Add infores api endpoints

.github/workflows/codecov_main.yaml

@@ -37,7 +37,7 @@ jobs:
         run: uv lock --check
 
       - name: Install library
-        run: uv sync --extra dev
+        run: uv sync
 
       - name: Run tests
         run: uv run pytest tests

.github/workflows/deploy-documentation.yaml

@@ -35,7 +35,7 @@ jobs:
           uv lock --directory backend --check
 
       - name: Install Dependencies
-        run: uv sync --directory backend --extra dev
+        run: uv sync --directory backend 
 
       - name: Build Documentation
         run: make docs

.github/workflows/test-backend.yaml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Install library
         run: |
-          uv sync --extra dev
+          uv sync
 
       - name: Run tests
         run: |

Makefile

@@ -65,7 +65,7 @@ install: install-backend install-frontend
 .PHONY: install-backend
 install-backend:
 	cd backend && \
-		uv sync --extra dev && \
+		uv sync && \
 		uv pip install -e .[dev]
 
 
@@ -78,7 +78,7 @@ install-frontend:
 
 .PHONY: model
 model: install-backend	
-	$(RUN) gen-pydantic --meta None --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
+	$(RUN) gen-pydantic --meta NONE --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
 	$(RUN) gen-typescript $(SCHEMADIR)/model.yaml > $(ROOTDIR)/frontend/src/api/model.ts
 	make format
 

backend/pyproject.toml

@@ -20,7 +20,7 @@ dependencies = [
     "docker>=7.1.0",
     "fastapi>=0.115.12,<1",
     "gunicorn>=23.0.0",
-    "linkml==1.8.3",
+    "linkml==1.9.2",
     "loguru",
     "oaklib>=0.6.6",
     "prefixmaps==0.2.4",
@@ -32,7 +32,7 @@ dependencies = [
     "typer>=0.12.0",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "pytest>=8.2.0",
     "mkdocs>=1.6.0",

backend/src/monarch_py/api/infores.py

@@ -0,0 +1,91 @@
+from typing import Union, List
+
+from fastapi import APIRouter, HTTPException, Path, Query, Response
+
+from monarch_py.api.config import solr
+from monarch_py.api.additional_models import OutputFormat
+from monarch_py.datamodels.model import InformationResource
+
+router = APIRouter(tags=["infores"], responses={404: {"description": "Not Found"}})
+
+
+@router.get("/")
+async def _get_infores_catalog(
+    format: OutputFormat = Query(
+        default=OutputFormat.json,
+        title="Output format for the response",
+        examples=["json", "tsv"],
+    ),
+) -> Union[List[InformationResource], str]:
+    """Retrieves all information resources from the catalog
+
+    <b>Returns:</b> <br>
+        List[InformationResource]: Complete collection of information resources
+    """
+    response = solr().get_infores_catalog()
+    if format == OutputFormat.json:
+        return response
+    elif format == OutputFormat.tsv:
+        if not response:
+            return Response(content="", media_type="text/tab-separated-values")
+
+        # Create TSV from pydantic models
+        headers = list(response[0].model_dump().keys()) if response else []
+        tsv_lines = ["\t".join(headers)]
+
+        for item in response:
+            row = []
+            for header in headers:
+                value = getattr(item, header, "")
+                if isinstance(value, list):
+                    value = ";".join(str(v) for v in value) if value else ""
+                row.append(str(value) if value is not None else "")
+            tsv_lines.append("\t".join(row))
+
+        tsv_content = "\n".join(tsv_lines)
+        return Response(content=tsv_content, media_type="text/tab-separated-values")
+
+
+@router.get("/{id}")
+async def _get_entity(
+    id: str = Path(
+        title="ID of the information resource to retrieve",
+        examples=["infores:zfin"],
+    ),
+    format: OutputFormat = Query(
+        default=OutputFormat.json,
+        title="Output format for the response",
+        examples=["json", "tsv"],
+    ),
+) -> Union[InformationResource, str]:
+    """Retrieves the information resource with the specified id
+
+    <b>Args:</b> <br>
+        id (str): ID for the entity to retrieve, ex: infores:zfin
+
+    <b>Raises:</b> <br>
+        HTTPException: 404 if the entity is not found
+
+    <b>Returns:</b> <br>
+        InformationResource: Information resource details for the specified id
+    """
+    response = solr().get_infores(id)
+    if response is None:
+        raise HTTPException(status_code=404, detail="Information resource not found")
+    if format == OutputFormat.json:
+        return response
+    elif format == OutputFormat.tsv:
+        # Create TSV from pydantic model
+        headers = list(response.model_dump().keys())
+        tsv_lines = ["\t".join(headers)]
+
+        row = []
+        for header in headers:
+            value = getattr(response, header, "")
+            if isinstance(value, list):
+                value = ";".join(str(v) for v in value) if value else ""
+            row.append(str(value) if value is not None else "")
+        tsv_lines.append("\t".join(row))
+
+        tsv_content = "\n".join(tsv_lines)
+        return Response(content=tsv_content, media_type="text/tab-separated-values")

backend/src/monarch_py/api/main.py

@@ -4,8 +4,9 @@
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import RedirectResponse
 
-from monarch_py.api import association, entity, histopheno, search, semsim, text_annotation
+from monarch_py.api import association, entity, histopheno, infores, search, semsim, text_annotation
 from monarch_py.api.config import semsimian, spacyner, settings
+
 from monarch_py.api.middleware.logging_middleware import LoggingMiddleware
 from monarch_py.utils.utils import get_release_metadata, get_release_versions
 
@@ -28,6 +29,7 @@ async def lifespan(app: FastAPI):
 app.include_router(association.router, prefix=f"{PREFIX}/association")
 app.include_router(entity.router, prefix=f"{PREFIX}/entity")
 app.include_router(histopheno.router, prefix=f"{PREFIX}/histopheno")
+app.include_router(infores.router, prefix=f"{PREFIX}/infores")
 app.include_router(search.router, prefix=PREFIX)
 app.include_router(semsim.router, prefix=f"{PREFIX}/semsim")
 app.include_router(text_annotation.router, prefix=PREFIX)