opentargets-py 0.1.0__tar.gz

opentargets_py-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.11", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          pip install -e ".[dev,pandas]"
+
+      - name: Lint (ruff)
+        run: ruff check src tests
+
+      - name: Format check (ruff)
+        run: ruff format --check src tests
+
+      - name: Type check (mypy)
+        run: mypy src/opentargets
+
+      - name: Run tests
+        run: pytest --cov=opentargets --cov-report=xml -v -m "not integration"
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.11'
+        with:
+          files: coverage.xml

opentargets_py-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,32 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build tools
+        run: pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Check distribution
+        run: twine check dist/*
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: twine upload dist/*

opentargets_py-0.1.0/.gitignore

@@ -0,0 +1,81 @@
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*.manifest
+*.spec
+pip-log.txt
+pip-delete-this-directory.txt
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+*.mo
+*.pot
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+instance/
+.webassets-cache
+.scrapy
+docs/_build/
+.pybuilder/
+target/
+.ipynb_checkpoints
+profile_default/
+ipython_config.py
+.pdm.toml
+.pdm-python
+.pdm-build/
+__pypackages__/
+celerybeat-schedule
+celerybeat.pid
+*.sage.py
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.spyderproject.db
+.spyproject
+.ropeproject
+/site
+.mypy_cache/
+.dmypy.json
+dmypy.json
+.pyre/
+.pytype/
+cython_debug/
+.idea/
+.vscode/
+*.iml

opentargets_py-0.1.0/CHANGELOG.md

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+# Changelog
+
+## [0.1.0] - 2026-04-19
+
+### Added
+- Initial release
+- `OpenTargetsClient` with sync support
+- Target, disease, drug, association, and search queries
+- Auto-pagination for association endpoints
+- Symbol-to-Ensembl ID resolution with caching
+- In-memory LRU cache with TTL
+- Exponential backoff retry (no third-party dependencies)
+- Pydantic v2 response models (frozen, fully typed)
+- Optional pandas DataFrame output
+- GitHub Actions CI (Python 3.9, 3.11, 3.13) and PyPI publish workflow

opentargets_py-0.1.0/CLAUDE.md

@@ -0,0 +1,50 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Commands
+
+```bash
+# Install all dependencies (from repo root)
+pip install -e ".[dev,pandas]"
+
+# Run tests (no real API calls)
+pytest
+
+# Run a single test file
+pytest tests/test_client.py -v
+
+# Run a single test
+pytest tests/test_client.py::test_get_target_by_ensembl_id -v
+
+# Run integration tests (hits the real API)
+pytest -m integration
+
+# Lint + format check
+ruff check src tests
+ruff format --check src tests
+
+# Type check
+mypy src/opentargets
+```
+
+## Architecture
+
+The package lives under `src/opentargets/` (PEP 517 src layout).
+
+**Request flow:**  
+`OpenTargetsClient` (public API) → `GraphQLClient` (`_graphql.py`) → `with_retry()` → `httpx`
+
+**Key design decisions:**
+
+- `client.py` contains all public methods and delegates to `_graphql.py` for HTTP. Parse helpers (`_parse_target`, `_parse_disease`, etc.) live at the bottom of `client.py` to keep method bodies short.
+- `_graphql.py` has two entry points: `execute()` for single queries and `paginate()` for cursor-based pagination. Pagination injects `index`/`size` variables and walks pages until `count` is exhausted.
+- `_queries/` holds only GraphQL string constants — no logic. One module per entity type.
+- `_retry.py` implements backoff without `tenacity`. It wraps a zero-argument callable, so it's usable with any function via a lambda.
+- `_cache.py` is a standalone LRU+TTL cache. `OpenTargetsClient` uses two instances: one for symbol→Ensembl ID mapping (`_symbol_cache`) and one for full entity responses (`_result_cache`). Passing `cache=False` swaps both for `_NoCache` (same interface, no-ops).
+- Symbol resolution: if `target_id` starts with `ENSG`, it's used directly. Otherwise the search endpoint is called and the result cached.
+- Models in `models.py` use Pydantic v2 `model_validate()` with `populate_by_name=True` so both camelCase API fields and snake_case aliases work.
+
+## Testing
+
+Tests use `respx` to mock `httpx` — no real API calls unless `@pytest.mark.integration`. Fixtures in `conftest.py` provide raw API response dicts that mirror the actual GraphQL schema shape.

opentargets_py-0.1.0/LICENSE

@@ -0,0 +1,181 @@
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+   9. Accepting Warranty or Liability. While redistributing the Work or
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+   END OF TERMS AND CONDITIONS
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+   Copyright 2024 Göknur Arıcan
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+   See the License for the specific language governing permissions and
+   limitations under the License.

opentargets_py-0.1.0/PKG-INFO

@@ -0,0 +1,120 @@
+Metadata-Version: 2.4
+Name: opentargets-py
+Version: 0.1.0
+Summary: Unofficial community-maintained Python client for the Open Targets Platform GraphQL API
+Project-URL: Homepage, https://github.com/goknurarican/opentargets-py
+Project-URL: Documentation, https://opentargets-py.readthedocs.io
+Project-URL: Repository, https://github.com/goknurarican/opentargets-py
+Project-URL: Issues, https://github.com/goknurarican/opentargets-py/issues
+Author-email: Göknur Arıcan <gknrperiarican@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: bioinformatics,drug-discovery,genomics,graphql,opentargets,python-client,sdk,target-identification
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: httpx>=0.24
+Requires-Dist: pydantic>=2.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.0; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: respx>=0.20; extra == 'dev'
+Requires-Dist: ruff>=0.1; extra == 'dev'
+Provides-Extra: pandas
+Requires-Dist: pandas>=1.5; extra == 'pandas'
+Description-Content-Type: text/markdown
+
+# opentargets-py
+
+[![PyPI version](https://badge.fury.io/py/opentargets-py.svg)](https://pypi.org/project/opentargets-py/)
+[![Python versions](https://img.shields.io/pypi/pyversions/opentargets-py)](https://pypi.org/project/opentargets-py/)
+[![CI](https://github.com/goknurarican/opentargets-py/actions/workflows/ci.yml/badge.svg)](https://github.com/goknurarican/opentargets-py/actions/workflows/ci.yml)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+
+Modern Python client for the [Open Targets Platform](https://platform.opentargets.org) GraphQL API.
+
+> **Disclaimer:** This is an **unofficial, community-maintained** client and is not affiliated with, endorsed by, or supported by the Open Targets consortium. For the official platform, visit [platform.opentargets.org](https://platform.opentargets.org).
+
+The official `opentargets` package was deprecated when Open Targets migrated to GraphQL in 2021 and has since been removed from PyPI. This library fills that gap — it is the only Python SDK targeting the current GraphQL API.
+
+## Installation
+
+```bash
+pip install opentargets-py
+```
+
+With pandas support:
+
+```bash
+pip install opentargets-py[pandas]
+```
+
+## Quick Start
+
+```python
+from opentargets import OpenTargetsClient
+
+client = OpenTargetsClient()
+
+# Look up a target by gene symbol
+target = client.get_target("EGFR")
+print(target.approved_name)  # epidermal growth factor receptor
+
+# Get associated diseases
+associations = client.get_target_associations("EGFR", limit=10)
+for a in associations:
+    print(a.disease_name, a.score)
+
+# Get drugs for a target
+drugs = client.get_target_drugs("EGFR")
+
+# Look up a disease
+disease = client.get_disease("EFO_0003060")
+
+# Search across the platform
+results = client.search("lung cancer", entity_type="disease", limit=5)
+```
+
+## Features
+
+- **Type-safe** — full Pydantic v2 models, `py.typed` marker, `mypy --strict` compliant
+- **Symbol resolution** — pass `"EGFR"` instead of `"ENSG00000146648"`
+- **Auto-pagination** — fetches all pages transparently
+- **In-memory cache** — LRU cache with TTL, reduces redundant API calls
+- **Retry with backoff** — automatic retries on 429/5xx with exponential backoff
+- **Pandas integration** — `as_dataframe=True` on any list method
+- **Minimal dependencies** — only `httpx` and `pydantic`
+
+## More Examples
+
+See the [`examples/`](examples/) directory:
+
+- [`basic_usage.py`](examples/basic_usage.py) — targets, diseases, drugs, search
+- [`batch_query.py`](examples/batch_query.py) — batch fetch + DataFrame output
+- [`network_analysis.py`](examples/network_analysis.py) — build a target–disease network
+
+## API Reference
+
+See [`docs/api-reference.md`](docs/api-reference.md).
+
+## Contributing
+
+1. Fork the repo and create a feature branch.
+2. Install dev dependencies: `pip install -e ".[dev,pandas]"`
+3. Run tests: `pytest`
+4. Run linting: `ruff check src tests && ruff format src tests`
+5. Open a pull request.
+
+## License
+
+Apache 2.0 — see [LICENSE](LICENSE).

opentargets_py-0.1.0/README.md

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+# opentargets-py
+
+[![PyPI version](https://badge.fury.io/py/opentargets-py.svg)](https://pypi.org/project/opentargets-py/)
+[![Python versions](https://img.shields.io/pypi/pyversions/opentargets-py)](https://pypi.org/project/opentargets-py/)
+[![CI](https://github.com/goknurarican/opentargets-py/actions/workflows/ci.yml/badge.svg)](https://github.com/goknurarican/opentargets-py/actions/workflows/ci.yml)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+
+Modern Python client for the [Open Targets Platform](https://platform.opentargets.org) GraphQL API.
+
+> **Disclaimer:** This is an **unofficial, community-maintained** client and is not affiliated with, endorsed by, or supported by the Open Targets consortium. For the official platform, visit [platform.opentargets.org](https://platform.opentargets.org).
+
+The official `opentargets` package was deprecated when Open Targets migrated to GraphQL in 2021 and has since been removed from PyPI. This library fills that gap — it is the only Python SDK targeting the current GraphQL API.
+
+## Installation
+
+```bash
+pip install opentargets-py
+```
+
+With pandas support:
+
+```bash
+pip install opentargets-py[pandas]
+```
+
+## Quick Start
+
+```python
+from opentargets import OpenTargetsClient
+
+client = OpenTargetsClient()
+
+# Look up a target by gene symbol
+target = client.get_target("EGFR")
+print(target.approved_name)  # epidermal growth factor receptor
+
+# Get associated diseases
+associations = client.get_target_associations("EGFR", limit=10)
+for a in associations:
+    print(a.disease_name, a.score)
+
+# Get drugs for a target
+drugs = client.get_target_drugs("EGFR")
+
+# Look up a disease
+disease = client.get_disease("EFO_0003060")
+
+# Search across the platform
+results = client.search("lung cancer", entity_type="disease", limit=5)
+```
+
+## Features
+
+- **Type-safe** — full Pydantic v2 models, `py.typed` marker, `mypy --strict` compliant
+- **Symbol resolution** — pass `"EGFR"` instead of `"ENSG00000146648"`
+- **Auto-pagination** — fetches all pages transparently
+- **In-memory cache** — LRU cache with TTL, reduces redundant API calls
+- **Retry with backoff** — automatic retries on 429/5xx with exponential backoff
+- **Pandas integration** — `as_dataframe=True` on any list method
+- **Minimal dependencies** — only `httpx` and `pydantic`
+
+## More Examples
+
+See the [`examples/`](examples/) directory:
+
+- [`basic_usage.py`](examples/basic_usage.py) — targets, diseases, drugs, search
+- [`batch_query.py`](examples/batch_query.py) — batch fetch + DataFrame output
+- [`network_analysis.py`](examples/network_analysis.py) — build a target–disease network
+
+## API Reference
+
+See [`docs/api-reference.md`](docs/api-reference.md).
+
+## Contributing
+
+1. Fork the repo and create a feature branch.
+2. Install dev dependencies: `pip install -e ".[dev,pandas]"`
+3. Run tests: `pytest`
+4. Run linting: `ruff check src tests && ruff format src tests`
+5. Open a pull request.
+
+## License
+
+Apache 2.0 — see [LICENSE](LICENSE).

opentargets_py-0.1.0/docs/api-reference.md

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+# API Reference
+
+## OpenTargetsClient
+
+```python
+OpenTargetsClient(
+    base_url: str = "https://api.platform.opentargets.org/api/v4/graphql",
+    timeout: float = 30.0,
+    cache: bool = True,
+    cache_ttl: float = 300.0,
+)
+```
+
+### Target methods
+
+| Method | Returns |
+|---|---|
+| `get_target(target_id)` | `Target` |
+| `get_targets(target_ids)` | `list[Target]` |
+| `get_target_associations(target_id, limit, as_dataframe)` | `list[Association]` or `DataFrame` |
+| `get_target_drugs(target_id)` | `list[Drug]` |
+
+### Disease methods
+
+| Method | Returns |
+|---|---|
+| `get_disease(disease_id)` | `Disease` |
+| `get_disease_targets(disease_id, limit, as_dataframe)` | `list[Association]` or `DataFrame` |
+
+### Drug methods
+
+| Method | Returns |
+|---|---|
+| `get_drug(drug_id)` | `Drug` |
+| `get_drug_indications(drug_id)` | `list[DrugIndication]` |
+
+### Search
+
+| Method | Returns |
+|---|---|
+| `search(query_string, entity_type, limit)` | `list[SearchResult]` |
+
+### Associations
+
+| Method | Returns |
+|---|---|
+| `get_associations(target_id, disease_id)` | `Association \| None` |
+
+## Models
+
+### Target
+`id`, `approved_symbol`, `approved_name`, `biotype`, `description`, `function_descriptions`
+
+### Disease
+`id`, `name`, `description`, `therapeutic_areas`, `db_x_refs`
+
+### Drug
+`id`, `name`, `drug_type`, `mechanism_of_action`, `synonyms`, `trade_names`, `max_clinical_trial_phase`
+
+### Association
+`target_id`, `target_symbol`, `disease_id`, `disease_name`, `score`, `datasource_scores`, `evidence_count`
+
+### SearchResult
+`id`, `name`, `entity_type`, `description`, `score`
+
+### DrugIndication
+`disease_id`, `disease_name`, `max_phase_for_indication`
+
+## Exceptions
+
+| Exception | When |
+|---|---|
+| `OpenTargetsError` | Base class |
+| `APIError` | HTTP error (non-2xx) |
+| `QueryError` | GraphQL `errors` in response |
+| `NotFoundError` | Entity not found |
+| `RateLimitError` | HTTP 429 |