diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml index ec1bc81..eedb345 100644 --- a/.github/workflows/deploy-docs.yaml +++ b/.github/workflows/deploy-docs.yaml @@ -15,23 +15,22 @@ jobs: id-token: write # to verify the deployment originates from an appropriate source steps: - - name: Checkout - uses: actions/checkout@v4 + - uses: actions/checkout@v4 with: - fetch-depth: 0 # otherwise, you will failed to push refs to dest repo + fetch-depth: 0 # otherwise, it will fail to push refs to dest repo - - name: Set up Python. - uses: actions/setup-python@v4 - with: - python-version: 3.9 - - - name: Install Poetry. + - name: Install Poetry run: pipx install poetry - - name: Install dependencies. - run: poetry install -E docs + - uses: actions/setup-python@v5 + with: + python-version: '3.12' + cache: 'poetry' + + - name: Install dependencies + run: poetry install - - name: Build documentation. + - name: Build documentation run: | mkdir -p docs touch docs/.nojekyll diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index d5332e8..9a3e511 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -11,26 +11,21 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10"] + python-version: ["3.9", "3.12"] steps: + - uses: actions/checkout@v4 - - name: Check out repository - uses: actions/checkout@v3 + - name: Install Poetry + run: pipx install poetry - - name: Set up Python - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - - name: Install Poetry - run: pipx install poetry + cache: 'poetry' - name: Install dependencies - run: poetry install --no-interaction --no-root - - - name: Install project - run: poetry install --no-interaction + run: poetry install - name: Run test suite run: make test diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml index 22d5a69..7a23432 100644 --- a/.github/workflows/pypi-publish.yaml +++ b/.github/workflows/pypi-publish.yaml @@ -9,28 +9,37 @@ jobs: build-n-publish: name: Build and publish Python 🐍 distributions 📦 to PyPI runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/gocam + permissions: + # this permission is mandatory for trusted publishing + id-token: write steps: - - uses: actions/checkout@v3 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: 3.9 + - uses: actions/checkout@v4 - name: Install Poetry run: | pipx install poetry - poetry self add "poetry-dynamic-versioning[plugin]" + pipx inject poetry "poetry-dynamic-versioning[plugin]" + + - uses: actions/setup-python@v5 + with: + python-version: '3.12' + cache: 'poetry' - # - name: Install dependencies - # run: poetry install --no-interaction + - name: Install dependencies + run: poetry install + + - name: Generate project files + run: make clean all + + - name: Test project + run: make test - name: Build source and wheel archives run: poetry build - name: Publish distribution 📦 to PyPI - uses: pypa/gh-action-pypi-publish@v1.2.2 - with: - user: __token__ - password: ${{ secrets.PYPI_PASSWORD }} + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/test_pages_build.yaml b/.github/workflows/test_pages_build.yaml index 0a2ccd0..b1f0119 100644 --- a/.github/workflows/test_pages_build.yaml +++ b/.github/workflows/test_pages_build.yaml @@ -13,21 +13,20 @@ jobs: run: runs-on: ubuntu-latest steps: - - name: Checkout - uses: actions/checkout@v4 + - uses: actions/checkout@v4 with: fetch-depth: 0 - - name: Set up Python 3 - uses: actions/setup-python@v4 - with: - python-version: 3.9 - - name: Install Poetry run: pipx install poetry + - uses: actions/setup-python@v5 + with: + python-version: '3.12' + cache: 'poetry' + - name: Install dependencies - run: poetry install -E docs + run: poetry install - name: Build documentation run: | diff --git a/Makefile b/Makefile index 957f9ea..1549bb0 100644 --- a/Makefile +++ b/Makefile @@ -105,7 +105,7 @@ create-data-harmonizer: npm init data-harmonizer $(SOURCE_SCHEMA_PATH) all: site -site: gen-project gendoc +site: gen-project gendoc $(PYDANTIC) %.yaml: gen-project deploy: all mkd-gh-deploy @@ -143,7 +143,7 @@ test-schema: $(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH) test-python: - $(RUN) python -m unittest discover + $(RUN) pytest tests lint: $(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) @@ -219,6 +219,6 @@ clean: rm -rf $(DEST) rm -rf tmp rm -fr docs/* - rm -fr $(PYMODEL)/* + rm -fr $(PYDANTIC) include project.Makefile diff --git a/poetry.lock b/poetry.lock index 8d8005a..df78108 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,20 +1,5 @@ # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. -[[package]] -name = "airium" -version = "0.2.6" -description = "Easy and quick html builder with natural syntax correspondence (python->html). 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a/pyproject.toml b/pyproject.toml index e25f7b7..b45f2ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,35 +1,43 @@ [tool.poetry] name = "gocam" -version = "0.1.0" +version = "0.0.0" description = "GO CAM Data Model (Python)" -authors = ["My Name "] +authors = ["The Gene Ontology Consortium "] license = "BSD-3" readme = "README.md" include = ["README.md", "src/gocam/schema", "project"] [tool.poetry.dependencies] python = "^3.9" +click = "^8" linkml-runtime = "^1.1.24" -oaklib = "^0.6.10" +pydantic = "^2" +pyyaml = "^6" +requests = "^2" -[tool.poetry-dynamic-versioning] -enable = true -vcs = "git" -style = "pep440" - -[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] linkml = "^1.3.5" mkdocs-material = "^8.2.8" mkdocs-mermaid2-plugin = ">=1.1.1" schemasheets = "^0.1.14" +[tool.poetry.group.test.dependencies] +pytest = "^8.2.2" +requests-mock = "^1.12.1" + +[tool.poetry-dynamic-versioning] +enable = true +vcs = "git" +style = "pep440" + [build-system] requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] build-backend = "poetry_dynamic_versioning.backend" -[tool.poetry.extras] -docs = ["linkml", "mkdocs-material"] - [tool.poetry.scripts] gocam = "gocam.cli:cli" +[tool.pytest.ini_options] +markers = [ + "integration" +] diff --git a/src/gocam/__init__.py b/src/gocam/__init__.py new file mode 100644 index 0000000..651774b --- /dev/null +++ b/src/gocam/__init__.py @@ -0,0 +1 @@ +from gocam._version import __version__ diff --git a/src/gocam/_version.py b/src/gocam/_version.py index 7edc9ee..fe5022e 100644 --- a/src/gocam/_version.py +++ b/src/gocam/_version.py @@ -1,7 +1,7 @@ from importlib.metadata import version, PackageNotFoundError try: - __version__ = version(__name__) + __version__ = version(__package__) except PackageNotFoundError: # package not installed __version__ = "0.0.0" diff --git a/src/gocam/cli.py b/src/gocam/cli.py index 5f7a654..a7b7985 100644 --- a/src/gocam/cli.py +++ b/src/gocam/cli.py @@ -1,36 +1,12 @@ import json import logging import sys -import warnings -from typing import Optional import click import yaml -from linkml_runtime.dumpers import json_dumper -from pydantic import BaseModel -from gocam.translation.minerva_wrapper import MinervaWrapper - -index_type_option = click.option( - "--index-type", - "-t", - default="simple", - show_default=True, - help="Type of index to create. Values: simple, llm", -) - -logger = logging.getLogger(__name__) - -warnings.filterwarnings("ignore", module="duckdb_engine") - -def get_wrapper(): - return MinervaWrapper() - - -format_choice = click.Choice(["json", "yaml", "tsv"]) - - -include_internal_option = click.option("--include-internal/--no-include-internal", default=False, show_default=True) +from gocam import __version__ +from gocam.translation import MinervaWrapper @click.group() @@ -42,15 +18,18 @@ def get_wrapper(): show_default=True, help="If set then show full stacktrace on error", ) -@click.pass_context -def cli(ctx, verbose: int, quiet: bool, stacktrace: bool): - """A CLI for interacting with the linkml-store.""" +@click.version_option(__version__) +def cli(verbose: int, quiet: bool, stacktrace: bool): + """A CLI for interacting with GO-CAMs.""" if not stacktrace: sys.tracebacklimit = 0 + logger = logging.getLogger() # Set handler for the root logger to output to the console console_handler = logging.StreamHandler() - console_handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")) + console_handler.setFormatter( + logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") + ) # Clear existing handlers to avoid duplicate messages if function runs multiple times logger.handlers = [] @@ -68,22 +47,31 @@ def cli(ctx, verbose: int, quiet: bool, stacktrace: bool): @cli.command() -@click.option("--format", "-f", type=format_choice, help="Input format") +@click.option( + "--format", + "-f", + type=click.Choice(["json", "yaml"]), + default="yaml", + show_default=True, + help="Input format", +) @click.argument("model_ids", nargs=-1) def fetch(model_ids, format): - wrapper = get_wrapper() + """Fetch GO-CAM models.""" + wrapper = MinervaWrapper() + if not model_ids: model_ids = wrapper.models_ids() + for model_id in model_ids: - model = wrapper.object_by_id(model_id) + model = wrapper.fetch_model(model_id) model_dict = model.model_dump(exclude_none=True, exclude_unset=True) - if format is None: - format = "yaml" + if format == "json": - print(json.dumps(model_dict, indent=2)) + click.echo(json.dumps(model_dict, indent=2)) elif format == "yaml": - print("---") - print(yaml.dump(model_dict, sort_keys=False)) + click.echo("---") + click.echo(yaml.dump(model_dict, sort_keys=False)) else: click.echo(model.model_dump()) diff --git a/src/gocam/datamodel/__init__.py b/src/gocam/datamodel/__init__.py index c1b179c..104cdc8 100644 --- a/src/gocam/datamodel/__init__.py +++ b/src/gocam/datamodel/__init__.py @@ -1,5 +1,5 @@ from pathlib import Path -from .gocam import * +from gocam.datamodel.gocam import * THIS_PATH = Path(__file__).parent diff --git a/src/gocam/datamodel/gocam.py.old b/src/gocam/datamodel/gocam.py.old deleted file mode 100644 index 54fab54..0000000 --- a/src/gocam/datamodel/gocam.py.old +++ /dev/null @@ -1,345 +0,0 @@ -from __future__ import annotations -from datetime import ( - datetime, - date -) -from decimal import Decimal -from enum import Enum -import re -import sys -from typing import ( - Any, - List, - Literal, - Dict, - Optional, - Union -) -from pydantic.version import VERSION as PYDANTIC_VERSION -if int(PYDANTIC_VERSION[0])>=2: - from pydantic import ( - BaseModel, - ConfigDict, - Field, - field_validator - ) -else: - from pydantic import ( - BaseModel, - Field, - validator - ) - -metamodel_version = "None" -version = "None" - - -class ConfiguredBaseModel(BaseModel): - model_config = ConfigDict( - validate_assignment = True, - validate_default = True, - extra = "forbid", - arbitrary_types_allowed = True, - use_enum_values = True, - strict = False, - ) - pass - - -class ModelStateEnum(str, Enum): - """ - Status of a model - """ - production = "production" - development = "development" - - -class InformationBiomacromoleculeCategory(str, Enum): - GeneOrReferenceProtein = "GeneOrReferenceProtein" - ProteinIsoform = "ProteinIsoform" - MacromolecularComplex = "MacromolecularComplex" - Unknown = "Unknown" - - -class CausalPredicateEnum(str, Enum): - causally_upstream_of_positive_effect = "causally upstream of, positive effect" - causally_upstream_of_negative_effect = "causally upstream of, negative effect" - causally_upstream_of = "causally upstream of" - immediately_causally_upstream_of = "immediately causally upstream of" - causally_upstream_of_or_within = "causally upstream of or within" - causally_upstream_of_or_within_negative_effect = "causally upstream of or within, negative effect" - causally_upstream_of_or_within_positive_effect = "causally upstream of or within, positive effect" - regulates = "regulates" - negatively_regulates = "negatively regulates" - positively_regulates = "positively regulates" - - -class Model(ConfiguredBaseModel): - """ - A model of a biological program consisting of a set of causally connected activities - """ - title: Optional[str] = Field(None) - status: Optional[ModelStateEnum] = Field(None) - objects: Optional[List[Union[Object,TermObject,PublicationObject,EvidenceTermObject,MolecularFunctionTermObject,BiologicalProcessTermObject,CellularAnatomicalEntityTermObject,MoleculeTermObject,CellTypeTermObject,GrossAnatomicalStructureTermObject,PhaseTermObject,InformationBiomacromoleculeTermObject,GeneProductTermObject,ProteinComplexTermObject]]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class Activity(ConfiguredBaseModel): - """ - An individual activity in a causal model, representing the individual molecular activity of a single gene product or complex - """ - enabled_by: Optional[Union[InformationBiomacromoleculeTermObject,GeneProductTermObject,ProteinComplexTermObject]] = Field(None, description="""The gene product or complex that carries out the activity""") - molecular_function: Optional[MolecularFunctionAssociation] = Field(None, description="""The molecular function that is carried out by the gene product or complex""") - occurs_in: Optional[CellularAnatomicalEntityAssociation] = Field(None, description="""The cellular location in which the activity occurs""") - part_of: Optional[BiologicalProcessAssociation] = Field(None, description="""The larger biological process in which the activity is a part""") - has_direct_input: Optional[MoleculeAssociation] = Field(None, description="""The input molecules that are directly consumed by the activity""") - causal_associations: Optional[CausalAssociation] = Field(None, description="""The causal associations that connect this activity to other activities""") - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list, description="""Provenance information for the activity""") - - -class Association(ConfiguredBaseModel): - """ - An abstract grouping for different kinds of evidence-associated provenance - """ - type: Literal["Association"] = Field("Association") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class CausalAssociation(Association): - """ - A causal association between two activities - """ - predicate: Optional[CausalPredicateEnum] = Field(None) - type: Literal["CausalAssociation"] = Field("CausalAssociation") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class TermAssociation(Association): - """ - An association between an activity and a term, potentially with extensions - """ - term: Optional[str] = Field(None) - type: Literal["TermAssociation"] = Field("TermAssociation") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class MolecularFunctionAssociation(TermAssociation): - """ - An association between an activity and a molecular function term - """ - term: Optional[str] = Field(None) - type: Literal["MolecularFunctionAssociation"] = Field("MolecularFunctionAssociation") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class BiologicalProcessAssociation(TermAssociation): - """ - An association between an activity and a biological process term - """ - term: Optional[str] = Field(None) - type: Literal["BiologicalProcessAssociation"] = Field("BiologicalProcessAssociation") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class CellularAnatomicalEntityAssociation(TermAssociation): - """ - An association between an activity and a cellular anatomical entity term - """ - term: Optional[str] = Field(None) - type: Literal["CellularAnatomicalEntityAssociation"] = Field("CellularAnatomicalEntityAssociation") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class MoleculeAssociation(TermAssociation): - """ - An association between an activity and a molecule term - """ - term: Optional[str] = Field(None) - type: Literal["MoleculeAssociation"] = Field("MoleculeAssociation") - evidence: Optional[str] = Field(None) - reference: Optional[str] = Field(None) - with_objects: Optional[List[str]] = Field(default_factory=list) - provenances: Optional[List[ProvenanceInfo]] = Field(default_factory=list) - - -class Object(ConfiguredBaseModel): - """ - An abstract class for all identified objects in a model - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/Object","gocam:Object"] = Field("gocam:Object") - - -class TermObject(Object): - """ - An abstract class for all ontology term objects - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/TermObject","gocam:TermObject"] = Field("gocam:TermObject") - - -class PublicationObject(Object): - """ - An object that represents a publication or other kind of reference - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/PublicationObject","gocam:PublicationObject"] = Field("gocam:PublicationObject") - - -class EvidenceTermObject(TermObject): - """ - A term object that represents an evidence term from ECO - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/EvidenceTermObject","gocam:EvidenceTermObject"] = Field("gocam:EvidenceTermObject") - - -class MolecularFunctionTermObject(TermObject): - """ - A term object that represents a molecular function term from GO - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/MolecularFunctionTermObject","gocam:MolecularFunctionTermObject"] = Field("gocam:MolecularFunctionTermObject") - - -class BiologicalProcessTermObject(TermObject): - """ - A termm object that represents a biological process term from GO - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/BiologicalProcessTermObject","gocam:BiologicalProcessTermObject"] = Field("gocam:BiologicalProcessTermObject") - - -class CellularAnatomicalEntityTermObject(TermObject): - """ - A term object that represents a cellular anatomical entity term from GO - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/CellularAnatomicalEntityTermObject","gocam:CellularAnatomicalEntityTermObject"] = Field("gocam:CellularAnatomicalEntityTermObject") - - -class MoleculeTermObject(TermObject): - """ - A term object that represents a molecule term from CHEBI or UniProtKB - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/MoleculeTermObject","gocam:MoleculeTermObject"] = Field("gocam:MoleculeTermObject") - - -class CellTypeTermObject(TermObject): - """ - A term object that represents a cell type term from CL - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/CellTypeTermObject","gocam:CellTypeTermObject"] = Field("gocam:CellTypeTermObject") - - -class GrossAnatomicalStructureTermObject(TermObject): - """ - A term object that represents a gross anatomical structure term from UBERON - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/GrossAnatomicalStructureTermObject","gocam:GrossAnatomicalStructureTermObject"] = Field("gocam:GrossAnatomicalStructureTermObject") - - -class PhaseTermObject(TermObject): - """ - A term object that represents a phase term from GO or UBERON - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/PhaseTermObject","gocam:PhaseTermObject"] = Field("gocam:PhaseTermObject") - - -class InformationBiomacromoleculeTermObject(TermObject): - """ - An abstract class for all information biomacromolecule term objects - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/InformationBiomacromoleculeTermObject","gocam:InformationBiomacromoleculeTermObject"] = Field("gocam:InformationBiomacromoleculeTermObject") - - -class GeneProductTermObject(InformationBiomacromoleculeTermObject): - """ - A term object that represents a gene product term from GO or UniProtKB - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/GeneProductTermObject","gocam:GeneProductTermObject"] = Field("gocam:GeneProductTermObject") - - -class ProteinComplexTermObject(InformationBiomacromoleculeTermObject): - """ - A term object that represents a protein complex term from GO - """ - id: str = Field(...) - label: Optional[str] = Field(None) - type: Literal["https://w3id.org/gocam/ProteinComplexTermObject","gocam:ProteinComplexTermObject"] = Field("gocam:ProteinComplexTermObject") - - -class ProvenanceInfo(ConfiguredBaseModel): - """ - Provenance information for an object - """ - contributor: Optional[str] = Field(None) - created: Optional[str] = Field(None) - date: Optional[str] = Field(None) - provided_by: Optional[str] = Field(None) - - -# Model rebuild -# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model -Model.model_rebuild() -Activity.model_rebuild() -Association.model_rebuild() -CausalAssociation.model_rebuild() -TermAssociation.model_rebuild() -MolecularFunctionAssociation.model_rebuild() -BiologicalProcessAssociation.model_rebuild() -CellularAnatomicalEntityAssociation.model_rebuild() -MoleculeAssociation.model_rebuild() -Object.model_rebuild() -TermObject.model_rebuild() -PublicationObject.model_rebuild() -EvidenceTermObject.model_rebuild() -MolecularFunctionTermObject.model_rebuild() -BiologicalProcessTermObject.model_rebuild() -CellularAnatomicalEntityTermObject.model_rebuild() -MoleculeTermObject.model_rebuild() -CellTypeTermObject.model_rebuild() -GrossAnatomicalStructureTermObject.model_rebuild() -PhaseTermObject.model_rebuild() -InformationBiomacromoleculeTermObject.model_rebuild() -GeneProductTermObject.model_rebuild() -ProteinComplexTermObject.model_rebuild() -ProvenanceInfo.model_rebuild() - diff --git a/src/gocam/translation/__init__.py b/src/gocam/translation/__init__.py index e69de29..fb2b2d0 100644 --- a/src/gocam/translation/__init__.py +++ b/src/gocam/translation/__init__.py @@ -0,0 +1 @@ +from gocam.translation.minerva_wrapper import MinervaWrapper diff --git a/src/gocam/translation/minerva_wrapper.py b/src/gocam/translation/minerva_wrapper.py index ea6d65a..4e682a1 100644 --- a/src/gocam/translation/minerva_wrapper.py +++ b/src/gocam/translation/minerva_wrapper.py @@ -1,18 +1,22 @@ import logging from collections import defaultdict from dataclasses import dataclass, field -from typing import ClassVar, Dict, Iterable, Iterator, Optional, Tuple, List +from typing import Dict, Iterator, Optional, List, DefaultDict import requests -import requests_cache import yaml -from oaklib import BasicOntologyInterface, get_adapter -from gocam.datamodel import Model, Activity, MolecularFunctionAssociation, BiologicalProcessAssociation, \ - CellularAnatomicalEntityAssociation, CausalAssociation, Object, EvidenceItem, ProvenanceInfo - -INDEX_URL = "https://go-public.s3.amazonaws.com/files/gocam-models.json" -GOCAM_ENDPOINT = "https://api.geneontology.org/api/go-cam/" +from gocam.datamodel import ( + Model, + Activity, + MolecularFunctionAssociation, + BiologicalProcessAssociation, + CellularAnatomicalEntityAssociation, + CausalAssociation, + Object, + EvidenceItem, + ProvenanceInfo, +) ENABLED_BY = "RO:0002333" PART_OF = "BFO:0000050" @@ -31,7 +35,8 @@ def _normalize_property(prop: str) -> str: return prop.split("/")[-1] return prop -def _annotations(obj: Dict) -> Dict: + +def _annotations(obj: Dict) -> Dict[str, str]: """ Extract annotations from an object (assumes single-valued). @@ -39,7 +44,8 @@ def _annotations(obj: Dict) -> Dict: """ return {_normalize_property(a["key"]): a["value"] for a in obj["annotations"]} -def _annotations_multivalued(obj: Dict) -> Dict: + +def _annotations_multivalued(obj: Dict) -> Dict[str, List[str]]: """ Extract annotations from an object (assumes multi-valued). @@ -50,6 +56,7 @@ def _annotations_multivalued(obj: Dict) -> Dict: anns[a["key"]].append(a["value"]) return anns + MAIN_TYPES = [ "molecular_function", "biological_process", @@ -60,16 +67,6 @@ def _annotations_multivalued(obj: Dict) -> Dict: "anatomical entity", ] -TYPE_MAPPING = { - "molecular_function": "MolecularFunctionTermObject", - "biological_process": "BiologicalProcessTermObject", - "cellular_component": "CellularComponentTermObject", - "information biomacromolecule": "InformationBiomacromoleculeTermObject", - "evidence": "EvidenceTermObject", - "chemical entity": "ChemicalEntityTermObject", - "anatomical entity": "AnatomicalEntityTermObject", -} - @dataclass class MinervaWrapper: @@ -79,77 +76,92 @@ class MinervaWrapper: TODO: Implement a fact counter to ensure all facts are encountered for and nothing dropped on floor """ - name: ClassVar[str] = "gocam" + session: requests.Session = field(default_factory=lambda: requests.Session()) + gocam_index_url: str = "https://go-public.s3.amazonaws.com/files/gocam-models.json" + gocam_endpoint_base: str = "https://api.geneontology.org/api/go-cam/" - default_object_type = "Activity" + def models(self) -> Iterator[Model]: + """Iterator over all GO-CAM models from the index. - _label_adapter: BasicOntologyInterface = None + This method fetches the list of all GO-CAM models from the index URL. For each model, the + Minerva JSON object is fetched and converted to a Model object. - session: requests.Session = field(default_factory=lambda: requests.Session()) + :return: Iterator over GO-CAM models + :rtype: Iterator[Model] + """ + for gocam_id in self.models_ids(): + yield self.fetch_model(gocam_id) - def models( - self, **kwargs - ) -> Iterator[Model]: - """ - Fetch all models from the API. + def models_ids(self) -> Iterator[str]: + """Iterator over all GO-CAM IDs from the index. + + This method fetches the list of all GO-CAM models from the index URL and returns an + iterator over the IDs of each model. - :param kwargs: - :return: + :return: Iterator over GO-CAM IDs + :rtype: Iterator[str] """ - models = requests.get(INDEX_URL).json() - for model in models: - if "gocam" not in model: - raise ValueError(f"Missing gocam in {model}") - gocam = model["gocam"] - yield self.object_by_id(gocam.replace("http://model.geneontology.org/", "")) - - def models_ids( - self, **kwargs - ) -> Iterator[Model]: - models = requests.get(INDEX_URL).json() - for model in models: - if "gocam" not in model: + response = self.session.get(self.gocam_index_url) + response.raise_for_status() + for model in response.json(): + gocam = model.get("gocam") + if gocam is None: raise ValueError(f"Missing gocam in {model}") - gocam = model["gocam"] yield gocam.replace("http://model.geneontology.org/", "") + def fetch_minerva_object(self, gocam_id: str) -> Dict: + """Fetch a Minerva JSON object for a given GO-CAM ID. - def internal_object_by_id(self, object_id: str) -> Optional[Dict]: - session = self.session - if not object_id: - raise ValueError(f"Missing object ID: {object_id}") - logger.info(f"Fetch object: {object_id}") - # response = session.get(MODEL_URL_TEMPLATE.format(model_id=object_id)) - local_id = object_id.replace("gocam:", "") - response = session.get(f"{GOCAM_ENDPOINT}/{local_id}") - response.raise_for_status() - obj = response.json() - return obj - - def object_by_id(self, object_id: str) -> Optional[Model]: - session = self.session - if not object_id: - raise ValueError(f"Missing object ID: {object_id}") - logger.info(f"Fetch object: {object_id}") - local_id = object_id.replace("gocam:", "") - response = session.get(f"{GOCAM_ENDPOINT}/{local_id}") + :param gocam_id: GO-CAM ID + :type gocam_id: str + :return: Minerva JSON object + :rtype: Dict + """ + if not gocam_id: + raise ValueError(f"Missing GO-CAM ID: {gocam_id}") + local_id = gocam_id.replace("gocam:", "") + url = f"{self.gocam_endpoint_base}{local_id}" + logger.info(f"Fetch Minerva JSON from: {url}") + response = self.session.get(url) response.raise_for_status() - obj = response.json() - return self.object_from_dict(obj) + return response.json() + + def fetch_model(self, gocam_id: str) -> Model: + """Fetch a GO-CAM Model for a given GO-CAM ID. - def object_from_dict(self, obj: Dict) -> Optional[Model]: + :param gocam_id: GO-CAM ID + :type gocam_id: str + :return: GO-CAM Model + :rtype: Model + """ + minerva_object = self.fetch_minerva_object(gocam_id) + return self.minerva_object_to_model(minerva_object) + + @staticmethod + def minerva_object_to_model(obj: Dict) -> Model: + """Convert a Minerva JSON object to a GO-CAM Model. + + :param obj: Minerva JSON object + :type obj: Dict + :return: GO-CAM Model + :rtype: Model + """ id = obj["id"] logger.info(f"Processing model id: {id}") logger.debug(f"Model: {yaml.dump(obj)}") - individuals = obj["individuals"] - individual_to_type = {} # individual ID to "root" type / category, e.g Evidence, BP, .. - individual_to_term = {} - individual_to_annotations = {} - sources = set() - id2obj = {} + # Bookkeeping variables + + # individual ID to "root" type / category, e.g Evidence, BP + individual_to_type: Dict[str, Optional[str]] = {} + individual_to_term: Dict[str, str] = {} + individual_to_annotations: Dict[str, Dict] = {} + id2obj: Dict[str, Dict] = {} + activities: List[Activity] = [] + activities_by_mf_id: DefaultDict[str, List[Activity]] = defaultdict(list) + facts_by_property = defaultdict(list) def _cls(obj: Dict) -> Optional[str]: if obj.get("type", None) == "complement": @@ -162,61 +174,56 @@ def _cls(obj: Dict) -> Optional[str]: id2obj[id] = obj return id - def _evidence_from_fact(fact: Dict) -> Tuple[EvidenceItem, List[ProvenanceInfo]]: + def _evidence_from_fact(fact: Dict) -> List[EvidenceItem]: anns_mv = _annotations_multivalued(fact) evidence_inst_ids = anns_mv.get("evidence", []) - evs = [] - provs = [] + evs: List[EvidenceItem] = [] for evidence_inst_id in evidence_inst_ids: - with_obj = individual_to_annotations.get(evidence_inst_id, {}).get("with", None) + evidence_inst_annotations = individual_to_annotations.get( + evidence_inst_id, {} + ) + with_obj: Optional[str] = evidence_inst_annotations.get("with", None) if with_obj: with_objs = with_obj.split(" | ") else: with_objs = None prov = ProvenanceInfo( - contributor=individual_to_annotations.get(evidence_inst_id, {}).get("contributor", None), - date=individual_to_annotations.get(evidence_inst_id, {}).get("date", None), + contributor=evidence_inst_annotations.get("contributor", None), + date=evidence_inst_annotations.get("date", None), ) ev = EvidenceItem( term=individual_to_term.get(evidence_inst_id, None), - reference=individual_to_annotations.get(evidence_inst_id, {}).get("source", None), + reference=evidence_inst_annotations.get("source", None), with_objects=with_objs, - provenances=[prov] + provenances=[prov], ) evs.append(ev) - return evs, provs + return evs - for i in individuals: - typs = [x["label"] for x in i.get("root-type", []) if x] - typ = None + for individual in obj["individuals"]: + typs = [x["label"] for x in individual.get("root-type", []) if x] + typ: Optional[str] = None for t in typs: if t in MAIN_TYPES: typ = t break if not typ: - logger.warning(f"Could not find type for {i}") + logger.warning(f"Could not find type for {individual}") continue - individual_to_type[i["id"]] = typ - terms = [_cls(x) for x in i.get("type", [])] - terms = [x for x in terms if x] + individual_to_type[individual["id"]] = typ + terms = list(filter(None, (_cls(x) for x in individual.get("type", [])))) if len(terms) > 1: - logger.warning(f"Multiple terms for {i}: {terms}") + logger.warning(f"Multiple terms for {individual}: {terms}") if not terms: - logger.warning(f"No terms for {i}") + logger.warning(f"No terms for {individual}") continue - individual_to_term[i["id"]] = terms[0] - anns = _annotations(i) - individual_to_annotations[i["id"]] = anns - if "source" in anns: - sources.add(anns["source"]) - activities = [] - relationships = [] - gene_ids = set() - process_ids = set() - activities_by_mf_id: Dict[str, Activity] = defaultdict(list) - facts_by_property = defaultdict(list) + individual_to_term[individual["id"]] = terms[0] + anns = _annotations(individual) + individual_to_annotations[individual["id"]] = anns + for fact in obj["facts"]: facts_by_property[fact["property"]].append(fact) + enabled_by_facts = facts_by_property.get(ENABLED_BY, []) if not enabled_by_facts: raise ValueError(f"Missing {ENABLED_BY} in {facts_by_property}") @@ -230,15 +237,14 @@ def _evidence_from_fact(fact: Dict) -> Tuple[EvidenceItem, List[ProvenanceInfo]] continue gene_id = individual_to_term[o] - evs, provs = _evidence_from_fact(fact) + evs = _evidence_from_fact(fact) activity = Activity( id=s, enabled_by=gene_id, - molecular_function=MolecularFunctionAssociation(term=individual_to_term[s], - provenances=provs, - evidence=evs), + molecular_function=MolecularFunctionAssociation( + term=individual_to_term[s], evidence=evs + ), ) - gene_ids.add(gene_id) activities.append(activity) activities_by_mf_id[s].append(activity) @@ -248,10 +254,10 @@ def _evidence_from_fact(fact: Dict) -> Tuple[EvidenceItem, List[ProvenanceInfo]] logger.warning(f"Missing {o} in {individual_to_term}") continue for a in activities_by_mf_id.get(s, []): - evs, _provs = _evidence_from_fact(fact) - a.part_of = BiologicalProcessAssociation(term=individual_to_term[o], - evidence=evs) - process_ids.add(individual_to_term[o]) + evs = _evidence_from_fact(fact) + a.part_of = BiologicalProcessAssociation( + term=individual_to_term[o], evidence=evs + ) for fact in facts_by_property.get(OCCURS_IN, []): s, o = fact["subject"], fact["object"] @@ -259,48 +265,43 @@ def _evidence_from_fact(fact: Dict) -> Tuple[EvidenceItem, List[ProvenanceInfo]] logger.warning(f"Missing {o} in {individual_to_term}") continue for a in activities_by_mf_id.get(s, []): - evs, _provs = _evidence_from_fact(fact) - a.occurs_in = CellularAnatomicalEntityAssociation(term=individual_to_term[o], - evidence=evs) + evs = _evidence_from_fact(fact) + a.occurs_in = CellularAnatomicalEntityAssociation( + term=individual_to_term[o], evidence=evs + ) - for p, facts in facts_by_property.items(): + for fact_property, facts in facts_by_property.items(): for fact in facts: s, o = fact["subject"], fact["object"] - sas = activities_by_mf_id.get(s, []) - oas = activities_by_mf_id.get(o, []) - if not sas or not oas: + subject_activities = activities_by_mf_id.get(s, []) + object_activities = activities_by_mf_id.get(o, []) + + if not subject_activities or not object_activities: continue if individual_to_type.get(s, None) != "molecular_function": continue if individual_to_type.get(o, None) != "molecular_function": continue - sa = sas[0] - oa = oas[0] - evs, _provs = _evidence_from_fact(fact) + if len(subject_activities) > 1: + logger.warning(f"Multiple activities for subject: {s}") + if len(object_activities) > 1: + logger.warning(f"Multiple activities for object: {o}") + + subject_activity = subject_activities[0] + object_activity = object_activities[0] + evs = _evidence_from_fact(fact) rel = CausalAssociation( - predicate=p, - downstream_activity=oa.id, + predicate=fact_property, + downstream_activity=object_activity.id, evidence=evs, ) - if not sa.causal_associations: - sa.causal_associations = [] - sa.causal_associations.append(rel) - # raise ValueError(f"{rel} in {sa}") - relationships.append(rel) - #pmids = {a.reference for a in activities if "reference" in a} - #pmids = [p for p in pmids if p and p.startswith("PMID")] - #pubs = self.pubmed_wrapper.objects_by_ids(pmids) - #pubs_by_id = {p["id"]: p for p in pubs} - #for a in activities: - # if "reference" in a: - # ref = a["reference"] - # if ref in pubs_by_id: - # a["reference_title"] = pubs_by_id[ref]["title"] + if not subject_activity.causal_associations: + subject_activity.causal_associations = [] + subject_activity.causal_associations.append(rel) + annotations = _annotations(obj) annotations_mv = _annotations_multivalued(obj) - objs = [ - Object(id=obj["id"], label=obj["label"]) for obj in id2obj.values() - ] + objs = [Object(id=obj["id"], label=obj["label"]) for obj in id2obj.values()] cam = Model( id=id, title=annotations["title"], diff --git a/src/gocam/utils/__init__.py b/src/gocam/utils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/gocam/utils/pubmed_utils.py b/src/gocam/utils/pubmed_utils.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/input/minerva-5b91dbd100002057.json b/tests/input/minerva-5b91dbd100002057.json new file mode 100644 index 0000000..2437c57 --- /dev/null +++ b/tests/input/minerva-5b91dbd100002057.json @@ -0,0 +1 @@ +{"id":"gomodel:5b91dbd100002057","individuals":[{"id":"gomodel:5b91dbd100002057/5b91dbd100002058","type":[{"type":"class","id":"WB:WBGene00010700","label":"nipi-3 Cele"}],"root-type":[{"type":"class","id":"CHEBI:33695","label":"information biomacromolecule"},{"type":"class","id":"CHEBI:24431","label":"chemical entity"}],"annotations":[{"key":"contributor","value":"https://orcid.org/0000-0002-3013-9906"},{"key":"date","value":"2018-12-18"},{"key":"providedBy","value":"http://www.wormbase.org"}]},{"id":"gomodel:5b91dbd100002057/5b91dbd100002059","type":[{"type":"class","id":"GO:0031434","label":"mitogen-activated protein kinase kinase binding"}],"root-type":[{"type":"class","id":"GO:0003674","label":"molecular_function"},{"type":"class","id":"obo:go/extensions/reacto.owl#molecular_event","label":"Molecular Event"}],"annotations":[{"key":"hint-layout-y","value":"146"},{"key":"date","value":"2019-05-17"},{"key":"contributor","value":"https://orcid.org/0000-0002-3013-9906"},{"key":"hint-layout-x","value":"345"},{"key":"providedBy","value":"http://www.wormbase.org"}]},{"id":"gomodel:5b91dbd100002057/5b91dbd100002061","type":[{"type":"class","id":"ECO:0000318","label":"biological aspect of ancestor evidence used in manual 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innate immune response in the hypodermis via MAPK cascade (C. elegans)"},{"key":"providedBy","value":"http://www.wormbase.org"},{"key":"http://www.geneontology.org/formats/oboInOwl#id","value":"gomodel:5b91dbd100002057"},{"key":"https://w3id.org/biolink/vocab/in_taxon","value":"NCBITaxon:6239","value-type":"IRI"}]} \ No newline at end of file diff --git a/tests/input/minerva-example.json b/tests/input/minerva-663d668500002178.json similarity index 100% rename from tests/input/minerva-example.json rename to tests/input/minerva-663d668500002178.json diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..09644d0 --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,46 @@ +import json + +import pytest +import yaml +from click.testing import CliRunner + +from gocam import __version__ +from gocam.cli import fetch, cli +from tests import INPUT_DIR + + +@pytest.fixture +def runner(): + return CliRunner() + + +@pytest.fixture +def api_mock(requests_mock): + gocam_id = "5b91dbd100002057" + with open(INPUT_DIR / f"minerva-{gocam_id}.json", "r") as f: + minerva_object = json.load(f) + requests_mock.get( + f"https://api.geneontology.org/api/go-cam/{gocam_id}", json=minerva_object + ) + + +def test_fetch_yaml(runner, api_mock): + result = runner.invoke(fetch, ["--format", "yaml", "5b91dbd100002057"]) + assert result.exit_code == 0 + + parsed_output = yaml.safe_load(result.output) + assert parsed_output["id"] == "gomodel:5b91dbd100002057" + + +def test_fetch_json(runner, api_mock): + result = runner.invoke(fetch, ["--format", "json", "5b91dbd100002057"]) + assert result.exit_code == 0 + + parsed_output = json.loads(result.output) + assert parsed_output["id"] == "gomodel:5b91dbd100002057" + + +def test_version(runner): + result = runner.invoke(cli, ["--version"]) + assert result.exit_code == 0 + assert __version__ in result.output diff --git a/tests/test_data.py b/tests/test_data.py index 636bc14..f0b8406 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -1,10 +1,9 @@ """Data test.""" import os import glob -import unittest from linkml_runtime.loaders import yaml_loader -from gocam.datamodel.gocam import Model +from gocam.datamodel import Model ROOT = os.path.join(os.path.dirname(__file__), '..') DATA_DIR = os.path.join(ROOT, "src", "data", "examples") @@ -12,11 +11,8 @@ EXAMPLE_FILES = glob.glob(os.path.join(DATA_DIR, '*.yaml')) -class TestData(unittest.TestCase): - """Test data and datamodel.""" - - def test_data(self): - """Data test.""" - for path in EXAMPLE_FILES: - obj = yaml_loader.load(path, target_class=Model) - assert obj +def test_data(): + """Data test.""" + for path in EXAMPLE_FILES: + obj = yaml_loader.load(path, target_class=Model) + assert obj diff --git a/tests/test_translation/test_minerva_wrapper.py b/tests/test_translation/test_minerva_wrapper.py index e3987aa..c2374f7 100644 --- a/tests/test_translation/test_minerva_wrapper.py +++ b/tests/test_translation/test_minerva_wrapper.py @@ -1,10 +1,11 @@ import json import pytest -import yaml from gocam.translation.minerva_wrapper import MinervaWrapper -from tests import OUTPUT_DIR, INPUT_DIR +from tests import INPUT_DIR + +ENABLED_BY = "RO:0002333" # mark as integration test @@ -12,20 +13,21 @@ @pytest.mark.parametrize("model_local_id", ["663d668500002178"]) def test_api(model_local_id): mw = MinervaWrapper() - d = mw.internal_object_by_id(model_local_id) - OUTPUT_DIR.mkdir(parents=True, exist_ok=True) - with(open(OUTPUT_DIR / "t.json", "w")) as f: - json.dump(d, f) - model = mw.object_by_id(model_local_id) + model = mw.fetch_model(model_local_id) assert model is not None -@pytest.mark.parametrize("base_name", ["minerva-example"]) +@pytest.mark.parametrize("base_name", ["minerva-663d668500002178", "minerva-5b91dbd100002057"]) def test_object(base_name): mw = MinervaWrapper() - d = json.load(open(INPUT_DIR / f"{base_name}.json", "r")) - model = mw.object_from_dict(d) - assert model is not None - md = model.model_dump(exclude_unset=True) - print(yaml.dump(md, sort_keys=False)) + with open(INPUT_DIR / f"{base_name}.json", "r") as f: + minerva_object = json.load(f) + model = mw.minerva_object_to_model(minerva_object) + # TODO: add more sanity checks here + assert model is not None + assert model.id == minerva_object["id"] + enabled_by_facts = [ + fact for fact in minerva_object["facts"] if fact["property"] == ENABLED_BY + ] + assert len(model.activities) == len(enabled_by_facts)