interopdb 0.1.0__tar.gz

interopdb-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: interopdb
+Version: 0.1.0
+Summary: Python client for the Interop DB Registry API
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: httpx>=0.24
+Requires-Dist: click>=8.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-httpx>=0.21; extra == "dev"
+
+# interopdb
+
+Python client and CLI for the [Interop DB Registry](https://interopdb-staging-f-ca.salmonpebble-cac1724c.northeurope.azurecontainerapps.io/) API.
+
+Interop DB is a federated registry that assigns unified identifiers to genes and strains across multiple biological databases, enabling cross-database queries with a single search. It integrates data from:
+
+- **ALEdb** -- Adaptive Laboratory Evolution Database 
+- **BiGGr** -- Knowledgebase of genome-scale metabolic network reconstructions
+- **PanKB** -- Pangenome Knowledge Base (genes, strains, pangenomics)
+- **PMkbase** -- Phenotype MicroArray Knowledge Base (strains, phenotypes)
+
+## Installation
+
+```bash
+pip install interopdb
+```
+
+## Python API
+
+```python
+from interopdb import InteropClient
+
+client = InteropClient()
+
+# Query a gene
+result = client.get_gene("rpoB")
+print(result["uid"], result["attributes"])
+
+# Query a strain
+result = client.get_strain("511145")
+
+# Query a gene-strain pair
+result = client.get_pair("rpoB", "511145")
+for source in result["sources"]:
+    print(source["source"], source["data"])
+
+# Save result to JSON
+client.save_json(result, "output.json")
+```
+
+## CLI
+
+```bash
+# Query entities
+interopdb gene rpoB
+interopdb strain 511145
+
+# Query a gene-strain pair
+interopdb pair rpoB 511145
+
+# Save to file
+interopdb gene rpoB -o result.json
+```

interopdb-0.1.0/README.md

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+# interopdb
+
+Python client and CLI for the [Interop DB Registry](https://interopdb-staging-f-ca.salmonpebble-cac1724c.northeurope.azurecontainerapps.io/) API.
+
+Interop DB is a federated registry that assigns unified identifiers to genes and strains across multiple biological databases, enabling cross-database queries with a single search. It integrates data from:
+
+- **ALEdb** -- Adaptive Laboratory Evolution Database 
+- **BiGGr** -- Knowledgebase of genome-scale metabolic network reconstructions
+- **PanKB** -- Pangenome Knowledge Base (genes, strains, pangenomics)
+- **PMkbase** -- Phenotype MicroArray Knowledge Base (strains, phenotypes)
+
+## Installation
+
+```bash
+pip install interopdb
+```
+
+## Python API
+
+```python
+from interopdb import InteropClient
+
+client = InteropClient()
+
+# Query a gene
+result = client.get_gene("rpoB")
+print(result["uid"], result["attributes"])
+
+# Query a strain
+result = client.get_strain("511145")
+
+# Query a gene-strain pair
+result = client.get_pair("rpoB", "511145")
+for source in result["sources"]:
+    print(source["source"], source["data"])
+
+# Save result to JSON
+client.save_json(result, "output.json")
+```
+
+## CLI
+
+```bash
+# Query entities
+interopdb gene rpoB
+interopdb strain 511145
+
+# Query a gene-strain pair
+interopdb pair rpoB 511145
+
+# Save to file
+interopdb gene rpoB -o result.json
+```

interopdb-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "interopdb"
+version = "0.1.0"
+description = "Python client for the Interop DB Registry API"
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    "httpx>=0.24",
+    "click>=8.0",
+]
+
+[project.optional-dependencies]
+dev = ["pytest>=7.0", "pytest-httpx>=0.21"]
+
+[project.scripts]
+interopdb = "interopdb.cli:cli"
+
+[tool.setuptools.packages.find]
+where = ["src"]

interopdb-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

interopdb-0.1.0/src/interopdb/__init__.py

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+from interopdb.client import InteropClient
+
+__all__ = ["InteropClient"]
+__version__ = "0.1.0"

interopdb-0.1.0/src/interopdb/cli.py

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+"""Command-line interface for querying the Interop DB Registry."""
+
+import json
+import sys
+
+import click
+from interopdb.client import DEFAULT_BASE_URL, InteropClient, InteropError
+
+
+@click.group()
+@click.option("--url", default=DEFAULT_BASE_URL, show_default=True, help="Interop DB server URL.")
+@click.pass_context
+def cli(ctx, url):
+    """Query the Interop DB Registry."""
+    ctx.ensure_object(dict)
+    ctx.obj["client"] = InteropClient(base_url=url)
+
+
+@cli.command()
+@click.argument("identifier")
+@click.option("-o", "--output", type=click.Path(), help="Save result to a JSON file.")
+@click.pass_context
+def gene(ctx, identifier, output):
+    """Query a gene by local ID or UID."""
+    _query(ctx.obj["client"].get_gene, identifier, output)
+
+
+@cli.command()
+@click.argument("identifier")
+@click.option("-o", "--output", type=click.Path(), help="Save result to a JSON file.")
+@click.pass_context
+def strain(ctx, identifier, output):
+    """Query a strain by local ID or UID."""
+    _query(ctx.obj["client"].get_strain, identifier, output)
+
+
+@cli.command()
+@click.argument("gene_id")
+@click.argument("strain_id")
+@click.option("-o", "--output", type=click.Path(), help="Save result to a JSON file.")
+@click.pass_context
+def pair(ctx, gene_id, strain_id, output):
+    """Query a gene-strain pair across all source databases."""
+    _query(lambda _=None: ctx.obj["client"].get_pair(gene_id, strain_id), None, output)
+
+
+def _query(func, identifier, output):
+    try:
+        result = func(identifier) if identifier is not None else func()
+    except InteropError as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+    formatted = json.dumps(result, indent=2, ensure_ascii=False)
+
+    if output:
+        InteropClient.save_json(result, output)
+        click.echo(f"Saved to {output}")
+    else:
+        click.echo(formatted)

interopdb-0.1.0/src/interopdb/client.py

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+"""Interop DB Registry API client."""
+
+import json
+from pathlib import Path
+
+import httpx
+
+DEFAULT_BASE_URL = "https://interopdb-staging-f-ca.salmonpebble-cac1724c.northeurope.azurecontainerapps.io"
+DEFAULT_TIMEOUT = 120.0
+
+
+class InteropError(Exception):
+    """Raised when an API request fails."""
+
+    def __init__(self, status_code: int, detail: str):
+        self.status_code = status_code
+        self.detail = detail
+        super().__init__(f"HTTP {status_code}: {detail}")
+
+
+class InteropClient:
+    """Client for querying the Interop DB Registry API.
+
+    Args:
+        base_url: Base URL of the Interop DB server.
+        timeout: Request timeout in seconds.
+    """
+
+    def __init__(
+        self,
+        base_url: str = DEFAULT_BASE_URL,
+        timeout: float = DEFAULT_TIMEOUT,
+    ):
+        self.base_url = base_url.rstrip("/")
+        self._client = httpx.Client(base_url=self.base_url, timeout=timeout)
+
+    def get_gene(self, identifier: str) -> dict:
+        """Query a gene by local ID or UID.
+
+        Args:
+            identifier: Gene local ID (e.g. ``"rpoB"``) or UID (e.g. ``"G-6EE9A9CD8006"``).
+
+        Returns:
+            Registry item with ``local_id``, ``uid``, ``entity_type``, and ``attributes`` from all source databases.
+        """
+        return self._get(f"/gene/{identifier}")
+
+    def get_strain(self, identifier: str) -> dict:
+        """Query a strain by local ID or UID.
+
+        Args:
+            identifier: Strain local ID (e.g. ``"511145"``) or UID (e.g. ``"S-6AC722234E99"``).
+
+        Returns:
+            Registry item with ``local_id``, ``uid``, ``entity_type``, and ``attributes`` from all source databases.
+        """
+        return self._get(f"/strain/{identifier}")
+
+    def get_pair(self, gene_id: str, strain_id: str) -> dict:
+        """Query a gene-strain pair across all source databases.
+
+        Args:
+            gene_id: Gene local ID or UID.
+            strain_id: Strain local ID or UID.
+
+        Returns:
+            Pair result with ``gene``, ``strain``, and ``sources`` list containing data from each database.
+        """
+        return self._get(f"/pair/{gene_id},{strain_id}")
+
+    def _get(self, path: str) -> dict:
+        response = self._client.get(path)
+        if response.status_code == 200:
+            return response.json()
+        detail = response.text or response.reason_phrase
+        raise InteropError(response.status_code, detail)
+
+    @staticmethod
+    def save_json(data: dict, path: str | Path) -> None:
+        """Save a result dictionary to a JSON file.
+
+        Args:
+            data: Result from ``get_gene``, ``get_strain``, or ``get_pair``.
+            path: Output file path.
+        """
+        path = Path(path)
+        path.write_text(json.dumps(data, indent=2, ensure_ascii=False) + "\n")
+
+    def close(self) -> None:
+        self._client.close()
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args):
+        self.close()

interopdb-0.1.0/src/interopdb.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: interopdb
+Version: 0.1.0
+Summary: Python client for the Interop DB Registry API
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: httpx>=0.24
+Requires-Dist: click>=8.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-httpx>=0.21; extra == "dev"
+
+# interopdb
+
+Python client and CLI for the [Interop DB Registry](https://interopdb-staging-f-ca.salmonpebble-cac1724c.northeurope.azurecontainerapps.io/) API.
+
+Interop DB is a federated registry that assigns unified identifiers to genes and strains across multiple biological databases, enabling cross-database queries with a single search. It integrates data from:
+
+- **ALEdb** -- Adaptive Laboratory Evolution Database 
+- **BiGGr** -- Knowledgebase of genome-scale metabolic network reconstructions
+- **PanKB** -- Pangenome Knowledge Base (genes, strains, pangenomics)
+- **PMkbase** -- Phenotype MicroArray Knowledge Base (strains, phenotypes)
+
+## Installation
+
+```bash
+pip install interopdb
+```
+
+## Python API
+
+```python
+from interopdb import InteropClient
+
+client = InteropClient()
+
+# Query a gene
+result = client.get_gene("rpoB")
+print(result["uid"], result["attributes"])
+
+# Query a strain
+result = client.get_strain("511145")
+
+# Query a gene-strain pair
+result = client.get_pair("rpoB", "511145")
+for source in result["sources"]:
+    print(source["source"], source["data"])
+
+# Save result to JSON
+client.save_json(result, "output.json")
+```
+
+## CLI
+
+```bash
+# Query entities
+interopdb gene rpoB
+interopdb strain 511145
+
+# Query a gene-strain pair
+interopdb pair rpoB 511145
+
+# Save to file
+interopdb gene rpoB -o result.json
+```

interopdb-0.1.0/src/interopdb.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+src/interopdb/__init__.py
+src/interopdb/cli.py
+src/interopdb/client.py
+src/interopdb.egg-info/PKG-INFO
+src/interopdb.egg-info/SOURCES.txt
+src/interopdb.egg-info/dependency_links.txt
+src/interopdb.egg-info/entry_points.txt
+src/interopdb.egg-info/requires.txt
+src/interopdb.egg-info/top_level.txt

interopdb-0.1.0/src/interopdb.egg-info/dependency_links.txt

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+

interopdb-0.1.0/src/interopdb.egg-info/entry_points.txt

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+[console_scripts]
+interopdb = interopdb.cli:cli

interopdb-0.1.0/src/interopdb.egg-info/requires.txt

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+httpx>=0.24
+click>=8.0
+
+[dev]
+pytest>=7.0
+pytest-httpx>=0.21

interopdb-0.1.0/src/interopdb.egg-info/top_level.txt

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+interopdb