Add new features viewer

Author: ddomingof

src/pathme_viewer/constants.py

@@ -5,7 +5,13 @@
 import os
 
 from pathme.cli import WIKIPATHWAYS_FILES
-from pathme.constants import get_connection
+from pathme.constants import get_connection, KEGG, REACTOME, WIKIPATHWAYS
+
+DATABASE_STYLE_DICT = {
+    KEGG: 'KEGG',
+    REACTOME: 'Reactome',
+    WIKIPATHWAYS: 'WikiPathways',
+}
 
 MODULE_NAME = 'pathme_viewer'
 PATHME_DIR = os.environ.get('PATHME_DIRECTORY', os.path.join(os.path.expanduser('~'), '.pathme'))

src/pathme_viewer/models.py

@@ -4,12 +4,12 @@
 
 import datetime
 
-from pybel import from_bytes
 from sqlalchemy import Column, DateTime, Integer, String
 from sqlalchemy import LargeBinary, Text
 from sqlalchemy.ext.declarative import declarative_base
 
-from .constants import MODULE_NAME
+from pybel import from_bytes
+from .constants import MODULE_NAME, DATABASE_STYLE_DICT
 
 LONGBLOB = 4294967295
 
@@ -43,8 +43,19 @@ class Pathway(Base):
     blob = Column(LargeBinary(LONGBLOB), doc='A pickled version of this pathway')
 
     def __str__(self):
-        """Return Pathway name."""
-        return self.name
+        """Return pathway name."""
+        return '{} ({})'.format(
+            self.name,
+            DATABASE_STYLE_DICT.get(self.resource_name, self.resource_name)
+        )
+
+    @property
+    def display_name(self):
+        """Return pathway name."""
+        return '{} ({})'.format(
+            self.name,
+            DATABASE_STYLE_DICT.get(self.resource_name, self.resource_name)
+        )
 
     def as_bel(self):
         """Get this network and loads it into a :class:`BELGraph`.

src/pathme_viewer/templates/pathme_viewer.html

@@ -59,7 +59,7 @@
 
         <div class="col-lg-12 col-md-12 col-sm-12">
             <div class="row">
-                <h2 class="title text-center"> {{ subgraph_name_string }}</h2>
+                <h2 class="title text-center"> {{ pathways_name }}</h2>
             </div>
             <div class="row" style="margin-right: 0; margin-bottom:20px"><!-- visualization row -->
                 <div class="panel panel-default">  <!-- / Panel d3 Force -->

src/pathme_viewer/web/views.py

@@ -16,8 +16,8 @@
 from flask_admin.contrib.sqla import ModelView
 from pkg_resources import resource_filename
 
-from ..graph_utils import export_graph, merge_pathways, get_tree_annotations, process_request
-from ..models import Pathway
+from pathme_viewer.graph_utils import export_graph, merge_pathways, get_tree_annotations, process_request
+from pathme_viewer.models import Pathway
 
 log = logging.getLogger(__name__)
 time_instantiated = str(datetime.datetime.now())
@@ -106,9 +106,20 @@ def viewer():
     """PathMe page."""
     pathways = process_request(request)
 
+    # List of all pathway names
+    pathway_names = []
+    for pathway_id, resource in pathways.items():
+        pathway = current_app.pathme_manager.get_pathway_by_id(pathway_id, resource)
+
+        if not pathway:
+            continue
+
+        pathway_names.append(pathway.display_name)
+
     return render_template(
         'pathme_viewer.html',
         pathways=pathways,
+        pathways_name='+'.join(pathway_names),
         pathway_ids=list(pathways.keys())
     )
 
@@ -120,7 +131,8 @@ def get_network():
 
     graph = merge_pathways(pathways)
 
-    log.info('Exporting merged graph with {} nodes and {} edges'.format(graph.number_of_nodes(), graph.number_of_edges()))
+    log.info(
+        'Exporting merged graph with {} nodes and {} edges'.format(graph.number_of_nodes(), graph.number_of_edges()))
 
     return export_graph(graph, request.args.get('format'))