From 5dff098df76cc583fb4540c0677b57334f265158 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Wed, 26 Mar 2025 12:42:18 +0000 Subject: [PATCH 01/10] Use pre-computed component inchis and promote inchi fields to lists --- src/csd_optimade/fields.py | 10 +++++----- src/csd_optimade/mappers.py | 8 +++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/src/csd_optimade/fields.py b/src/csd_optimade/fields.py index 6f9a09b..400e45e 100644 --- a/src/csd_optimade/fields.py +++ b/src/csd_optimade/fields.py @@ -78,18 +78,18 @@ def generate_csd_provider_fields(): }, { "name": "_csd_inchi", - "type": "string", - "description": "CSD InChI string.", + "type": "list", + "description": "A list of InChI strings for individual components in the structure.", }, { "name": "_csd_inchi_key", - "type": "string", - "description": "CSD InChIKey.", + "type": "list", + "description": "A list of InChIKeys for individual components in the structure.", }, { "name": "_csd_smiles", "type": "string", - "description": "CSD SMILES string.", + "description": "A SMILES string computed for the 3D structure.", }, { "name": "_csd_z_value", diff --git a/src/csd_optimade/mappers.py b/src/csd_optimade/mappers.py index 91d92c3..423a152 100644 --- a/src/csd_optimade/mappers.py +++ b/src/csd_optimade/mappers.py @@ -168,9 +168,7 @@ def from_csd_entry_directly( } } - inchi = entry.crystal.generate_inchi() - if not inchi.success: - inchi = None + inchis = entry.component_inchis structure_features = [] try: @@ -252,8 +250,8 @@ def from_csd_entry_directly( _csd_crystal_system=entry.crystal.crystal_system, _csd_space_group_symbol_hermann_mauginn=entry.crystal.spacegroup_symbol, # Need to double-check if this matches OPTIMADE 1.2 definition _csd_chemical_name=entry.chemical_name, - _csd_inchi=inchi.inchi if inchi else None, - _csd_inchi_key=inchi.key if inchi else None, + _csd_inchi=[inchi.inchi for inchi in inchis] if inchis else None, + _csd_inchi_key=[inchi.key for inchi in inchis] if inchis else None, _csd_smiles=asym_unit.smiles, _csd_z_value=entry.crystal.z_value, _csd_z_prime=entry.crystal.z_prime, From 7b60655535bfcb15bda11d44dbcce21c8be68302 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Thu, 27 Mar 2025 09:58:38 +0000 Subject: [PATCH 02/10] Add debug logging per chunk --- src/csd_optimade/ingest.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/csd_optimade/ingest.py b/src/csd_optimade/ingest.py index 68949a2..8efde72 100644 --- a/src/csd_optimade/ingest.py +++ b/src/csd_optimade/ingest.py @@ -15,6 +15,7 @@ import glob import itertools import json +import logging import math import os import tempfile @@ -39,6 +40,8 @@ from csd_optimade.mappers import from_csd_entry_directly +logging.basicConfig() + def from_csd_database( reader: ccdc.io.EntryReader, @@ -69,7 +72,8 @@ def handle_chunk(args, run_name: str = "test", num_chunks: int | None = None): bad_count: int = 0 total_count: int = 0 str_chunk_id = f"{chunk_id:0{len(str(num_chunks))}d}" - with open(f"data/{run_name}-optimade-{str_chunk_id}.jsonl", "w") as f: + chunk_path = Path(f"data/{run_name}-optimade-{str_chunk_id}.jsonl") + with open(chunk_path, "w") as f: try: for entry in from_csd_database(ccdc.io.EntryReader("CSD"), range_): total_count += 1 @@ -84,6 +88,8 @@ def handle_chunk(args, run_name: str = "test", num_chunks: int | None = None): if total_count == 0 and bad_count != 0: raise RuntimeError("No good entries found in chunk; something went wrong.") + logging.info("Wrote chunk % to %", chunk_id, chunk_path) + return chunk_id, total_count, bad_count @@ -178,7 +184,7 @@ def cli(): output_file = output_dir / f"{run_name}-optimade.jsonl" tmp_dir = tempfile.TemporaryDirectory() tmp_jsonl_path = Path(tmp_dir.name) / output_file.name - print(f"Collecting results into {output_file}") + logging.info(f"Collecting results into {output_file}") pattern = f"{run_name}-optimade-*.jsonl" input_files = sorted( From 44cd4ac3c4959937c717b940d2349e34c285a27d Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Thu, 27 Mar 2025 12:06:31 +0000 Subject: [PATCH 03/10] Force use of /tmp --- src/csd_optimade/ingest.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/csd_optimade/ingest.py b/src/csd_optimade/ingest.py index 8efde72..306b99c 100644 --- a/src/csd_optimade/ingest.py +++ b/src/csd_optimade/ingest.py @@ -18,7 +18,6 @@ import logging import math import os -import tempfile import time import warnings from functools import partial @@ -40,7 +39,9 @@ from csd_optimade.mappers import from_csd_entry_directly -logging.basicConfig() +LOG = logging.getLogger(__name__) +LOG.handlers = [logging.StreamHandler()] +LOG.setLevel(logging.INFO) def from_csd_database( @@ -88,7 +89,7 @@ def handle_chunk(args, run_name: str = "test", num_chunks: int | None = None): if total_count == 0 and bad_count != 0: raise RuntimeError("No good entries found in chunk; something went wrong.") - logging.info("Wrote chunk % to %", chunk_id, chunk_path) + LOG.info("Wrote chunk % to %", chunk_id, chunk_path) return chunk_id, total_count, bad_count @@ -182,9 +183,9 @@ def cli(): # Combine all results into a single JSONL file, first temporary output_dir = Path("data") output_file = output_dir / f"{run_name}-optimade.jsonl" - tmp_dir = tempfile.TemporaryDirectory() - tmp_jsonl_path = Path(tmp_dir.name) / output_file.name - logging.info(f"Collecting results into {output_file}") + tmp_dir = "/tmp/csd-optimade" + tmp_jsonl_path = Path(tmp_dir) / output_file.name + LOG.info(f"Collecting results into {output_file}") pattern = f"{run_name}-optimade-*.jsonl" input_files = sorted( @@ -251,7 +252,7 @@ def cli(): ids_by_type[_type].add(json_entry["id"]) final_jsonl.write(line_entry) - tmp_dir.cleanup() + Path(tmp_dir).rmdir() # Final scan to remove duplicates an empty lines print( From 8ee6c2f3f85f7693aa5f58045f2e606304bf4e02 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Thu, 27 Mar 2025 13:47:59 +0000 Subject: [PATCH 04/10] Make tmp if missing --- src/csd_optimade/ingest.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/csd_optimade/ingest.py b/src/csd_optimade/ingest.py index 306b99c..ef1ba2c 100644 --- a/src/csd_optimade/ingest.py +++ b/src/csd_optimade/ingest.py @@ -183,8 +183,9 @@ def cli(): # Combine all results into a single JSONL file, first temporary output_dir = Path("data") output_file = output_dir / f"{run_name}-optimade.jsonl" - tmp_dir = "/tmp/csd-optimade" - tmp_jsonl_path = Path(tmp_dir) / output_file.name + tmp_dir = Path("/tmp/csd-optimade") + tmp_dir.mkdir(exist_ok=True, parents=True) + tmp_jsonl_path = tmp_dir / output_file.name LOG.info(f"Collecting results into {output_file}") pattern = f"{run_name}-optimade-*.jsonl" @@ -252,7 +253,7 @@ def cli(): ids_by_type[_type].add(json_entry["id"]) final_jsonl.write(line_entry) - Path(tmp_dir).rmdir() + tmp_dir.rmdir() # Final scan to remove duplicates an empty lines print( From 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Path("data") output_file = output_dir / f"{run_name}-optimade.jsonl" - tmp_dir = Path("/tmp/csd-optimade") + tmp_dir = Path(f"/tmp/csd-optimade/{run_name}") tmp_dir.mkdir(exist_ok=True, parents=True) tmp_jsonl_path = tmp_dir / output_file.name LOG.info(f"Collecting results into {output_file}") @@ -253,7 +253,12 @@ def cli(): ids_by_type[_type].add(json_entry["id"]) final_jsonl.write(line_entry) - tmp_dir.rmdir() + # Remove the temporary directory + try: + tmp_jsonl_path.unlink() + tmp_dir.rmdir() + except OSError: + raise OSError(f"Dir entries: {os.listdir(tmp_dir)}") # Final scan to remove duplicates an empty lines print( From 448926b4148f5934beb96daaf695a678def5cefa Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Sun, 12 Oct 2025 14:20:15 +0100 Subject: [PATCH 08/10] Rename output JSONL file to `optimade.jsonl` and support mock backend from Docker --- Dockerfile | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 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| gunzip > /opt/csd-optimade/csd-optimade.jsonl; - exec uv run --no-sync csd-serve --port 5001 --exit-after-insert --drop-first /opt/csd-optimade/csd-optimade.jsonl) & + (gpg --batch --passphrase ${CSD_ACTIVATION_KEY} --decrypt /opt/csd-optimade/csd-optimade.jsonl.gz.gpg | gunzip > /opt/csd-optimade/optimade.jsonl; + exec uv run --no-sync csd-serve --port 5001 --exit-after-insert --drop-first /opt/csd-optimade/optimade.jsonl) & fi -# Run CLI with 'fake' file -touch /tmp/csd-optimade.jsonl -exec uv run --no-sync csd-serve --no-insert /tmp/csd-optimade.jsonl +if [ "$OPTIMAKE_DATABASE_BACKEND" = "mongomock" ]; then + gpg --batch --passphrase ${CSD_ACTIVATION_KEY} --decrypt /opt/csd-optimade/csd-optimade.jsonl.gz.gpg | gunzip > /opt/csd-optimade/optimade.jsonl + echo "File size" + du -sh /opt/csd-optimade/optimade.jsonl + echo "Number of lines" + wc -l /opt/csd-optimade/optimade.jsonl + exec uv run --no-sync csd-serve --port 5001 /opt/csd-optimade/optimade.jsonl +else + # Run CLI with 'fake' file + touch /tmp/optimade.jsonl + exec uv run --no-sync csd-serve --no-insert /tmp/optimade.jsonl +fi EOF From 5705268886c11d81cfc0084d960f061b37d94568 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Sun, 12 Oct 2025 14:47:07 +0100 Subject: [PATCH 09/10] Add a dev server build that does not write to cache by default and can trigger reingestion --- docker-bake.hcl | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/docker-bake.hcl b/docker-bake.hcl index 798eef9..8521848 100644 --- a/docker-bake.hcl +++ b/docker-bake.hcl @@ -1,5 +1,5 @@ variable "CI" { - // Set to true if running in a CI environment; this affects how secrets are mounted + // Set to true if running in a CI environment; this affects how caching is handled default = false } @@ -13,6 +13,11 @@ variable "VERSION" { default = "latest" } +variable "CSD_REINGEST" { + // Whether to reingest the CSD data even if it already exists in the image + default = "false" +} + variable "CSD_NUM_STRUCTURES" { // Number of structures to ingest (default: all) default = "" @@ -51,11 +56,26 @@ target "csd-ingester-test" { secret = ["type=env,id=csd-activation-key,env=CSD_ACTIVATION_KEY", "id=csd-installer-url,env=CSD_INSTALLER_URL"] } +target "csd-optimade-dev" { + inherits = ["docker-metadata-action"] + context = "." + dockerfile = "Dockerfile" + args = {CSD_NUM_STRUCTURES = CSD_NUM_STRUCTURES, REINGEST = CSD_REINGEST} + target = "csd-optimade-server" + tags = ["${IMAGE_BASE}-dev:${VERSION}"] + cache-from = [ + "type=registry,ref=${IMAGE_BASE}:${VERSION}", + "type=registry,ref=${IMAGE_BASE}:cache", + ] + cache-to = [] + secret = ["type=env,id=csd-activation-key,env=CSD_ACTIVATION_KEY", "id=csd-installer-url,env=CSD_INSTALLER_URL"] +} + target "csd-optimade-server" { inherits = ["docker-metadata-action"] context = "." dockerfile = "Dockerfile" - args = {CSD_NUM_STRUCTURES = CSD_NUM_STRUCTURES} + args = {CSD_NUM_STRUCTURES = CSD_NUM_STRUCTURES, REINGEST = CSD_REINGEST} 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