/HMDB01270 + - http://identifiers.org/kegg.compound/C00236 + - http://identifiers.org/pubchem.substance/3535 + - http://identifiers.org/reactome/REACT_29800 + - http://identifiers.org/seed.compound/cpd00203 + - http://identifiers.org/unipathway.compound/UPC00236 + nested_data: !!omap [] + - !!omap + - id: M_2pg_c - name: D-Glycerate 2-phosphate - compartment: c - charge: -3 - formula: C3H4O7P - annotation: !!omap - - bigg.metabolite: 2pg - - biocyc: 2-PG - - chebi: - - CHEBI:1267 - - CHEBI:58289 - - CHEBI:17835 - - CHEBI:21028 - - CHEBI:11651 - - CHEBI:12986 - - CHEBI:24344 - - CHEBI:39868 - - hmdb: - - HMDB03391 - - HMDB00362 - - kegg.compound: C00631 - - pubchem.substance: '3904' - - reactome: REACT_30485 - - seed.compound: cpd00482 - - unipathway.compound: UPC00631 - - !!omap - - id: 3pg_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/2pg + - http://identifiers.org/biocyc/2-PG + - http://identifiers.org/chebi/CHEBI:1267 + - http://identifiers.org/chebi/CHEBI:58289 + - http://identifiers.org/chebi/CHEBI:17835 + - http://identifiers.org/chebi/CHEBI:21028 + - http://identifiers.org/chebi/CHEBI:11651 + - http://identifiers.org/chebi/CHEBI:12986 + - http://identifiers.org/chebi/CHEBI:24344 + - http://identifiers.org/chebi/CHEBI:39868 + - http://identifiers.org/hmdb/HMDB03391 + - http://identifiers.org/hmdb/HMDB00362 + - http://identifiers.org/kegg.compound/C00631 + - http://identifiers.org/pubchem.substance/3904 + - http://identifiers.org/reactome/REACT_30485 + - http://identifiers.org/seed.compound/cpd00482 + - http://identifiers.org/unipathway.compound/UPC00631 + nested_data: !!omap [] + - !!omap + - id: M_3pg_c - name: 3-Phospho-D-glycerate - compartment: c - charge: -3 - formula: C3H4O7P - annotation: !!omap - - bigg.metabolite: 3pg - - biocyc: G3P - - chebi: - - CHEBI:40016 - - CHEBI:58272 - - CHEBI:57998 - - CHEBI:11879 - - CHEBI:1657 - - CHEBI:1659 - - CHEBI:17050 - - CHEBI:21029 - - CHEBI:11882 - - CHEBI:11880 - - CHEBI:12987 - - CHEBI:17794 - - CHEBI:24345 - - hmdb: HMDB00807 - - kegg.compound: - - C00197 - - C00597 - - pubchem.substance: '3497' - - reactome: REACT_29728 - - seed.compound: cpd00169 - - unipathway.compound: - - UPC00597 - - UPC00197 - - !!omap - - id: adp_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/3pg + - http://identifiers.org/biocyc/G3P + - http://identifiers.org/chebi/CHEBI:40016 + - http://identifiers.org/chebi/CHEBI:58272 + - http://identifiers.org/chebi/CHEBI:57998 + - http://identifiers.org/chebi/CHEBI:11879 + - http://identifiers.org/chebi/CHEBI:1657 + - http://identifiers.org/chebi/CHEBI:1659 + - http://identifiers.org/chebi/CHEBI:17050 + - http://identifiers.org/chebi/CHEBI:21029 + - http://identifiers.org/chebi/CHEBI:11882 + - http://identifiers.org/chebi/CHEBI:11880 + - http://identifiers.org/chebi/CHEBI:12987 + - http://identifiers.org/chebi/CHEBI:17794 + - http://identifiers.org/chebi/CHEBI:24345 + - http://identifiers.org/hmdb/HMDB00807 + - http://identifiers.org/kegg.compound/C00197 + - http://identifiers.org/kegg.compound/C00597 + - http://identifiers.org/pubchem.substance/3497 + - http://identifiers.org/reactome/REACT_29728 + - http://identifiers.org/seed.compound/cpd00169 + - http://identifiers.org/unipathway.compound/UPC00597 + - http://identifiers.org/unipathway.compound/UPC00197 + nested_data: !!omap [] + - !!omap + - id: M_adp_c - name: ADP - compartment: c - charge: -3 - formula: C10H12N5O10P2 - annotation: !!omap - - bigg.metabolite: adp - - biocyc: - - ADP - - ADP-GROUP - - cas: - - 58-64-0 - - chebi: - - CHEBI:13222 - - CHEBI:16761 - - CHEBI:2342 - - CHEBI:22244 - - CHEBI:40553 - - CHEBI:456216 - - hmdb: HMDB01341 - - kegg.compound: C00008 - - kegg.glycan: G11113 - - pubchem.substance: '3310' - - reactome: - - REACT_190072 - - REACT_481002 - - REACT_211606 - - REACT_429160 - - REACT_29370 - - REACT_196180 - - REACT_113581 - - REACT_113582 - - REACT_114564 - - REACT_114565 - - REACT_429153 - - seed.compound: cpd00008 - - unipathway.compound: UPC00008 - - !!omap - - id: atp_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/adp + - http://identifiers.org/biocyc/ADP + - http://identifiers.org/biocyc/ADP-GROUP + - http://identifiers.org/cas/58-64-0 + - http://identifiers.org/cas/58-64-0 + - http://identifiers.org/chebi/CHEBI:13222 + - http://identifiers.org/chebi/CHEBI:16761 + - http://identifiers.org/chebi/CHEBI:2342 + - http://identifiers.org/chebi/CHEBI:22244 + - http://identifiers.org/chebi/CHEBI:40553 + - http://identifiers.org/chebi/CHEBI:456216 + - http://identifiers.org/hmdb/HMDB01341 + - http://identifiers.org/kegg.compound/C00008 + - http://identifiers.org/kegg.glycan/G11113 + - http://identifiers.org/pubchem.substance/3310 + - http://identifiers.org/reactome/REACT_190072 + - http://identifiers.org/reactome/REACT_481002 + - http://identifiers.org/reactome/REACT_211606 + - http://identifiers.org/reactome/REACT_429160 + - http://identifiers.org/reactome/REACT_29370 + - http://identifiers.org/reactome/REACT_196180 + - http://identifiers.org/reactome/REACT_113581 + - http://identifiers.org/reactome/REACT_113582 + - http://identifiers.org/reactome/REACT_114564 + - http://identifiers.org/reactome/REACT_114565 + - http://identifiers.org/reactome/REACT_429153 + - http://identifiers.org/seed.compound/cpd00008 + - http://identifiers.org/unipathway.compound/UPC00008 + nested_data: !!omap [] + - !!omap + - id: M_atp_c - name: ATP - compartment: c - charge: -4 - formula: C10H12N5O13P3 - annotation: !!omap - - bigg.metabolite: atp - - biocyc: ATP - - cas: - - 56-65-5 - - chebi: - - CHEBI:40938 - - CHEBI:15422 - - CHEBI:57299 - - CHEBI:13236 - - CHEBI:10789 - - CHEBI:30616 - - CHEBI:22249 - - CHEBI:10841 - - CHEBI:2359 - - hmdb: HMDB00538 - - kegg.compound: C00002 - - kegg.drug: D08646 - - pubchem.substance: '3304' - - reactome: - - REACT_190078 - - REACT_113592 - - REACT_113593 - - REACT_114570 - - REACT_29358 - - REACT_389573 - - REACT_139836 - - REACT_211579 - - seed.compound: cpd00002 - - unipathway.compound: UPC00002 - - !!omap - - id: dhap_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/atp + - http://identifiers.org/biocyc/ATP + - http://identifiers.org/cas/56-65-5 + - http://identifiers.org/cas/56-65-5 + - http://identifiers.org/chebi/CHEBI:40938 + - http://identifiers.org/chebi/CHEBI:15422 + - http://identifiers.org/chebi/CHEBI:57299 + - http://identifiers.org/chebi/CHEBI:13236 + - http://identifiers.org/chebi/CHEBI:10789 + - http://identifiers.org/chebi/CHEBI:30616 + - http://identifiers.org/chebi/CHEBI:22249 + - http://identifiers.org/chebi/CHEBI:10841 + - http://identifiers.org/chebi/CHEBI:2359 + - http://identifiers.org/hmdb/HMDB00538 + - http://identifiers.org/kegg.compound/C00002 + - http://identifiers.org/kegg.drug/D08646 + - http://identifiers.org/pubchem.substance/3304 + - http://identifiers.org/reactome/REACT_190078 + - http://identifiers.org/reactome/REACT_113592 + - http://identifiers.org/reactome/REACT_113593 + - http://identifiers.org/reactome/REACT_114570 + - http://identifiers.org/reactome/REACT_29358 + - http://identifiers.org/reactome/REACT_389573 + - http://identifiers.org/reactome/REACT_139836 + - http://identifiers.org/reactome/REACT_211579 + - http://identifiers.org/seed.compound/cpd00002 + - http://identifiers.org/unipathway.compound/UPC00002 + nested_data: !!omap [] + - !!omap + - id: M_dhap_c - name: Dihydroxyacetone phosphate - compartment: c - charge: -2 - formula: C3H5O6P - annotation: !!omap - - bigg.metabolite: dhap - - biocyc: DIHYDROXY-ACETONE-PHOSPHATE - - cas: - - 57-04-5 - - chebi: - - CHEBI:14341 - - CHEBI:57642 - - CHEBI:14342 - - CHEBI:16108 - - CHEBI:5454 - - CHEBI:24355 - - CHEBI:39571 - - hmdb: - - HMDB01473 - - HMDB11735 - - kegg.compound: C00111 - - pubchem.substance: '3411' - - reactome: - - REACT_188451 - - REACT_75970 - - REACT_390404 - - seed.compound: cpd00095 - - unipathway.compound: UPC00111 - - !!omap - - id: f6p_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/dhap + - http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE + - http://identifiers.org/cas/57-04-5 + - http://identifiers.org/cas/57-04-5 + - http://identifiers.org/chebi/CHEBI:14341 + - http://identifiers.org/chebi/CHEBI:57642 + - http://identifiers.org/chebi/CHEBI:14342 + - http://identifiers.org/chebi/CHEBI:16108 + - http://identifiers.org/chebi/CHEBI:5454 + - http://identifiers.org/chebi/CHEBI:24355 + - http://identifiers.org/chebi/CHEBI:39571 + - http://identifiers.org/hmdb/HMDB01473 + - http://identifiers.org/hmdb/HMDB11735 + - http://identifiers.org/kegg.compound/C00111 + - http://identifiers.org/pubchem.substance/3411 + - http://identifiers.org/reactome/REACT_188451 + - http://identifiers.org/reactome/REACT_75970 + - http://identifiers.org/reactome/REACT_390404 + - http://identifiers.org/seed.compound/cpd00095 + - http://identifiers.org/unipathway.compound/UPC00111 + nested_data: !!omap [] + - !!omap + - id: M_f6p_c - name: D-Fructose 6-phosphate - compartment: c - charge: -2 - formula: C6H11O9P - annotation: !!omap - - bigg.metabolite: f6p - - biocyc: FRUCTOSE-6P - - cas: - - 643-13-0 - - chebi: - - CHEBI:57634 - - CHEBI:12352 - - CHEBI:45804 - - CHEBI:61527 - - CHEBI:61553 - - CHEBI:10375 - - CHEBI:16084 - - CHEBI:42378 - - CHEBI:22768 - - hmdb: HMDB03971 - - kegg.compound: - - C05345 - - C00085 - - pubchem.substance: '3385' - - seed.compound: cpd00072 - - unipathway.compound: - - UPC05345 - - UPC00085 - - !!omap - - id: fdp_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/f6p + - http://identifiers.org/biocyc/FRUCTOSE-6P + - http://identifiers.org/cas/643-13-0 + - http://identifiers.org/cas/643-13-0 + - http://identifiers.org/chebi/CHEBI:57634 + - http://identifiers.org/chebi/CHEBI:12352 + - http://identifiers.org/chebi/CHEBI:45804 + - http://identifiers.org/chebi/CHEBI:61527 + - http://identifiers.org/chebi/CHEBI:61553 + - http://identifiers.org/chebi/CHEBI:10375 + - http://identifiers.org/chebi/CHEBI:16084 + - http://identifiers.org/chebi/CHEBI:42378 + - http://identifiers.org/chebi/CHEBI:22768 + - http://identifiers.org/hmdb/HMDB03971 + - http://identifiers.org/kegg.compound/C05345 + - http://identifiers.org/kegg.compound/C00085 + - http://identifiers.org/pubchem.substance/3385 + - http://identifiers.org/seed.compound/cpd00072 + - http://identifiers.org/unipathway.compound/UPC05345 + - http://identifiers.org/unipathway.compound/UPC00085 + nested_data: !!omap [] + - !!omap + - id: M_fdp_c - name: D-Fructose 1,6-bisphosphate - compartment: c - charge: -4 - formula: C6H10O12P2 - annotation: !!omap - - bigg.metabolite: fdp - - biocyc: FRUCTOSE-16-DIPHOSPHATE - - cas: - - 488-69-7 - - chebi: - - CHEBI:32968 - - CHEBI:49299 - - CHEBI:42553 - - CHEBI:32966 - - CHEBI:37736 - - CHEBI:28013 - - CHEBI:32967 - - CHEBI:41014 - - CHEBI:22767 - - CHEBI:10374 - - CHEBI:40595 - - CHEBI:40591 - - kegg.compound: - - C05378 - - C00354 - - pubchem.substance: '3647' - - seed.compound: cpd00290 - - unipathway.compound: UPC00354 - - !!omap - - id: g3p_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/fdp + - http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE + - http://identifiers.org/cas/488-69-7 + - http://identifiers.org/cas/488-69-7 + - http://identifiers.org/chebi/CHEBI:32968 + - http://identifiers.org/chebi/CHEBI:49299 + - http://identifiers.org/chebi/CHEBI:42553 + - http://identifiers.org/chebi/CHEBI:32966 + - http://identifiers.org/chebi/CHEBI:37736 + - http://identifiers.org/chebi/CHEBI:28013 + - http://identifiers.org/chebi/CHEBI:32967 + - http://identifiers.org/chebi/CHEBI:41014 + - http://identifiers.org/chebi/CHEBI:22767 + - http://identifiers.org/chebi/CHEBI:10374 + - http://identifiers.org/chebi/CHEBI:40595 + - http://identifiers.org/chebi/CHEBI:40591 + - http://identifiers.org/kegg.compound/C05378 + - http://identifiers.org/kegg.compound/C00354 + - http://identifiers.org/pubchem.substance/3647 + - http://identifiers.org/seed.compound/cpd00290 + - http://identifiers.org/unipathway.compound/UPC00354 + nested_data: !!omap [] + - !!omap + - id: M_g3p_c - name: Glyceraldehyde 3-phosphate - compartment: c - charge: -2 - formula: C3H5O6P - annotation: !!omap - - bigg.metabolite: g3p - - cas: - - 142-10-9 - - chebi: - - CHEBI:17138 - - CHEBI:14333 - - CHEBI:5446 - - CHEBI:58027 - - hmdb: HMDB01112 - - kegg.compound: - - C00661 - - C00118 - - pubchem.substance: '3930' - - seed.compound: cpd00102 - - unipathway.compound: - - UPC00661 - - UPC00118 - - !!omap - - id: g6p_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/g3p + - http://identifiers.org/cas/142-10-9 + - http://identifiers.org/cas/142-10-9 + - http://identifiers.org/chebi/CHEBI:17138 + - http://identifiers.org/chebi/CHEBI:14333 + - http://identifiers.org/chebi/CHEBI:5446 + - http://identifiers.org/chebi/CHEBI:58027 + - http://identifiers.org/hmdb/HMDB01112 + - http://identifiers.org/kegg.compound/C00661 + - http://identifiers.org/kegg.compound/C00118 + - http://identifiers.org/pubchem.substance/3930 + - http://identifiers.org/seed.compound/cpd00102 + - http://identifiers.org/unipathway.compound/UPC00661 + - http://identifiers.org/unipathway.compound/UPC00118 + nested_data: !!omap [] + - !!omap + - id: M_g6p_c - name: D-Glucose 6-phosphate - compartment: c - charge: -2 - formula: C6H11O9P - annotation: !!omap - - bigg.metabolite: g6p - - biocyc: - - D-glucose-6-phosphate - - GLC-6-P - - cas: - - 56-73-5 - - chebi: - - CHEBI:10399 - - CHEBI:22797 - - CHEBI:41041 - - CHEBI:17719 - - CHEBI:4170 - - CHEBI:61548 - - CHEBI:58247 - - CHEBI:12375 - - hmdb: - - HMDB03498 - - HMDB06793 - - HMDB01401 - - HMDB01549 - - kegg.compound: - - C00092 - - C01172 - - pubchem.substance: '3392' - - reactome: REACT_1629756 - - seed.compound: cpd00079 - - unipathway.compound: UPC00092 - - !!omap - - id: glc__D_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/g6p + - http://identifiers.org/biocyc/D-glucose-6-phosphate + - http://identifiers.org/biocyc/GLC-6-P + - http://identifiers.org/cas/56-73-5 + - http://identifiers.org/cas/56-73-5 + - http://identifiers.org/chebi/CHEBI:10399 + - http://identifiers.org/chebi/CHEBI:22797 + - http://identifiers.org/chebi/CHEBI:41041 + - http://identifiers.org/chebi/CHEBI:17719 + - http://identifiers.org/chebi/CHEBI:4170 + - http://identifiers.org/chebi/CHEBI:61548 + - http://identifiers.org/chebi/CHEBI:58247 + - http://identifiers.org/chebi/CHEBI:12375 + - http://identifiers.org/hmdb/HMDB03498 + - http://identifiers.org/hmdb/HMDB06793 + - http://identifiers.org/hmdb/HMDB01401 + - http://identifiers.org/hmdb/HMDB01549 + - http://identifiers.org/kegg.compound/C00092 + - http://identifiers.org/kegg.compound/C01172 + - http://identifiers.org/pubchem.substance/3392 + - http://identifiers.org/reactome/REACT_1629756 + - http://identifiers.org/seed.compound/cpd00079 + - http://identifiers.org/unipathway.compound/UPC00092 + nested_data: !!omap [] + - !!omap + - id: M_glc__D_e - name: D-Glucose - compartment: e - charge: 0 - formula: C6H12O6 - annotation: !!omap - - bigg.metabolite: glc__D - - cas: - - 50-99-7 - - kegg.compound: C00031 - - pubchem.substance: '3333' - - !!omap - - id: h2o_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/glc__D + - http://identifiers.org/cas/50-99-7 + - http://identifiers.org/cas/50-99-7 + - http://identifiers.org/kegg.compound/C00031 + - http://identifiers.org/pubchem.substance/3333 + nested_data: !!omap [] + - !!omap + - id: M_h2o_c - name: H2O - compartment: c - charge: 0 - formula: H2O - annotation: !!omap - - bigg.metabolite: h2o - - biocyc: - - WATER - - OH - - OXONIUM - - cas: - - 7732-18-5 - - chebi: - - CHEBI:15377 - - CHEBI:13365 - - CHEBI:41979 - - CHEBI:16234 - - CHEBI:36385 - - CHEBI:42857 - - CHEBI:27313 - - CHEBI:44819 - - CHEBI:29373 - - CHEBI:10743 - - CHEBI:5594 - - CHEBI:29356 - - CHEBI:53442 - - CHEBI:29375 - - CHEBI:29374 - - CHEBI:13419 - - CHEBI:43228 - - CHEBI:44292 - - CHEBI:13352 - - CHEBI:41981 - - CHEBI:29412 - - CHEBI:42043 - - CHEBI:33811 - - CHEBI:33813 - - CHEBI:35511 - - CHEBI:5585 - - CHEBI:44641 - - CHEBI:44701 - - hmdb: - - HMDB01039 - - HMDB02111 - - kegg.compound: - - C01328 - - C00001 - - C18714 - - C18712 - - kegg.drug: - - D00001 - - D06322 - - D03703 - - pubchem.substance: '3303' - - reactome: - - REACT_947593 - - REACT_189422 - - REACT_141343 - - REACT_113518 - - REACT_1605715 - - REACT_109276 - - REACT_113521 - - REACT_113519 - - REACT_2022884 - - REACT_351603 - - REACT_29356 - - seed.compound: - - cpd15275 - - cpd00001 - - unipathway.compound: - - UPC00001 - - UPC01328 - - !!omap - - id: h2o_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h2o + - http://identifiers.org/biocyc/WATER + - http://identifiers.org/biocyc/OH + - http://identifiers.org/biocyc/OXONIUM + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/chebi/CHEBI:15377 + - http://identifiers.org/chebi/CHEBI:13365 + - http://identifiers.org/chebi/CHEBI:41979 + - http://identifiers.org/chebi/CHEBI:16234 + - http://identifiers.org/chebi/CHEBI:36385 + - http://identifiers.org/chebi/CHEBI:42857 + - http://identifiers.org/chebi/CHEBI:27313 + - http://identifiers.org/chebi/CHEBI:44819 + - http://identifiers.org/chebi/CHEBI:29373 + - http://identifiers.org/chebi/CHEBI:10743 + - http://identifiers.org/chebi/CHEBI:5594 + - 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charge: 0 - formula: H2O - annotation: !!omap - - bigg.metabolite: h2o - - biocyc: - - WATER - - OH - - OXONIUM - - cas: - - 7732-18-5 - - chebi: - - CHEBI:15377 - - CHEBI:13365 - - CHEBI:41979 - - CHEBI:16234 - - CHEBI:36385 - - CHEBI:42857 - - CHEBI:27313 - - CHEBI:44819 - - CHEBI:29373 - - CHEBI:10743 - - CHEBI:5594 - - CHEBI:29356 - - CHEBI:53442 - - CHEBI:29375 - - CHEBI:29374 - - CHEBI:13419 - - CHEBI:43228 - - CHEBI:44292 - - CHEBI:13352 - - CHEBI:41981 - - CHEBI:29412 - - CHEBI:42043 - - CHEBI:33811 - - CHEBI:33813 - - CHEBI:35511 - - CHEBI:5585 - - CHEBI:44641 - - CHEBI:44701 - - hmdb: - - HMDB01039 - - HMDB02111 - - kegg.compound: - - C01328 - - C00001 - - C18714 - - C18712 - - kegg.drug: - - D00001 - - D06322 - - D03703 - - pubchem.substance: '3303' - - reactome: - - REACT_947593 - - REACT_189422 - - REACT_141343 - - REACT_113518 - - REACT_1605715 - - REACT_109276 - - REACT_113521 - - REACT_113519 - - REACT_2022884 - - REACT_351603 - - REACT_29356 - - seed.compound: - - cpd15275 - - cpd00001 - - unipathway.compound: - - UPC00001 - - UPC01328 - - !!omap - - id: h_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h2o + - http://identifiers.org/biocyc/WATER + - http://identifiers.org/biocyc/OH + - http://identifiers.org/biocyc/OXONIUM + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/chebi/CHEBI:15377 + - http://identifiers.org/chebi/CHEBI:13365 + - http://identifiers.org/chebi/CHEBI:41979 + - http://identifiers.org/chebi/CHEBI:16234 + - http://identifiers.org/chebi/CHEBI:36385 + - http://identifiers.org/chebi/CHEBI:42857 + - http://identifiers.org/chebi/CHEBI:27313 + - http://identifiers.org/chebi/CHEBI:44819 + - http://identifiers.org/chebi/CHEBI:29373 + - http://identifiers.org/chebi/CHEBI:10743 + - http://identifiers.org/chebi/CHEBI:5594 + - http://identifiers.org/chebi/CHEBI:29356 + - http://identifiers.org/chebi/CHEBI:53442 + - http://identifiers.org/chebi/CHEBI:29375 + - 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- CHEBI:24636 - - CHEBI:15378 - - CHEBI:10744 - - CHEBI:13357 - - CHEBI:5584 - - kegg.compound: C00080 - - pubchem.substance: '3380' - - reactome: - - REACT_194688 - - REACT_425978 - - REACT_193465 - - REACT_374900 - - REACT_74722 - - REACT_425999 - - REACT_428040 - - REACT_163953 - - REACT_372511 - - REACT_2000349 - - REACT_70106 - - REACT_1470067 - - REACT_113529 - - REACT_425969 - - REACT_428548 - - REACT_156540 - - REACT_1614597 - - REACT_351626 - - REACT_427899 - - seed.compound: cpd00067 - - unipathway.compound: UPC00080 - - !!omap - - id: h_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h + - http://identifiers.org/biocyc/PROTON + - http://identifiers.org/cas/12408-02-5 + - http://identifiers.org/cas/12408-02-5 + - http://identifiers.org/chebi/CHEBI:24636 + - http://identifiers.org/chebi/CHEBI:15378 + - http://identifiers.org/chebi/CHEBI:10744 + - http://identifiers.org/chebi/CHEBI:13357 + - http://identifiers.org/chebi/CHEBI:5584 + - 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http://identifiers.org/chebi/CHEBI:11001 + - http://identifiers.org/chebi/CHEBI:16004 + - http://identifiers.org/chebi/CHEBI:18684 + - http://identifiers.org/chebi/CHEBI:341 + - http://identifiers.org/chebi/CHEBI:42105 + - http://identifiers.org/chebi/CHEBI:42111 + - http://identifiers.org/chebi/CHEBI:43701 + - http://identifiers.org/hmdb/HMDB00171 + - http://identifiers.org/hmdb/HMDB01311 + - http://identifiers.org/kegg.compound/C00256 + - http://identifiers.org/metanetx.chemical/MNXM285 + - http://identifiers.org/seed.compound/cpd00221 + nested_data: !!omap [] + - !!omap + - id: M_lac__D_e - name: D-Lactate - compartment: e - charge: -1 - formula: C3H5O3 - annotation: !!omap - - bigg.metabolite: lac__D - - biocyc: META:D-LACTATE - - chebi: - - CHEBI:11001 - - CHEBI:16004 - - CHEBI:18684 - - CHEBI:341 - - CHEBI:42105 - - CHEBI:42111 - - CHEBI:43701 - - hmdb: - - HMDB00171 - - HMDB01311 - - kegg.compound: C00256 - - metanetx.chemical: MNXM285 - - seed.compound: cpd00221 - - !!omap - - id: nad_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/lac__D + - http://identifiers.org/biocyc/META:D-LACTATE + - http://identifiers.org/chebi/CHEBI:11001 + - http://identifiers.org/chebi/CHEBI:16004 + - http://identifiers.org/chebi/CHEBI:18684 + - http://identifiers.org/chebi/CHEBI:341 + - http://identifiers.org/chebi/CHEBI:42105 + - http://identifiers.org/chebi/CHEBI:42111 + - http://identifiers.org/chebi/CHEBI:43701 + - http://identifiers.org/hmdb/HMDB00171 + - http://identifiers.org/hmdb/HMDB01311 + - http://identifiers.org/kegg.compound/C00256 + - http://identifiers.org/metanetx.chemical/MNXM285 + - http://identifiers.org/seed.compound/cpd00221 + nested_data: !!omap [] + - !!omap + - id: M_nad_c - name: Nicotinamide adenine dinucleotide - compartment: c - charge: -1 - formula: C21H26N7O14P2 - annotation: !!omap - - bigg.metabolite: nad - - biocyc: NAD - - cas: - - 53-84-9 - - chebi: - - CHEBI:21901 - - CHEBI:7422 - - CHEBI:44214 - - CHEBI:15846 - - CHEBI:13394 - - CHEBI:13393 - - CHEBI:44215 - - CHEBI:13389 - - CHEBI:57540 - - CHEBI:44281 - - hmdb: HMDB00902 - - kegg.compound: C00003 - - kegg.drug: D00002 - - pubchem.substance: '3305' - - reactome: - - REACT_192307 - - REACT_29360 - - REACT_427523 - - REACT_194653 - - REACT_113526 - - seed.compound: cpd00003 - - unipathway.compound: UPC00003 - - !!omap - - id: nadh_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/nad + - http://identifiers.org/biocyc/NAD + - http://identifiers.org/cas/53-84-9 + - http://identifiers.org/cas/53-84-9 + - http://identifiers.org/chebi/CHEBI:21901 + - http://identifiers.org/chebi/CHEBI:7422 + - http://identifiers.org/chebi/CHEBI:44214 + - http://identifiers.org/chebi/CHEBI:15846 + - http://identifiers.org/chebi/CHEBI:13394 + - http://identifiers.org/chebi/CHEBI:13393 + - http://identifiers.org/chebi/CHEBI:44215 + - http://identifiers.org/chebi/CHEBI:13389 + - http://identifiers.org/chebi/CHEBI:57540 + - http://identifiers.org/chebi/CHEBI:44281 + - 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- REACT_73473 - - REACT_194697 - - REACT_29362 - - seed.compound: cpd00004 - - unipathway.compound: UPC00004 - - !!omap - - id: pep_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/nadh + - http://identifiers.org/biocyc/NADH + - http://identifiers.org/cas/58-68-4 + - http://identifiers.org/cas/58-68-4 + - http://identifiers.org/chebi/CHEBI:13395 + - http://identifiers.org/chebi/CHEBI:21902 + - http://identifiers.org/chebi/CHEBI:16908 + - http://identifiers.org/chebi/CHEBI:7423 + - http://identifiers.org/chebi/CHEBI:44216 + - http://identifiers.org/chebi/CHEBI:57945 + - http://identifiers.org/chebi/CHEBI:13396 + - http://identifiers.org/hmdb/HMDB01487 + - http://identifiers.org/kegg.compound/C00004 + - http://identifiers.org/pubchem.substance/3306 + - http://identifiers.org/reactome/REACT_192305 + - http://identifiers.org/reactome/REACT_73473 + - http://identifiers.org/reactome/REACT_194697 + - http://identifiers.org/reactome/REACT_29362 + - http://identifiers.org/seed.compound/cpd00004 + - http://identifiers.org/unipathway.compound/UPC00004 + nested_data: !!omap [] + - !!omap + - id: M_pep_c - name: Phosphoenolpyruvate - compartment: c - charge: -3 - formula: C3H2O6P - annotation: !!omap - - bigg.metabolite: pep - - biocyc: PHOSPHO-ENOL-PYRUVATE - - cas: - - 138-08-9 - - chebi: - - CHEBI:44897 - - CHEBI:44894 - - CHEBI:14812 - - CHEBI:8147 - - CHEBI:26055 - - CHEBI:26054 - - CHEBI:58702 - - CHEBI:18021 - - hmdb: HMDB00263 - - kegg.compound: C00074 - - pubchem.substance: '3374' - - reactome: - - REACT_29492 - - REACT_372364 - - seed.compound: cpd00061 - - unipathway.compound: UPC00074 - - !!omap - - id: pi_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/pep + - http://identifiers.org/biocyc/PHOSPHO-ENOL-PYRUVATE + - http://identifiers.org/cas/138-08-9 + - http://identifiers.org/cas/138-08-9 + - http://identifiers.org/chebi/CHEBI:44897 + - http://identifiers.org/chebi/CHEBI:44894 + - http://identifiers.org/chebi/CHEBI:14812 + - http://identifiers.org/chebi/CHEBI:8147 + - http://identifiers.org/chebi/CHEBI:26055 + - http://identifiers.org/chebi/CHEBI:26054 + - http://identifiers.org/chebi/CHEBI:58702 + - http://identifiers.org/chebi/CHEBI:18021 + - http://identifiers.org/hmdb/HMDB00263 + - http://identifiers.org/kegg.compound/C00074 + - http://identifiers.org/pubchem.substance/3374 + - http://identifiers.org/reactome/REACT_29492 + - http://identifiers.org/reactome/REACT_372364 + - http://identifiers.org/seed.compound/cpd00061 + - http://identifiers.org/unipathway.compound/UPC00074 + nested_data: !!omap [] + - !!omap + - id: M_pi_c - name: Phosphate - compartment: c - charge: -2 - formula: HO4P - annotation: !!omap - - bigg.metabolite: pi - - biocyc: - - Pi - - PHOSPHATE-GROUP - - CPD0-1421 - - cas: - - 14265-44-2 - - chebi: - - CHEBI:37583 - - CHEBI:7793 - - CHEBI:37585 - - CHEBI:34683 - - CHEBI:14791 - - CHEBI:34855 - - CHEBI:29137 - - CHEBI:29139 - - CHEBI:63036 - - CHEBI:26020 - - CHEBI:39739 - - CHEBI:32597 - - CHEBI:32596 - - CHEBI:43474 - - CHEBI:63051 - - CHEBI:43470 - - CHEBI:9679 - - CHEBI:35433 - - CHEBI:4496 - - CHEBI:45024 - - CHEBI:18367 - - CHEBI:26078 - - CHEBI:39745 - - CHEBI:24838 - - hmdb: HMDB02142 - - kegg.compound: - - C13556 - - C13558 - - C00009 - - kegg.drug: D05467 - - pubchem.substance: '3311' - - reactome: - - REACT_947590 - - REACT_109277 - - REACT_113548 - - REACT_2255331 - - REACT_29372 - - REACT_113550 - - REACT_113551 - - seed.compound: - - cpd09464 - - cpd09463 - - cpd00009 - - unipathway.compound: UPC00009 - - !!omap - - id: pi_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/pi + - http://identifiers.org/biocyc/Pi + - http://identifiers.org/biocyc/PHOSPHATE-GROUP + - http://identifiers.org/biocyc/CPD0-1421 + - http://identifiers.org/cas/14265-44-2 + - http://identifiers.org/cas/14265-44-2 + - http://identifiers.org/chebi/CHEBI:37583 + - http://identifiers.org/chebi/CHEBI:7793 + - http://identifiers.org/chebi/CHEBI:37585 + - http://identifiers.org/chebi/CHEBI:34683 + - http://identifiers.org/chebi/CHEBI:14791 + - http://identifiers.org/chebi/CHEBI:34855 + - http://identifiers.org/chebi/CHEBI:29137 + - http://identifiers.org/chebi/CHEBI:29139 + - http://identifiers.org/chebi/CHEBI:63036 + - http://identifiers.org/chebi/CHEBI:26020 + - http://identifiers.org/chebi/CHEBI:39739 + - http://identifiers.org/chebi/CHEBI:32597 + - http://identifiers.org/chebi/CHEBI:32596 + - http://identifiers.org/chebi/CHEBI:43474 + - http://identifiers.org/chebi/CHEBI:63051 + - http://identifiers.org/chebi/CHEBI:43470 + - http://identifiers.org/chebi/CHEBI:9679 + - http://identifiers.org/chebi/CHEBI:35433 + - http://identifiers.org/chebi/CHEBI:4496 + - http://identifiers.org/chebi/CHEBI:45024 + - http://identifiers.org/chebi/CHEBI:18367 + - http://identifiers.org/chebi/CHEBI:26078 + - http://identifiers.org/chebi/CHEBI:39745 + - http://identifiers.org/chebi/CHEBI:24838 + - http://identifiers.org/hmdb/HMDB02142 + - http://identifiers.org/kegg.compound/C13556 + - http://identifiers.org/kegg.compound/C13558 + - http://identifiers.org/kegg.compound/C00009 + - http://identifiers.org/kegg.drug/D05467 + - http://identifiers.org/pubchem.substance/3311 + - http://identifiers.org/reactome/REACT_947590 + - http://identifiers.org/reactome/REACT_109277 + - http://identifiers.org/reactome/REACT_113548 + - http://identifiers.org/reactome/REACT_2255331 + - http://identifiers.org/reactome/REACT_29372 + - http://identifiers.org/reactome/REACT_113550 + - http://identifiers.org/reactome/REACT_113551 + - http://identifiers.org/seed.compound/cpd09464 + - http://identifiers.org/seed.compound/cpd09463 + - http://identifiers.org/seed.compound/cpd00009 + - http://identifiers.org/unipathway.compound/UPC00009 + nested_data: !!omap [] + - !!omap + - id: M_pi_e - name: Phosphate - compartment: e - charge: -2 - formula: HO4P - annotation: !!omap - - bigg.metabolite: pi - - biocyc: - - Pi - - PHOSPHATE-GROUP - - CPD0-1421 - - cas: - - 14265-44-2 - - chebi: - - CHEBI:37583 - - CHEBI:7793 - - CHEBI:37585 - - CHEBI:34683 - - CHEBI:14791 - - CHEBI:34855 - - CHEBI:29137 - - CHEBI:29139 - - CHEBI:63036 - - CHEBI:26020 - - CHEBI:39739 - - CHEBI:32597 - - CHEBI:32596 - - CHEBI:43474 - - CHEBI:63051 - - CHEBI:43470 - - CHEBI:9679 - - CHEBI:35433 - - CHEBI:4496 - - CHEBI:45024 - - CHEBI:18367 - - CHEBI:26078 - - CHEBI:39745 - - CHEBI:24838 - - hmdb: HMDB02142 - - kegg.compound: - - C13556 - - C13558 - - C00009 - - kegg.drug: D05467 - - pubchem.substance: '3311' - - reactome: - - REACT_947590 - - REACT_109277 - - REACT_113548 - - REACT_2255331 - - REACT_29372 - - REACT_113550 - - REACT_113551 - - seed.compound: - - cpd09464 - - cpd09463 - - cpd00009 - - unipathway.compound: UPC00009 - - !!omap - - id: pyr_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/pi + - http://identifiers.org/biocyc/Pi + - http://identifiers.org/biocyc/PHOSPHATE-GROUP + - http://identifiers.org/biocyc/CPD0-1421 + - http://identifiers.org/cas/14265-44-2 + - http://identifiers.org/cas/14265-44-2 + - http://identifiers.org/chebi/CHEBI:37583 + - http://identifiers.org/chebi/CHEBI:7793 + - http://identifiers.org/chebi/CHEBI:37585 + - http://identifiers.org/chebi/CHEBI:34683 + - http://identifiers.org/chebi/CHEBI:14791 + - http://identifiers.org/chebi/CHEBI:34855 + - http://identifiers.org/chebi/CHEBI:29137 + - http://identifiers.org/chebi/CHEBI:29139 + - http://identifiers.org/chebi/CHEBI:63036 + - http://identifiers.org/chebi/CHEBI:26020 + - http://identifiers.org/chebi/CHEBI:39739 + - http://identifiers.org/chebi/CHEBI:32597 + - http://identifiers.org/chebi/CHEBI:32596 + - http://identifiers.org/chebi/CHEBI:43474 + - http://identifiers.org/chebi/CHEBI:63051 + - http://identifiers.org/chebi/CHEBI:43470 + - http://identifiers.org/chebi/CHEBI:9679 + - http://identifiers.org/chebi/CHEBI:35433 + - http://identifiers.org/chebi/CHEBI:4496 + - http://identifiers.org/chebi/CHEBI:45024 + - http://identifiers.org/chebi/CHEBI:18367 + - http://identifiers.org/chebi/CHEBI:26078 + - http://identifiers.org/chebi/CHEBI:39745 + - http://identifiers.org/chebi/CHEBI:24838 + - http://identifiers.org/hmdb/HMDB02142 + - http://identifiers.org/kegg.compound/C13556 + - http://identifiers.org/kegg.compound/C13558 + - http://identifiers.org/kegg.compound/C00009 + - http://identifiers.org/kegg.drug/D05467 + - http://identifiers.org/pubchem.substance/3311 + - http://identifiers.org/reactome/REACT_947590 + - http://identifiers.org/reactome/REACT_109277 + - http://identifiers.org/reactome/REACT_113548 + - http://identifiers.org/reactome/REACT_2255331 + - http://identifiers.org/reactome/REACT_29372 + - http://identifiers.org/reactome/REACT_113550 + - http://identifiers.org/reactome/REACT_113551 + - http://identifiers.org/seed.compound/cpd09464 + - http://identifiers.org/seed.compound/cpd09463 + - http://identifiers.org/seed.compound/cpd00009 + - http://identifiers.org/unipathway.compound/UPC00009 + nested_data: !!omap [] + - !!omap + - id: M_pyr_c - name: Pyruvate - compartment: c - charge: -1 - formula: C3H3O3 - annotation: !!omap - 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upper_bound: 1000.0 - gene_reaction_rule: '' - !!omap - - id: ENO + - id: R_ENO - name: enolase - metabolites: !!omap - - 2pg_c: -1.0 - - h2o_c: 1.0 - - pep_c: 1.0 + - M_2pg_c: -1.0 + - M_h2o_c: 1.0 + - M_pep_c: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b2779 - annotation: !!omap - - bigg.reaction: ENO + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/ENO + nested_data: !!omap [] - !!omap - - id: EX_glc__D_e + - id: R_EX_glc__D_e - name: D-Glucose exchange - metabolites: !!omap - - glc__D_e: -1.0 + - M_glc__D_e: -1.0 - lower_bound: -10.0 - upper_bound: 1000.0 - gene_reaction_rule: '' - annotation: !!omap - - bigg.reaction: glc + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/glc + nested_data: !!omap [] - sbo: SBO:0000627 - !!omap - - id: EX_h_e + - id: R_EX_h_e - name: H+ exchange - metabolites: !!omap - - h_e: -1.0 + - M_h_e: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: '' - annotation: !!omap - - bigg.reaction: h + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/h + nested_data: !!omap [] - sbo: SBO:0000627 - !!omap - - id: EX_lac__D_e + - id: R_EX_lac__D_e - name: D-lactate exchange - metabolites: !!omap - - lac__D_e: -1.0 + - M_lac__D_e: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: '' - annotation: !!omap - - bigg.reaction: lac__D + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/lac__D + nested_data: !!omap [] - sbo: SBO:0000627 - !!omap - - id: FBA + - id: R_FBA - name: fructose-bisphosphate aldolase - metabolites: !!omap - - dhap_c: 1.0 - - fdp_c: -1.0 - - g3p_c: 1.0 + - M_dhap_c: 1.0 + - M_fdp_c: -1.0 + - M_g3p_c: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b1773 or b2097 or b2925 - annotation: !!omap - - bigg.reaction: FBA + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/FBA + nested_data: !!omap [] - !!omap - - id: GAPD + - id: R_GAPD - name: glyceraldehyde-3-phosphate dehydrogenase - metabolites: !!omap - - 13dpg_c: 1.0 - - g3p_c: -1.0 - - h_c: 1.0 - - nad_c: -1.0 - - nadh_c: 1.0 - - pi_c: -1.0 + - M_13dpg_c: 1.0 + - M_g3p_c: -1.0 + - M_h_c: 1.0 + - M_nad_c: -1.0 + - M_nadh_c: 1.0 + - M_pi_c: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b1779 - annotation: !!omap - - bigg.reaction: GAPD + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/GAPD + nested_data: !!omap [] - !!omap - - id: GLCpts + - id: R_GLCpts - name: D-glucose transport via PEP:Pyr PTS - metabolites: !!omap - - g6p_c: 1.0 - - glc__D_e: -1.0 - - pep_c: -1.0 - - pyr_c: 1.0 + - M_g6p_c: 1.0 + - M_glc__D_e: -1.0 + - M_pep_c: -1.0 + - M_pyr_c: 1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: (b2415 and b2417 and b1101 and b2416) or (b2415 and b2417 and b1621 and b2416) or (b2415 and b1818 and b1817 and b1819 and b2416) - annotation: !!omap - - bigg.reaction: GLCpts + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/GLCpts + nested_data: !!omap [] - !!omap - - id: H2Ot + - id: R_H2Ot - name: R H2O transport via - diffusion - metabolites: !!omap - - h2o_c: 1.0 - - h2o_e: -1.0 + - M_h2o_c: 1.0 + - M_h2o_e: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b0875 or s0001 - annotation: !!omap - - bigg.reaction: H2Ot + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/H2Ot + nested_data: !!omap [] - !!omap - - id: LDH_D + - id: R_LDH_D - name: D-lactate dehydrogenase - metabolites: !!omap - - h_c: 1.0 - - lac__D_c: -1.0 - - nad_c: -1.0 - - nadh_c: 1.0 - - pyr_c: 1.0 + - M_h_c: 1.0 + - M_lac__D_c: -1.0 + - M_nad_c: -1.0 + - M_nadh_c: 1.0 + - M_pyr_c: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b2133 or b1380 + - subsystem: Pyruvate Metabolism - annotation: !!omap - - bigg.reaction: LDH_D - - biocyc: META:DLACTDEHYDROGNAD-RXN - - ec-code: 1.1.1.28 - - kegg.reaction: R00704 - - metanetx.reaction: MNXR101037 - - rhea: - - '16369' - - '16370' - - '16371' - - '16372' + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/LDH_D + - http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN + - http://identifiers.org/ec-code/1.1.1.28 + - http://identifiers.org/kegg.reaction/R00704 + - http://identifiers.org/metanetx.reaction/MNXR101037 + - http://identifiers.org/rhea/16369 + - http://identifiers.org/rhea/16370 + - http://identifiers.org/rhea/16371 + - http://identifiers.org/rhea/16372 + nested_data: !!omap [] - sbo: SBO:0000375 - !!omap - - id: PFK + - id: R_PFK - name: phosphofructokinase - metabolites: !!omap - - adp_c: 1.0 - - atp_c: -1.0 - - f6p_c: -1.0 - - fdp_c: 1.0 - - h_c: 1.0 + - M_adp_c: 1.0 + - M_atp_c: -1.0 + - M_f6p_c: -1.0 + - M_fdp_c: 1.0 + - M_h_c: 1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: b3916 or b1723 - objective_coefficient: 1.0 - annotation: !!omap - - bigg.reaction: PFK + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/PFK + nested_data: !!omap [] - !!omap - - id: PGI + - id: R_PGI - name: glucose-6-phosphate isomerase - metabolites: !!omap - - f6p_c: 1.0 - - g6p_c: -1.0 + - M_f6p_c: 1.0 + - M_g6p_c: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b4025 - annotation: !!omap - - bigg.reaction: PGI + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/PGI + nested_data: !!omap [] - !!omap - - id: PGK + - id: R_PGK - name: phosphoglycerate kinase - metabolites: !!omap - - 13dpg_c: 1.0 - - 3pg_c: -1.0 - - adp_c: 1.0 - - atp_c: -1.0 + - M_13dpg_c: 1.0 + - M_3pg_c: -1.0 + - M_adp_c: 1.0 + - M_atp_c: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b2926 - annotation: !!omap - - bigg.reaction: PGK + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/PGK + nested_data: !!omap [] - !!omap - - id: PGM + - id: R_PGM - name: phosphoglycerate mutase - metabolites: !!omap - - 2pg_c: -1.0 - - 3pg_c: 1.0 + - M_2pg_c: -1.0 + - M_3pg_c: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b4395 or b3612 or b0755 - annotation: !!omap - - bigg.reaction: PGM + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/PGM + nested_data: !!omap [] - !!omap - - id: PIt2r + - id: R_PIt2r - name: R phosphate reversible transport via - symport - metabolites: !!omap - - h_c: 1.0 - - h_e: -1.0 - - pi_c: 1.0 - - pi_e: -1.0 + - M_h_c: 1.0 + - M_h_e: -1.0 + - M_pi_c: 1.0 + - M_pi_e: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b2987 or b3493 - annotation: !!omap - - bigg.reaction: PIt2r + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/PIt2r + nested_data: !!omap [] - !!omap - - id: PYK + - id: R_PYK - name: pyruvate kinase - metabolites: !!omap - - adp_c: -1.0 - - atp_c: 1.0 - - h_c: -1.0 - - pep_c: -1.0 - - pyr_c: 1.0 + - M_adp_c: -1.0 + - M_atp_c: 1.0 + - M_h_c: -1.0 + - M_pep_c: -1.0 + - M_pyr_c: 1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: b1854 or b1676 - annotation: !!omap - - bigg.reaction: PYK + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/PYK + nested_data: !!omap [] - !!omap - - id: TPI + - id: R_TPI - name: triose-phosphate isomerase - metabolites: !!omap - - dhap_c: -1.0 - - g3p_c: 1.0 + - M_dhap_c: -1.0 + - M_g3p_c: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: b3919 - annotation: !!omap - - bigg.reaction: TPI + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.reaction/TPI + nested_data: !!omap [] - genes: - !!omap - - id: b0755 + - id: G_b0755 - name: gpmA - !!omap - - id: b0875 + - id: G_b0875 - name: aqpZ - !!omap - - id: b1101 + - id: G_b1101 - name: ptsG - !!omap - - id: b1380 + - id: G_b1380 - name: ldhA - !!omap - - id: b1621 + - id: G_b1621 - name: malX - !!omap - - id: b1676 + - id: G_b1676 - name: pykF - annotation: !!omap - - ncbigi: - - GI:1208453 - - GI:1652654 - - !!omap - - id: b1723 + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/ncbiprotein/1208453 + - http://identifiers.org/ncbiprotein/1652654 + nested_data: !!omap [] + - !!omap + - id: G_b1723 - name: pfkB - !!omap - - id: b1773 + - id: G_b1773 - name: ydjI - !!omap - - id: b1779 + - id: G_b1779 - name: gapA - !!omap - - id: b1817 + - id: G_b1817 - name: manX - !!omap - - id: b1818 + - id: G_b1818 - name: manY - !!omap - - id: b1819 + - id: G_b1819 - name: manZ - !!omap - - id: b1854 + - id: G_b1854 - name: pykA - !!omap - - id: b2097 + - id: G_b2097 - name: fbaB - !!omap - - id: b2133 + - id: G_b2133 - name: dld - !!omap - - id: b2415 + - id: G_b2415 - name: ptsH - !!omap - - id: b2416 + - id: G_b2416 - name: ptsI - !!omap - - id: b2417 + - id: G_b2417 - name: crr - !!omap - - id: b2779 + - id: G_b2779 - name: eno - annotation: !!omap - - ncbigi: GI:1653839 + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/ncbiprotein/1653839 + nested_data: !!omap [] - !!omap - - id: b2925 + - id: G_b2925 - name: fbaA - !!omap - - id: b2926 + - id: G_b2926 - name: pgk - annotation: !!omap - - ncbigi: GI:1653609 + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/ncbiprotein/1653609 + nested_data: !!omap [] - !!omap - - id: b2987 + - id: G_b2987 - name: pitB - !!omap - - id: b3493 + - id: G_b3493 - name: pitA - !!omap - - id: b3612 + - id: G_b3612 - name: gpmM - !!omap - - id: b3916 + - id: G_b3916 - name: pfkA - annotation: !!omap - - ncbigi: - - GI:1006614 - - GI:1651919 - - !!omap - - id: b3919 + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/ncbiprotein/1006614 + - http://identifiers.org/ncbiprotein/1651919 + nested_data: !!omap [] + - !!omap + - id: G_b3919 - name: tpiA - !!omap - - id: b4025 + - id: G_b4025 - name: pgi - annotation: !!omap - - ncbigi: GI:1653253 + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/ncbiprotein/1653253 + nested_data: !!omap [] - !!omap - - id: b4395 + - id: G_b4395 - name: ytjC - !!omap - - id: s0001 + - id: G_s0001 - name: G_s0001 +- groups: [] - id: mini_textbook - compartments: !!omap - c: cytosol diff --git a/src/cobra/data/mini_cobra.xml b/src/cobra/data/mini_cobra.xml index 5f2e7b547..7163c331a 100644 --- a/src/cobra/data/mini_cobra.xml +++ b/src/cobra/data/mini_cobra.xml @@ -1,5 +1,5 @@ - + @@ -21,19 +21,19 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + @@ -46,23 +46,23 @@ - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + @@ -75,29 +75,29 @@ - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + @@ -110,33 +110,34 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -149,32 +150,33 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -187,25 +189,26 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -218,25 +221,26 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -249,26 +253,27 @@ - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + @@ -281,19 +286,20 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -306,28 +312,29 @@ - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + @@ -340,10 +347,11 @@ - - - - + + + + + @@ -356,64 +364,65 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -426,64 +435,65 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -496,37 +506,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -539,37 +550,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -582,20 +594,20 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -608,20 +620,20 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -634,30 +646,31 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -670,25 +683,26 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -701,24 +715,25 @@ - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -731,52 +746,53 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -789,52 +805,53 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -847,25 +864,26 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -889,7 +907,7 @@ - + @@ -905,14 +923,14 @@ - + - + @@ -929,13 +947,13 @@ - + - + @@ -945,13 +963,13 @@ - + - + @@ -961,13 +979,13 @@ - + - + @@ -983,7 +1001,7 @@ - + @@ -1010,7 +1028,7 @@ - + @@ -1036,7 +1054,7 @@ - + @@ -1080,7 +1098,7 @@ - + @@ -1099,21 +1117,21 @@ - + - - - - - - - - - + + + + + + + + + @@ -1141,7 +1159,7 @@ - + @@ -1169,7 +1187,7 @@ - + @@ -1191,7 +1209,7 @@ - + @@ -1215,7 +1233,7 @@ - + @@ -1241,7 +1259,7 @@ - + @@ -1268,7 +1286,7 @@ - + @@ -1296,7 +1314,7 @@ - + @@ -1322,97 +1340,97 @@ - - - - - + + + + + - - + + - - - - - - - - - - - - + + + + + + + + + + + + - + - + - + - - - + + + - - + + - + - + - - + + diff --git a/src/cobra/data/textbook.xml.gz b/src/cobra/data/textbook.xml.gz index a5d1fbc51..40452b55b 100644 Binary files a/src/cobra/data/textbook.xml.gz and b/src/cobra/data/textbook.xml.gz differ diff --git a/src/cobra/io/__init__.py b/src/cobra/io/__init__.py index 66d8a1b92..4c7ac6135 100644 --- a/src/cobra/io/__init__.py +++ b/src/cobra/io/__init__.py @@ -2,8 +2,14 @@ from cobra.io.dict import model_from_dict, model_to_dict -from cobra.io.json import from_json, load_json_model, save_json_model, to_json -from cobra.io.mat import load_matlab_model, save_matlab_model +from cobra.io.json import ( + from_json, + load_json_model, + save_json_model, + to_json, + validate_json_model, +) +from cobra.io.mat import load_matlab_model, save_matlab_model, create_mat_dict from cobra.io.sbml import read_sbml_model, write_sbml_model, validate_sbml_model from cobra.io.yaml import from_yaml, load_yaml_model, save_yaml_model, to_yaml from cobra.io.web import AbstractModelRepository, BiGGModels, BioModels, load_model diff --git a/src/cobra/io/dict.py b/src/cobra/io/dict.py index b0f009d4c..8dde2d916 100644 --- a/src/cobra/io/dict.py +++ b/src/cobra/io/dict.py @@ -1,75 +1,96 @@ """Provide functions for cobrapy objects to generic Python objects and vice-versa.""" - -from collections import OrderedDict -from operator import attrgetter, itemgetter -from typing import TYPE_CHECKING, Dict, List, Sequence, Set, Union +import itertools +import re +from collections import OrderedDict, defaultdict +from functools import partial +from typing import TYPE_CHECKING, Callable, Dict, List, Set, Tuple, Union import numpy as np -from ..core import Gene, Metabolite, Model, Reaction +from ..core import Gene, Group, Metabolite, Model, Reaction +from ..core.metadata import MetaData, Notes +from ..core.metadata.helper import URL_IDENTIFIERS_PATTERN, parse_identifiers_uri +from ..io.sbml import ( + F_GENE, + F_GENE_REV, + F_GROUP, + F_GROUP_REV, + F_REACTION, + F_REACTION_REV, + F_REPLACE, + F_SPECIE, + F_SPECIE_REV, +) from ..util.solver import set_objective if TYPE_CHECKING: from cobra import Object -_REQUIRED_REACTION_ATTRIBUTES = [ - "id", - "name", - "metabolites", - "lower_bound", - "upper_bound", - "gene_reaction_rule", -] -_ORDERED_OPTIONAL_REACTION_KEYS = [ - "objective_coefficient", - "subsystem", - "notes", - "annotation", -] -_OPTIONAL_REACTION_ATTRIBUTES = { - "objective_coefficient": 0, +_REACTION_DICT = { + "id": "", + "name": None, + "lower_bound": None, + "upper_bound": None, "subsystem": "", - "notes": {}, + "notes": Notes(), "annotation": {}, } -_REQUIRED_METABOLITE_ATTRIBUTES = ["id", "name", "compartment"] -_ORDERED_OPTIONAL_METABOLITE_KEYS = [ - "charge", - "formula", - "_bound", - "notes", - "annotation", -] -_OPTIONAL_METABOLITE_ATTRIBUTES = { +_METABOLITE_DICT = { + "id": "", + "name": None, + "compartment": None, "charge": None, "formula": None, "_bound": 0, - "notes": {}, + "notes": Notes(), + "annotation": {}, +} + +_GENE_DICT = { + "id": "", + "name": None, + "notes": Notes(), "annotation": {}, } -_REQUIRED_GENE_ATTRIBUTES = ["id", "name"] -_ORDERED_OPTIONAL_GENE_KEYS = ["notes", "annotation"] -_OPTIONAL_GENE_ATTRIBUTES = { - "notes": {}, +_GROUP_DICT = { + "id": "", + "name": "", + "kind": "", + "notes": Notes(), "annotation": {}, } -_ORDERED_OPTIONAL_MODEL_KEYS = ["name", "compartments", "notes", "annotation"] -_OPTIONAL_MODEL_ATTRIBUTES = { +_MODEL_DICT = { + "id": "", "name": None, - # "description": None, should not actually be included "compartments": [], - "notes": {}, + "notes": Notes(), "annotation": {}, } +def flatten(list_of_lists: Union[List, Tuple]) -> List: + """Flatten lists of lists. + + Parameters + ---------- + list_of_lists: List or Tuple + List or Tuple of lists or tuples to flatten. + + Returns + ------- + list: flattened list + + """ + return list(itertools.chain.from_iterable(list_of_lists)) + + def _fix_type( value: Union[str, np.float, np.bool, Set, Dict] -) -> Union[str, float, bool, List, OrderedDict]: +) -> Union[str, float, bool, List, OrderedDict, Dict]: """Convert possible types to correct Python types. Parameters @@ -86,6 +107,8 @@ def _fix_type( # Because numpy floats can not be pickled to json if isinstance(value, str): return str(value) + if isinstance(value, np.float) and (np.isnan(value) or np.isinf(value)): + return str(value) if isinstance(value, np.float): return float(value) if isinstance(value, np.bool): @@ -94,6 +117,10 @@ def _fix_type( return list(value) if isinstance(value, dict): return OrderedDict((key, value[key]) for key in sorted(value)) + if isinstance(value, Notes): + return str(value) + if isinstance(value, MetaData): + return value.to_dict() # handle legacy Formula type if value.__class__.__name__ == "Formula": return str(value) @@ -102,24 +129,86 @@ def _fix_type( return value -def _update_optional( - cobra_object: "Object", - new_dict: Dict, - optional_attribute_dict: Dict, - ordered_keys: Sequence, -) -> None: +def _f_replace_object_id(cobra_object, f_replace=F_REPLACE) -> str: # noqa: W0102 + if f_replace is None: + f_replace = {} + if f_replace: + if isinstance(cobra_object, Reaction): + return F_REPLACE[F_REACTION_REV](cobra_object.id) + elif isinstance(cobra_object, Gene): + return F_REPLACE[F_GENE_REV](cobra_object.id) + elif isinstance(cobra_object, Metabolite): + return F_REPLACE[F_SPECIE_REV](cobra_object.id) + elif isinstance(cobra_object, Group): + return F_REPLACE[F_GROUP_REV](cobra_object.id) + return cobra_object.id + + +def _fix_id_from_dict( + _id_to_fix: str, + _class_to_fix_to: str, + f_replace: dict = F_REPLACE, # noqa: W0102 +): + if f_replace is None: + f_replace = {} + if not f_replace: + return _id_to_fix + if _class_to_fix_to == "Metabolite": + return F_REPLACE[F_SPECIE](_id_to_fix) + elif _class_to_fix_to == "Reaction": + return F_REPLACE[F_REACTION](_id_to_fix) + elif _class_to_fix_to == "Gene": + return F_REPLACE[F_GENE](_id_to_fix) + elif _class_to_fix_to == "Group": + return F_REPLACE[F_GROUP](_id_to_fix) + + +def _fix_value_from_dict(_key: str, _value_to_fix: Union[List, str]): + if _key == "annotation": + # if annotation is in the form of list of list, modify the format + # https://github.com/opencobra/cobrapy/issues/736 + if isinstance(_value_to_fix, list) and isinstance(_value_to_fix[0], list): + _value_to_fix = flatten(_value_to_fix) + anno_dict = defaultdict(list) + if isinstance(_value_to_fix, list): + for item in _value_to_fix: + if re.match(URL_IDENTIFIERS_PATTERN, item): + provider, identifier = parse_identifiers_uri(item) + anno_dict[provider].append(identifier) + _value_to_fix = anno_dict + _value_to_fix = MetaData.from_dict(_value_to_fix) + elif _key == "notes": + _value_to_fix = Notes(_value_to_fix) + elif _key == "lower_bound" or _key == "upper_bound": + _value_to_fix = float(_value_to_fix) + + return _value_to_fix + + +def _get_by_id( + _id: str, _object_to_get: str, model: Model +) -> Union[Gene, Metabolite, Group, Reaction]: + if _object_to_get == "Reaction": + return model.reactions.get_by_id(_id) + elif _object_to_get == "Metabolite": + return model.metabolites.get_by_id(_id) + elif _object_to_get == "Group": + return model.groups.get_by_id(_id) + elif _object_to_get == "Gene": + return model.genes.get_by_id(_id) + + +def _object_to_dict( + cobra_object: "Object", optional_attribute_dict: Dict, _f_replace_function: Callable +) -> OrderedDict: """Update `new_dict` with optional attributes from `cobra_object`. Parameters ---------- cobra_object : cobra.Object The cobra Object to update optional attributes from. - new_dict : dict - The dictionary to update optional attributes for. optional_attribute_dict : dict The dictionary to use as default value lookup store. - ordered_keys : list, tuple - The keys to update values for. Raises ------ @@ -129,21 +218,51 @@ def _update_optional( If key in `ordered_keys` is not found in `cobra_object`. """ - for key in ordered_keys: - default = optional_attribute_dict[key] - value = getattr(cobra_object, key) - if value is None or value == default: - continue - new_dict[key] = _fix_type(value) + state = cobra_object.__getstate__() + state["id"] = _f_replace_function(cobra_object) + state_fixed = { + (re.sub("^_", "", key) if key != "_bound" else key): state[key] + for key in state.keys() + } + cobra_dict = OrderedDict( + { + key: _fix_type(state_fixed[key]) + for key, default in optional_attribute_dict.items() + if state_fixed[key] is not None and state_fixed[key] != default + } + ) + return cobra_dict + + +def object_from_dict(new_object: "Object", object_dict: Dict): + [ + setattr(new_object, k, _fix_value_from_dict(k, v)) + for k, v in object_dict.items() + if k + not in { + "id", + "objective_coefficient", + "reversibility", + "reaction", + "metabolites", + "members", + } + ] -def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict: +def _metabolite_to_dict( + metabolite: Metabolite, f_replace_func: Callable +) -> OrderedDict: """Convert a cobra Metabolite object to dictionary. Parameters ---------- metabolite : cobra.Metabolite The cobra.Metabolite to convert to dictionary. + f_replace_func : partial replacement function for id replacement + By default, the following id changes are performed on import: + clip G_ from genes, clip M_ from species, clip R_ from reactions + If no replacements should be performed, set f_replace={} or None Returns ------- @@ -155,19 +274,14 @@ def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict: _metabolite_from_dict : Convert a dictionary to cobra Metabolite object. """ - new_metabolite = OrderedDict() - for key in _REQUIRED_METABOLITE_ATTRIBUTES: - new_metabolite[key] = _fix_type(getattr(metabolite, key)) - _update_optional( - metabolite, - new_metabolite, - _OPTIONAL_METABOLITE_ATTRIBUTES, - _ORDERED_OPTIONAL_METABOLITE_KEYS, + return _object_to_dict( + metabolite, _METABOLITE_DICT, _f_replace_function=f_replace_func ) - return new_metabolite -def _metabolite_from_dict(metabolite: Dict) -> Metabolite: +def _metabolite_from_dict( + metabolite: Dict, f_replace: dict = F_REPLACE # noqa: W0102 +) -> Metabolite: """Convert a dictionary to cobra Metabolite object. Parameters @@ -184,19 +298,28 @@ def _metabolite_from_dict(metabolite: Dict) -> Metabolite: _metabolite_to_dict : Convert a cobra Metabolite object to dictionary. """ - new_metabolite = Metabolite() - for k, v in metabolite.items(): - setattr(new_metabolite, k, v) + if f_replace is None: + f_replace = {} + + new_metabolite = Metabolite( + _fix_id_from_dict(metabolite["id"], "Metabolite", f_replace) + ) + object_from_dict(new_metabolite, metabolite) return new_metabolite -def _gene_to_dict(gene: Gene) -> OrderedDict: +def _gene_to_dict(gene: Gene, f_replace_func: Callable) -> OrderedDict: """Convert a cobra Gene object to dictionary. Parameters ---------- gene : cobra.Gene The cobra.Gene to convert to dictionary. + f_replace_func : Callable + partial replacement function for id replacement + By default, the following id changes are performed on import: + clip G_ from genes, clip M_ from species, clip R_ from reactions + If no replacements should be performed, set f_replace={} or None Returns ------- @@ -208,16 +331,10 @@ def _gene_to_dict(gene: Gene) -> OrderedDict: _gene_from_dict : Convert a dictionary to cobra Gene object. """ - new_gene = OrderedDict() - for key in _REQUIRED_GENE_ATTRIBUTES: - new_gene[key] = _fix_type(getattr(gene, key)) - _update_optional( - gene, new_gene, _OPTIONAL_GENE_ATTRIBUTES, _ORDERED_OPTIONAL_GENE_KEYS - ) - return new_gene + return _object_to_dict(gene, _GENE_DICT, _f_replace_function=f_replace_func) -def gene_from_dict(gene: Dict) -> Gene: +def gene_from_dict(gene: Dict, f_replace: dict = F_REPLACE) -> Gene: # noqa: W0102 """Convert a dictionary to cobra Gene object. Parameters @@ -235,19 +352,26 @@ def gene_from_dict(gene: Dict) -> Gene: _gene_to_dict : Convert a cobra Gene object to a dictionary. """ - new_gene = Gene(gene["id"]) - for k, v in gene.items(): - setattr(new_gene, k, v) + if f_replace is None: + f_replace = {} + + new_gene = Gene(_fix_id_from_dict(gene["id"], "Gene", f_replace)) + object_from_dict(new_gene, gene) return new_gene -def _reaction_to_dict(reaction: Reaction) -> OrderedDict: +def _reaction_to_dict(reaction: Reaction, f_replace_func: Callable) -> OrderedDict: """Convert a cobra Reaction object to a dictionary. Parameters ---------- reaction : cobra.Reaction The cobra.Reaction to convert to dictionary. + f_replace_func : Callable + partial replacement function for id replacement + By default, the following id changes are performed on import: + clip G_ from genes, clip M_ from species, clip R_ from reactions + If no replacements should be performed, set f_replace={} or None Returns ------- @@ -259,34 +383,20 @@ def _reaction_to_dict(reaction: Reaction) -> OrderedDict: _reaction_from_dict : Convert a dictionary to a cobra Reaction object. """ - new_reaction = OrderedDict() - for key in _REQUIRED_REACTION_ATTRIBUTES: - if key != "metabolites": - if key == "lower_bound" and ( - np.isnan(reaction.lower_bound) or np.isinf(reaction.lower_bound) - ): - new_reaction[key] = str(_fix_type(getattr(reaction, key))) - elif key == "upper_bound" and ( - np.isnan(reaction.upper_bound) or np.isinf(reaction.upper_bound) - ): - new_reaction[key] = str(_fix_type(getattr(reaction, key))) - else: - new_reaction[key] = _fix_type(getattr(reaction, key)) - continue - mets = OrderedDict() - for met in sorted(reaction.metabolites, key=attrgetter("id")): - mets[str(met)] = reaction.metabolites[met] - new_reaction["metabolites"] = mets - _update_optional( - reaction, - new_reaction, - _OPTIONAL_REACTION_ATTRIBUTES, - _ORDERED_OPTIONAL_REACTION_KEYS, + new_reaction = _object_to_dict( + reaction, _REACTION_DICT, _f_replace_function=f_replace_func + ) + new_reaction["metabolites"] = OrderedDict( + {f_replace_func(met): stoic for met, stoic in reaction.metabolites.items()} ) + new_reaction["gene_reaction_rule"] = _fix_type(reaction.gene_reaction_rule) + new_reaction["objective_coefficient"] = _fix_type(reaction.objective_coefficient) return new_reaction -def _reaction_from_dict(reaction: Dict, model: Model) -> Reaction: +def _reaction_from_dict( + reaction: Dict, model: Model, f_replace: Dict = F_REPLACE # noqa: W0102 +) -> Reaction: """Convert a dictionary to a cobra Reaction object. Parameters @@ -306,26 +416,55 @@ def _reaction_from_dict(reaction: Dict, model: Model) -> Reaction: _reaction_to_dict : Convert a cobra Reaction object to a dictionary. """ - new_reaction = Reaction() - for k, v in reaction.items(): - if k in {"objective_coefficient", "reversibility", "reaction"}: - continue - elif k == "metabolites": - new_reaction.add_metabolites( - OrderedDict( - (model.metabolites.get_by_id(str(met)), coeff) - for met, coeff in v.items() - ) - ) - else: - if k == "lower_bound" or k == "upper_bound": - setattr(new_reaction, k, float(v)) - else: - setattr(new_reaction, k, v) + if f_replace is None: + f_replace = {} + + new_reaction = Reaction(_fix_id_from_dict(reaction["id"], "Reaction", f_replace)) + object_from_dict(new_reaction, reaction) + + new_reaction.add_metabolites( + { + model.metabolites.get_by_id( + _fix_id_from_dict(str(met), "Metabolite", f_replace) + ): coeff + for met, coeff in reaction.get("metabolites", {}).items() + } + ) return new_reaction -def model_to_dict(model: Model, sort: bool = False) -> OrderedDict: +def group_to_dict(group: "Group", f_replace_func: Callable) -> Dict: + new_group = _object_to_dict(group, _GROUP_DICT, _f_replace_function=f_replace_func) + new_group["members"] = [ + {"idRef": f_replace_func(member), "type": type(member).__name__} + for member in group.members + ] + return new_group + + +def group_from_dict( + group: Dict, model: Model, f_replace=F_REPLACE # noqa: W0102 +) -> Group: + if f_replace is None: + f_replace = {} + + new_group = Group(_fix_id_from_dict(group["id"], "Group")) + object_from_dict(new_group, group) + cobra_members = [ + _get_by_id( + _fix_id_from_dict(member["idRef"], member["type"], f_replace), + member["type"], + model, + ) + for member in group["members"] + ] + new_group.add_members(cobra_members) + return new_group + + +def model_to_dict( + model: Model, sort: bool = False, f_replace: dict = F_REPLACE # noqa: W0102 +) -> OrderedDict: """Convert a cobra Model to a dictionary. Parameters @@ -335,6 +474,11 @@ def model_to_dict(model: Model, sort: bool = False) -> OrderedDict: sort : bool, optional Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False). + f_replace : dict of replacement functions for id replacement + Dictionary of replacement functions for gene, specie, and reaction. + By default, the following id changes are performed on import: + clip G_ from genes, clip M_ from species, clip R_ from reactions + If no replacements should be performed, set f_replace={} or None Returns ------- @@ -349,23 +493,37 @@ def model_to_dict(model: Model, sort: bool = False) -> OrderedDict: model_from_dict : Convert a dictionary to a cobra Model. """ - obj = OrderedDict() - obj["metabolites"] = list(map(_metabolite_to_dict, model.metabolites)) - obj["reactions"] = list(map(_reaction_to_dict, model.reactions)) - obj["genes"] = list(map(_gene_to_dict, model.genes)) - obj["id"] = model.id - _update_optional( - model, obj, _OPTIONAL_MODEL_ATTRIBUTES, _ORDERED_OPTIONAL_MODEL_KEYS - ) + if f_replace is None: + f_replace = {} + + _f_replace_function = partial(_f_replace_object_id, f_replace=f_replace) + + obj = _object_to_dict(model, _MODEL_DICT, _f_replace_function) + obj["metabolites"] = [ + _metabolite_to_dict(met, _f_replace_function) for met in model.metabolites + ] + obj["reactions"] = [ + _reaction_to_dict(rxn, _f_replace_function) for rxn in model.reactions + ] + obj["genes"] = [_gene_to_dict(gene, _f_replace_function) for gene in model.genes] + obj["groups"] = [ + group_to_dict(group, _f_replace_function) for group in model.groups + ] + + # sbml meta info + if hasattr(model, "_sbml"): + obj["sbml_info"] = OrderedDict( + {key: _fix_type(value) for key, value in model._sbml.items()} + ) if sort: - get_id = itemgetter("id") - obj["metabolites"].sort(key=get_id) - obj["reactions"].sort(key=get_id) - obj["genes"].sort(key=get_id) + obj["metabolites"].sort(key=lambda x: x["id"]) + obj["reactions"].sort(key=lambda x: x["id"]) + obj["genes"].sort(key=lambda x: x["id"]) + obj["groups"].sort(key=lambda x: x["id"]) return obj -def model_from_dict(obj: Dict) -> Model: +def model_from_dict(obj: Dict, f_replace=F_REPLACE) -> Model: """Build a cobra Model from a dictionary. Models stored in JSON are first formulated as a dictionary that can be read @@ -408,11 +566,25 @@ def model_from_dict(obj: Dict) -> Model: rxn for rxn in obj["reactions"] if rxn.get("objective_coefficient", 0) != 0 ] coefficients = { - model.reactions.get_by_id(rxn["id"]): rxn["objective_coefficient"] + model.reactions.get_by_id( + _fix_id_from_dict(rxn["id"], "Reaction", f_replace) + ): rxn["objective_coefficient"] for rxn in objective_reactions } + if "groups" in obj: + model.add_groups([group_from_dict(group, model) for group in obj["groups"]]) set_objective(model, coefficients) - for k, v in obj.items(): - if k in {"id", "name", "notes", "compartments", "annotation"}: - setattr(model, k, v) + + # sbml meta info + if "sbml_info" in obj: + model._sbml = { + k: _fix_value_from_dict(k, v) for k, v in obj["sbml_info"].items() + } + + [ + setattr(model, k, _fix_value_from_dict(k, v)) + for k, v in obj.items() + if k in {"id", "name", "compartments", "annotation", "notes"} + ] + return model diff --git a/src/cobra/io/json.py b/src/cobra/io/json.py index 8fec5191d..42fa7f3c2 100644 --- a/src/cobra/io/json.py +++ b/src/cobra/io/json.py @@ -1,6 +1,11 @@ """Provide functions for I/O in JSON format.""" from pathlib import Path -from typing import TYPE_CHECKING, Any, Union +from typing import IO, TYPE_CHECKING, Any, Dict, List, Union + +import jsonschema +from importlib_resources import open_text + +from cobra import io as cio from .dict import model_from_dict, model_to_dict @@ -17,6 +22,18 @@ JSON_SPEC = "1" +def json_schema_v1() -> Dict: + with open_text(cio, "schema_v1.json") as handle: + schema_v1 = json.load(handle) + return schema_v1 + + +def json_schema_v2() -> Dict: + with open_text(cio, "schema_v2.json") as handle: + schema_v2 = json.load(handle) + return schema_v2 + + def to_json(model: "Model", sort: bool = False, **kwargs: Any) -> str: """Return the model as a JSON string. @@ -69,10 +86,10 @@ def from_json(document: str) -> "Model": def save_json_model( model: "Model", - filename: Union[str, Path], + filename: Union[str, Path, IO[str]], sort: bool = False, pretty: bool = False, - **kwargs: Any + **kwargs: Any, ) -> None: """Write the cobra model to a file in JSON format. @@ -80,8 +97,8 @@ def save_json_model( ---------- model : cobra.Model The cobra model to represent. - filename : str or file-like - File path or descriptor that the JSON representation should be + filename : str or file-like (IO[str]) or Path + File path or file handle or str that the JSON representation should be written to. sort : bool, optional Whether to sort the metabolites, reactions, and genes or maintain the @@ -125,12 +142,12 @@ def save_json_model( json.dump(obj, filename, **dump_opts) -def load_json_model(filename: Union[str, Path]) -> "Model": +def load_json_model(filename: Union[str, Path, IO[str]]) -> "Model": """Load a cobra model from a file in JSON format. Parameters ---------- - filename : str or file-like + filename : str or file-like or Path File path or descriptor that contains the JSON document describing the cobra model. @@ -149,3 +166,48 @@ def load_json_model(filename: Union[str, Path]) -> "Model": return model_from_dict(json.load(file_handle)) else: return model_from_dict(json.load(filename)) + + +def validate_json_model( + filename: Union[str, Path, IO[str]], json_schema_version: int = 1 +) -> List: + """ + Validate a model in json format against the schema with given version + Parameters + ---------- + filename : str or Path or file-like + File path or descriptor that contains the JSON document describing the + cobra model. + json_schema_version : int {1, 2} + the version of schema to be used for validation. + Currently we have v1 and v2 only and v2 is under development + Returns + ------- + errors : list + The list of errors encountered while validating + """ + + if json_schema_version == 1: + schema = json_schema_v1() + elif json_schema_version == 2: + schema = json_schema_v2() + else: + raise ValueError( + f"Only v1 and v2 of JSON schema are available. JSON " + f"schema v{json_schema_version} is not supported." + ) + + # TODO - Should the validator be picked by schema? + # Something like validators.validator_for + validator = jsonschema.Draft7Validator(schema) + + try: + if isinstance(filename, (str, Path)): + with open(filename, "r") as file_handle: + errors = validator.iter_errors(json.load(file_handle)) + else: + errors = validator.iter_errors(json.load(filename)) + except OSError: + errors = validator.iter_errors(json.loads(filename)) + + return list(errors) diff --git a/src/cobra/io/mat.py b/src/cobra/io/mat.py index 73f52e417..84f6ddcea 100644 --- a/src/cobra/io/mat.py +++ b/src/cobra/io/mat.py @@ -7,7 +7,7 @@ import numpy as np -from ..core import Gene, Group, Metabolite, Model, Object, Reaction +from ..core import Gene, Group, Metabolite, Model, Notes, Object, Reaction from ..util import create_stoichiometric_matrix from ..util.solver import set_objective @@ -35,7 +35,7 @@ "metUniPathway": "unipathway.compound", "metPubChemID": "pubchem.compound", "metPubChemSubstance": "pubchem.substance", - "metCHEBIID": "CHEBI", + "metCHEBIID": "chebi", "metMetaNetXID": "metanetx.chemical", "metSEEDID": "seed.compound", "metBiGGID": "bigg.metabolite", @@ -44,9 +44,9 @@ "metLIPIDMAPSID": "lipidmaps", "metReactomeID": "reactome", "metSABIORKID": "sabiork.compound", - "metSLMID": "SLM", + "metSLMID": "slm", "metSMILES": "SMILES", - "metSBOTerm": "SBO", + "metSBOTerms": "sbo", "metCasNumber": "cas", } @@ -73,21 +73,22 @@ "rxnReactomeID": "reactome", "rxnSABIORKID": "sabiork.reaction", "rxnBRENDAID": "brenda", - "rxnSBOTerms": "SBO", + "rxnSBOTerms": "sbo", } RXN_PROVIDERS_TO_MATLAB = { RXN_MATLAB_TO_PROVIDERS[k]: k for k in RXN_MATLAB_TO_PROVIDERS.keys() } +CONFIDENCE_STR = "Confidence Level" RXN_MATLAB_TO_NOTES = { "rxnReferences": "References", "rxnNotes": "NOTES", - "rxnConfidenceScores": "Confidence Level", + "rxnConfidenceScores": CONFIDENCE_STR, } RXN_NOTES_TO_MATLAB = { - "Confidence Level": "rxnConfidenceScores", + CONFIDENCE_STR: "rxnConfidenceScores", "NOTES": "rxnNotes", "References": "rxnNotes", } @@ -141,6 +142,7 @@ _double_punctuation_re = re.compile(r"[;,.'\"]{2,}") _ec_re = re.compile(r"([\d\-]+.[\d\-]+.[\d\-]+.[\d-]+)") _chebi_re = re.compile(r"\D*(\d+),?") +_sbo_re = re.compile(r"\D*(\d+),?") def _get_id_compartment(_id: str) -> str: @@ -233,7 +235,9 @@ def _cell_to_str_list( def _cell_to_float_list( - m_cell: np.ndarray, empty_value: Optional[float] = None + m_cell: np.ndarray, + empty_value: Optional[float] = None, + inf_value: Optional[float] = None, ) -> List: """Turn an ndarray (cell) to a list of floats. @@ -242,13 +246,41 @@ def _cell_to_float_list( m_cell: np.ndarray empty_value: float, optional What value to replace empty cells with. Default None. + inf_value: float, optional + Replace infinite values with defined inf. Default None (don't replace), will be + replaced by given value if given. Returns ------- List A list of processed floats. """ - return [float(x[0]) if np.size(x[0]) else empty_value for x in m_cell] + + def fix_inf(val: str, _inf_value: float): + """Fix inf value, used for rxn.lb and rxn.ub. + + Parameters + ---------- + val: str + the str to process into float + _inf_value: float + A value to replace infite values with. + """ + val = float(val) + if np.isinf(val) and val < 0: + return -_inf_value + elif np.isinf(val) and val > 0: + return _inf_value + else: + return val + + if inf_value: + return [ + fix_inf(x[0], _inf_value=inf_value) if np.size(x[0]) else empty_value + for x in m_cell + ] + else: + return [float(x[0]) if np.size(x[0]) else empty_value for x in m_cell] def load_matlab_model( @@ -302,7 +334,6 @@ def load_matlab_model( except ValueError as e: print(f"Some problem with the model, causing error {e}") # TODO: use custom cobra exception to handle exception - pass # If code here is executed, then no model was found. raise IOError(f"No COBRA model found at {infile_path}.") @@ -382,6 +413,14 @@ def mat_parse_annotations( annotations[name] = _cell_to_str_list( mat_struct[caseunfold[mat_key]][0, 0], None, _chebi_re, "CHEBI:" ) + elif mat_key == "metSBOTerms".casefold() or mat_key == "rxnSBOTerms".casefold(): + annotations[name] = _cell_to_str_list( + mat_struct[caseunfold[mat_key]][0, 0], None, _sbo_re, "SBO:" + ) + elif mat_key == "metSLMID".casefold(): + annotations[name] = _cell_to_str_list( + mat_struct[caseunfold[mat_key]][0, 0], None, _sbo_re, "SLM:" + ) else: # If it something else, which may have commas, turn it into a list annotations[name] = [ @@ -395,9 +434,6 @@ def mat_parse_annotations( prov: annotations[prov][i] for prov in providers if annotations[prov][i] } - # TODO - When cobrapy.notes are revised not be a dictionary (possibly when - # annotations are fully SBML compliant, revise this function. - def mat_parse_notes( target_list: List[Object], @@ -454,7 +490,9 @@ def mat_parse_notes( for x in notes[name] ] for i, obj in enumerate(target_list): - obj.notes = {prov: notes[prov][i] for prov in note_providers if notes[prov][i]} + obj.notes = Notes.notes_from_dict( + {prov: notes[prov][i] for prov in note_providers if notes[prov][i]} + ) def annotations_to_mat( @@ -479,42 +517,36 @@ def annotations_to_mat( """ providers_used = set() for i in range(len(annotation_list)): - if annotation_list[i]: - providers_used.update(annotation_list[i].keys()) + providers_used.update(annotation_list[i].keys()) providers_used = providers_used.intersection(DICT_REPLACE[d_replace].keys()) providers_used = list(providers_used) annotation_matlab = {prov: DICT_REPLACE[d_replace][prov] for prov in providers_used} - empty_lists = [[""] * len(annotation_list) for x in annotation_matlab] + empty_lists = [[""] * len(annotation_list) for _ in annotation_matlab] annotation_cells_to_be = dict(zip(annotation_matlab.values(), empty_lists)) for i in range(len(annotation_list)): - if annotation_list[i]: - for provider_key, v in annotation_list[i].items(): - if isinstance(v, str): - v = [v] - if provider_key == "pubmed": - v = ", ".join( - [ - "PMID:" + annot if "PMID:" not in annot else annot - for annot in v - ] - ) - elif provider_key == "CHEBI": - v = ", ".join( - [ - "CHEBI:" + annot if "CHBEI:" not in annot else annot - for annot in v - ] - ) - elif provider_key == "ec-code": - v = " or ".join(v) - else: - v = ", ".join(v) - if provider_key not in providers_used: - continue - annotation_cells_to_be[annotation_matlab[provider_key]][i] = v + for provider_key, v in annotation_list[i].items(): + if isinstance(v, str): + v = [v] + if provider_key == "pubmed": + v = ", ".join( + ["PMID:" + annot if "PMID:" not in annot else annot for annot in v] + ) + elif provider_key == "CHEBI": + v = ", ".join( + [ + "CHEBI:" + annot if "CHBEI:" not in annot else annot + for annot in v + ] + ) + elif provider_key == "ec-code": + v = " or ".join(v) + else: + v = ", ".join(v) + if provider_key not in providers_used: + continue + annotation_cells_to_be[annotation_matlab[provider_key]][i] = v for annotation_key, item_list in annotation_cells_to_be.items(): - if annotation_key not in mat_dict: - mat_dict[annotation_key] = _cell(item_list) + mat_dict[annotation_key] = _cell(item_list) # TODO - When cobrapy.notes are revised not be a dictionary (possibly when # annotations are fully SBML compliant, revise this function. @@ -542,28 +574,26 @@ def notes_to_mat( """ providers_used = set() for i in range(len(note_list)): - if note_list[i]: - providers_used.update(note_list[i].keys()) + providers_used.update(note_list[i].keys()) providers_used = providers_used.intersection(DICT_REPLACE[d_replace].keys()) providers_used = list(providers_used) annotation_matlab = {prov: DICT_REPLACE[d_replace][prov] for prov in providers_used} - empty_lists = [[""] * len(note_list) for x in annotation_matlab] + empty_lists = [[""] * len(note_list) for _ in annotation_matlab] annotation_cells_to_be = dict(zip(annotation_matlab.values(), empty_lists)) for i in range(len(note_list)): - if note_list[i]: - for provider_key, v in note_list[i].items(): - if provider_key not in providers_used: - continue - if provider_key == "Confidence Level": - v = float(v) - if not len(annotation_cells_to_be[annotation_matlab[provider_key]][i]): - annotation_cells_to_be[annotation_matlab[provider_key]][i] = v - else: - # References that aren't MIRIAM compliant will go to rxnNotes - annotation_cells_to_be[annotation_matlab[provider_key]][i] = ( - annotation_cells_to_be[annotation_matlab[provider_key]][i] - + f"; {v}" - ) + for provider_key, v in note_list[i].items(): + if provider_key not in providers_used: + continue + if provider_key == CONFIDENCE_STR: + v = float(v) + if not len(annotation_cells_to_be[annotation_matlab[provider_key]][i]): + annotation_cells_to_be[annotation_matlab[provider_key]][i] = v + else: + # References that aren't MIRIAM compliant will go to rxnNotes + annotation_cells_to_be[annotation_matlab[provider_key]][i] = ( + annotation_cells_to_be[annotation_matlab[provider_key]][i] + + f"; {v}" + ) for annotation_key, item_list in annotation_cells_to_be.items(): mat_dict[annotation_key] = _cell(item_list) @@ -588,13 +618,11 @@ def create_mat_dict(model: Model) -> OrderedDict: mat = OrderedDict() mat["mets"] = _cell(mets.list_attr("id")) model_has_compartment_names = False - for comp, compName in model.compartments.items(): - if comp != compName: - model_has_compartment_names = True - if ( - set([_get_id_compartment(met_id) for met_id in mets.list_attr("id")]) == {None} - or model_has_compartment_names - ): + if list(model.compartments.keys()) != list(model.compartments.values()): + model_has_compartment_names = True + if {_get_id_compartment(met_id) for met_id in mets.list_attr("id")} == { + None + } or model_has_compartment_names: comps = list(model.compartments.keys()) mat["comps"] = _cell(comps) mat["compNames"] = _cell([model.compartments[comp] for comp in comps]) @@ -629,7 +657,28 @@ def create_mat_dict(model: Model) -> OrderedDict: mat["rxnNames"] = _cell(rxns.list_attr("name")) annotations_to_mat(mat, rxns.list_attr("annotation"), DICT_REACTION_REV) notes_to_mat(mat, rxns.list_attr("notes"), DICT_REACTION_NOTES_REV) - mat["subSystems"] = _cell(rxns.list_attr("subsystem")) # TODO - output groups + rxn_subsystems = _cell(rxns.list_attr("subsystem")) + group_ids = model.groups.list_attr("id") + group_names = model.groups.list_attr("name") + group_ids = [ + _id if not _name else _name for _id, _name in zip(group_ids, group_names) + ] + group_members_list = model.groups.list_attr("members") + if set(rxn_subsystems) == {""} and set(group_ids) != {""}: + subsystems = [[] for _ in rxns] + for group_id, group_members in zip(group_ids, group_members_list): + group = model.groups.get_by_id(group_id) + if group.kind == "partonomy": + for member in group_members: + if isinstance(member, Reaction): + rxn_ind = model.reactions.index(member) + # noinspection PyTypeChecker + subsystems[rxn_ind].append(group_id) + mat["subSystems"] = _cell( + [", ".join(subsystem_list) for subsystem_list in subsystems] + ) + else: + mat["subSystems"] = _cell(rxns.list_attr("subsystem")) stoich_mat = create_stoichiometric_matrix(model) mat["S"] = stoich_mat if stoich_mat is not None else [[]] # multiply by 1 to convert to float, working around scipy bug @@ -674,9 +723,7 @@ def from_mat_struct( """ m = mat_struct - if m.dtype.names is None or not {"rxns", "mets", "S", "lb", "ub"} <= set( - m.dtype.names - ): + if m.dtype.names is None or {"rxns", "mets", "S", "lb", "ub"} > set(m.dtype.names): raise ValueError("Invalid MATLAB struct.") old_cobratoolbox_fields = [ @@ -705,7 +752,9 @@ def from_mat_struct( new_names[new_names.index(old_field)] = new_field m.dtype.names = new_names - model = Model() + model = ( + Model() + ) # TODO - Model() creates models with name=None, while SBML creates them with name='' if model_id is not None: model.id = model_id elif "description" in m.dtype.names: @@ -721,7 +770,7 @@ def from_mat_struct( model.name = m["modelName"][0, 0][0] met_ids = _cell_to_str_list(m["mets"][0, 0]) - if all(var in m.dtype.names for var in ["metComps", "comps", "compNames"]): + if {"metComps", "comps", "compNames"}.issubset(m.dtype.names): met_comp_index = [x[0] - 1 for x in m["metComps"][0][0]] comps = _cell_to_str_list(m["comps"][0, 0]) comp_names = _cell_to_str_list(m["compNames"][0][0]) @@ -760,7 +809,7 @@ def from_mat_struct( except (IndexError, ValueError): # TODO: use custom cobra exception to handle exception pass - new_metabolites = list() + new_metabolites = [] for i in range(len(met_ids)): new_metabolite = Metabolite(met_ids[i], compartment=met_comps[i]) if met_names: @@ -775,7 +824,6 @@ def from_mat_struct( model.add_metabolites(new_metabolites) if "genes" in m.dtype.names: - new_genes = [] gene_names = None gene_ids = _cell_to_str_list(m["genes"][0, 0]) try: @@ -783,12 +831,10 @@ def from_mat_struct( except (IndexError, ValueError): # TODO: use custom cobra exception to handle exception pass - for i in range(len(gene_ids)): - if gene_names: - new_gene = Gene(gene_ids[i], name=gene_names[i]) - else: - new_gene = Gene(gene_ids[i]) - new_genes.append(new_gene) + new_genes = [ + Gene(gene_ids[i], name=gene_names[i]) if gene_names else Gene(gene_ids[i]) + for i in range(len(gene_ids)) + ] mat_parse_annotations(new_genes, m, d_replace=DICT_GENE) for current_gene in new_genes: current_gene._model = model @@ -796,10 +842,8 @@ def from_mat_struct( new_reactions = [] rxn_ids = _cell_to_str_list(m["rxns"][0, 0]) - rxn_lbs = _cell_to_float_list(m["lb"][0, 0]) - rxn_lbs = [-inf if np.isinf(x) and x < 0 else x for x in rxn_lbs] - rxn_ubs = _cell_to_float_list(m["ub"][0, 0]) - rxn_ubs = [inf if np.isinf(x) and x > 0 else x for x in rxn_ubs] + rxn_lbs = _cell_to_float_list(m["lb"][0, 0], empty_value=None, inf_value=inf) + rxn_ubs = _cell_to_float_list(m["ub"][0, 0], empty_value=None, inf_value=inf) rxn_gene_rules, rxn_names, rxn_subsystems = None, None, None try: rxn_gene_rules = _cell_to_str_list(m["grRules"][0, 0], "") @@ -815,14 +859,16 @@ def from_mat_struct( # RECON3.0 mat has an array within an array for subsystems. # If we find a model that has multiple subsytems per reaction, this should be # modified - if isinstance(m["subSystems"][0, 0][0][0][0], np.ndarray): + if np.sctype2char(m["subSystems"][0, 0][0][0]) == "O" and isinstance( + m["subSystems"][0, 0][0][0][0], np.ndarray + ): rxn_subsystems = [ - each_cell[0][0][0][0] if each_cell else None + each_cell[0][0][0][0] if each_cell else "" for each_cell in m["subSystems"][0, 0] ] # Other matlab files seem normal. else: - rxn_subsystems = _cell_to_str_list(m["subSystems"][0, 0]) + rxn_subsystems = _cell_to_str_list(m["subSystems"][0, 0], "") except (IndexError, ValueError): # TODO: use custom cobra exception to handle exception pass @@ -856,11 +902,13 @@ def from_mat_struct( rxn_group_names = set(rxn_subsystems).difference({None}) new_groups = [] for g_name in sorted(rxn_group_names): - group_members = model.reactions.query(lambda x: x.subsystem == g_name) + group_members = model.reactions.query( + lambda x, g_n=g_name: x.subsystem == g_n + ) new_group = Group( id=g_name, name=g_name, members=group_members, kind="partonomy" ) - new_group.annotation["sbo"] = "SBO:0000633" + new_group.annotation["sbo"] = ["SBO:0000633"] new_groups.append(new_group) model.add_groups(new_groups) diff --git a/src/cobra/io/sbml.py b/src/cobra/io/sbml.py index 081d8f672..ce6a07699 100644 --- a/src/cobra/io/sbml.py +++ b/src/cobra/io/sbml.py @@ -19,8 +19,6 @@ Annotations are read in the Object.annotation fields. Some SBML related issues are still open, please refer to the respective issue: -- update annotation format and support qualifiers (depends on decision - for new annotation format; https://github.com/opencobra/cobrapy/issues/684) - write compartment annotations and notes (depends on updated first-class compartments; see https://github.com/opencobra/cobrapy/issues/760) - support compression on file handles (depends on solution for @@ -35,14 +33,30 @@ from collections import defaultdict, namedtuple from copy import deepcopy from io import StringIO +from pathlib import Path from sys import platform -from typing import IO, Match, Optional, Pattern, Tuple, Type, Union +from typing import IO, List, Match, Optional, Pattern, Tuple, Type, Union +from warnings import warn import libsbml import cobra -from ..core import GPR, Gene, Group, Metabolite, Model, Reaction +from ..core import ( + GPR, + Creator, + CVTerm, + CVTerms, + ExternalResources, + Gene, + Group, + HistoryDatetime, + Metabolite, + MetaData, + Model, + Notes, + Reaction, +) from ..manipulation.validate import check_metabolite_compartment_formula from ..util.solver import linear_reaction_coefficients, set_objective @@ -394,7 +408,7 @@ def _f_group_rev(sid: str, prefix: str = "G_") -> str: # ----------------------------------------------------------------------------- # noinspection PyDefaultArgument def read_sbml_model( - filename: Union[str, IO], + filename: Union[str, IO, Path], number: Type = float, f_replace: dict = F_REPLACE, **kwargs, @@ -472,7 +486,7 @@ def read_sbml_model( raise cobra_error from original_error -def _get_doc_from_filename(filename: Union[str, IO]) -> "libsbml.SBMLDocument": +def _get_doc_from_filename(filename: Union[str, IO, Path]) -> "libsbml.SBMLDocument": """Get SBMLDocument from given filename. Parameters @@ -517,6 +531,8 @@ def _get_doc_from_filename(filename: Union[str, IO]) -> "libsbml.SBMLDocument": doc = libsbml.readSBMLFromString( filename.read() ) # noqa: E501 type: libsbml.SBMLDocument + elif isinstance(filename, Path): + doc = libsbml.readSBMLFromString(filename.read_text()) else: raise CobraSBMLError( f"Input type '{type(filename)}' for '{filename}' is not supported." @@ -598,41 +614,7 @@ def _sbml_to_model( if not libsbml.SyntaxChecker.isValidSBMLSId(model_id): LOGGER.error(f"'{model_id}' is not a valid SBML 'SId'.") cobra_model = Model(model_id) - cobra_model.name = model.getName() - - # meta information - meta = { - "model.id": model_id, - "level": model.getLevel(), - "version": model.getVersion(), - "packages": [], - } - # History - creators = [] - created = None - if model.isSetModelHistory(): - history: "libsbml.ModelHistory" = model.getModelHistory() - - if history.isSetCreatedDate(): - created = history.getCreatedDate() - - c: "libsbml.ModelCreator" - for c in history.getListCreators(): - creators.append( - { - "familyName": c.getFamilyName() if c.isSetFamilyName() else None, - "givenName": c.getGivenName() if c.isSetGivenName() else None, - "organisation": c.getOrganisation() - if c.isSetOrganisation() - else None, - "email": c.getEmail() if c.isSetEmail() else None, - } - ) - - meta["creators"] = creators - meta["created"] = created - meta["notes"] = _parse_notes_dict(doc) - meta["annotation"] = _parse_annotations(doc) + cobra_model.name = model.getName() or None info = f"<{model_id}> SBML L{model.getLevel()}V{model.getVersion()}" packages = {} @@ -646,20 +628,28 @@ def _sbml_to_model( f"SBML package '{key}' not supported by cobrapy, " f"information is not parsed" ) - meta["info"] = info - meta["packages"] = packages + + # meta information + meta = { + "model.id": model_id, + "level": model.getLevel(), + "version": model.getVersion(), + "packages": packages, + "notes": _parse_notes_info(doc), + "annotation": _parse_annotations(doc), + "info": info, + } cobra_model._sbml = meta # notes and annotations - cobra_model.notes = _parse_notes_dict(model) + cobra_model.notes = _parse_notes_info(model) cobra_model.annotation = _parse_annotations(model) # Compartments # FIXME: update with new compartments compartments = {} - for ( - compartment - ) in model.getListOfCompartments(): # noqa: E501 type: libsbml.Compartment + compartment: libsbml.Compartment + for compartment in model.getListOfCompartments(): cid = _check_required(compartment, compartment.getIdAttribute(), "id") compartments[cid] = compartment.getName() cobra_model.compartments = compartments @@ -678,14 +668,14 @@ def _sbml_to_model( met = Metabolite(sid) met.name = specie.getName() - met.notes = _parse_notes_dict(specie) + met.notes = _parse_notes_info(specie) met.annotation = _parse_annotations(specie) met.compartment = specie.getCompartment() specie_fbc: "libsbml.FbcSpeciesPlugin" = specie.getPlugin("fbc") if specie_fbc: met.charge = specie_fbc.getCharge() - met.formula = specie_fbc.getChemicalFormula() + met.formula = specie_fbc.getChemicalFormula() or None else: if specie.isSetCharge(): LOGGER.warning( @@ -693,24 +683,23 @@ def _sbml_to_model( f"discouraged, use fbc:charge instead: {specie}" ) met.charge = specie.getCharge() - else: - if "CHARGE" in met.notes: - LOGGER.warning( - f"Use of CHARGE in the notes element is " - f"discouraged, use fbc:charge instead: {specie}" - ) - try: - met.charge = int(met.notes["CHARGE"]) - except ValueError: - # handle nan, na, NA, ... - pass + elif "CHARGE" in met.notes: + LOGGER.warning( + f"Use of CHARGE in the notes element is " + f"discouraged, use fbc:charge instead: {specie}" + ) + try: + met.charge = int(met.notes["CHARGE"]) + except ValueError: + # handle nan, na, NA, ... + pass if "FORMULA" in met.notes: LOGGER.warning( f"Use of FORMULA in the notes element is " f"discouraged, use fbc:chemicalFormula instead: {specie}" ) - met.formula = met.notes["FORMULA"] + met.formula = met.notes["FORMULA"] or None # Detect boundary metabolites if specie.getBoundaryCondition() is True: @@ -726,7 +715,7 @@ def _sbml_to_model( ex_rid = f"EX_{met.id}" ex_reaction = Reaction(ex_rid) ex_reaction.name = ex_rid - ex_reaction.annotation = {"sbo": SBO_EXCHANGE_REACTION} + ex_reaction.annotation = {"sbo": [SBO_EXCHANGE_REACTION]} ex_reaction.lower_bound = config.lower_bound ex_reaction.upper_bound = config.upper_bound LOGGER.warning( @@ -751,7 +740,7 @@ def _sbml_to_model( if cobra_gene.name is None: cobra_gene.name = gid cobra_gene.annotation = _parse_annotations(gp) - cobra_gene.notes = _parse_notes_dict(gp) + cobra_gene.notes = _parse_notes_info(gp) cobra_model.genes.append(cobra_gene) else: @@ -759,7 +748,7 @@ def _sbml_to_model( cobra_reaction ) in model.getListOfReactions(): # noqa: E501 type: libsbml.Reaction # fallback to notes information - notes = _parse_notes_dict(cobra_reaction) + notes = _parse_notes_info(cobra_reaction) if "GENE ASSOCIATION" in notes: gpr = notes["GENE ASSOCIATION"] elif "GENE_ASSOCIATION" in notes: @@ -829,9 +818,9 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]: if f_replace and F_REACTION in f_replace: rid = f_replace[F_REACTION](rid) cobra_reaction = Reaction(rid) - cobra_reaction.name = reaction.getName() + cobra_reaction.name = reaction.getName().strip() cobra_reaction.annotation = _parse_annotations(reaction) - cobra_reaction.notes = _parse_notes_dict(reaction) + cobra_reaction.notes = _parse_notes_info(reaction) # set bounds p_ub, p_lb = None, None @@ -1065,7 +1054,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]: if group.isSetKind(): cobra_group.kind = group.getKindAsString() cobra_group.annotation = _parse_annotations(group) - cobra_group.notes = _parse_notes_dict(group) + cobra_group.notes = _parse_notes_info(group) cobra_members = [] member: "libsbml.Member" @@ -1089,6 +1078,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]: if f_replace and F_REACTION in f_replace: obj_id = f_replace[F_REACTION](obj_id) cobra_member = cobra_model.reactions.get_by_id(obj_id) + cobra_member.subsystem = group.name elif typecode == libsbml.SBML_FBC_GENEPRODUCT: if f_replace and F_GENE in f_replace: obj_id = f_replace[F_GENE](obj_id) @@ -1110,6 +1100,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]: for cobra_reaction in cobra_model.reactions: if "SUBSYSTEM" in cobra_reaction.notes: g_name = cobra_reaction.notes["SUBSYSTEM"] + cobra_reaction.subsystem = g_name if g_name in groups_dict: groups_dict[g_name].append(cobra_reaction) else: @@ -1118,7 +1109,8 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]: for gid, cobra_members in groups_dict.items(): if f_replace and F_GROUP in f_replace: gid = f_replace[F_GROUP](gid) - cobra_group = Group(gid, name=gid, kind="collection") + cobra_group = Group(gid, name=gid, kind="partonomy") + cobra_group.annotation["sbo"] = ["SBO:0000633"] cobra_group.add_members(cobra_members) groups.append(cobra_group) @@ -1140,7 +1132,10 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]: # ----------------------------------------------------------------------------- # noinspection PyDefaultArgument def write_sbml_model( - cobra_model: Model, filename: Union[str, IO], f_replace: dict = F_REPLACE, **kwargs + cobra_model: Model, + filename: Union[str, IO, Path], + f_replace: dict = F_REPLACE, + **kwargs, ) -> None: """Write cobra model to filename. @@ -1182,6 +1177,10 @@ def write_sbml_model( sbml_str = libsbml.writeSBMLToString(doc) filename.write(sbml_str) + elif isinstance(filename, Path): + sbml_str = libsbml.writeSBMLToString(doc) + filename.write_text(sbml_str) + def _model_to_sbml( cobra_model: Model, f_replace: Optional[dict] = None, units: bool = True @@ -1226,7 +1225,7 @@ def _model_to_sbml( # for parsing annotation corresponding to the model _sbase_annotations(model, cobra_model.annotation) # for parsing notes corresponding to the model - _sbase_notes_dict(model, cobra_model.notes) + _set_notes(model, cobra_model.notes) # Meta information (ModelHistory) related to SBMLDocument if hasattr(cobra_model, "_sbml"): @@ -1234,7 +1233,7 @@ def _model_to_sbml( if "annotation" in meta: _sbase_annotations(doc, meta["annotation"]) if "notes" in meta: - _sbase_notes_dict(doc, meta["notes"]) + _set_notes(doc, meta["notes"]) history: "libsbml.ModelHistory" = libsbml.ModelHistory() if "created" in meta and meta["created"]: @@ -1251,10 +1250,10 @@ def _model_to_sbml( "creators" ]: # noqa: E501 type: libsbml.ModelCreator creator = libsbml.ModelCreator() - if cobra_creator.get("familyName", None): - creator.setFamilyName(cobra_creator["familyName"]) - if cobra_creator.get("givenName", None): - creator.setGivenName(cobra_creator["givenName"]) + if cobra_creator.get("family_name", None): + creator.setFamilyName(cobra_creator["family_name"]) + if cobra_creator.get("given_name", None): + creator.setGivenName(cobra_creator["given_name"]) if cobra_creator.get("organisation", None): creator.setOrganisation(cobra_creator["organisation"]) if cobra_creator.get("email", None): @@ -1264,6 +1263,7 @@ def _model_to_sbml( # TODO: Will be implemented as part of # https://github.com/opencobra/cobrapy/issues/810 + # I think this should be uncommented and under the if, like # _check(model.setModelHistory(history), 'set model history') # Units @@ -1332,7 +1332,7 @@ def _model_to_sbml( s_fbc.setChemicalFormula(metabolite.formula) _sbase_annotations(specie, metabolite.annotation) - _sbase_notes_dict(specie, metabolite.notes) + _set_notes(specie, metabolite.notes) # Genes for cobra_gene in cobra_model.genes: @@ -1348,7 +1348,7 @@ def _model_to_sbml( gp.setLabel(gid) _sbase_annotations(gp, cobra_gene.annotation) - _sbase_notes_dict(gp, cobra_gene.notes) + _set_notes(gp, cobra_gene.notes) # Objective objective: "libsbml.Objective" = model_fbc.createObjective() @@ -1368,7 +1368,7 @@ def _model_to_sbml( reaction.setFast(False) reaction.setReversible((cobra_reaction.lower_bound < 0)) _sbase_annotations(reaction, cobra_reaction.annotation) - _sbase_notes_dict(reaction, cobra_reaction.notes) + _set_notes(reaction, cobra_reaction.notes) # stoichiometry for metabolite, stoichiometry in cobra_reaction.metabolites.items(): @@ -1444,9 +1444,7 @@ def _model_to_sbml( "http://www.sbml.org/sbml/level3/version1/groups/version1", "groups", True ) doc.setPackageRequired("groups", False) - model_group = model.getPlugin( - "groups" - ) # noqa: E501 type: libsbml.GroupsModelPlugin + model_group: "libsbml.GroupsModelPlugin" = model.getPlugin("groups") for cobra_group in cobra_model.groups: group: "libsbml.Group" = model_group.createGroup() if f_replace and F_GROUP_REV in f_replace: @@ -1457,7 +1455,7 @@ def _model_to_sbml( group.setName(cobra_group.name) group.setKind(cobra_group.kind) - _sbase_notes_dict(group, cobra_group.notes) + _set_notes(group, cobra_group.notes) _sbase_annotations(group, cobra_group.annotation) for cobra_member in cobra_group.members: @@ -1466,15 +1464,12 @@ def _model_to_sbml( m_type = str(type(cobra_member)) # id replacements - if "Reaction" in m_type: - if f_replace and F_REACTION_REV in f_replace: - mid = f_replace[F_REACTION_REV](mid) - if "Metabolite" in m_type: - if f_replace and F_SPECIE_REV in f_replace: - mid = f_replace[F_SPECIE_REV](mid) - if "Gene" in m_type: - if f_replace and F_GENE_REV in f_replace: - mid = f_replace[F_GENE_REV](mid) + if "Reaction" in m_type and f_replace and F_REACTION_REV in f_replace: + mid = f_replace[F_REACTION_REV](mid) + if "Metabolite" in m_type and f_replace and F_SPECIE_REV in f_replace: + mid = f_replace[F_SPECIE_REV](mid) + if "Gene" in m_type and f_replace and F_GENE_REV in f_replace: + mid = f_replace[F_GENE_REV](mid) member.setIdRef(mid) if cobra_member.name and len(cobra_member.name) > 0: @@ -1612,9 +1607,8 @@ def _check_required(sbase: "libsbml.Base", value: str, attribute: str) -> str: elif hasattr(sbase, "getMetaId") and sbase.getMetaId(): msg += f" with metaId '{sbase.getName()}'" raise CobraSBMLError(msg) - if attribute == "id": - if not libsbml.SyntaxChecker.isValidSBMLSId(value): - LOGGER.error(f"'{value}' is not a valid SBML 'SId'.") + if attribute == "id" and not libsbml.SyntaxChecker.isValidSBMLSId(value): + LOGGER.error(f"'{value}' is not a valid SBML 'SId'.") return value @@ -1656,8 +1650,8 @@ def _check(value: Union[None, int], message: str) -> None: # ----------------------------------------------------------------------------- # Notes # ----------------------------------------------------------------------------- -def _parse_notes_dict(sbase) -> dict: - """Create dictionary of COBRA notes. +def _parse_notes_info(sbase: libsbml.SBase) -> Notes: + """Create COBRA Notes object. Parameters ---------- @@ -1665,28 +1659,15 @@ def _parse_notes_dict(sbase) -> dict: Returns ------- - dict of notes + Notes object """ - notes = sbase.getNotesString() - if notes and len(notes) > 0: - notes_store = dict() - for match in pattern_notes.finditer(notes): - _content = match.group("content") - try: - # Python 2.7 does not allow keywords for split. - # Python 3 can have (":", maxsplit=1) - key, value = _content.split(":", maxsplit=1) - except ValueError: - LOGGER.debug(f"Unexpected content format '{_content}'.") - continue - notes_store[key.strip()] = value.strip() - return {k: v for k, v in notes_store.items() if len(v) > 0} - else: - return {} + notes = sbase.getNotesString() or None + cobra_notes = Notes(notes) + return cobra_notes -def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None: - """Set SBase notes based on dictionary. +def _set_notes(sbase: libsbml.SBase, notes: Notes) -> None: + """Set SBase notes based on the COBRA notes object. Parameters ---------- @@ -1695,16 +1676,11 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None: notes : dict Notes information from cobra object. """ - if notes and len(notes) > 0: - tokens = ( - [''] - + [f"

{k}: {v}

" for (k, v) in notes.items()] - + [""] - ) - _check( - sbase.setNotes("\n".join(tokens)), - f"Setting notes on sbase: {sbase}", - ) + if notes.notes_xhtml is None or len(notes.notes_xhtml) == 0: + return + _check( + sbase.setNotes(notes.notes_xhtml), "Setting notes on sbase: {}".format(sbase) + ) # ----------------------------------------------------------------------------- @@ -1731,21 +1707,21 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None: URL_IDENTIFIERS_PATTERN = re.compile(r"^https?://identifiers.org/(.+?)[:/](.+)") URL_IDENTIFIERS_PREFIX = "https://identifiers.org" -QUALIFIER_TYPES = { - "is": libsbml.BQB_IS, - "hasPart": libsbml.BQB_HAS_PART, - "isPartOf": libsbml.BQB_IS_PART_OF, - "isVersionOf": libsbml.BQB_IS_VERSION_OF, - "hasVersion": libsbml.BQB_HAS_VERSION, - "isHomologTo": libsbml.BQB_IS_HOMOLOG_TO, - "isDescribedBy": libsbml.BQB_IS_DESCRIBED_BY, - "isEncodedBy": libsbml.BQB_IS_ENCODED_BY, - "encodes": libsbml.BQB_ENCODES, - "occursIn": libsbml.BQB_OCCURS_IN, - "hasProperty": libsbml.BQB_HAS_PROPERTY, - "isPropertyOf": libsbml.BQB_IS_PROPERTY_OF, - "hasTaxon": libsbml.BQB_HAS_TAXON, - "unknown": libsbml.BQB_UNKNOWN, +QUALIFIER_TYPES_COBRA_SBML_DICT = { + "bqb_is": libsbml.BQB_IS, + "bqb_hasPart": libsbml.BQB_HAS_PART, + "bqb_isPartOf": libsbml.BQB_IS_PART_OF, + "bqb_isVersionOf": libsbml.BQB_IS_VERSION_OF, + "bqb_hasVersion": libsbml.BQB_HAS_VERSION, + "bqb_isHomologTo": libsbml.BQB_IS_HOMOLOG_TO, + "bqb_isDescribedBy": libsbml.BQB_IS_DESCRIBED_BY, + "bqb_isEncodedBy": libsbml.BQB_IS_ENCODED_BY, + "bqb_encodes": libsbml.BQB_ENCODES, + "bqb_occursIn": libsbml.BQB_OCCURS_IN, + "bqb_hasProperty": libsbml.BQB_HAS_PROPERTY, + "bqb_isPropertyOf": libsbml.BQB_IS_PROPERTY_OF, + "bqb_hasTaxon": libsbml.BQB_HAS_TAXON, + "bqb_unknown": libsbml.BQB_UNKNOWN, "bqm_is": libsbml.BQM_IS, "bqm_isDescribedBy": libsbml.BQM_IS_DESCRIBED_BY, "bqm_isDerivedFrom": libsbml.BQM_IS_DERIVED_FROM, @@ -1755,10 +1731,21 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None: } -def _parse_annotations(sbase: libsbml.SBase) -> dict: - """Parse cobra annotations from a given SBase object. +def _parse_annotations(sbase: libsbml.SBase) -> MetaData: + """Parses cobra annotations from a given SBase object. - Annotations are dictionaries with the providers as keys. + The annotation format has been changed. We no longer have + simple dictionaries for storing annotation data. Dedicated + classes for storing CVTerm data, History data and key-value + pair data corresponding to an SBase object have been made. + The metadata classes inside cobra.core directory contains + of them. All the existing issues in old annotation format have + been solved. The new format annotation is completely backward + compatible. It can read models with old annotation format, + can convert old format annotation to new format annotation, + and writes annotation in new format only (for JSON and other + formats). The JSON schema v2 specifies the new format annotation + whereas JSON schema v1 have annotation data defined in old format. Parameters ---------- @@ -1767,15 +1754,13 @@ def _parse_annotations(sbase: libsbml.SBase) -> dict: Returns ------- - dict (annotation dictionary) + MetaData + a metadata object storing COBRA annotation """ - # FIXME: annotation format must be updated (this is a big collection of - # fixes) - see: https://github.com/opencobra/cobrapy/issues/684) - annotation = {} + annotation = MetaData() # SBO term if sbase.isSetSBOTerm(): - # FIXME: correct handling of annotations annotation["sbo"] = sbase.getSBOTermID() # RDF annotation @@ -1783,27 +1768,69 @@ def _parse_annotations(sbase: libsbml.SBase) -> dict: if cvterms is None: return annotation - cvterm: "libsbml.CVTerm" - for cvterm in cvterms: - for k in range(cvterm.getNumResources()): - # FIXME: read and store the qualifier + def _cvterm_to_cobra(_cvterm: "libsbml.CVTerm") -> CVTerm: + """Parses the libsbml.CVTerm object to cobra CVTerm. - uri = cvterm.getResourceURI(k) - data = _parse_annotation_info(uri) - if data is None: - continue - else: - provider, identifier = data - - if provider in annotation: - if isinstance(annotation[provider], str): - annotation[provider] = [annotation[provider]] - # FIXME: use a list - if identifier not in annotation[provider]: - annotation[provider].append(identifier) - else: - # FIXME: always in list - annotation[provider] = identifier + Parameters + ---------- + _cvterm : libsbml.CVTerm + The libsbml.CVTerm object from which data is to be parsed. + + Returns + ------- + CVTerm + The parsed data of the given libsbml.CVTerm object as CVTerm. + """ + qualifier_type = _cvterm.getQualifierType() + if qualifier_type == 0: + mq_type = _cvterm.getModelQualifierType() + qualifier = "bqm_" + libsbml.ModelQualifierType_toString(mq_type) + elif qualifier_type == 1: + bq_type = _cvterm.getBiologicalQualifierType() + qualifier = "bqb_" + libsbml.BiolQualifierType_toString(bq_type) + else: + qualifier = "unknown_qualifier" + ext_res = {"resources": []} + for k in range(_cvterm.getNumResources()): + uri = _cvterm.getResourceURI(k) + ext_res["resources"].append(uri) + nested_cv_terms = [ + _cvterm.getNestedCVTerm(index) + for index in range(_cvterm.getNumNestedCVTerms()) + ] + # This kludge is necessary since _cvterm.getListNestedCVTerms() doesn't give a + # python list, but a Swig List_t * and then SwigPyObject is not iterable + ext_res["nested_data"] = CVTerms( + [_cvterm_to_cobra(_nested_cvterm) for _nested_cvterm in nested_cv_terms] + ) + return CVTerm(ExternalResources.from_dict(ext_res), qualifier) + + annotation.add_cvterms([_cvterm_to_cobra(cvterm) for cvterm in cvterms]) + + # history of the component + if sbase.isSetModelHistory(): + model_history: "libsbml.ModelHistory" = sbase.getModelHistory() + + annotation.history.creators = [ + Creator.from_data( + { + "family_name": creator.getFamilyName() or None, + "given_name": creator.getGivenName() or None, + "organisation": creator.getOrganisation() or None, + "email": creator.getEmail() or None, + } + ) + for creator in model_history.getListCreators() + ] + + if model_history.isSetCreatedDate(): + date: libsbml.Date = model_history.getCreatedDate() + annotation.history.created_date = HistoryDatetime(date.getDateAsString()) + + annotation.history.modified_dates = [ + HistoryDatetime(_date.getDateAsString()) + for _date in model_history.getListModifiedDates() + ] return annotation @@ -1819,7 +1846,15 @@ def _parse_annotation_info(uri: str) -> Union[None, Tuple[str, str]]: Returns ------- (provider, identifier) if resolvable, None otherwise + + .. deprecated :: + Use cobra.core.metadata.helper.parse_identifiers_uri() """ + warn( + "_parse_annotation_info() is being replaced by " + "cobra.core.metadata.helper.parse_identifiers_uri()", + DeprecationWarning, + ) match = URL_IDENTIFIERS_PATTERN.match(uri) if match: provider, identifier = match.group(1), match.group(2) @@ -1837,7 +1872,53 @@ def _parse_annotation_info(uri: str) -> Union[None, Tuple[str, str]]: return provider, identifier -def _sbase_annotations(sbase: libsbml.SBase, annotation: dict) -> None: +def _cvterms_to_sbml(cvterms: CVTerms) -> List["libsbml.CVTerm"]: + """Convert cobra CVTerms to libsbml.CVTerm list. + + Parameters + ---------- + cvterms: CVTerms + cobra CVTerms object + + Returns + ------- + list + List of libsbml.cvTerm objects + """ + cv_list = [] + for cvterm in cvterms: + qualifier = cvterm.qualifier + if qualifier.name.startswith("bqb"): + qualifier_type = libsbml.BIOLOGICAL_QUALIFIER + elif qualifier.name.startswith("bqm"): + qualifier_type = libsbml.MODEL_QUALIFIER + else: + raise CobraSBMLError(f"Unsupported qualifier: {qualifier}") + + cv: "libsbml.CVTerm" = libsbml.CVTerm() + cv.setQualifierType(qualifier_type) + if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER: + cv.setBiologicalQualifierType( + QUALIFIER_TYPES_COBRA_SBML_DICT[qualifier.name] + ) + elif qualifier_type == libsbml.MODEL_QUALIFIER: + cv.setModelQualifierType(QUALIFIER_TYPES_COBRA_SBML_DICT[qualifier.name]) + else: + raise CobraSBMLError(f"Unsupported qualifier: {qualifier}") + for uri in cvterm.external_resources.resources: + cv.addResource(uri) + + [ + _check(cv.addNestedCVTerm(_cv), f"Adding nested cvterm: {_cv}") + for _cv in _cvterms_to_sbml(cvterm.external_resources.nested_data) + ] + + cv_list.append(cv) + + return cv_list + + +def _sbase_annotations(sbase: libsbml.SBase, annotation: MetaData) -> None: """Set SBase annotations based on cobra annotations. Parameters @@ -1851,72 +1932,62 @@ def _sbase_annotations(sbase: libsbml.SBase, annotation: dict) -> None: ------ CobraSBMLError for unsupported qualifier """ - # FIXME: annotation format must be updated - # (https://github.com/opencobra/cobrapy/issues/684) - if not annotation or len(annotation) == 0: - return - - # standardize annotations annotation_data = deepcopy(annotation) + # TODO - devel has formatting of float and to str, and str to ["is", str] - does this happen in CVterm? + + if not isinstance(annotation_data, MetaData): + raise TypeError( + f"The annotation object must be of type 'Metadata': {annotation_data}" + ) - for key, value in annotation_data.items(): - # handling of non-string annotations (e.g. integers) - if isinstance(value, (float, int)): - value = str(value) - if isinstance(value, str): - annotation_data[key] = [("is", value)] + if "SBO" in annotation_data: + LOGGER.warning( + "'SBO' provider is deprecated, use 'sbo' provider instead. Converting to" + "'sbo' for writing." + ) + annotation_data["sbo"] = annotation_data.pop("SBO") - for _key, value in annotation_data.items(): - for idx, item in enumerate(value): - if isinstance(item, str): - value[idx] = ("is", item) + if "sbo" in annotation and annotation.sbo: + sbo_term = annotation_data.sbo + if isinstance(sbo_term, list): + sbo_term = sbo_term[0] + _check(sbase.setSBOTerm(sbo_term), f"Setting SBOTerm: {sbo_term}") # set metaId meta_id = f"meta_{sbase.getId()}" sbase.setMetaId(meta_id) - # rdf_items = [] - for provider, data in annotation_data.items(): - - # set SBOTerm - if provider in ["SBO", "sbo"]: - if provider == "SBO": - LOGGER.warning( - "'SBO' provider is deprecated, use 'sbo' provider instead" - ) - sbo_term = data[0][1] - _check(sbase.setSBOTerm(sbo_term), f"Setting SBOTerm: {sbo_term}") - - # FIXME: sbo should also be written as CVTerm - continue - - for item in data: - qualifier_str, entity = item[0], item[1] - qualifier = QUALIFIER_TYPES.get(qualifier_str, None) - if qualifier is None: - qualifier = libsbml.BQB_IS - LOGGER.error( - f"Qualifier type is not supported on annotation: '{qualifier_str}'" - ) - - qualifier_type = libsbml.BIOLOGICAL_QUALIFIER - if qualifier_str.startswith("bqm_"): - qualifier_type = libsbml.MODEL_QUALIFIER - - cv: "libsbml.CVTerm" = libsbml.CVTerm() - cv.setQualifierType(qualifier_type) - if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER: - cv.setBiologicalQualifierType(qualifier) - elif qualifier_type == libsbml.MODEL_QUALIFIER: - cv.setModelQualifierType(qualifier) - else: - raise CobraSBMLError(f"Unsupported qualifier: {qualifier}") - resource = f"{URL_IDENTIFIERS_PREFIX}/{provider}/{entity}" - cv.addResource(resource) - _check( - sbase.addCVTerm(cv), - f"Setting cvterm: {cv}, resource: {resource}", - ) + # set cvterms + [ + _check(sbase.addCVTerm(cv), f"Setting cvterm: {cv}") + for cv in _cvterms_to_sbml(annotation.cvterms) + ] + + # set history + if not annotation.history.is_empty(): + comp_history = libsbml.ModelHistory() + + for creator in annotation.history.creators: + comp_creator = libsbml.ModelCreator() + comp_creator.setGivenName(creator.given_name) + comp_creator.setFamilyName(creator.family_name) + creator.email and comp_creator.setEmail(creator.email) + creator.organisation and comp_creator.setOrganisation(creator.organisation) + comp_history.addCreator(comp_creator) + + if annotation.history.created_date.datetime is not None: + date = libsbml.Date(annotation.history.created_date.datetime) + comp_history.setCreatedDate(date) + + for modified_date in annotation.history.modified_dates: + date = libsbml.Date(modified_date.datetime) + comp_history.addModifiedDate(date) + + # finally add the compo_history + _check( + sbase.setModelHistory(comp_history), + f"Setting ModelHistory: {comp_history}", + ) # ----------------------------------------------------------------------------- diff --git a/src/cobra/io/schema_v1.json b/src/cobra/io/schema_v1.json index edc9756fb..8fd7cb0a4 100644 --- a/src/cobra/io/schema_v1.json +++ b/src/cobra/io/schema_v1.json @@ -153,5 +153,5 @@ "metabolites", "genes" ], - "additionalProperties": false + "additionalProperties": true } diff --git a/src/cobra/io/schema_v2.json b/src/cobra/io/schema_v2.json new file mode 100644 index 000000000..2aaadfbe9 --- /dev/null +++ b/src/cobra/io/schema_v2.json @@ -0,0 +1,370 @@ +{ + "$schema": "http://json-schema.org/draft-04/schema#", + "title": "COBRA", + "description": "JSON representation of COBRA model", + "definitions": { + "annotation": { + "type": "object", + "properties": { + "sbo": { + "type": "string" + }, + "cvterms": { + "type": "object", + "additionalProperties": { + "type": "array", + "items": { + "type": "object", + "properties": { + "resources": { + "type": "array", + "items": { + "type": "string" + } + }, + "nested_data": { + "$ref": "#/definitions/annotation" + } + } + } + } + }, + "history": { + "type": "object", + "properties": { + "creators": { + "type": "array", + "items": { + "type": "object", + "properties": { + "email": { + "type": "string" + }, + "given_name": { + "type": "string" + }, + "family_name": { + "type": "string" + }, + "organisation": { + "type": "string" + } + }, + "required": [ + "given_name", + "family_name" + ], + "additionalProperties": false + } + }, + "created_date": { + "type": "string", + "format": "date-time" + }, + "modified_dates": { + "type": "array", + "items": { + "type": "string", + "format": "date-time" + } + } + }, + "required": [ + "creators", + "created_date", + "modified_dates" + ], + "additionalProperties": false + }, + "listofkeyvalue": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "key": { + "type": "string" + }, + "value": { + "type": "string" + }, + "uri": { + "type": "string" + } + }, + "required": [ + "key" + ], + "additionalProperties": false + } + } + } + } + }, + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "version": { + "type": "string", + "default": "1" + }, + "reactions": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "metabolites": { + "type": "object", + "patternProperties": { + ".*": { + "type": "number" + } + } + }, + "gene_reaction_rule": { + "type": "string" + }, + "lower_bound": { + "type": "number" + }, + "upper_bound": { + "type": "number" + }, + "objective_coefficient": { + "type": "number", + "default": 0 + }, + "subsystem": { + "type": "string" + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + } + }, + "required": [ + "id", + "name", + "metabolites", + "lower_bound", + "upper_bound", + "gene_reaction_rule" + ], + "additionalProperties": false + } + }, + "metabolites": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "compartment": { + "type": "string", + "pattern": "[a-z]{1,2}" + }, + "charge": { + "type": "integer" + }, + "formula": { + "type": "string" + }, + "_bound": { + "type": "number", + "default": 0 + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + } + }, + "required": [ + "id", + "name", + "compartment" + ], + "additionalProperties": false + } + }, + "genes": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + } + }, + "required": [ + "id", + "name" + ], + "additionalProperties": false + } + }, + "compartments": { + "type": "object", + "patternProperties": { + "[a-z]{1,2}": { + "type": "string" + } + } + }, + "groups": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + }, + "kind": { + "type": "string", + "enum": ["collection", "classification", "partonomy"] + }, + "members": { + "type": "array", + "items": { + "type": "object", + "properties": { + "idRef": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "type": { + "type": "string" + } + }, + "required": ["idRef", "type"] + } + } + }, + "required": ["kind", "members"] + } + }, + "user_defined_constraints": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "lower_bound": { + "type": "number" + }, + "upper_bound": { + "type": "number" + }, + "constraint_comps": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$" + }, + "name": { + "type": "string" + }, + "coefficient": { + "type": "number" + }, + "variable": { + "type": "string" + }, + "variable_type": { + "type": "string", + "enum": ["linear", "quadratic"] + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + } + }, + "required": ["variable"], + "additionalProperties": false + } + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + } + }, + "required": ["lower_bound", "upper_bound", "constraint_comps"], + "additionalProperties": false + } + }, + "notes": { + "type": "string" + }, + "annotation": { + "$ref": "#/definitions/annotation" + } + }, + "required": [ + "id", + "reactions", + "metabolites", + "genes" + ], + "additionalProperties": true +} diff --git a/src/cobra/manipulation/annotate.py b/src/cobra/manipulation/annotate.py index 6f989dd2a..9bad70d41 100644 --- a/src/cobra/manipulation/annotate.py +++ b/src/cobra/manipulation/annotate.py @@ -22,15 +22,18 @@ def add_SBO(model: "Model") -> None: The model whose demand and exchange reactions need to be annotated. """ + # ??? Should this be done with boundary? for r in model.reactions: # don't annotate already annotated reactions - if r.annotation.get("sbo"): + if len(r.annotation.get("sbo")) != 0 and r.annotation.sbo: continue # only doing exchanges if len(r.metabolites) != 1: continue met_id = list(r._metabolites)[0].id if r.id.startswith("EX_") and r.id == "EX_" + met_id: - r.annotation["sbo"] = "SBO:0000627" + r.annotation["sbo"] = ["SBO:0000627"] elif r.id.startswith("DM_") and r.id == "DM_" + met_id: - r.annotation["sbo"] = "SBO:0000628" + r.annotation["sbo"] = ["SBO:0000628"] + elif r.id.startswith("SK_") and r.id == "SK_" + met_id: + r.annotation["sbo"] = ["SBO:0000632"] diff --git a/src/cobra/manipulation/validate.py b/src/cobra/manipulation/validate.py index 344a05437..34c821690 100644 --- a/src/cobra/manipulation/validate.py +++ b/src/cobra/manipulation/validate.py @@ -33,7 +33,7 @@ def check_mass_balance(model: "Model") -> Dict["Reaction", Dict["Metabolite", fl """ unbalanced = {} for reaction in model.reactions: - if reaction.annotation.get("sbo") not in _NOT_MASS_BALANCED_TERMS: + if set(reaction.annotation.get("sbo", [])).isdisjoint(_NOT_MASS_BALANCED_TERMS): balance = reaction.check_mass_balance() if balance: unbalanced[reaction] = balance diff --git a/src/cobra/medium/boundary_types.py b/src/cobra/medium/boundary_types.py index 0229b4bb4..2b327d82a 100644 --- a/src/cobra/medium/boundary_types.py +++ b/src/cobra/medium/boundary_types.py @@ -125,9 +125,9 @@ def is_boundary_type( """ # Check if the reaction has an annotation. Annotations dominate everything. sbo_term = reaction.annotation.get("sbo", "") - if isinstance(sbo_term, list): + if isinstance(sbo_term, list) and len(sbo_term) != 0: sbo_term = sbo_term[0] - sbo_term = sbo_term.upper() + sbo_term = sbo_term.upper() if sbo_term == sbo_terms[boundary_type]: return True diff --git a/tests/data/annotation.xml b/tests/data/annotation.xml index 8be18e5b1..ae00ba3c5 100644 --- a/tests/data/annotation.xml +++ b/tests/data/annotation.xml @@ -148,7 +148,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + diff --git a/tests/data/cvterms_nested.json b/tests/data/cvterms_nested.json new file mode 100644 index 000000000..4c0ff5996 --- /dev/null +++ b/tests/data/cvterms_nested.json @@ -0,0 +1,32 @@ +{ + "bqb_hasPart": [ + { + "resources": [ + "https://identifiers.org/uniprot/P69905", + "https://identifiers.org/uniprot/P68871", + "https://identifiers.org/kegg.compound/C00032" + ] + }, + { + "resources": [ + "https://identifiers.org/uniprot/P69905", + "https://www.uniprot.org/uniprot/P68871", + "https://identifiers.org/chebi/CHEBI:17627" + ], + "nested_data": { + "bqb_isDescribedBy": [ + { + "resources": [ + "https://identifiers.org/pubmed/1111111" + ] + }, + { + "resources": [ + "https://identifiers.org/eco/000000" + ] + } + ] + } + } + ] +} diff --git a/tests/data/e_coli_core.json b/tests/data/e_coli_core.json new file mode 100644 index 000000000..39db77321 --- /dev/null +++ b/tests/data/e_coli_core.json @@ -0,0 +1,14786 @@ +{ +"metabolites":[ +{ +"id":"glc__D_e", +"name":"D-Glucose", +"compartment":"e", +"charge":0, +"formula":"C6H12O6", +"notes":{ +"original_bigg_ids":[ +"glc_D_e" +] +}, +"annotation":{ +"bigg.metabolite":[ +"glc__D" +], +"biocyc":[ +"META:Glucopyranose" +], +"chebi":[ +"CHEBI:12965", +"CHEBI:20999", +"CHEBI:4167", +"CHEBI:17634" +], +"hmdb":[ +"HMDB00122", +"HMDB06564" +], +"inchi_key":[ +"WQZGKKKJIJFFOK-GASJEMHNSA-N" +], +"kegg.compound":[ +"C00031" +], 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+"refseq_synonym":[ +"glu", +"ECK3947", +"asp", +"JW3928" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P00864" +] +} +}, +{ +"id":"b3403", +"name":"pck", +"notes":{ +"original_bigg_ids":[ +"b3403" +] +}, +"annotation":{ +"asap":[ +"ABE-0011106" +], +"ecogene":[ +"EG10688" +], +"ncbigene":[ +"945667" +], +"ncbigi":[ +"16131280" +], +"refseq_locus_tag":[ +"b3403" +], +"refseq_name":[ +"pck" +], +"refseq_synonym":[ +"JW3366", +"pckA", +"ECK3390" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P22259" +] +} +}, +{ +"id":"b1702", +"name":"ppsA", +"notes":{ +"original_bigg_ids":[ +"b1702" +] +}, +"annotation":{ +"asap":[ +"ABE-0005678" +], +"ecogene":[ +"EG10759" +], +"ncbigene":[ +"946209" +], +"ncbigi":[ +"16129658" +], +"refseq_locus_tag":[ +"b1702" +], +"refseq_name":[ +"ppsA" +], +"refseq_synonym":[ +"pps", +"ECK1700", +"JW1692" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P23538" +] +} +}, +{ +"id":"b2297", +"name":"pta", +"notes":{ +"original_bigg_ids":[ +"b2297" +] +}, +"annotation":{ +"asap":[ +"ABE-0007582" +], +"ecogene":[ +"EG20173" +], +"ncbigene":[ +"946778" +], +"ncbigi":[ +"16130232" +], +"refseq_locus_tag":[ +"b2297" +], +"refseq_name":[ +"pta" +], +"refseq_synonym":[ +"JW2294", +"ECK2291" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A9M8" +] +} +}, +{ +"id":"b2458", +"name":"eutD", +"notes":{ +"original_bigg_ids":[ +"b2458" +] +}, +"annotation":{ +"asap":[ +"ABE-0008097" +], +"ecogene":[ +"EG14188" +], +"ncbigene":[ +"946940" +], +"ncbigi":[ +"16130383" +], +"refseq_locus_tag":[ +"b2458" +], +"refseq_name":[ +"eutD" +], +"refseq_synonym":[ +"eutI", +"ypfA", +"ECK2453", +"JW2442" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P77218" +] +} +}, +{ +"id":"b1676", +"name":"pykF", +"notes":{ +"original_bigg_ids":[ +"b1676" +] +}, +"annotation":{ +"asap":[ +"ABE-0005600" +], +"ecogene":[ +"EG10804" +], +"ncbigene":[ +"946179" +], +"ncbigi":[ +"16129632" +], +"refseq_locus_tag":[ +"b1676" +], +"refseq_name":[ +"pykF" +], +"refseq_synonym":[ +"ECK1672", +"JW1666" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AD61" +] +} +}, +{ +"id":"b1854", +"name":"pykA", +"notes":{ +"original_bigg_ids":[ +"b1854" +] +}, +"annotation":{ +"asap":[ +"ABE-0006182" +], +"ecogene":[ +"EG10803" +], +"ncbigene":[ +"946527" +], +"ncbigi":[ +"16129807" +], +"refseq_locus_tag":[ +"b1854" +], +"refseq_name":[ +"pykA" +], +"refseq_synonym":[ +"JW1843", +"ECK1855" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P21599" +] +} +}, +{ +"id":"b3386", +"name":"rpe", +"notes":{ +"original_bigg_ids":[ +"b3386" +] +}, +"annotation":{ +"asap":[ +"ABE-0011061" +], +"ecogene":[ +"EG11960" +], +"ncbigene":[ +"947896" +], +"ncbigi":[ +"16131264" +], +"refseq_locus_tag":[ +"b3386" +], +"refseq_name":[ +"rpe" +], +"refseq_synonym":[ +"yhfD", +"ECK3373", +"JW3349", +"dod" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AG07" +] +} +}, +{ +"id":"b4301", +"name":"sgcE", +"notes":{ +"original_bigg_ids":[ +"b4301" +] +}, +"annotation":{ +"asap":[ +"ABE-0014097" +], +"ecogene":[ +"EG12553" +], +"ncbigene":[ +"948829" +], +"ncbigi":[ +"16132122" +], +"refseq_locus_tag":[ +"b4301" +], +"refseq_name":[ +"sgcE" +], +"refseq_synonym":[ +"JW4263", +"ECK4290", +"yjhK" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P39362" +] +} +}, +{ +"id":"b2914", +"name":"rpiA", +"notes":{ +"original_bigg_ids":[ +"b2914" +] +}, +"annotation":{ +"asap":[ +"ABE-0009567" +], +"ecogene":[ +"EG11443" +], +"ncbigene":[ +"947407" +], +"ncbigi":[ +"16130815" +], +"refseq_locus_tag":[ +"b2914" +], +"refseq_name":[ +"rpiA" +], +"refseq_synonym":[ +"ECK2910", +"JW5475", +"ygfC" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A7Z0" +] +} +}, +{ +"id":"b4090", +"name":"rpiB", +"notes":{ +"original_bigg_ids":[ +"b4090" +] +}, +"annotation":{ +"asap":[ +"ABE-0013405" +], +"ecogene":[ +"EG11827" +], +"ncbigene":[ +"948602" +], +"ncbigi":[ +"16131916" +], +"refseq_locus_tag":[ +"b4090" +], +"refseq_name":[ +"rpiB" +], +"refseq_synonym":[ +"JW4051", +"alsB", +"alsI", +"yjcA", +"ECK4083" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P37351" +] +} +}, +{ +"id":"b0721", +"name":"sdhC", +"notes":{ +"original_bigg_ids":[ +"b0721" +] +}, +"annotation":{ +"asap":[ +"ABE-0002460" +], +"ecogene":[ +"EG10933" +], +"ncbigene":[ +"945316" +], +"ncbigi":[ +"16128696" +], +"refseq_locus_tag":[ +"b0721" +], +"refseq_name":[ +"sdhC" +], +"refseq_synonym":[ +"JW0711", +"ECK0710", +"cybA" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P69054" +] +} +}, +{ +"id":"b0722", +"name":"sdhD", +"notes":{ +"original_bigg_ids":[ +"b0722" +] +}, +"annotation":{ +"asap":[ +"ABE-0002464" +], +"ecogene":[ +"EG10934" +], +"ncbigene":[ +"945322" +], +"ncbigi":[ +"16128697" +], +"refseq_locus_tag":[ +"b0722" +], +"refseq_name":[ +"sdhD" +], +"refseq_synonym":[ +"JW0712", +"ECK0711" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC44" +] +} +}, +{ +"id":"b0724", +"name":"sdhB", +"notes":{ +"original_bigg_ids":[ +"b0724" +] +}, +"annotation":{ +"asap":[ +"ABE-0002468" +], +"ecogene":[ +"EG10932" +], +"ncbigene":[ +"945300" +], +"ncbigi":[ +"16128699" +], +"refseq_locus_tag":[ +"b0724" +], +"refseq_name":[ +"sdhB" +], +"refseq_synonym":[ +"ECK0713", +"JW0714" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P07014" +] +} +}, +{ +"id":"b0723", +"name":"sdhA", +"notes":{ +"original_bigg_ids":[ +"b0723" +] +}, +"annotation":{ +"asap":[ +"ABE-0002466" +], +"ecogene":[ +"EG10931" +], +"ncbigene":[ +"945402" +], +"ncbigi":[ +"16128698" +], +"refseq_locus_tag":[ +"b0723" +], +"refseq_name":[ +"sdhA" +], +"refseq_synonym":[ +"JW0713", +"ECK0712" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AC41" +] +} +}, +{ +"id":"b0729", +"name":"sucD", +"notes":{ +"original_bigg_ids":[ +"b0729" +] +}, +"annotation":{ +"asap":[ +"ABE-0002485" +], +"ecogene":[ +"EG10982" +], +"ncbigene":[ +"945314" +], +"ncbigi":[ +"16128704" +], +"refseq_locus_tag":[ +"b0729" +], +"refseq_name":[ +"sucD" +], +"refseq_synonym":[ +"JW0718", +"ECK0717" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0AGE9" +] +} +}, +{ +"id":"b0728", +"name":"sucC", +"notes":{ +"original_bigg_ids":[ +"b0728" +] +}, +"annotation":{ +"asap":[ +"ABE-0002483" +], +"ecogene":[ +"EG10981" +], +"ncbigene":[ +"945312" +], +"ncbigi":[ +"16128703" +], +"refseq_locus_tag":[ +"b0728" +], +"refseq_name":[ +"sucC" +], +"refseq_synonym":[ +"JW0717", +"ECK0716" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A836" +] +} +}, +{ +"id":"b0008", +"name":"talB", +"notes":{ +"original_bigg_ids":[ +"b0008" +] +}, +"annotation":{ +"asap":[ +"ABE-0000027" +], +"ecogene":[ +"EG11556" +], +"ncbigene":[ +"944748" +], +"ncbigi":[ +"16128002" +], +"refseq_locus_tag":[ +"b0008" +], +"refseq_name":[ +"talB" +], +"refseq_synonym":[ +"yaaK", +"JW0007", +"ECK0008" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A870" +] +} +}, +{ +"id":"b2464", +"name":"talA", +"notes":{ +"original_bigg_ids":[ +"b2464" +] +}, +"annotation":{ +"asap":[ +"ABE-0008115" +], +"ecogene":[ +"EG11797" +], +"ncbigene":[ +"947006" +], +"ncbigi":[ +"16130389" +], +"refseq_locus_tag":[ +"b2464" +], +"refseq_name":[ +"talA" +], +"refseq_synonym":[ +"ECK2459", +"JW2448" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A867" +] +} +}, +{ +"id":"b2465", +"name":"tktB", +"notes":{ +"original_bigg_ids":[ +"b2465" +] +}, +"annotation":{ +"asap":[ +"ABE-0008117" +], +"ecogene":[ +"EG12100" +], +"ncbigene":[ +"945865" +], +"ncbigi":[ +"16130390" +], +"refseq_locus_tag":[ +"b2465" +], +"refseq_name":[ +"tktB" +], +"refseq_synonym":[ +"JW2449", +"ECK2460" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P33570" +] +} +}, +{ +"id":"b2935", +"name":"tktA", +"notes":{ +"original_bigg_ids":[ +"b2935" +] +}, +"annotation":{ +"asap":[ +"ABE-0009625" +], +"ecogene":[ +"EG11427" +], +"ncbigene":[ +"947420" +], +"ncbigi":[ +"49176286" +], +"refseq_locus_tag":[ +"b2935" +], +"refseq_name":[ +"tktA" +], +"refseq_synonym":[ +"JW5478", +"tkt", +"ECK2930" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P27302" +] +} +}, +{ +"id":"b3919", +"name":"tpiA", +"notes":{ +"original_bigg_ids":[ +"b3919" +] +}, +"annotation":{ +"asap":[ +"ABE-0012799" +], +"ecogene":[ +"EG11015" +], +"ncbigene":[ +"948409" +], +"ncbigi":[ +"16131757" +], +"refseq_locus_tag":[ +"b3919" +], +"refseq_name":[ +"tpiA" +], +"refseq_synonym":[ +"JW3890", +"ECK3911", +"tpi" +], +"sbo":"SBO:0000243", +"uniprot":[ +"P0A858" +] +} +} +], +"id":"e_coli_core", +"compartments":{ +"c":"cytosol", +"e":"extracellular space" +}, +"version":"1" +} \ No newline at end of file diff --git a/tests/data/e_coli_core.xml b/tests/data/e_coli_core.xml index a50651aae..ab2494b5c 100644 --- a/tests/data/e_coli_core.xml +++ b/tests/data/e_coli_core.xml @@ -19,35 +19,35 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="

Description

-

This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in +

This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in SBML format.

-
The content of this model has been carefully created in a manual research effort. This file has been exported from the software - COBRApy and further processed with the - JSBML-based +
The content of this model has been carefully created in a manual research effort. This file has been exported from the software + COBRApy and further processed with the + JSBML-based ModelPolisher application.
-
This file has been produced by the - Systems Biology Research Group using +
This file has been produced by the + Systems Biology Research Group using BiGG Models knowledge-base version of Feb 24, 2018, where it is currently hosted and - identified by: + identified by: e_coli_core.

Terms of use

Copyright © 2017 The Regents of the University of California.
-

Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met: +

Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

-

For specific licensing terms about this particular model and regulations of commercial use, see +

For specific licensing terms about this particular model and regulations of commercial use, see this model in BiGG Models knowledge-base.

-

References

When using content from BiGG Models knowledge-base in your research works, please cite +

References

When using content from BiGG Models knowledge-base in your research works, please cite
-
King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015). -
BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. - Nucl Acids Res. +
King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015). +
BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. + Nucl Acids Res. doi:10.1093/nar/gkv1049
@@ -94,7 +94,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -115,7 +115,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -137,7 +137,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -158,7 +158,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -179,7 +179,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -200,7 +200,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -221,7 +221,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -242,7 +242,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -263,7 +263,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -284,7 +284,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -305,7 +305,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -326,7 +326,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -347,7 +347,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -368,7 +368,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -389,7 +389,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -410,7 +410,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -431,7 +431,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -452,7 +452,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -473,7 +473,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -494,7 +494,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -515,7 +515,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -536,7 +536,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -557,7 +557,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -578,7 +578,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -599,7 +599,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -620,7 +620,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -641,7 +641,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -662,7 +662,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -683,7 +683,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -704,7 +704,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -725,7 +725,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -746,7 +746,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -767,7 +767,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -788,7 +788,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -809,7 +809,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -830,7 +830,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -851,7 +851,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -872,7 +872,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -893,7 +893,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -914,7 +914,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -935,7 +935,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -956,7 +956,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -977,7 +977,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -998,7 +998,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1019,7 +1019,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1040,7 +1040,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1061,7 +1061,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1082,7 +1082,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1103,7 +1103,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1124,7 +1124,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1145,7 +1145,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1166,7 +1166,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1187,7 +1187,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1208,7 +1208,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1229,7 +1229,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1250,7 +1250,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1271,7 +1271,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1292,7 +1292,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1313,7 +1313,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1334,7 +1334,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1355,7 +1355,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1376,7 +1376,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1397,7 +1397,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1418,7 +1418,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1439,7 +1439,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1460,7 +1460,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1481,7 +1481,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1502,7 +1502,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1523,7 +1523,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1544,7 +1544,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1565,7 +1565,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1586,7 +1586,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1607,7 +1607,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1628,7 +1628,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1649,7 +1649,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1670,7 +1670,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1691,7 +1691,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1712,7 +1712,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1733,7 +1733,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1754,7 +1754,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1775,7 +1775,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1796,7 +1796,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1817,7 +1817,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1838,7 +1838,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1859,7 +1859,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1880,7 +1880,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1901,7 +1901,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1922,7 +1922,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1943,7 +1943,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1964,7 +1964,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -1985,7 +1985,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2006,7 +2006,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2027,7 +2027,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2048,7 +2048,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2069,7 +2069,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2090,7 +2090,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2111,7 +2111,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2132,7 +2132,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2153,7 +2153,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2174,7 +2174,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2195,7 +2195,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2216,7 +2216,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2237,7 +2237,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2258,7 +2258,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2279,7 +2279,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2300,7 +2300,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2321,7 +2321,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2342,7 +2342,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2363,7 +2363,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2384,7 +2384,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2405,7 +2405,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2426,7 +2426,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2447,7 +2447,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2468,7 +2468,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2489,7 +2489,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2510,7 +2510,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2531,7 +2531,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2552,7 +2552,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2573,7 +2573,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2594,7 +2594,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2615,7 +2615,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2636,7 +2636,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2657,7 +2657,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2678,7 +2678,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2699,7 +2699,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2720,7 +2720,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2741,7 +2741,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2762,7 +2762,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2783,7 +2783,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2804,7 +2804,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2825,7 +2825,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2846,7 +2846,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2867,7 +2867,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2888,7 +2888,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2909,7 +2909,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -2930,7 +2930,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6035,7 +6035,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6052,7 +6052,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6069,7 +6069,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6086,7 +6086,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6103,7 +6103,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6120,7 +6120,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6137,7 +6137,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6154,7 +6154,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6171,7 +6171,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6188,7 +6188,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6205,7 +6205,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6238,7 +6238,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6255,7 +6255,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6272,7 +6272,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6289,7 +6289,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6305,7 +6305,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6322,7 +6322,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6339,7 +6339,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -6356,7 +6356,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - + @@ -7423,7 +7423,7 @@ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups=" - diff --git a/tests/data/e_coli_core_for_annotation.xml b/tests/data/e_coli_core_for_annotation.xml new file mode 100644 index 000000000..3358ad622 --- /dev/null +++ b/tests/data/e_coli_core_for_annotation.xml @@ -0,0 +1,8367 @@ + + + + + +
+

Key1 : Value1

+
+

+
e_coli_core - Escherichia coli str. K-12 substr. MG1655
+

+
+
+ + + + + +

Description

+
+

This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in + SBML format.

+
+
The content of this model has been carefully created in a manual research effort. This file has been exported from the software + COBRApy and further processed with the + JSBML-based + ModelPolisher application.
+
This file has been produced by the + Systems Biology Research Group using + BiGG Models knowledge-base version of Feb 24, 2018, where it is currently hosted and + identified by: + e_coli_core.
+

Terms of use

+
Copyright © 2017 The Regents of the University of California.
+
+

Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met: +

    +
  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
    2. +
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided + with the distribution.
    3. +
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

+

For specific licensing terms about this particular model and regulations of commercial use, see + this model in BiGG Models knowledge-base.

+
+

References

When using content from BiGG Models knowledge-base in your research works, please cite +
+
King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015). +
BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. + Nucl Acids Res. + doi:10.1093/nar/gkv1049
+
+ + + + + + + + + Koenig + Matthias + + koenigmx@hu-berlin.de + + Humboldt-University Berlin, Institute for Theoretical Biology + + + + + Koenig + Matthias + + koenigmx@hu-berlin.de + + + + Koenig + Matthias + + + Humboldt-University Berlin, Institute for Theoretical Biology + + + + + Koenig + Matthias + + + + + + 2019-03-06T14:40:55Z + + + 2019-03-06T14:40:55Z + + + 2019-03-06T14:41:55Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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K-12 substr. MG1655", + "notes": "\n \n

Description

\n
\n

This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in\n SBML\u00a0format.

\n
\n
The content of this model has been carefully created in a manual research effort. This file has been exported from the software\n COBRApy\u00a0and further processed with the\n JSBML-based\n ModelPolisher\u00a0application.
\n
This file has been produced by the\n Systems Biology Research Group\u00a0using\n BiGG Models knowledge-base\u00a0version of Feb 24, 2018, where it is currently hosted and\n identified by:\n e_coli_core.
\n

Terms of use

\n
Copyright \u00a9 2017 The Regents of the University of California.
\n
\n

Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met:\n

    \n
  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
    2. \n
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided\n with the distribution.
    3. \n
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

\n

For specific licensing terms about this particular model and regulations of commercial use, see\n this model in BiGG Models knowledge-base.

\n
\n

References

When using content from BiGG Models knowledge-base in your research works, please cite\n
\n
King ZA, Lu JS, Dr\u00e4ger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and\u00a0Lewis NE. (2015).\n
BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models.\n Nucl Acids Res.\n doi:10.1093/nar/gkv1049
\n
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\n

Key1 : Value1

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Key2 : Value2

\n
\n

A Heading

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e_coli_core - Escherichia coli str. K-12 substr. MG1655
\n
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Key1 : Value1

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"lac__D_c": -1.0, - "nad_c": -1.0, - "nadh_c": 1.0, - "pyr_c": 1.0 + "M_h_c": 1.0, + "M_lac__D_c": -1.0, + "M_nad_c": -1.0, + "M_nadh_c": 1.0, + "M_pyr_c": 1.0 }, "name": "D-lactate dehydrogenase", + "objective_coefficient": 0.0, + "subsystem": "Pyruvate Metabolism", "upper_bound": 1000.0 }, { "annotation": { - "bigg.reaction": "PFK" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/PFK" + ] + } + ] + } }, "gene_reaction_rule": "b3916 or b1723", - "id": "PFK", + "id": "R_PFK", "lower_bound": 0.0, "metabolites": { - "adp_c": 1.0, - "atp_c": -1.0, - "f6p_c": -1.0, - "fdp_c": 1.0, - "h_c": 1.0 + "M_adp_c": 1.0, + "M_atp_c": -1.0, + "M_f6p_c": -1.0, + "M_fdp_c": 1.0, + "M_h_c": 1.0 }, "name": "phosphofructokinase", "objective_coefficient": 1.0, @@ -1300,93 +1464,147 @@ }, { "annotation": { - "bigg.reaction": "PGI" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/PGI" + ] + } + ] + } }, "gene_reaction_rule": "b4025", - "id": "PGI", + "id": "R_PGI", "lower_bound": -1000.0, "metabolites": { - "f6p_c": 1.0, - "g6p_c": -1.0 + "M_f6p_c": 1.0, + "M_g6p_c": -1.0 }, "name": "glucose-6-phosphate isomerase", + "objective_coefficient": 0.0, "upper_bound": 1000.0 }, { "annotation": { - "bigg.reaction": "PGK" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/PGK" + ] + } + ] + } }, "gene_reaction_rule": "b2926", - "id": "PGK", + "id": "R_PGK", "lower_bound": -1000.0, "metabolites": { - "13dpg_c": 1.0, - "3pg_c": -1.0, - "adp_c": 1.0, - "atp_c": -1.0 + "M_13dpg_c": 1.0, + "M_3pg_c": -1.0, + "M_adp_c": 1.0, + "M_atp_c": -1.0 }, "name": "phosphoglycerate kinase", + "objective_coefficient": 0.0, "upper_bound": 1000.0 }, { "annotation": { - "bigg.reaction": "PGM" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/PGM" + ] + } + ] + } }, "gene_reaction_rule": "b4395 or b3612 or b0755", - "id": "PGM", + "id": "R_PGM", "lower_bound": -1000.0, "metabolites": { - "2pg_c": -1.0, - "3pg_c": 1.0 + "M_2pg_c": -1.0, + "M_3pg_c": 1.0 }, "name": "phosphoglycerate mutase", + "objective_coefficient": 0.0, "upper_bound": 1000.0 }, { "annotation": { - "bigg.reaction": "PIt2r" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/PIt2r" + ] + } + ] + } }, "gene_reaction_rule": "b2987 or b3493", - "id": "PIt2r", + "id": "R_PIt2r", "lower_bound": -1000.0, "metabolites": { - "h_c": 1.0, - "h_e": -1.0, - "pi_c": 1.0, - "pi_e": -1.0 + "M_h_c": 1.0, + "M_h_e": -1.0, + "M_pi_c": 1.0, + "M_pi_e": -1.0 }, "name": "R phosphate reversible transport via - symport", + "objective_coefficient": 0.0, "upper_bound": 1000.0 }, { "annotation": { - "bigg.reaction": "PYK" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/PYK" + ] + } + ] + } }, "gene_reaction_rule": "b1854 or b1676", - "id": "PYK", + "id": "R_PYK", "lower_bound": 0.0, "metabolites": { - "adp_c": -1.0, - "atp_c": 1.0, - "h_c": -1.0, - "pep_c": -1.0, - "pyr_c": 1.0 + "M_adp_c": -1.0, + "M_atp_c": 1.0, + "M_h_c": -1.0, + "M_pep_c": -1.0, + "M_pyr_c": 1.0 }, "name": "pyruvate kinase", + "objective_coefficient": 0.0, "upper_bound": 1000.0 }, { "annotation": { - "bigg.reaction": "TPI" + "cvterms": { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.reaction/TPI" + ] + } + ] + } }, "gene_reaction_rule": "b3919", - "id": "TPI", + "id": "R_TPI", "lower_bound": -1000.0, "metabolites": { - "dhap_c": -1.0, - "g3p_c": 1.0 + "M_dhap_c": -1.0, + "M_g3p_c": 1.0 }, "name": "triose-phosphate isomerase", + "objective_coefficient": 0.0, "upper_bound": 1000.0 } ], diff --git a/tests/data/mini.mat b/tests/data/mini.mat index a92a1570b..7f1aeb3d7 100644 Binary files a/tests/data/mini.mat and b/tests/data/mini.mat differ diff --git a/tests/data/mini.pickle b/tests/data/mini.pickle index 135ce225e..861da1e13 100644 Binary files a/tests/data/mini.pickle and b/tests/data/mini.pickle differ diff --git a/tests/data/mini.yml b/tests/data/mini.yml index e5e9e3b05..bf8697043 100644 --- a/tests/data/mini.yml +++ b/tests/data/mini.yml @@ -1,1169 +1,1251 @@ !!omap +- id: mini_textbook +- compartments: !!omap + - c: cytosol + - e: extracellular - metabolites: - !!omap - - id: 13dpg_c + - id: M_13dpg_c - name: 3-Phospho-D-glyceroyl phosphate - compartment: c - charge: -4 - formula: C3H4O10P2 - annotation: !!omap - - bigg.metabolite: 13dpg - - biocyc: DPG - - chebi: - - CHEBI:16001 - - CHEBI:1658 - - CHEBI:20189 - - CHEBI:57604 - - CHEBI:11881 - - hmdb: HMDB01270 - - kegg.compound: C00236 - - pubchem.substance: '3535' - - reactome: REACT_29800 - - seed.compound: cpd00203 - - unipathway.compound: UPC00236 - - !!omap - - id: 2pg_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/13dpg + - http://identifiers.org/biocyc/DPG + - http://identifiers.org/chebi/CHEBI:16001 + - http://identifiers.org/chebi/CHEBI:1658 + - http://identifiers.org/chebi/CHEBI:20189 + - http://identifiers.org/chebi/CHEBI:57604 + - http://identifiers.org/chebi/CHEBI:11881 + - http://identifiers.org/hmdb/HMDB01270 + - http://identifiers.org/kegg.compound/C00236 + - http://identifiers.org/pubchem.substance/3535 + - http://identifiers.org/reactome/REACT_29800 + - http://identifiers.org/seed.compound/cpd00203 + - http://identifiers.org/unipathway.compound/UPC00236 + - !!omap + - id: M_2pg_c - name: D-Glycerate 2-phosphate - compartment: c - charge: -3 - formula: C3H4O7P - annotation: !!omap - - bigg.metabolite: 2pg - - biocyc: 2-PG - - chebi: - - CHEBI:1267 - - CHEBI:58289 - - CHEBI:17835 - - CHEBI:21028 - - CHEBI:11651 - - CHEBI:12986 - - CHEBI:24344 - - CHEBI:39868 - - hmdb: - - HMDB03391 - - HMDB00362 - - kegg.compound: C00631 - - pubchem.substance: '3904' - - reactome: REACT_30485 - - seed.compound: cpd00482 - - unipathway.compound: UPC00631 - - !!omap - - id: 3pg_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/2pg + - http://identifiers.org/biocyc/2-PG + - http://identifiers.org/chebi/CHEBI:1267 + - http://identifiers.org/chebi/CHEBI:58289 + - http://identifiers.org/chebi/CHEBI:17835 + - http://identifiers.org/chebi/CHEBI:21028 + - http://identifiers.org/chebi/CHEBI:11651 + - http://identifiers.org/chebi/CHEBI:12986 + - http://identifiers.org/chebi/CHEBI:24344 + - http://identifiers.org/chebi/CHEBI:39868 + - http://identifiers.org/hmdb/HMDB03391 + - http://identifiers.org/hmdb/HMDB00362 + - http://identifiers.org/kegg.compound/C00631 + - http://identifiers.org/pubchem.substance/3904 + - http://identifiers.org/reactome/REACT_30485 + - http://identifiers.org/seed.compound/cpd00482 + - http://identifiers.org/unipathway.compound/UPC00631 + - !!omap + - id: M_3pg_c - name: 3-Phospho-D-glycerate - compartment: c - charge: -3 - formula: C3H4O7P - annotation: !!omap - - bigg.metabolite: 3pg - - biocyc: G3P - - chebi: - - CHEBI:40016 - - CHEBI:58272 - - CHEBI:57998 - - CHEBI:11879 - - CHEBI:1657 - - CHEBI:1659 - - CHEBI:17050 - - CHEBI:21029 - - CHEBI:11882 - - CHEBI:11880 - - CHEBI:12987 - - CHEBI:17794 - - CHEBI:24345 - - hmdb: HMDB00807 - - kegg.compound: - - C00197 - - C00597 - - pubchem.substance: '3497' - - reactome: REACT_29728 - - seed.compound: cpd00169 - - unipathway.compound: - - UPC00597 - - UPC00197 - - !!omap - - id: adp_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/3pg + - http://identifiers.org/biocyc/G3P + - http://identifiers.org/chebi/CHEBI:40016 + - http://identifiers.org/chebi/CHEBI:58272 + - http://identifiers.org/chebi/CHEBI:57998 + - http://identifiers.org/chebi/CHEBI:11879 + - http://identifiers.org/chebi/CHEBI:1657 + - http://identifiers.org/chebi/CHEBI:1659 + - http://identifiers.org/chebi/CHEBI:17050 + - http://identifiers.org/chebi/CHEBI:21029 + - http://identifiers.org/chebi/CHEBI:11882 + - http://identifiers.org/chebi/CHEBI:11880 + - http://identifiers.org/chebi/CHEBI:12987 + - http://identifiers.org/chebi/CHEBI:17794 + - http://identifiers.org/chebi/CHEBI:24345 + - http://identifiers.org/hmdb/HMDB00807 + - http://identifiers.org/kegg.compound/C00197 + - http://identifiers.org/kegg.compound/C00597 + - http://identifiers.org/pubchem.substance/3497 + - http://identifiers.org/reactome/REACT_29728 + - http://identifiers.org/seed.compound/cpd00169 + - http://identifiers.org/unipathway.compound/UPC00597 + - http://identifiers.org/unipathway.compound/UPC00197 + - !!omap + - id: M_adp_c - name: ADP - compartment: c - charge: -3 - formula: C10H12N5O10P2 - annotation: !!omap - - bigg.metabolite: adp - - biocyc: - - ADP - - ADP-GROUP - - cas: - - 58-64-0 - - chebi: - - CHEBI:13222 - - CHEBI:16761 - - CHEBI:2342 - - CHEBI:22244 - - CHEBI:40553 - - CHEBI:456216 - - hmdb: HMDB01341 - - kegg.compound: C00008 - - kegg.glycan: G11113 - - pubchem.substance: '3310' - - reactome: - - REACT_190072 - - REACT_481002 - - REACT_211606 - - REACT_429160 - - REACT_29370 - - REACT_196180 - - REACT_113581 - - REACT_113582 - - REACT_114564 - - REACT_114565 - - REACT_429153 - - seed.compound: cpd00008 - - unipathway.compound: UPC00008 - - !!omap - - id: atp_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/adp + - http://identifiers.org/biocyc/ADP + - http://identifiers.org/biocyc/ADP-GROUP + - http://identifiers.org/cas/58-64-0 + - http://identifiers.org/cas/58-64-0 + - http://identifiers.org/chebi/CHEBI:13222 + - http://identifiers.org/chebi/CHEBI:16761 + - http://identifiers.org/chebi/CHEBI:2342 + - http://identifiers.org/chebi/CHEBI:22244 + - http://identifiers.org/chebi/CHEBI:40553 + - http://identifiers.org/chebi/CHEBI:456216 + - http://identifiers.org/hmdb/HMDB01341 + - http://identifiers.org/kegg.compound/C00008 + - http://identifiers.org/kegg.glycan/G11113 + - http://identifiers.org/pubchem.substance/3310 + - http://identifiers.org/reactome/REACT_190072 + - http://identifiers.org/reactome/REACT_481002 + - http://identifiers.org/reactome/REACT_211606 + - http://identifiers.org/reactome/REACT_429160 + - http://identifiers.org/reactome/REACT_29370 + - http://identifiers.org/reactome/REACT_196180 + - http://identifiers.org/reactome/REACT_113581 + - http://identifiers.org/reactome/REACT_113582 + - http://identifiers.org/reactome/REACT_114564 + - http://identifiers.org/reactome/REACT_114565 + - http://identifiers.org/reactome/REACT_429153 + - http://identifiers.org/seed.compound/cpd00008 + - http://identifiers.org/unipathway.compound/UPC00008 + - !!omap + - id: M_atp_c - name: ATP - compartment: c - charge: -4 - formula: C10H12N5O13P3 - annotation: !!omap - - bigg.metabolite: atp - - biocyc: ATP - - cas: - - 56-65-5 - - chebi: - - CHEBI:40938 - - CHEBI:15422 - - CHEBI:57299 - - CHEBI:13236 - - CHEBI:10789 - - CHEBI:30616 - - CHEBI:22249 - - CHEBI:10841 - - CHEBI:2359 - - hmdb: HMDB00538 - - kegg.compound: C00002 - - kegg.drug: D08646 - - pubchem.substance: '3304' - - reactome: - - REACT_190078 - - REACT_113592 - - REACT_113593 - - REACT_114570 - - REACT_29358 - - REACT_389573 - - REACT_139836 - - REACT_211579 - - seed.compound: cpd00002 - - unipathway.compound: UPC00002 - - !!omap - - id: dhap_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/atp + - http://identifiers.org/biocyc/ATP + - http://identifiers.org/cas/56-65-5 + - http://identifiers.org/cas/56-65-5 + - http://identifiers.org/chebi/CHEBI:40938 + - http://identifiers.org/chebi/CHEBI:15422 + - http://identifiers.org/chebi/CHEBI:57299 + - http://identifiers.org/chebi/CHEBI:13236 + - http://identifiers.org/chebi/CHEBI:10789 + - http://identifiers.org/chebi/CHEBI:30616 + - http://identifiers.org/chebi/CHEBI:22249 + - http://identifiers.org/chebi/CHEBI:10841 + - http://identifiers.org/chebi/CHEBI:2359 + - http://identifiers.org/hmdb/HMDB00538 + - http://identifiers.org/kegg.compound/C00002 + - http://identifiers.org/kegg.drug/D08646 + - http://identifiers.org/pubchem.substance/3304 + - http://identifiers.org/reactome/REACT_190078 + - http://identifiers.org/reactome/REACT_113592 + - http://identifiers.org/reactome/REACT_113593 + - http://identifiers.org/reactome/REACT_114570 + - http://identifiers.org/reactome/REACT_29358 + - http://identifiers.org/reactome/REACT_389573 + - http://identifiers.org/reactome/REACT_139836 + - http://identifiers.org/reactome/REACT_211579 + - http://identifiers.org/seed.compound/cpd00002 + - http://identifiers.org/unipathway.compound/UPC00002 + - !!omap + - id: M_dhap_c - name: Dihydroxyacetone phosphate - compartment: c - charge: -2 - formula: C3H5O6P - annotation: !!omap - - bigg.metabolite: dhap - - biocyc: DIHYDROXY-ACETONE-PHOSPHATE - - cas: - - 57-04-5 - - chebi: - - CHEBI:14341 - - CHEBI:57642 - - CHEBI:14342 - - CHEBI:16108 - - CHEBI:5454 - - CHEBI:24355 - - CHEBI:39571 - - hmdb: - - HMDB01473 - - HMDB11735 - - kegg.compound: C00111 - - pubchem.substance: '3411' - - reactome: - - REACT_188451 - - REACT_75970 - - REACT_390404 - - seed.compound: cpd00095 - - unipathway.compound: UPC00111 - - !!omap - - id: f6p_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/dhap + - http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE + - http://identifiers.org/cas/57-04-5 + - http://identifiers.org/cas/57-04-5 + - http://identifiers.org/chebi/CHEBI:14341 + - http://identifiers.org/chebi/CHEBI:57642 + - http://identifiers.org/chebi/CHEBI:14342 + - http://identifiers.org/chebi/CHEBI:16108 + - http://identifiers.org/chebi/CHEBI:5454 + - http://identifiers.org/chebi/CHEBI:24355 + - http://identifiers.org/chebi/CHEBI:39571 + - http://identifiers.org/hmdb/HMDB01473 + - http://identifiers.org/hmdb/HMDB11735 + - http://identifiers.org/kegg.compound/C00111 + - http://identifiers.org/pubchem.substance/3411 + - http://identifiers.org/reactome/REACT_188451 + - http://identifiers.org/reactome/REACT_75970 + - http://identifiers.org/reactome/REACT_390404 + - http://identifiers.org/seed.compound/cpd00095 + - http://identifiers.org/unipathway.compound/UPC00111 + - !!omap + - id: M_f6p_c - name: D-Fructose 6-phosphate - compartment: c - charge: -2 - formula: C6H11O9P - annotation: !!omap - - bigg.metabolite: f6p - - biocyc: FRUCTOSE-6P - - cas: - - 643-13-0 - - chebi: - - CHEBI:57634 - - CHEBI:12352 - - CHEBI:45804 - - CHEBI:61527 - - CHEBI:61553 - - CHEBI:10375 - - CHEBI:16084 - - CHEBI:42378 - - CHEBI:22768 - - hmdb: HMDB03971 - - kegg.compound: - - C05345 - - C00085 - - pubchem.substance: '3385' - - seed.compound: cpd00072 - - unipathway.compound: - - UPC05345 - - UPC00085 - - !!omap - - id: fdp_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/f6p + - http://identifiers.org/biocyc/FRUCTOSE-6P + - http://identifiers.org/cas/643-13-0 + - http://identifiers.org/cas/643-13-0 + - http://identifiers.org/chebi/CHEBI:57634 + - http://identifiers.org/chebi/CHEBI:12352 + - http://identifiers.org/chebi/CHEBI:45804 + - http://identifiers.org/chebi/CHEBI:61527 + - http://identifiers.org/chebi/CHEBI:61553 + - http://identifiers.org/chebi/CHEBI:10375 + - http://identifiers.org/chebi/CHEBI:16084 + - http://identifiers.org/chebi/CHEBI:42378 + - http://identifiers.org/chebi/CHEBI:22768 + - http://identifiers.org/hmdb/HMDB03971 + - http://identifiers.org/kegg.compound/C05345 + - http://identifiers.org/kegg.compound/C00085 + - http://identifiers.org/pubchem.substance/3385 + - http://identifiers.org/seed.compound/cpd00072 + - http://identifiers.org/unipathway.compound/UPC05345 + - http://identifiers.org/unipathway.compound/UPC00085 + - !!omap + - id: M_fdp_c - name: D-Fructose 1,6-bisphosphate - compartment: c - charge: -4 - formula: C6H10O12P2 - annotation: !!omap - - bigg.metabolite: fdp - - biocyc: FRUCTOSE-16-DIPHOSPHATE - - cas: - - 488-69-7 - - chebi: - - CHEBI:32968 - - CHEBI:49299 - - CHEBI:42553 - - CHEBI:32966 - - CHEBI:37736 - - CHEBI:28013 - - CHEBI:32967 - - CHEBI:41014 - - CHEBI:22767 - - CHEBI:10374 - - CHEBI:40595 - - CHEBI:40591 - - kegg.compound: - - C05378 - - C00354 - - pubchem.substance: '3647' - - seed.compound: cpd00290 - - unipathway.compound: UPC00354 - - !!omap - - id: g3p_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/fdp + - http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE + - http://identifiers.org/cas/488-69-7 + - http://identifiers.org/cas/488-69-7 + - http://identifiers.org/chebi/CHEBI:32968 + - http://identifiers.org/chebi/CHEBI:49299 + - http://identifiers.org/chebi/CHEBI:42553 + - http://identifiers.org/chebi/CHEBI:32966 + - http://identifiers.org/chebi/CHEBI:37736 + - http://identifiers.org/chebi/CHEBI:28013 + - http://identifiers.org/chebi/CHEBI:32967 + - http://identifiers.org/chebi/CHEBI:41014 + - http://identifiers.org/chebi/CHEBI:22767 + - http://identifiers.org/chebi/CHEBI:10374 + - http://identifiers.org/chebi/CHEBI:40595 + - http://identifiers.org/chebi/CHEBI:40591 + - http://identifiers.org/kegg.compound/C05378 + - http://identifiers.org/kegg.compound/C00354 + - http://identifiers.org/pubchem.substance/3647 + - http://identifiers.org/seed.compound/cpd00290 + - http://identifiers.org/unipathway.compound/UPC00354 + - !!omap + - id: M_g3p_c - name: Glyceraldehyde 3-phosphate - compartment: c - charge: -2 - formula: C3H5O6P - annotation: !!omap - - bigg.metabolite: g3p - - cas: - - 142-10-9 - - chebi: - - CHEBI:17138 - - CHEBI:14333 - - CHEBI:5446 - - CHEBI:58027 - - hmdb: HMDB01112 - - kegg.compound: - - C00661 - - C00118 - - pubchem.substance: '3930' - - seed.compound: cpd00102 - - unipathway.compound: - - UPC00661 - - UPC00118 - - !!omap - - id: g6p_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/g3p + - http://identifiers.org/cas/142-10-9 + - http://identifiers.org/cas/142-10-9 + - http://identifiers.org/chebi/CHEBI:17138 + - http://identifiers.org/chebi/CHEBI:14333 + - http://identifiers.org/chebi/CHEBI:5446 + - http://identifiers.org/chebi/CHEBI:58027 + - http://identifiers.org/hmdb/HMDB01112 + - http://identifiers.org/kegg.compound/C00661 + - http://identifiers.org/kegg.compound/C00118 + - http://identifiers.org/pubchem.substance/3930 + - http://identifiers.org/seed.compound/cpd00102 + - http://identifiers.org/unipathway.compound/UPC00661 + - http://identifiers.org/unipathway.compound/UPC00118 + - !!omap + - id: M_g6p_c - name: D-Glucose 6-phosphate - compartment: c - charge: -2 - formula: C6H11O9P - annotation: !!omap - - bigg.metabolite: g6p - - biocyc: - - D-glucose-6-phosphate - - GLC-6-P - - cas: - - 56-73-5 - - chebi: - - CHEBI:10399 - - CHEBI:22797 - - CHEBI:41041 - - CHEBI:17719 - - CHEBI:4170 - - CHEBI:61548 - - CHEBI:58247 - - CHEBI:12375 - - hmdb: - - HMDB03498 - - HMDB06793 - - HMDB01401 - - HMDB01549 - - kegg.compound: - - C00092 - - C01172 - - pubchem.substance: '3392' - - reactome: REACT_1629756 - - seed.compound: cpd00079 - - unipathway.compound: UPC00092 - - !!omap - - id: glc__D_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/g6p + - http://identifiers.org/biocyc/D-glucose-6-phosphate + - http://identifiers.org/biocyc/GLC-6-P + - http://identifiers.org/cas/56-73-5 + - http://identifiers.org/cas/56-73-5 + - http://identifiers.org/chebi/CHEBI:10399 + - http://identifiers.org/chebi/CHEBI:22797 + - http://identifiers.org/chebi/CHEBI:41041 + - http://identifiers.org/chebi/CHEBI:17719 + - http://identifiers.org/chebi/CHEBI:4170 + - http://identifiers.org/chebi/CHEBI:61548 + - http://identifiers.org/chebi/CHEBI:58247 + - http://identifiers.org/chebi/CHEBI:12375 + - http://identifiers.org/hmdb/HMDB03498 + - http://identifiers.org/hmdb/HMDB06793 + - http://identifiers.org/hmdb/HMDB01401 + - http://identifiers.org/hmdb/HMDB01549 + - http://identifiers.org/kegg.compound/C00092 + - http://identifiers.org/kegg.compound/C01172 + - http://identifiers.org/pubchem.substance/3392 + - http://identifiers.org/reactome/REACT_1629756 + - http://identifiers.org/seed.compound/cpd00079 + - http://identifiers.org/unipathway.compound/UPC00092 + - !!omap + - id: M_glc__D_e - name: D-Glucose - compartment: e - charge: 0 - formula: C6H12O6 - annotation: !!omap - - bigg.metabolite: glc__D - - cas: - - 50-99-7 - - kegg.compound: C00031 - - pubchem.substance: '3333' - - !!omap - - id: h2o_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/glc__D + - http://identifiers.org/cas/50-99-7 + - http://identifiers.org/cas/50-99-7 + - http://identifiers.org/kegg.compound/C00031 + - http://identifiers.org/pubchem.substance/3333 + - !!omap + - id: M_h2o_c - name: H2O - compartment: c - charge: 0 - formula: H2O - annotation: !!omap - - bigg.metabolite: h2o - - biocyc: - - WATER - - OH - - OXONIUM - - cas: - - 7732-18-5 - - chebi: - - CHEBI:15377 - - CHEBI:13365 - - CHEBI:41979 - - CHEBI:16234 - - CHEBI:36385 - - CHEBI:42857 - - CHEBI:27313 - - CHEBI:44819 - - CHEBI:29373 - - CHEBI:10743 - - CHEBI:5594 - - CHEBI:29356 - - CHEBI:53442 - - CHEBI:29375 - - CHEBI:29374 - - CHEBI:13419 - - CHEBI:43228 - - CHEBI:44292 - - CHEBI:13352 - - CHEBI:41981 - - CHEBI:29412 - - CHEBI:42043 - - CHEBI:33811 - - CHEBI:33813 - - CHEBI:35511 - - CHEBI:5585 - - CHEBI:44641 - - CHEBI:44701 - - hmdb: - - HMDB01039 - - HMDB02111 - - kegg.compound: - - C01328 - - C00001 - - C18714 - - C18712 - - kegg.drug: - - D00001 - - D06322 - - D03703 - - pubchem.substance: '3303' - - reactome: - - REACT_947593 - - REACT_189422 - - REACT_141343 - - REACT_113518 - - REACT_1605715 - - REACT_109276 - - REACT_113521 - - REACT_113519 - - REACT_2022884 - - REACT_351603 - - REACT_29356 - - seed.compound: - - cpd15275 - - cpd00001 - - unipathway.compound: - - UPC00001 - - UPC01328 - - !!omap - - id: h2o_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h2o + - http://identifiers.org/biocyc/WATER + - http://identifiers.org/biocyc/OH + - http://identifiers.org/biocyc/OXONIUM + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/chebi/CHEBI:15377 + - http://identifiers.org/chebi/CHEBI:13365 + - http://identifiers.org/chebi/CHEBI:41979 + - http://identifiers.org/chebi/CHEBI:16234 + - http://identifiers.org/chebi/CHEBI:36385 + - http://identifiers.org/chebi/CHEBI:42857 + - http://identifiers.org/chebi/CHEBI:27313 + - http://identifiers.org/chebi/CHEBI:44819 + - http://identifiers.org/chebi/CHEBI:29373 + - http://identifiers.org/chebi/CHEBI:10743 + - http://identifiers.org/chebi/CHEBI:5594 + - http://identifiers.org/chebi/CHEBI:29356 + - http://identifiers.org/chebi/CHEBI:53442 + - http://identifiers.org/chebi/CHEBI:29375 + - http://identifiers.org/chebi/CHEBI:29374 + - http://identifiers.org/chebi/CHEBI:13419 + - http://identifiers.org/chebi/CHEBI:43228 + - http://identifiers.org/chebi/CHEBI:44292 + - http://identifiers.org/chebi/CHEBI:13352 + - http://identifiers.org/chebi/CHEBI:41981 + - http://identifiers.org/chebi/CHEBI:29412 + - http://identifiers.org/chebi/CHEBI:42043 + - http://identifiers.org/chebi/CHEBI:33811 + - http://identifiers.org/chebi/CHEBI:33813 + - http://identifiers.org/chebi/CHEBI:35511 + - http://identifiers.org/chebi/CHEBI:5585 + - http://identifiers.org/chebi/CHEBI:44641 + - http://identifiers.org/chebi/CHEBI:44701 + - http://identifiers.org/hmdb/HMDB01039 + - http://identifiers.org/hmdb/HMDB02111 + - http://identifiers.org/kegg.compound/C01328 + - http://identifiers.org/kegg.compound/C00001 + - http://identifiers.org/kegg.compound/C18714 + - http://identifiers.org/kegg.compound/C18712 + - http://identifiers.org/kegg.drug/D00001 + - http://identifiers.org/kegg.drug/D06322 + - http://identifiers.org/kegg.drug/D03703 + - http://identifiers.org/pubchem.substance/3303 + - http://identifiers.org/reactome/REACT_947593 + - http://identifiers.org/reactome/REACT_189422 + - http://identifiers.org/reactome/REACT_141343 + - http://identifiers.org/reactome/REACT_113518 + - http://identifiers.org/reactome/REACT_1605715 + - http://identifiers.org/reactome/REACT_109276 + - http://identifiers.org/reactome/REACT_113521 + - http://identifiers.org/reactome/REACT_113519 + - http://identifiers.org/reactome/REACT_2022884 + - http://identifiers.org/reactome/REACT_351603 + - http://identifiers.org/reactome/REACT_29356 + - http://identifiers.org/seed.compound/cpd15275 + - http://identifiers.org/seed.compound/cpd00001 + - http://identifiers.org/unipathway.compound/UPC00001 + - http://identifiers.org/unipathway.compound/UPC01328 + - !!omap + - id: M_h2o_e - name: H2O - compartment: e - charge: 0 - formula: H2O - annotation: !!omap - - bigg.metabolite: h2o - - biocyc: - - WATER - - OH - - OXONIUM - - cas: - - 7732-18-5 - - chebi: - - CHEBI:15377 - - CHEBI:13365 - - CHEBI:41979 - - CHEBI:16234 - - CHEBI:36385 - - CHEBI:42857 - - CHEBI:27313 - - CHEBI:44819 - - CHEBI:29373 - - CHEBI:10743 - - CHEBI:5594 - - CHEBI:29356 - - CHEBI:53442 - - CHEBI:29375 - - CHEBI:29374 - - CHEBI:13419 - - CHEBI:43228 - - CHEBI:44292 - - CHEBI:13352 - - CHEBI:41981 - - CHEBI:29412 - - CHEBI:42043 - - CHEBI:33811 - - CHEBI:33813 - - CHEBI:35511 - - CHEBI:5585 - - CHEBI:44641 - - CHEBI:44701 - - hmdb: - - HMDB01039 - - HMDB02111 - - kegg.compound: - - C01328 - - C00001 - - C18714 - - C18712 - - kegg.drug: - - D00001 - - D06322 - - D03703 - - pubchem.substance: '3303' - - reactome: - - REACT_947593 - - REACT_189422 - - REACT_141343 - - REACT_113518 - - REACT_1605715 - - REACT_109276 - - REACT_113521 - - REACT_113519 - - REACT_2022884 - - REACT_351603 - - REACT_29356 - - seed.compound: - - cpd15275 - - cpd00001 - - unipathway.compound: - - UPC00001 - - UPC01328 - - !!omap - - id: h_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h2o + - http://identifiers.org/biocyc/WATER + - http://identifiers.org/biocyc/OH + - http://identifiers.org/biocyc/OXONIUM + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/cas/7732-18-5 + - http://identifiers.org/chebi/CHEBI:15377 + - http://identifiers.org/chebi/CHEBI:13365 + - http://identifiers.org/chebi/CHEBI:41979 + - http://identifiers.org/chebi/CHEBI:16234 + - http://identifiers.org/chebi/CHEBI:36385 + - http://identifiers.org/chebi/CHEBI:42857 + - http://identifiers.org/chebi/CHEBI:27313 + - http://identifiers.org/chebi/CHEBI:44819 + - http://identifiers.org/chebi/CHEBI:29373 + - http://identifiers.org/chebi/CHEBI:10743 + - http://identifiers.org/chebi/CHEBI:5594 + - http://identifiers.org/chebi/CHEBI:29356 + - http://identifiers.org/chebi/CHEBI:53442 + - http://identifiers.org/chebi/CHEBI:29375 + - http://identifiers.org/chebi/CHEBI:29374 + - http://identifiers.org/chebi/CHEBI:13419 + - http://identifiers.org/chebi/CHEBI:43228 + - http://identifiers.org/chebi/CHEBI:44292 + - http://identifiers.org/chebi/CHEBI:13352 + - http://identifiers.org/chebi/CHEBI:41981 + - http://identifiers.org/chebi/CHEBI:29412 + - http://identifiers.org/chebi/CHEBI:42043 + - http://identifiers.org/chebi/CHEBI:33811 + - http://identifiers.org/chebi/CHEBI:33813 + - http://identifiers.org/chebi/CHEBI:35511 + - http://identifiers.org/chebi/CHEBI:5585 + - http://identifiers.org/chebi/CHEBI:44641 + - http://identifiers.org/chebi/CHEBI:44701 + - http://identifiers.org/hmdb/HMDB01039 + - http://identifiers.org/hmdb/HMDB02111 + - http://identifiers.org/kegg.compound/C01328 + - http://identifiers.org/kegg.compound/C00001 + - http://identifiers.org/kegg.compound/C18714 + - http://identifiers.org/kegg.compound/C18712 + - http://identifiers.org/kegg.drug/D00001 + - http://identifiers.org/kegg.drug/D06322 + - http://identifiers.org/kegg.drug/D03703 + - http://identifiers.org/pubchem.substance/3303 + - http://identifiers.org/reactome/REACT_947593 + - http://identifiers.org/reactome/REACT_189422 + - http://identifiers.org/reactome/REACT_141343 + - http://identifiers.org/reactome/REACT_113518 + - http://identifiers.org/reactome/REACT_1605715 + - http://identifiers.org/reactome/REACT_109276 + - http://identifiers.org/reactome/REACT_113521 + - http://identifiers.org/reactome/REACT_113519 + - http://identifiers.org/reactome/REACT_2022884 + - http://identifiers.org/reactome/REACT_351603 + - http://identifiers.org/reactome/REACT_29356 + - http://identifiers.org/seed.compound/cpd15275 + - http://identifiers.org/seed.compound/cpd00001 + - http://identifiers.org/unipathway.compound/UPC00001 + - http://identifiers.org/unipathway.compound/UPC01328 + - !!omap + - id: M_h_c - name: H+ - compartment: c - charge: 1 - formula: H - annotation: !!omap - - bigg.metabolite: h - - biocyc: PROTON - - cas: - - 12408-02-5 - - chebi: - - CHEBI:24636 - - CHEBI:15378 - - CHEBI:10744 - - CHEBI:13357 - - CHEBI:5584 - - kegg.compound: C00080 - - pubchem.substance: '3380' - - reactome: - - REACT_194688 - - REACT_425978 - - REACT_193465 - - REACT_374900 - - REACT_74722 - - REACT_425999 - - REACT_428040 - - REACT_163953 - - REACT_372511 - - REACT_2000349 - - REACT_70106 - - REACT_1470067 - - REACT_113529 - - REACT_425969 - - REACT_428548 - - REACT_156540 - - REACT_1614597 - - REACT_351626 - - REACT_427899 - - seed.compound: cpd00067 - - unipathway.compound: UPC00080 - - !!omap - - id: h_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h + - http://identifiers.org/biocyc/PROTON + - http://identifiers.org/cas/12408-02-5 + - http://identifiers.org/cas/12408-02-5 + - http://identifiers.org/chebi/CHEBI:24636 + - http://identifiers.org/chebi/CHEBI:15378 + - http://identifiers.org/chebi/CHEBI:10744 + - http://identifiers.org/chebi/CHEBI:13357 + - http://identifiers.org/chebi/CHEBI:5584 + - http://identifiers.org/kegg.compound/C00080 + - http://identifiers.org/pubchem.substance/3380 + - http://identifiers.org/reactome/REACT_194688 + - http://identifiers.org/reactome/REACT_425978 + - http://identifiers.org/reactome/REACT_193465 + - http://identifiers.org/reactome/REACT_374900 + - http://identifiers.org/reactome/REACT_74722 + - http://identifiers.org/reactome/REACT_425999 + - http://identifiers.org/reactome/REACT_428040 + - http://identifiers.org/reactome/REACT_163953 + - http://identifiers.org/reactome/REACT_372511 + - http://identifiers.org/reactome/REACT_2000349 + - http://identifiers.org/reactome/REACT_70106 + - http://identifiers.org/reactome/REACT_1470067 + - http://identifiers.org/reactome/REACT_113529 + - http://identifiers.org/reactome/REACT_425969 + - http://identifiers.org/reactome/REACT_428548 + - http://identifiers.org/reactome/REACT_156540 + - http://identifiers.org/reactome/REACT_1614597 + - http://identifiers.org/reactome/REACT_351626 + - http://identifiers.org/reactome/REACT_427899 + - http://identifiers.org/seed.compound/cpd00067 + - http://identifiers.org/unipathway.compound/UPC00080 + - !!omap + - id: M_h_e - name: H+ - compartment: e - charge: 1 - formula: H - annotation: !!omap - - bigg.metabolite: h - - biocyc: PROTON - - cas: - - 12408-02-5 - - chebi: - - CHEBI:24636 - - CHEBI:15378 - - CHEBI:10744 - - CHEBI:13357 - - CHEBI:5584 - - kegg.compound: C00080 - - pubchem.substance: '3380' - - reactome: - - REACT_194688 - - REACT_425978 - - REACT_193465 - - REACT_374900 - - REACT_74722 - - REACT_425999 - - REACT_428040 - - REACT_163953 - - REACT_372511 - - REACT_2000349 - - REACT_70106 - - REACT_1470067 - - REACT_113529 - - REACT_425969 - - REACT_428548 - - REACT_156540 - - REACT_1614597 - - REACT_351626 - - REACT_427899 - - seed.compound: cpd00067 - - unipathway.compound: UPC00080 - - !!omap - - id: lac__D_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/h + - http://identifiers.org/biocyc/PROTON + - http://identifiers.org/cas/12408-02-5 + - http://identifiers.org/cas/12408-02-5 + - http://identifiers.org/chebi/CHEBI:24636 + - http://identifiers.org/chebi/CHEBI:15378 + - http://identifiers.org/chebi/CHEBI:10744 + - http://identifiers.org/chebi/CHEBI:13357 + - http://identifiers.org/chebi/CHEBI:5584 + - http://identifiers.org/kegg.compound/C00080 + - http://identifiers.org/pubchem.substance/3380 + - http://identifiers.org/reactome/REACT_194688 + - http://identifiers.org/reactome/REACT_425978 + - http://identifiers.org/reactome/REACT_193465 + - http://identifiers.org/reactome/REACT_374900 + - http://identifiers.org/reactome/REACT_74722 + - http://identifiers.org/reactome/REACT_425999 + - http://identifiers.org/reactome/REACT_428040 + - http://identifiers.org/reactome/REACT_163953 + - http://identifiers.org/reactome/REACT_372511 + - http://identifiers.org/reactome/REACT_2000349 + - http://identifiers.org/reactome/REACT_70106 + - http://identifiers.org/reactome/REACT_1470067 + - http://identifiers.org/reactome/REACT_113529 + - http://identifiers.org/reactome/REACT_425969 + - http://identifiers.org/reactome/REACT_428548 + - http://identifiers.org/reactome/REACT_156540 + - http://identifiers.org/reactome/REACT_1614597 + - http://identifiers.org/reactome/REACT_351626 + - http://identifiers.org/reactome/REACT_427899 + - http://identifiers.org/seed.compound/cpd00067 + - http://identifiers.org/unipathway.compound/UPC00080 + - !!omap + - id: M_lac__D_c - name: D-Lactate - compartment: c - charge: -1 - formula: C3H5O3 - annotation: !!omap - - bigg.metabolite: lac__D - - biocyc: META:D-LACTATE - - chebi: - - CHEBI:11001 - - CHEBI:16004 - - CHEBI:18684 - - CHEBI:341 - - CHEBI:42105 - - CHEBI:42111 - - CHEBI:43701 - - hmdb: - - HMDB00171 - - HMDB01311 - - kegg.compound: C00256 - - metanetx.chemical: MNXM285 - - seed.compound: cpd00221 - - !!omap - - id: lac__D_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/lac__D + - http://identifiers.org/biocyc/META:D-LACTATE + - http://identifiers.org/chebi/CHEBI:11001 + - http://identifiers.org/chebi/CHEBI:16004 + - http://identifiers.org/chebi/CHEBI:18684 + - http://identifiers.org/chebi/CHEBI:341 + - http://identifiers.org/chebi/CHEBI:42105 + - http://identifiers.org/chebi/CHEBI:42111 + - http://identifiers.org/chebi/CHEBI:43701 + - http://identifiers.org/hmdb/HMDB00171 + - http://identifiers.org/hmdb/HMDB01311 + - http://identifiers.org/kegg.compound/C00256 + - http://identifiers.org/metanetx.chemical/MNXM285 + - http://identifiers.org/seed.compound/cpd00221 + - !!omap + - id: M_lac__D_e - name: D-Lactate - compartment: e - charge: -1 - formula: C3H5O3 - annotation: !!omap - - bigg.metabolite: lac__D - - biocyc: META:D-LACTATE - - chebi: - - CHEBI:11001 - - CHEBI:16004 - - CHEBI:18684 - - CHEBI:341 - - CHEBI:42105 - - CHEBI:42111 - - CHEBI:43701 - - hmdb: - - HMDB00171 - - HMDB01311 - - kegg.compound: C00256 - - metanetx.chemical: MNXM285 - - seed.compound: cpd00221 - - !!omap - - id: nad_c + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/lac__D + - http://identifiers.org/biocyc/META:D-LACTATE + - http://identifiers.org/chebi/CHEBI:11001 + - http://identifiers.org/chebi/CHEBI:16004 + - http://identifiers.org/chebi/CHEBI:18684 + - http://identifiers.org/chebi/CHEBI:341 + - http://identifiers.org/chebi/CHEBI:42105 + - http://identifiers.org/chebi/CHEBI:42111 + - http://identifiers.org/chebi/CHEBI:43701 + - http://identifiers.org/hmdb/HMDB00171 + - http://identifiers.org/hmdb/HMDB01311 + - http://identifiers.org/kegg.compound/C00256 + - http://identifiers.org/metanetx.chemical/MNXM285 + - http://identifiers.org/seed.compound/cpd00221 + - !!omap + - id: M_nad_c - name: Nicotinamide adenine dinucleotide - compartment: c - charge: -1 - formula: C21H26N7O14P2 - annotation: !!omap - - bigg.metabolite: nad - - biocyc: NAD - - cas: - - 53-84-9 - - chebi: - - CHEBI:21901 - - CHEBI:7422 - - CHEBI:44214 - - CHEBI:15846 - - CHEBI:13394 - - CHEBI:13393 - - 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CHEBI:29139 - - CHEBI:63036 - - CHEBI:26020 - - CHEBI:39739 - - CHEBI:32597 - - CHEBI:32596 - - CHEBI:43474 - - CHEBI:63051 - - CHEBI:43470 - - CHEBI:9679 - - CHEBI:35433 - - CHEBI:4496 - - CHEBI:45024 - - CHEBI:18367 - - CHEBI:26078 - - CHEBI:39745 - - CHEBI:24838 - - hmdb: HMDB02142 - - kegg.compound: - - C13556 - - C13558 - - C00009 - - kegg.drug: D05467 - - pubchem.substance: '3311' - - reactome: - - REACT_947590 - - REACT_109277 - - REACT_113548 - - REACT_2255331 - - REACT_29372 - - REACT_113550 - - REACT_113551 - - seed.compound: - - cpd09464 - - cpd09463 - - cpd00009 - - unipathway.compound: UPC00009 - - !!omap - - id: pi_e + - cvterms: !!omap + - bqb_is: + - resources: + - http://identifiers.org/bigg.metabolite/pi + - http://identifiers.org/biocyc/Pi + - http://identifiers.org/biocyc/PHOSPHATE-GROUP + - http://identifiers.org/biocyc/CPD0-1421 + - http://identifiers.org/cas/14265-44-2 + - http://identifiers.org/cas/14265-44-2 + - http://identifiers.org/chebi/CHEBI:37583 + - 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+ + + + + + + + + + + + + + + + + + + + + + @@ -496,37 +506,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -539,37 +550,38 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -582,20 +594,20 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -608,20 +620,20 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -634,30 +646,31 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -670,25 +683,26 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -701,24 +715,25 @@ - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -731,52 +746,53 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -789,52 +805,53 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -847,25 +864,26 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -889,7 +907,7 @@ - + @@ -905,14 +923,14 @@ - + - + @@ -935,7 +953,7 @@ - + @@ -951,7 +969,7 @@ - + @@ -967,7 +985,7 @@ - + @@ -983,7 +1001,7 @@ - + @@ -1010,7 +1028,7 @@ - + @@ -1036,7 +1054,7 @@ - + @@ -1080,7 +1098,7 @@ - + @@ -1105,15 +1123,15 @@ - - - - - - - - - + + + + + + + + + @@ -1141,7 +1159,7 @@ - + @@ -1169,7 +1187,7 @@ - + @@ -1191,7 +1209,7 @@ - + @@ -1215,7 +1233,7 @@ - + @@ -1241,7 +1259,7 @@ - + @@ -1268,7 +1286,7 @@ - + @@ -1296,7 +1314,7 @@ - + @@ -1322,97 +1340,97 @@ - - - - - + + + + + - - + + - - - - - - - - - - - - + + + + + + + + + + + + - + - + - + - - - + + + - - + + - + - + - - + + diff --git a/tests/data/mini_fbc2.xml.bz2 b/tests/data/mini_fbc2.xml.bz2 index cdfa3736a..487855e44 100644 Binary files a/tests/data/mini_fbc2.xml.bz2 and b/tests/data/mini_fbc2.xml.bz2 differ diff --git a/tests/data/mini_fbc2.xml.gz b/tests/data/mini_fbc2.xml.gz index efdb5e4c5..a52c29193 100644 Binary files a/tests/data/mini_fbc2.xml.gz and b/tests/data/mini_fbc2.xml.gz differ diff --git a/tests/data/mini_wrong_key_caps.mat b/tests/data/mini_wrong_key_caps.mat index ef093934e..59931eb36 100644 Binary files a/tests/data/mini_wrong_key_caps.mat and b/tests/data/mini_wrong_key_caps.mat differ diff --git a/tests/data/raven.pickle b/tests/data/raven.pickle index 5bb891e73..a33a8e701 100644 Binary files a/tests/data/raven.pickle and b/tests/data/raven.pickle differ diff --git a/tests/data/salmonella.pickle b/tests/data/salmonella.pickle index 644fa8ee8..12db2a493 100644 Binary files a/tests/data/salmonella.pickle and b/tests/data/salmonella.pickle differ diff --git a/tests/data/salmonella_old.pickle b/tests/data/salmonella_old.pickle new file mode 100644 index 000000000..33b1e8f7a Binary files /dev/null and b/tests/data/salmonella_old.pickle differ diff --git a/tests/data/textbook.xml.gz b/tests/data/textbook.xml.gz index a5d1fbc51..40452b55b 100644 Binary files a/tests/data/textbook.xml.gz and b/tests/data/textbook.xml.gz differ diff --git a/tests/data/update_pickles.py b/tests/data/update_pickles.py index 035604c7c..b1270e984 100755 --- a/tests/data/update_pickles.py +++ b/tests/data/update_pickles.py @@ -14,8 +14,11 @@ from json import dump as json_dump from pickle import dump, load +import scipy.io as scipy_io + import cobra from cobra.io import ( + create_mat_dict, load_matlab_model, load_model, read_sbml_model, @@ -109,6 +112,40 @@ with open("raven.pickle", "wb") as outfile: dump(raven, outfile, protocol=2) + # Make mat model with wrong fields, which needs to happen every time the mini.mat + # model changes, i.e. every time update_pickles.py runs. + mat_dict = create_mat_dict(mini) + + old_new_fields = { + "metUniPathway": "metUNIPathway", + "metKEGGID": "metKeggID", + "metHMDBID": "methmdbid", + "metMetaNetXID": "metMETANETXID", + "metKEGGDrugID": "metKEGGDrugid", + "metKEGGGlycanID": "metkeggGlycanID", + "metBiGGID": "metBIGGID", + "metLIPIDMAPSID": "metLipidMapsID", + "metSEEDID": "metSEEDID".casefold(), + "metBioCycID": "metBioCYCID", + "metPubChemSubstance": "metPubChemSUBSTANCE", + "metReactomeID": "metREACTOMEid", + "metCasNumber": "metCASNumber".upper(), + "rxnECNumbers": "rxnECNumbers".upper(), + "rxnMetaNetXID": "rxnMetaNetXID".casefold(), + "rxnKEGGID": "rxnKeggID", + "rxnRheaID": "rxnRHEAID", + "rxnBioCycID": "rxnBIOCycID", + "rxnBiGGID": "rxnBIGGID", + } + for _old, _new in old_new_fields.items(): + mat_dict[_new] = mat_dict.pop(_old) + scipy_io.savemat( + "mini_wrong_key_caps.mat", + {"mini_textbook": mat_dict}, + appendmat=True, + oned_as="column", + ) + # TODO:these need a reference solutions rather than circular solution checking! # fva results diff --git a/tests/data/valid_annotation_format.json b/tests/data/valid_annotation_format.json index 8bbb6a38c..84107b755 100644 --- a/tests/data/valid_annotation_format.json +++ b/tests/data/valid_annotation_format.json @@ -5,9 +5,9 @@ "name":"", "compartment":"c", "annotation": { - "bigg.reaction": [["is", "PFK26"]], - "kegg.reaction": [["is", "R02732"]], - "rhea": [["is", "15656"]] + "bigg.reaction": [["bqb_is", "PFK26"]], + "kegg.reaction": [["bqb_is", "R02732"]], + "rhea": [["bqb_is", "15656"]] } } ], diff --git a/tests/test_core/test_group.py b/tests/test_core/test_group.py index 543df5960..9a0125c02 100644 --- a/tests/test_core/test_group.py +++ b/tests/test_core/test_group.py @@ -1,10 +1,12 @@ """Test functions of group via model.py.""" +from os.path import join import pytest from cobra import Model from cobra.core import Group +from cobra.io import load_json_model, read_sbml_model, save_json_model def test_group_add_elements(model: Model) -> None: @@ -38,3 +40,17 @@ def test_group_kind() -> None: group.kind = "collection" assert group.kind == "collection" + + +def test_read_write_json(data_directory, tmp_path): + model = read_sbml_model(join(data_directory, "e_coli_core.xml")) + assert model.groups is not None + assert len(model.groups) == 10 + assert len(model.groups[0].members) == 6 + + path_to_file = join(tmp_path, "group_ecoli.json") + save_json_model(model, path_to_file) + model_from_json = load_json_model(path_to_file) + assert model_from_json.groups is not None + assert len(model_from_json.groups) == 10 + assert len(model_from_json.groups[0].members) == 6 diff --git a/tests/test_core/test_metadata/test_history.py b/tests/test_core/test_metadata/test_history.py new file mode 100644 index 000000000..fda29e135 --- /dev/null +++ b/tests/test_core/test_metadata/test_history.py @@ -0,0 +1,119 @@ +import os +from datetime import datetime, timedelta, timezone + +import pytest + +from cobra.core.metadata.history import Creator, History, HistoryDatetime +from cobra.io import read_sbml_model + + +JUNE_26TH = "2020-06-26T12:34:11+00:00" +JUNE_26TH_530 = "2020-06-26T00:34:11+05:30" +TEST_COM = "test@test.com" + + +def _read_ecoli_annotation_model(data_directory): + """Read model with history elements.""" + test_xml = os.path.join(data_directory, "e_coli_core_for_annotation.xml") + model = read_sbml_model(test_xml) + return model + + +def test_create_history(): + history = History( + creators=[ + Creator( + given_name="Matthias", + family_name="Koenig", + organisation="HU", + email=TEST_COM, + ), + Creator( + given_name="Andreas", + family_name="Draeger", + organisation="University of Tübingen", + email="test2@test2.com", + ), + ], + created_date=HistoryDatetime(JUNE_26TH_530), + modified_dates=[ + HistoryDatetime(JUNE_26TH), + HistoryDatetime(JUNE_26TH_530), + ], + ) + assert len(history.creators) == 2 + assert isinstance(history.created_date, HistoryDatetime) + assert history.created_date.datetime == JUNE_26TH_530 + assert len(history.modified_dates) == 2 + + +def test_history_from_ecoli_xml(data_directory): + model = _read_ecoli_annotation_model(data_directory) + history = History( + creators=[ + Creator( + given_name="Matthias", + family_name="Koenig", + email="koenigmx@hu-berlin.de", + organisation="Humboldt-University Berlin, " + "Institute for Theoretical Biology", + ), + Creator( + given_name="Matthias", + family_name="Koenig", + email="koenigmx@hu-berlin.de", + ), + Creator( + given_name="Matthias", + family_name="Koenig", + organisation="Humboldt-University Berlin, " + "Institute for Theoretical Biology", + ), + Creator( + given_name="Matthias", + family_name="Koenig", + ), + ], + created_date=HistoryDatetime("2019-03-06T14:40:55Z"), + modified_dates=[ + HistoryDatetime("2019-03-06T14:40:55Z"), + HistoryDatetime("2019-03-06T14:41:55Z"), + ], + ) + assert model.annotation.history == history + + +def test_create_creator(): + creator = Creator( + given_name="Matthias", + family_name="König", + organisation="HU", + email=TEST_COM, + ) + assert creator.given_name == "Matthias" + assert creator.family_name == "König" + assert creator.organisation == "HU" + assert creator.email == TEST_COM + + +def test_historydatetime(): + # valid date + dt_str1 = JUNE_26TH_530 + datetime_obj = HistoryDatetime(dt_str1) + assert datetime_obj.datetime == dt_str1 + + # valid date + datetime_obj.datetime = JUNE_26TH + assert datetime_obj.datetime == JUNE_26TH + datetime_obj.datetime = None + assert datetime_obj.datetime is None + + # create from python datetime + datetime_obj.datetime = datetime.now() + assert datetime_obj.datetime is not None + + # incorrect format + with pytest.raises(ValueError): + datetime_obj.datetime = datetime.now(timezone(timedelta(hours=1))).strftime( + "%Y-%m-%dT%H:%M:%S%Z" + ) diff --git a/tests/test_core/test_metadata/test_keyvaluepair.py b/tests/test_core/test_metadata/test_keyvaluepair.py new file mode 100644 index 000000000..7f58250e4 --- /dev/null +++ b/tests/test_core/test_metadata/test_keyvaluepair.py @@ -0,0 +1,64 @@ +from cobra.core.metadata.keyvaluepairs import KeyValueEntry, KeyValuePairs + + +EXAMPLE_URL = "https://tinyurl.com/ybyr7b62" + + +def test_keyvalueentry(): + keyvaluedict = KeyValueEntry.from_data( + { + "id": "KV_id", + "name": "abc_xyz", + "key": "keyX", + "value": "45", + "uri": EXAMPLE_URL, + } + ) + assert isinstance(keyvaluedict, KeyValueEntry) + assert keyvaluedict.id == "KV_id" + assert keyvaluedict.name == "abc_xyz" + assert keyvaluedict.key == "keyX" + assert keyvaluedict.value == "45" + assert keyvaluedict.uri == EXAMPLE_URL + + +def test_keyvalueentry_empty_uri(): + keyvaluedict = KeyValueEntry.from_data( + { + "id": "KV_id", + "name": "abc_xyz", + "key": "keyX", + "value": "45", + } + ) + assert isinstance(keyvaluedict, KeyValueEntry) + assert keyvaluedict.id == "KV_id" + assert keyvaluedict.name == "abc_xyz" + assert keyvaluedict.key == "keyX" + assert keyvaluedict.value == "45" + assert keyvaluedict.uri is None + + +def test_keyvaluepairs(): + entry1 = { + "id": "id1", + "name": "abc_xyz", + "key": "key1", + "value": "45", + "uri": "https://tinyurl.com/ybyr7b62", + } + entry2 = KeyValueEntry.from_data( + { + "id": "id2", + "name": "abc_xyz2", + "key": "key2", + "value": "48", + "uri": EXAMPLE_URL, + } + ) + + kvp = KeyValuePairs(entries=[entry1, entry2]) + assert len(kvp) == 2 + for key in ["key1", "key2"]: + assert key in kvp + assert kvp["key2"] == entry2 diff --git a/tests/test_core/test_metadata/test_metadata.py b/tests/test_core/test_metadata/test_metadata.py new file mode 100644 index 000000000..2d0869069 --- /dev/null +++ b/tests/test_core/test_metadata/test_metadata.py @@ -0,0 +1,249 @@ +"""Tests for the metadata structures.""" + +import json +import os +from os.path import join +from pathlib import Path + +from cobra.core.metadata import CVTerm, CVTerms, ExternalResources +from cobra.core.species import Species +from cobra.io import load_json_model, read_sbml_model, save_json_model, write_sbml_model + + +PUBMED_EXAMPLE = "https://identifiers.org/pubmed/1111111" +ECO_EXAMPLE = "https://identifiers.org/eco/ECO:0000004" + +ecoli_model_annotation = { + "bqb_hasTaxon": [{"resources": ["http://identifiers.org/taxonomy/511145"]}], + "bqm_is": [ + { + "nested_data": { + "bqb_isDescribedBy": [ + {"resources": [PUBMED_EXAMPLE]}, + {"resources": [ECO_EXAMPLE]}, + ] + }, + "resources": ["http://identifiers.org/bigg.model/e_coli_core"], + } + ], + "bqm_isDescribedBy": [ + {"resources": ["http://identifiers.org/doi/10.1128/ecosalplus.10.2.1"]}, + {"resources": ["http://identifiers.org/ncbigi/gi:16128336"]}, + ], +} + + +def test_annotation(): + # a cobra component + s = Species() + assert s.annotation == {} # nothing set for annotation, so empty dict + assert s.annotation.cvterms == CVTerms() + assert not s.annotation.keys() + assert s.annotation.keyvaluepairs == {} + assert s.annotation.history.creators == [] + assert s.annotation.history.modified_dates == [] + + # setting annotation via old annotation format + s.annotation["chebi"] = ["CHEBI:43215", "CHEBI:11881"] + + assert s.annotation.cvterms.resources == { + "https://identifiers.org/chebi/CHEBI:43215", + "https://identifiers.org/chebi/CHEBI:11881", + } + + # checking old (fixed) annotation format + assert s.annotation == {"chebi": sorted(["CHEBI:43215", "CHEBI:11881"])} + + # checking new cvterms + cvt = CVTerms( + [ + CVTerm( + qualifier="bqb_is", + ex_res=ExternalResources( + resources=["https://identifiers.org/chebi/CHEBI:43215"] + ), + ), + CVTerm( + qualifier="bqb_is", + ex_res=ExternalResources( + resources=["https://identifiers.org/chebi/CHEBI:11881"] + ), + ), + ] + ) + + assert s.annotation.cvterms == cvt + + # adding an SBO term + s.annotation["sbo"] = ["SBO:0000123"] + assert "chebi" in s.annotation + assert "sbo" in s.annotation + assert s.annotation == { + "chebi": sorted(["CHEBI:43215", "CHEBI:11881"]), + "sbo": ["SBO:0000123"], + } + + +def test_nested_annotation(data_directory): + # testing via cvterms + with open(join(data_directory, "cvterms_nested.json"), "r") as f_cvterms: + cvterms_data = json.load(f_cvterms) + + s = Species() + s.annotation.add_cvterms(CVTerms.from_dict(cvterms_data)) + assert s.annotation == { + "chebi": ["CHEBI:17627"], + "eco": ["000000"], + "kegg.compound": ["C00032"], + "pubmed": ["1111111"], + "uniprot": ["P68871", "P69905"], + } + # check cvterms + main_cvt = CVTerms.from_dict( + { + "bqb_hasPart": [ + { + "resources": [ + "https://identifiers.org/uniprot/P69905", + "https://identifiers.org/uniprot/P68871", + "https://identifiers.org/kegg.compound/C00032", + ] + }, + { + "resources": [ + "https://identifiers.org/uniprot/P69905", + "https://www.uniprot.org/uniprot/P68871", + "https://identifiers.org/chebi/CHEBI:17627", + ], + "nested_data": { + "bqb_isDescribedBy": [ + {"resources": [PUBMED_EXAMPLE]}, + {"resources": ["https://identifiers.org/eco/000000"]}, + ], + }, + }, + ] + } + ) + nested_cvt = CVTerms.from_dict( + { + "bqb_isDescribedBy": [ + {"resources": [PUBMED_EXAMPLE]}, + {"resources": ["https://identifiers.org/eco/000000"]}, + ] + } + ) + assert s.annotation.cvterms == main_cvt + nested_data = s.annotation.cvterms.query_qualifier("bqb_hasPart")[ + 1 + ].external_resources.nested_data + assert nested_data == nested_cvt + + +def _read_ecoli_annotation_model(data_directory): + test_xml = os.path.join(data_directory, "e_coli_core_for_annotation.xml") + model = read_sbml_model(test_xml) + return model + + +def test_cvterms_from_ecoli_xml(data_directory): + model = _read_ecoli_annotation_model(data_directory) + qualifier_set = {"bqb_hasTaxon", "bqm_is", "bqm_isDescribedBy"} + nested_cvt = CVTerms.from_dict( + { + "bqb_isDescribedBy": [ + {"resources": [PUBMED_EXAMPLE]}, + {"resources": [ECO_EXAMPLE]}, + ] + } + ) + ecoli_model_cvterm = CVTerms.from_dict(ecoli_model_annotation) + xml_model_cvterms = model.annotation.cvterms + model_cvterms_qualifier_set = {qual.name for qual in xml_model_cvterms.qualifiers} + assert qualifier_set == model_cvterms_qualifier_set + assert xml_model_cvterms == ecoli_model_cvterm + assert len(xml_model_cvterms.query_qualifier("bqm_isDescribedBy")) == 2 + nested_data = xml_model_cvterms.query_qualifier("bqm_is")[ + 0 + ].external_resources.nested_data + assert nested_data == nested_cvt + + # check backwards compatibility + assert model.annotation == { + "bigg.model": ["e_coli_core"], + "doi": ["10.1128/ecosalplus.10.2.1"], + "eco": ["ECO:0000004"], + "ncbigi": ["gi:16128336"], + "pubmed": ["1111111"], + "taxonomy": ["511145"], + } + + +def test_writing_xml(data_directory, tmp_path): + model = _read_ecoli_annotation_model(data_directory) + assert write_sbml_model(model, tmp_path.joinpath("e_coli_core_writing.xml")) is None + + +def test_read_write_json(data_directory, tmp_path): + model = _read_ecoli_annotation_model(data_directory) + json_path = join(tmp_path, "e_coli_core_json_writing.json") + assert save_json_model(model, json_path, sort=False, pretty=True) is None + + model = load_json_model(json_path) + assert model.annotation == { + "bigg.model": ["e_coli_core"], + "doi": ["10.1128/ecosalplus.10.2.1"], + "eco": ["ECO:0000004"], + "ncbigi": ["gi:16128336"], + "pubmed": ["1111111"], + "taxonomy": ["511145"], + } + assert model.annotation.cvterms == CVTerms.from_dict(ecoli_model_annotation) + + +def test_read_old_json_model(data_directory): + model = load_json_model(Path(data_directory) / "mini.json") + meta = model.metabolites[0] + assert meta.annotation == { + "bigg.metabolite": ["13dpg"], + "biocyc": ["DPG"], + "chebi": [ + "CHEBI:11881", + "CHEBI:16001", + "CHEBI:1658", + "CHEBI:20189", + "CHEBI:57604", + ], + "hmdb": ["HMDB01270"], + "kegg.compound": ["C00236"], + "pubchem.substance": ["3535"], + "reactome": ["REACT_29800"], + "seed.compound": ["cpd00203"], + "unipathway.compound": ["UPC00236"], + } + + # testing cvterms + expected_cvterms = CVTerms.from_dict( + { + "bqb_is": [ + { + "resources": [ + "http://identifiers.org/bigg.metabolite/13dpg", + "http://identifiers.org/biocyc/DPG", + "http://identifiers.org/chebi/CHEBI:16001", + "http://identifiers.org/chebi/CHEBI:1658", + "http://identifiers.org/chebi/CHEBI:20189", + "http://identifiers.org/chebi/CHEBI:57604", + "http://identifiers.org/chebi/CHEBI:11881", + "http://identifiers.org/hmdb/HMDB01270", + "http://identifiers.org/kegg.compound/C00236", + "http://identifiers.org/pubchem.substance/3535", + "http://identifiers.org/reactome/REACT_29800", + "http://identifiers.org/seed.compound/cpd00203", + "http://identifiers.org/unipathway.compound/UPC00236", + ] + } + ] + } + ) + assert meta.annotation.cvterms == expected_cvterms diff --git a/tests/test_core/test_metadata/test_notes.py b/tests/test_core/test_metadata/test_notes.py new file mode 100644 index 000000000..aeea75265 --- /dev/null +++ b/tests/test_core/test_metadata/test_notes.py @@ -0,0 +1,154 @@ +from pathlib import Path + +import pytest + +from cobra import Metabolite, Model, Reaction +from cobra.core import Notes +from cobra.io import load_json_model, read_sbml_model, save_json_model, write_sbml_model + + +def test_notes_io(tmp_path: Path) -> None: + """Test if model notes are written and read from/to SBML. + + Parameters + ---------- + tmp_path : pathlib.Path + The path to the temporary test assets store. + + """ + path_to_file = tmp_path / "model_notes.xml" + + # making a minimal cobra model to test notes + model = Model("e_coli_core") + model.notes = Notes().notes_from_dict({"Remark": "...Model Notes..."}) + met = Metabolite("pyr_c", compartment="c") + model.add_metabolites([met]) + met.notes = Notes().notes_from_dict({"Remark": "Note with \n newline"}) + rxn = Reaction("R_ATPM") + model.add_reactions([rxn]) + rxn.notes = Notes().notes_from_dict({"Remark": "What about me?"}) + model.objective_direction = "max" + model.objective = rxn + write_sbml_model(model, str(path_to_file.resolve())) + + # reading the model back + model_after_reading = read_sbml_model(str(path_to_file.resolve())) + met_after_reading = model_after_reading.metabolites.get_by_id("pyr_c") + reaction_after_reading = model_after_reading.reactions.get_by_id("R_ATPM") + + # checking if notes are written to model + assert model_after_reading.notes["Remark"] == "...Model Notes..." + + # checking notes for metabolite and reaction + assert met_after_reading.notes["Remark"] == "Note with \n newline" + assert reaction_after_reading.notes["Remark"] == "What about me?" + + +NEW_VALUE1 = "New Value 1" +NEW_VALUE3 = "New Value 3" + + +incoming_notes_str = ( + '\ +\n\ + \n\ +
\n\ +

Key1 : Value1

\n\ +

Key2 : Value2

\n\ +
\n\ +

A Heading

\n\ +
e_coli_core - Escherichia coli ' + "str. K-12 substr. MG1655
\n\ +
\n\ +

Key3 : Value3

\n\ +
\n\ + \n\ +" +) + +modified_notes_str = ( + '\ +\n\ + \n\ +
\n\ +

Key1 : New Value 1

\n\ +

Key2 : Value2

\n\ +
\n\ +

A Heading

\n\ +
e_coli_core - Escherichia coli ' + "str. K-12 substr. MG1655
\n\ +
\n\ +

Key3 : New Value 3

\n\ +
\n\ + \n\ +" +) + + +def test_notes(data_directory, tmp_path): + """Test creating notes from SBML to cobra model.""" + model_path = data_directory / "e_coli_core_for_annotation.xml" + assert model_path.exists() + model = read_sbml_model(model_path) + rx1 = model.reactions[0] + # making notes object to test equality check of + # two notes object + notes = Notes(incoming_notes_str) + + assert rx1.notes.notes_xhtml == incoming_notes_str + assert rx1.notes == notes + + # keys inside notes dict + list_of_keys = ["Key1", "Key2", "Key3"] + + for key in list_of_keys: + assert key in rx1.notes + + assert rx1.notes["Key1"] == "Value1" + assert rx1.notes["Key2"] == "Value2" + assert rx1.notes["Key3"] == "Value3" + + # modifying already present key-value + rx1.notes["Key1"] = NEW_VALUE1 + rx1.notes["Key3"] = NEW_VALUE3 + + # trying to insert a new key-value + with pytest.raises(ValueError): + rx1.notes["Key4"] = NEW_VALUE3 + + # checking modified notes dict and string + assert rx1.notes.notes_xhtml == modified_notes_str + assert rx1.notes["Key1"] == NEW_VALUE1 + assert rx1.notes["Key2"] == "Value2" + assert rx1.notes["Key3"] == NEW_VALUE3 + + # writing and reading back the model + path_to_file = tmp_path / "model_notes.xml" + write_sbml_model(model, path_to_file) + + model_after_reading = read_sbml_model(path_to_file) + rx1_after_reading = model_after_reading.reactions[0] + + # checks after reading model back again + assert rx1_after_reading.notes.notes_xhtml == modified_notes_str + assert rx1_after_reading.notes["Key1"] == NEW_VALUE1 + assert rx1_after_reading.notes["Key2"] == "Value2" + assert rx1_after_reading.notes["Key3"] == NEW_VALUE3 + + +def test_reading_writing_notes(data_directory, tmp_path): + # reading model with notes + model = read_sbml_model(data_directory / "e_coli_core_for_annotation.xml") + + # checking notes data + rx1 = model.reactions[0] + assert rx1.notes.notes_xhtml == incoming_notes_str + + # reading and writing in json format + path_to_json = tmp_path / "json_notes.json" + save_json_model(model, path_to_json) + model_from_json = load_json_model(path_to_json) + rx1_from_json = model_from_json.reactions[0] + assert rx1_from_json.notes.notes_xhtml == incoming_notes_str diff --git a/tests/test_io/test_annotation.py b/tests/test_io/test_annotation.py index f58e267ec..9fd005e4f 100644 --- a/tests/test_io/test_annotation.py +++ b/tests/test_io/test_annotation.py @@ -27,24 +27,28 @@ def _check_sbml_annotations(model: "Model") -> None: annotation = model.annotation assert annotation is not None assert len(annotation) == 3 - for key in ["bigg.model", "doi", "taxonomy"]: - assert key in annotation - assert annotation["bigg.model"] == "e_coli_core" - assert annotation["doi"] == "10.1128/ecosalplus.10.2.1" - assert annotation["taxonomy"] == "511145" + assert set(annotation.keys()) == {"bigg.model", "doi", "taxonomy"} + assert annotation["bigg.model"] == ["e_coli_core"] + assert annotation["doi"] == ["10.1128/ecosalplus.10.2.1"] + assert annotation["taxonomy"] == ["511145"] # gene annotation # {'asap': 'ABE-0006162', 'ncbigene': '946368', 'uniprot': 'P33221', - # 'ncbigi': 'gi:16129802', 'ecogene': 'EG11809'} + # 'ncbiprotein': 'gi:16129802', 'ecogene': 'EG11809'} annotation = model.genes.G1.annotation assert len(annotation) == 5 - for key in ["asap", "ncbigene", "uniprot", "ncbigi", "ecogene"]: - assert key in annotation - assert annotation["asap"] == "ABE-0006162" - assert annotation["ncbigene"] == "946368" - assert annotation["uniprot"] == "P33221" - assert annotation["ncbigi"] == "gi:16129802" - assert annotation["ecogene"] == "EG11809" + assert set(annotation.keys()) == { + "asap", + "ncbigene", + "uniprot", + "ncbiprotein", + "ecogene", + } + assert annotation["asap"] == ["ABE-0006162"] + assert annotation["ncbigene"] == ["946368"] + assert annotation["uniprot"] == ["P33221"] + assert annotation["ncbiprotein"] == ["16129802"] + assert annotation["ecogene"] == ["EG11809"] # compartment annotation # FIXME: add tests with first class compartment model @@ -63,7 +67,7 @@ def _check_sbml_annotations(model: "Model") -> None: # 'seed.compound': 'cpd00203', 'hmdb': ['HMDB62758', 'HMDB06213'], # 'biocyc': 'META:DPG'} annotation = model.metabolites.A.annotation - for key in [ + assert set(annotation.keys()) == { "inchi", "bigg.metabolite", "chebi", @@ -72,11 +76,10 @@ def _check_sbml_annotations(model: "Model") -> None: "seed.compound", "hmdb", "biocyc", - ]: - assert key in annotation - assert ( - annotation["inchi"] == "InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1" - ) # noqa: E501 + } + assert annotation["inchi"] == [ + "InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1" + ] # noqa: E501 # reaction annotation # {'kegg.reaction': 'R00228', 'sbo': 'SBO:0000375', @@ -84,7 +87,7 @@ def _check_sbml_annotations(model: "Model") -> None: # 'metanetx.reaction': 'MNXR95210', 'bigg.reaction': 'ACALD', # 'biocyc': 'META:ACETALD-DEHYDROG-RXN'} annotation = model.reactions.R1.annotation - for key in [ + assert set(annotation.keys()) == { "kegg.reaction", "sbo", "ec-code", @@ -92,9 +95,8 @@ def _check_sbml_annotations(model: "Model") -> None: "metanetx.reaction", "bigg.reaction", "biocyc", - ]: - assert key in annotation - assert annotation["biocyc"] == "META:ACETALD-DEHYDROG-RXN" + } + assert annotation["biocyc"] == ["META:ACETALD-DEHYDROG-RXN"] def test_read_sbml_annotations(data_directory: Path) -> None: diff --git a/tests/test_io/test_annotation_format.py b/tests/test_io/test_annotation_format.py index 9b9d039cd..0a678bc28 100644 --- a/tests/test_io/test_annotation_format.py +++ b/tests/test_io/test_annotation_format.py @@ -2,8 +2,6 @@ from pathlib import Path -import pytest - from cobra.io import load_json_model, write_sbml_model @@ -19,9 +17,9 @@ def test_load_json_model_valid(data_directory: Path, tmp_path: Path) -> None: path_to_file = data_directory / "valid_annotation_format.json" model = load_json_model(path_to_file) expected = { - "bigg.reaction": [["is", "PFK26"]], - "kegg.reaction": [["is", "R02732"]], - "rhea": [["is", "15656"]], + "bigg.reaction": ["PFK26"], + "kegg.reaction": ["R02732"], + "rhea": ["15656"], } for metabolite in model.metabolites: assert metabolite.annotation == expected @@ -37,5 +35,6 @@ def test_load_json_model_invalid(data_directory: Path) -> None: """ path = data_directory / "invalid_annotation_format.json" - with pytest.raises(TypeError): - load_json_model(path) + model = load_json_model(path) + anno = model.metabolites[0].annotation + assert anno == {"kegg.compound": ["C01468"], "chebi": ["CHEBI:11981"]} diff --git a/tests/test_io/test_json.py b/tests/test_io/test_json.py index 866a8f5b1..b2fee1f86 100644 --- a/tests/test_io/test_json.py +++ b/tests/test_io/test_json.py @@ -1,33 +1,32 @@ """Test functionalities of I/O in JSON format.""" -import json from os.path import join from pathlib import Path -from typing import Any, Callable, Dict, Union - -import pytest -from importlib_resources import files +from typing import Callable from cobra import Model from cobra import io as cio -@pytest.fixture(scope="module") -def json_schema_v1() -> Dict[str, Union[str, bool, Any]]: - """Fixture for cobra JSON-schema.""" - with files(cio).joinpath("schema_v1.json").open("r") as handle: - schema_v1 = json.load(handle) - return schema_v1 +def test_validate_json(data_directory: Path) -> None: + """Validate file according to JSON-schema.""" + path_old_format = join(data_directory, "e_coli_core.json") + # validate the model using JSON schema v1 + list_errors = cio.validate_json_model( + filename=path_old_format, json_schema_version=1 + ) + assert len(list_errors) == 0 + path_new_format = join(data_directory, "e_coli_new_format.json") + # validate the model using JSON schema v2 + errors = cio.validate_json_model(filename=path_new_format, json_schema_version=2) + assert len(errors) == 0 -def test_validate_json( - data_directory: Path, json_schema_v1: Dict[str, Union[str, bool, Any]] -) -> None: - """Validate file according to JSON-schema.""" - jsonschema = pytest.importorskip("jsonschema") - with open(data_directory.joinpath("mini.json"), "r", encoding="utf-8") as infile: - loaded = json.load(infile) - assert jsonschema.validate(loaded, json_schema_v1) is None + # test for invalid json model according to schema + errors_invalid = cio.validate_json_model( + filename=path_old_format, json_schema_version=2 + ) + assert len(errors_invalid) == 309 def test_load_json_model( @@ -38,30 +37,26 @@ def test_load_json_model( assert compare_models(mini_model, json_model) is None -def test_save_json_model( - tmp_path: Path, - mini_model: Model, - json_schema_v1: Dict[str, Union[str, bool, Any]], -) -> None: +def test_save_json_model(tmp_path: Path, mini_model: Model) -> None: """Test the writing of JSON model.""" - jsonschema = pytest.importorskip("jsonschema") output_file = tmp_path.joinpath("mini.json") cio.save_json_model(mini_model, output_file, pretty=True) # validate against JSONSchema - with open(str(output_file), "r") as infile: - loaded = json.load(infile) - assert jsonschema.validate(loaded, json_schema_v1) is None + errors = cio.validate_json_model(output_file, 1) + assert len(errors) == 0 def test_reaction_bounds_json(data_directory: Path, tmp_path: Path) -> None: """Test reading and writing of model with inf bounds in JSON.""" - # Path to XML file with INF bounds + """Path to XML file with INF bounds""" path_to_xml_inf_file = join(data_directory, "fbc_ex1.xml") model_xml_inf = cio.read_sbml_model(path_to_xml_inf_file) path_to_output = tmp_path.joinpath("fbc_ex1_json.json") - # Saving model with inf bounds in json form without error + + """Saving model with inf bounds in json form without error""" cio.save_json_model(model_xml_inf, path_to_output) - # Path to JSON file with INF bounds + + """Path to JSON file with INF bounds""" path_to_JSON_inf_file = data_directory.joinpath("JSON_with_inf_bounds.json") model_json_inf = cio.load_json_model(path_to_JSON_inf_file) assert model_json_inf.reactions[0].upper_bound == float("inf") diff --git a/tests/test_io/test_mat.py b/tests/test_io/test_mat.py index 4e392e92e..4f540e6e9 100644 --- a/tests/test_io/test_mat.py +++ b/tests/test_io/test_mat.py @@ -14,10 +14,12 @@ except ImportError: scipy = None - if TYPE_CHECKING: from cobra import Model +MINI_MAT = "mini.mat" +RAVEN_MAT = "raven.mat" + @pytest.fixture(scope="function") def raven_model(data_directory: Path) -> "Model": @@ -29,9 +31,9 @@ def raven_model(data_directory: Path) -> "Model": @pytest.mark.skipif(scipy is None, reason="scipy unavailable") # @pytest.mark.parametrize("ref_model, filename", # [(pytest.fixture_request("mini_model"), -# "mini.mat"), +# MINI_MAT), # (pytest.fixture_request("raven_model"), -# "raven.mat")]) +# RAVEN_MAT)]) # TODO: wait for pytest.fixture_request() to get approved def test_load_matlab_model( compare_models: Callable, @@ -49,8 +51,8 @@ def test_load_matlab_model( The path to the test data directory. """ - mini_mat_model = load_matlab_model(str((data_directory / "mini.mat").resolve())) - raven_mat_model = load_matlab_model(str((data_directory / "raven.mat").resolve())) + mini_mat_model = load_matlab_model(str((data_directory / MINI_MAT).resolve())) + raven_mat_model = load_matlab_model(str((data_directory / RAVEN_MAT).resolve())) assert compare_models(mini_model, mini_mat_model) is None assert compare_models(raven_model, raven_mat_model) is None @@ -59,9 +61,9 @@ def test_load_matlab_model( @pytest.mark.skipif(scipy is None, reason="scipy unavailable") # @pytest.mark.parametrize("model, filename", # [(pytest.fixture_request("mini_model"), -# "mini.mat"), +# MINI_MAT), # (pytest.fixture_request("raven_model"), -# "raven.mat")]) +# RAVEN_MAT)]) # TODO: wait for pytest.fixture_request() to get approved def test_save_matlab_model( tmp_path: Path, mini_model: "Model", raven_model: "Model" @@ -78,8 +80,8 @@ def test_save_matlab_model( The RAVEN model. """ - mini_output_file = tmp_path / "mini.mat" - raven_output_file = tmp_path / "raven.mat" + mini_output_file = tmp_path / MINI_MAT + raven_output_file = tmp_path / RAVEN_MAT # scipy.io.savemat() doesn't support anything other than # str or file-stream object, hence the str conversion save_matlab_model(mini_model, str(mini_output_file.resolve())) @@ -123,10 +125,10 @@ def test_read_rewrite_matlab_model( The path to the test data directory. """ - mini_mat_model = load_matlab_model(str((data_directory / "mini.mat").resolve())) - raven_mat_model = load_matlab_model(str((data_directory / "raven.mat").resolve())) - mini_output_file = tmp_path.joinpath("mini.mat") - raven_output_file = tmp_path.joinpath("raven.mat") + mini_mat_model = load_matlab_model(str((data_directory / MINI_MAT).resolve())) + raven_mat_model = load_matlab_model(str((data_directory / RAVEN_MAT).resolve())) + mini_output_file = tmp_path.joinpath(MINI_MAT) + raven_output_file = tmp_path.joinpath(RAVEN_MAT) # scipy.io.savemat() doesn't support anything other than # str or file-stream object, hence the str conversion save_matlab_model(mini_mat_model, str(mini_output_file)) @@ -137,60 +139,12 @@ def test_read_rewrite_matlab_model( assert compare_models(raven_mat_model, raven_mat_model_reload) is None -def _fix_xml_annotation_to_identifiers(model: "Model") -> None: - """Fix XML annotations to respect identifiers.org . - - This function will fix the dict keys of annotations to match identifiers.org. - Eventually, the XML models should be fixed and cobrapy should be strict, but this is - part of SBML rewriting of annotations - see: https://github.com/opencobra/cobrapy/issues/684 - - It also changes met formulas from empty string to None (which is the default - when creating a metabolite with no fomula given) and strips spaces from reaction - names. - - Parameters - ---------- - model : cobra.Model - The model to fix. - - """ - for met in model.metabolites: - if met.formula == "": - met.formula = None - if len(met.annotation): - if "chebi" in met.annotation.keys(): - met.annotation["CHEBI"] = met.annotation.pop("chebi") - if "sbo" in met.annotation.keys(): - met.annotation["SBO"] = met.annotation.pop("sbo") - for annot, val in met.annotation.items(): - if isinstance(val, str): - met.annotation[annot] = [val] - for rxn in model.reactions: - rxn.name = rxn.name.strip() - if "sbo" in rxn.annotation.keys(): - rxn.annotation["SBO"] = rxn.annotation.pop("sbo") - if len(rxn.annotation): - for annot, val in rxn.annotation.items(): - if isinstance(val, str): - rxn.annotation[annot] = [val] - for gene in model.genes: - if len(gene.annotation): - if "ncbigi" in gene.annotation.keys(): - gene.annotation["ncbiprotein"] = gene.annotation.pop("ncbigi") - for annot, val in gene.annotation.items(): - if isinstance(val, str): - gene.annotation[annot] = [val] - - @pytest.mark.skipif(scipy is None, reason="scipy unavailable") @pytest.mark.parametrize( "xml_file", ["e_coli_core.xml", "salmonella.xml", "mini_cobra.xml", "mini_fbc2.xml"] ) # When using a better comparison function, can run test on # "annotation.xml", "example_notes.xml", "fbc_ex1.xml", "fbc_ex2.xml", "validation.xml" -# "example_notes.xml" contains a group and groups are not yet correctly exported to -# matlab # "valid_annotation_output.xml" has reaction annotations in a metabolite, so they would # be thrown out by matlab def test_compare_xml_to_written_matlab_model( @@ -214,11 +168,8 @@ def test_compare_xml_to_written_matlab_model( """ xml_model = read_sbml_model(str((data_directory / xml_file).resolve())) - _fix_xml_annotation_to_identifiers(xml_model) mat_output_file = tmp_path / xml_file.replace(".xml", ".mat") - save_matlab_model( - xml_model, str(mat_output_file.resolve()) - ) # lac__D_e_boundary confuses the reading of matlab + save_matlab_model(xml_model, str(mat_output_file.resolve())) mat_model = load_matlab_model(str(mat_output_file.resolve())) assert compare_models(xml_model, mat_model) is None @@ -326,36 +277,65 @@ def test_mat_model_wrong_caps(compare_models: Callable, data_directory: Path) -> The path to the test data directory. """ - mat_model = load_matlab_model(str(Path(data_directory / "mini.mat").resolve())) + mat_model = load_matlab_model(str(Path(data_directory / MINI_MAT).resolve())) mat_wrong_caps_model = load_matlab_model( str(Path(data_directory, "mini_wrong_key_caps.mat").resolve()) ) assert compare_models(mat_model, mat_wrong_caps_model) is None - assert mat_wrong_caps_model.reactions.get_by_id("LDH_D").annotation == { + EXPECTED_RXN_ANNOTATION = { "rhea": ["16369", "16370", "16371", "16372"], "metanetx.reaction": ["MNXR101037"], "kegg.reaction": ["R00704"], "bigg.reaction": ["LDH_D"], "ec-code": ["1.1.1.28"], "biocyc": ["META:DLACTDEHYDROGNAD-RXN"], + "sbo": ["SBO:0000375"], } + actual_rxn_annotation = dict( + mat_wrong_caps_model.reactions.get_by_id("LDH_D").annotation + ) + expected_rxn_keys = EXPECTED_RXN_ANNOTATION.keys() + actual_rxn_keys = actual_rxn_annotation.keys() + assert expected_rxn_keys == actual_rxn_keys + for key in actual_rxn_keys: + assert EXPECTED_RXN_ANNOTATION[key] == actual_rxn_annotation[key] for rxn in mat_model.reactions.list_attr("id"): assert ( mat_wrong_caps_model.reactions.get_by_id(rxn).annotation == mat_model.reactions.get_by_id(rxn).annotation ) - assert mat_wrong_caps_model.metabolites.get_by_id("pyr_c").annotation == { + + EXPECTED_MAT_ANNOTATION = { "seed.compound": ["cpd00020"], "unipathway.compound": ["UPC00022"], "lipidmaps": ["LMFA01060077"], - "reactome": ["REACT_113557", "REACT_389680", "REACT_29398"], + "reactome": sorted(["REACT_113557", "REACT_389680", "REACT_29398"]), "biocyc": ["PYRUVATE"], + "chebi": sorted( + [ + "CHEBI:15361", + "CHEBI:14987", + "CHEBI:8685", + "CHEBI:32816", + "CHEBI:45253", + "CHEBI:26466", + "CHEBI:26462", + ] + ), "pubchem.substance": ["3324"], "bigg.metabolite": ["pyr"], "cas": ["127-17-3"], "hmdb": ["HMDB00243"], "kegg.compound": ["C00022"], } + actual_met_annotation = mat_wrong_caps_model.metabolites.get_by_id( + "pyr_c" + ).annotation.annotations + expected_met_keys = EXPECTED_MAT_ANNOTATION.keys() + actual_met_keys = actual_met_annotation.keys() + assert expected_met_keys == actual_met_keys + for key in actual_met_keys: + assert EXPECTED_MAT_ANNOTATION[key] == actual_met_annotation[key] for met in mat_model.metabolites.list_attr("id"): assert ( mat_wrong_caps_model.metabolites.get_by_id(met).annotation diff --git a/tests/test_io/test_notes.py b/tests/test_io/test_notes.py deleted file mode 100644 index 7a15640c0..000000000 --- a/tests/test_io/test_notes.py +++ /dev/null @@ -1,43 +0,0 @@ -"""Test proper reading of SBML notes.""" - -from pathlib import Path - -from cobra import Metabolite, Model, Reaction -from cobra.io import read_sbml_model, write_sbml_model - - -def test_notes(tmp_path: Path) -> None: - """Test if model notes are written in SBML. - - Parameters - ---------- - tmp_path : pathlib.Path - The path to the temporary test assets store. - - """ - path_to_file = tmp_path / "model_notes.xml" - - # making a minimal cobra model to test notes - model = Model("e_coli_core") - model.notes["Remark"] = "...Model Notes..." - met = Metabolite("pyr_c", compartment="c") - model.add_metabolites([met]) - met.notes["Remark"] = "Note with \n newline" - rxn = Reaction("R_ATPM") - model.add_reactions([rxn]) - rxn.notes["Remark"] = "What about me?" - model.objective_direction = "max" - model.objective = rxn - write_sbml_model(model, str(path_to_file.resolve())) - - # reading the model back - model_after_reading = read_sbml_model(str(path_to_file.resolve())) - met_after_reading = model_after_reading.metabolites.get_by_id("pyr_c") - reaction_after_reading = model_after_reading.reactions.get_by_id("R_ATPM") - - # checking if notes are written to model - assert model_after_reading.notes["Remark"] == "...Model Notes..." - - # checking notes for metabolite and reaction - assert met_after_reading.notes["Remark"] == "Note with \n newline" - assert reaction_after_reading.notes["Remark"] == "What about me?" diff --git a/tests/test_io/test_sbml.py b/tests/test_io/test_sbml.py index 776c3dcb8..c633e962f 100644 --- a/tests/test_io/test_sbml.py +++ b/tests/test_io/test_sbml.py @@ -6,13 +6,14 @@ from pathlib import Path from pickle import load from tempfile import gettempdir -from typing import List, Tuple +from typing import Callable, List, Tuple import pytest from _pytest.fixtures import SubRequest import cobra from cobra import Model +from cobra.core.metadata import MetaData from cobra.io import read_sbml_model, validate_sbml_model, write_sbml_model @@ -23,6 +24,8 @@ except ImportError: jsonschema = None +TEST_XML = "test.xml" + # ---------------------------------- # Definition of SBML files to test # ---------------------------------- @@ -76,7 +79,7 @@ def test_validate(trial: IOTrial, data_directory: str) -> None: Parameters ---------- - IOTrial: + trial: IOTrial Which model trial to check. data_directory: str Directory where the data is. @@ -318,7 +321,6 @@ def test_from_sbml_string(data_directory: str) -> None: TestCobraIO.compare_models(name="read from string", model1=model1, model2=model2) -@pytest.mark.skip(reason="Model history currently not written") def test_model_history(tmp_path: Path) -> None: """Testing reading and writing of ModelHistory. @@ -328,31 +330,45 @@ def test_model_history(tmp_path: Path) -> None: Directory to use for temporary data. """ model = Model("test") - model._sbml = { + history = { "creators": [ { - "familyName": "Mustermann", - "givenName": "Max", + "family_name": "Mustermann", + "given_name": "Max", "organisation": "Muster University", "email": "muster@university.com", } - ] + ], + "created_date": "2019-10-20T12:34:32Z", + "modified_dates": ["2019-10-20T12:35:32Z"], } + annotation = MetaData(history=history) + model._sbml = {"annotation": annotation} - sbml_path = join(str(tmp_path), "test.xml") + sbml_path = join(str(tmp_path), TEST_XML) with open(sbml_path, "w") as f_out: write_sbml_model(model, f_out) with open(sbml_path, "r") as f_in: model2 = read_sbml_model(f_in) - assert "creators" in model2._sbml - assert len(model2._sbml["creators"]) == 1 - c = model2._sbml["creators"][0] - assert c["familyName"] == "Mustermann" - assert c["givenName"] == "Max" - assert c["organisation"] == "Muster University" - assert c["email"] == "muster@university.com" + assert "annotation" in model2._sbml + assert len(model2._sbml["annotation"].history.creators) == 1 + c = model2._sbml["annotation"].history.creators[0] + assert c.family_name == "Mustermann" + assert c.given_name == "Max" + assert c.organisation == "Muster University" + assert c.email == "muster@university.com" + + assert ( + model2._sbml["annotation"].history.created_date.datetime + == "2019-10-20T12:34:32Z" + ) + assert len(model2._sbml["annotation"].history._modified_dates) == 1 + assert ( + model2._sbml["annotation"].history._modified_dates[0].datetime + == "2019-10-20T12:35:32Z" + ) def test_groups(data_directory: str, tmp_path: Path) -> None: @@ -372,7 +388,7 @@ def test_groups(data_directory: str, tmp_path: Path) -> None: g1 = model.groups[0] assert len(g1.members) == 6 - temp_path = join(str(tmp_path), "test.xml") + temp_path = join(str(tmp_path), TEST_XML) with open(temp_path, "w") as f_out: write_sbml_model(model, f_out) @@ -478,7 +494,7 @@ def test_infinity_bounds(data_directory: str, tmp_path: Path) -> None: assert r.lower_bound == -float("Inf") assert r.upper_bound == float("Inf") - temp_path = join(str(tmp_path), "test.xml") + temp_path = join(str(tmp_path), TEST_XML) with open(temp_path, "w") as f_out: write_sbml_model(model, f_out) @@ -525,7 +541,7 @@ def test_gprs(data_directory: str, tmp_path: Path) -> None: """ model1 = read_sbml_model(join(data_directory, "iJO1366.xml.gz")) - sbml_path = join(str(tmp_path), "test.xml") + sbml_path = join(str(tmp_path), TEST_XML) with open(sbml_path, "w") as f_out: write_sbml_model(model1, f_out) @@ -543,7 +559,7 @@ def test_gprs(data_directory: str, tmp_path: Path) -> None: def test_identifiers_annotation() -> None: """Test annotation with identifiers.""" - from cobra.io.sbml import _parse_annotation_info + from cobra.core.metadata.helper import parse_identifiers_uri for uri in [ "http://identifiers.org/chebi/CHEBI:000123", @@ -551,7 +567,7 @@ def test_identifiers_annotation() -> None: "http://identifiers.org/CHEBI:000123", "https://identifiers.org/CHEBI:000123", ]: - data = _parse_annotation_info(uri) + data = parse_identifiers_uri(uri) assert data assert data[0] == "chebi" assert data[1] == "CHEBI:000123" @@ -562,7 +578,7 @@ def test_identifiers_annotation() -> None: "http://identifiers.org/taxonomy:9602", "https://identifiers.org/taxonomy:9602", ]: - data = _parse_annotation_info(uri) + data = parse_identifiers_uri(uri) assert data assert data[0] == "taxonomy" assert data[1] == "9602" @@ -571,19 +587,17 @@ def test_identifiers_annotation() -> None: "http://identifier.org/taxonomy/9602", "https://test.com", ]: - data = _parse_annotation_info(uri) + data = parse_identifiers_uri(uri) assert data is None -def test_smbl_with_notes(data_directory: str, tmp_path: Path) -> None: +def test_smbl_with_notes(data_directory: str) -> None: """Test that NOTES in the RECON 2.2 style are written and read correctly. Parameters ---------- data_directory: str Directory where the data is. - tmp_path: Path - Directory to use for temporary data. """ sbml_path = join(data_directory, "example_notes.xml") model = read_sbml_model(sbml_path) @@ -609,52 +623,56 @@ def test_smbl_with_notes(data_directory: str, tmp_path: Path) -> None: } metabolite_annotations = { "2hb_e": { - "sbo": "SBO:0000247", - "inchi": "InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3," "(H,6,7)", - "chebi": "CHEBI:1148", + "sbo": ["SBO:0000247"], + "inchi": ["InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)"], + "chebi": ["CHEBI:1148"], }, "nad_e": { - "sbo": "SBO:0000247", - "inchi": "InChI=1S/C21H27N7O14P2/c22-17-12-19(" - "25-7-24-17)28(8-26-12)21-16(32)14(30)11(" - "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(" - "31)20(40-10)27-3-1-2-9(4-27)18(" - "23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2," - "(H5-,22,23,24,25,33,34,35,36,37)/p-1/t10-," - "11-,13-,14-,15-,16-,20-,21-/m1/s1", - "chebi": "CHEBI:57540", + "sbo": ["SBO:0000247"], + "inchi": [ + "InChI=1S/C21H27N7O14P2/c22-17-12-19(" + "25-7-24-17)28(8-26-12)21-16(32)14(30)11(" + "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(" + "31)20(40-10)27-3-1-2-9(4-27)18(" + "23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2," + "(H5-,22,23,24,25,33,34,35,36,37)/p-1/t10-," + "11-,13-,14-,15-,16-,20-,21-/m1/s1" + ], + "chebi": ["CHEBI:57540"], }, "h_e": { - "sbo": "SBO:0000247", - "inchi": "InChI=1S/p+1/i/hH", - "chebi": "CHEBI:24636", + "sbo": ["SBO:0000247"], + "inchi": ["InChI=1S/p+1/i/hH"], + "chebi": ["CHEBI:24636"], }, "2obut_e": { - "sbo": "SBO:0000247", - "inchi": "InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6," "7)/p-1", - "chebi": "CHEBI:16763", + "sbo": ["SBO:0000247"], + "inchi": ["InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)/p-1"], + "chebi": ["CHEBI:16763"], }, "nadh_e": { - "sbo": "SBO:0000247", - "inchi": "InChI=1S/C21H29N7O14P2/c22-17-12-19(" - "25-7-24-17)28(8-26-12)21-16(32)14(30)11(" - "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(" - "29)15(31)20(40-10)27-3-1-2-9(4-27)18(" - "23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2," - "5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24," - "25)/p-2/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1", - "chebi": "CHEBI:57945", + "sbo": ["SBO:0000247"], + "inchi": [ + "InChI=1S/C21H29N7O14P2/c22-17-12-19(" + "25-7-24-17)28(8-26-12)21-16(32)14(30)11(" + "41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(" + "29)15(31)20(40-10)27-3-1-2-9(4-27)18(" + "23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2," + "5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24," + "25)/p-2/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1" + ], + "chebi": ["CHEBI:57945"], }, } reaction_notes = { "CONFIDENCE_LEVEL": "4", "NOTES": "NCD", "SUBSYSTEM": "Propanoate metabolism", - "GENE_ASSOCIATION": "(HGNC:8546 and HGNC:8548) or" " (HGNC:8547 and HGNC:8548)", + "GENE_ASSOCIATION": "(HGNC:8546 and HGNC:8548) or (HGNC:8547 and HGNC:8548)", } reaction_annotations = { - "sbo": "SBO:0000176", - "ec-code": "1.1.1.27", + "sbo": ["SBO:0000176"], + "ec-code": ["1.1.1.27"], "pubmed": ["10108", "21765"], } @@ -708,3 +726,12 @@ def test_stable_gprs(data_directory: str, tmp_path: Path) -> None: assert ( fixed_model.reactions.GLCpts.gene_reaction_rule == "(b2415 and b2417) or b2416" ) + + +def test_writing_xml_with_annotation( + compare_models: Callable, data_directory: Path, tmp_path: Path +): + model = read_sbml_model(data_directory.joinpath("e_coli_core_for_annotation.xml")) + write_sbml_model(model, tmp_path.joinpath("e_coli_core_writing.xml")) + reread_model = read_sbml_model(tmp_path.joinpath("e_coli_core_writing.xml")) + compare_models(model, reread_model) diff --git a/tests/test_io/test_yaml.py b/tests/test_io/test_yaml.py index 4bb2e593e..956e895a5 100644 --- a/tests/test_io/test_yaml.py +++ b/tests/test_io/test_yaml.py @@ -4,7 +4,6 @@ from pathlib import Path from typing import Callable -import pytest from ruamel.yaml import YAML from cobra import Model @@ -19,10 +18,8 @@ def test_load_yaml_model( assert compare_models(mini_model, yaml_model) is None -@pytest.mark.xfail(reason="schema outdated") def test_save_yaml_model(tmp_path: Path, mini_model: Model) -> None: """Test the writing of YAML model.""" - jsonschema = pytest.importorskip("jsonschema") output_file = tmp_path.joinpath("mini.yml") cio.save_yaml_model(mini_model, str(output_file), sort=True) # validate against JSONSchema @@ -30,5 +27,6 @@ def test_save_yaml_model(tmp_path: Path, mini_model: Model) -> None: with open(output_file, "r") as infile: yaml_to_dict = yaml.load(infile) dict_to_json = json.dumps(yaml_to_dict) - loaded = json.loads(dict_to_json) - assert jsonschema.validate(loaded, cio.json.json_schema) + # Validate according to schema version 1 + errors = cio.validate_json_model(filename=dict_to_json, json_schema_version=1) + assert len(errors) == 0 diff --git a/tests/test_manipulation/test_annotate.py b/tests/test_manipulation/test_annotate.py index f1fa0d85e..c344d7255 100644 --- a/tests/test_manipulation/test_annotate.py +++ b/tests/test_manipulation/test_annotate.py @@ -7,7 +7,7 @@ def test_sbo_annotation(model: Model) -> None: """Test SBO annotation function.""" rxns = model.reactions - rxns.EX_o2_e.annotation.clear() + rxns.get_by_id("EX_o2_e").annotation.sbo = "" fake_DM = Reaction("DM_h_c") model.add_reactions([fake_DM]) fake_DM.add_metabolites({model.metabolites.get_by_id("h_c"): -1}) @@ -15,6 +15,6 @@ def test_sbo_annotation(model: Model) -> None: # an existing SBO annotation rxns.get_by_id("EX_h_e").annotation["sbo"] = "SBO:0000628" add_SBO(model) - assert rxns.EX_o2_e.annotation["sbo"] == "SBO:0000627" - assert rxns.DM_h_c.annotation["sbo"] == "SBO:0000628" - assert rxns.EX_h_e.annotation["sbo"] == "SBO:0000628" + assert rxns.EX_o2_e.annotation["sbo"] == ["SBO:0000627"] + assert rxns.DM_h_c.annotation["sbo"] == ["SBO:0000628"] + assert rxns.EX_h_e.annotation["sbo"] == ["SBO:0000628"] diff --git a/tests/test_manipulation/test_delete.py b/tests/test_manipulation/test_delete.py index c745a1efb..cc18a4865 100644 --- a/tests/test_manipulation/test_delete.py +++ b/tests/test_manipulation/test_delete.py @@ -11,6 +11,13 @@ ) +A_AND_B_OR_C_AND_A = "(a and b) or (c and a)" +A_AND_B_AND_D_AND_E = "(a and b and d and e)" +A_AND_B_OR_B_AND_C = "(a and b) or (b and c)" +F_AND_B_OR_B_AND_C = "(f and b) or (b and c)" +B_AND_C = "b and c" + + def test_prune_unused_metabolites_output_type(model: Model) -> None: """Test the output type of unused metabolites pruning.""" [model.reactions.get_by_id(x).remove_from_model() for x in ["RPI", "RPE", "GND"]] @@ -110,7 +117,7 @@ def test_gene_knockout(salmonella: Model) -> None: assert expected_reactions == knocked_out_reactions with salmonella: expected_reactions = [salmonella.reactions.get_by_id("4PEPTabcpp")] - knocked_out_reactions = knock_out_model_genes(salmonella, ["STM1746.S"]) + knocked_out_reactions = knock_out_model_genes(salmonella, ["STM1746_S"]) assert expected_reactions == knocked_out_reactions knocked_out_reactions = knock_out_model_genes(salmonella, gene_list) assert len(knocked_out_reactions) == 13 @@ -128,7 +135,7 @@ def test_gene_knockout(salmonella: Model) -> None: test_model.add_reactions([test_reaction_1]) with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["eggs"]) - assert knocked_out_reactions == list() + assert knocked_out_reactions == [] with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["eggs", "spam"]) expected_reactions = [test_model.reactions.get_by_id("test1")] @@ -137,13 +144,13 @@ def test_gene_knockout(salmonella: Model) -> None: test_reaction_1.gene_reaction_rule = "g1 and g2 and (g3 or g4 or (g5 and g6))" with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["g3"]) - assert knocked_out_reactions == list() + assert knocked_out_reactions == [] with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["g1"]) assert knocked_out_reactions == [test_reaction_1] with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["g5"]) - assert knocked_out_reactions == list() + assert knocked_out_reactions == [] with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["g3", "g4", "g5"]) assert knocked_out_reactions == [test_reaction_1] @@ -154,7 +161,7 @@ def test_gene_knockout(salmonella: Model) -> None: assert knocked_out_reactions == [test_reaction_1] with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["for"]) - assert knocked_out_reactions == list() + assert knocked_out_reactions == [] test_reaction_1.gene_reaction_rule = "g1 and g2 and g2.conjugate" with test_model: knocked_out_reactions = knock_out_model_genes(test_model, ["g2"]) @@ -179,10 +186,10 @@ def test_remove_genes() -> None: m.add_reactions([Reaction("r" + str(i + 1)) for i in range(8)]) assert len(m.reactions) == 8 rxns = m.reactions - rxns.r1.gene_reaction_rule = "(a and b) or (c and a)" - rxns.r2.gene_reaction_rule = "(a and b and d and e)" - rxns.r3.gene_reaction_rule = "(a and b) or (b and c)" - rxns.r4.gene_reaction_rule = "(f and b) or (b and c)" + rxns.r1.gene_reaction_rule = A_AND_B_OR_C_AND_A + rxns.r2.gene_reaction_rule = A_AND_B_AND_D_AND_E + rxns.r3.gene_reaction_rule = A_AND_B_OR_B_AND_C + rxns.r4.gene_reaction_rule = F_AND_B_OR_B_AND_C rxns.r5.gene_reaction_rule = "x" rxns.r6.gene_reaction_rule = "y" rxns.r7.gene_reaction_rule = "x or z" @@ -194,8 +201,8 @@ def test_remove_genes() -> None: assert "x" in m.genes assert rxns.r1.gene_reaction_rule == "" assert rxns.r2.gene_reaction_rule == "" - assert rxns.r3.gene_reaction_rule == "b and c" - assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)" + assert rxns.r3.gene_reaction_rule == B_AND_C + assert rxns.r4.gene_reaction_rule == F_AND_B_OR_B_AND_C assert rxns.r5.gene_reaction_rule == "x" assert rxns.r6.gene_reaction_rule == "y" assert rxns.r7.genes == {m.genes.x, m.genes.z} @@ -206,8 +213,8 @@ def test_remove_genes() -> None: assert "x" not in m.genes assert rxns.r1.gene_reaction_rule == "" assert rxns.r2.gene_reaction_rule == "" - assert rxns.r3.gene_reaction_rule == "b and c" - assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)" + assert rxns.r3.gene_reaction_rule == B_AND_C + assert rxns.r4.gene_reaction_rule == F_AND_B_OR_B_AND_C assert rxns.r6.gene_reaction_rule == "y" assert rxns.r7.gene_reaction_rule == "z" assert rxns.r7.genes == {m.genes.z} @@ -220,10 +227,10 @@ def test_remove_genes_with_context() -> None: m.add_reactions([Reaction("r" + str(i + 1)) for i in range(8)]) assert len(m.reactions) == 8 rxns = m.reactions - rxns.r1.gene_reaction_rule = "(a and b) or (c and a)" - rxns.r2.gene_reaction_rule = "(a and b and d and e)" - rxns.r3.gene_reaction_rule = "(a and b) or (b and c)" - rxns.r4.gene_reaction_rule = "(f and b) or (b and c)" + rxns.r1.gene_reaction_rule = A_AND_B_OR_C_AND_A + rxns.r2.gene_reaction_rule = A_AND_B_AND_D_AND_E + rxns.r3.gene_reaction_rule = A_AND_B_OR_B_AND_C + rxns.r4.gene_reaction_rule = F_AND_B_OR_B_AND_C rxns.r5.gene_reaction_rule = "x" rxns.r6.gene_reaction_rule = "y" rxns.r7.gene_reaction_rule = "x or z" @@ -234,18 +241,18 @@ def test_remove_genes_with_context() -> None: assert "x" in m.genes assert rxns.r1.gene_reaction_rule == "" assert rxns.r2.gene_reaction_rule == "" - assert rxns.r3.gene_reaction_rule == "b and c" - assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)" + assert rxns.r3.gene_reaction_rule == B_AND_C + assert rxns.r4.gene_reaction_rule == F_AND_B_OR_B_AND_C assert rxns.r5.gene_reaction_rule == "x" assert rxns.r6.gene_reaction_rule == "y" assert rxns.r7.genes == {m.genes.x, m.genes.z} assert rxns.r8.gene_reaction_rule == "" assert "a" in m.genes assert "x" in m.genes - assert rxns.r1.gene_reaction_rule == "(a and b) or (c and a)" - assert rxns.r2.gpr == GPR.from_string("(a and b and d and e)") - assert rxns.r3.gene_reaction_rule == "(a and b) or (b and c)" - assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)" + assert rxns.r1.gene_reaction_rule == A_AND_B_OR_C_AND_A + assert rxns.r2.gpr == GPR.from_string(A_AND_B_AND_D_AND_E) + assert rxns.r3.gene_reaction_rule == A_AND_B_OR_B_AND_C + assert rxns.r4.gene_reaction_rule == F_AND_B_OR_B_AND_C assert rxns.r5.gene_reaction_rule == "x" assert rxns.r6.gene_reaction_rule == "y" assert rxns.r7.genes == {m.genes.x, m.genes.z} @@ -259,8 +266,8 @@ def test_remove_genes_with_context() -> None: assert "x" not in m.genes assert rxns.r1.gene_reaction_rule == "" assert rxns.r2.gene_reaction_rule == "" - assert rxns.r3.gene_reaction_rule == "b and c" - assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)" + assert rxns.r3.gene_reaction_rule == B_AND_C + assert rxns.r4.gene_reaction_rule == F_AND_B_OR_B_AND_C assert rxns.r6.gene_reaction_rule == "y" assert rxns.r7.gene_reaction_rule == "z" assert rxns.r7.genes == {m.genes.z} @@ -268,10 +275,10 @@ def test_remove_genes_with_context() -> None: assert "a" in m.genes assert "x" in m.genes assert len(m.reactions) == 8 - assert rxns.r1.gene_reaction_rule == "(a and b) or (c and a)" - assert rxns.r2.gpr == GPR.from_string("(a and b and d and e)") - assert rxns.r3.gene_reaction_rule == "(a and b) or (b and c)" - assert rxns.r4.gene_reaction_rule == "(f and b) or (b and c)" + assert rxns.r1.gene_reaction_rule == A_AND_B_OR_C_AND_A + assert rxns.r2.gpr == GPR.from_string(A_AND_B_AND_D_AND_E) + assert rxns.r3.gene_reaction_rule == A_AND_B_OR_B_AND_C + assert rxns.r4.gene_reaction_rule == F_AND_B_OR_B_AND_C assert rxns.r5.gene_reaction_rule == "x" assert rxns.r6.gene_reaction_rule == "y" assert rxns.r7.genes == {m.genes.x, m.genes.z} diff --git a/tox.ini b/tox.ini index adca66347..5d73515af 100644 --- a/tox.ini +++ b/tox.ini @@ -123,6 +123,7 @@ known_third_party = ruamel.yaml scipy swiglpk + jsonschema [flake8] exclude =