Experiment info retrieval

transcriptomics_data_service/db.py

@@ -88,6 +88,102 @@ async def delete_experiment_result(self, exp_id: str):
         await self._execute(*("DELETE FROM experiment_results WHERE experiment_result_id = $1", exp_id))
         self.logger.info(f"Deleted experiment_result row {exp_id}")
 
+    ############################
+    # fetch experiment_results
+    ############################
+
+    async def fetch_experiment_results(
+        self,
+        paginate: bool = False,
+        page: int = 1,
+        page_size: int = 100,
+    ) -> Tuple[List[ExperimentResult], int]:
+
+        order_clause = " ORDER BY experiment_result_id"
+        base_query = "SELECT * FROM experiment_results"
+        count_query = "SELECT COUNT(*) FROM experiment_results"
+
+        async with self.connect() as conn:
+            total_records = await conn.fetchval(count_query)
+            query = base_query + order_clause
+            params = []
+            if paginate:
+                offset = (page - 1) * page_size
+                query += " LIMIT $1 OFFSET $2"
+                params = [page_size, offset]
+
+            rows = await conn.fetch(query, *params)
+
+        items = [
+            ExperimentResult(
+                experiment_result_id=r["experiment_result_id"],
+                assembly_id=r["assembly_id"],
+                assembly_name=r["assembly_name"],
+            )
+            for r in rows
+        ]
+        return items, total_records
+
+    async def fetch_experiment_samples(
+        self, experiment_result_id: str, paginate: bool = True, page: int = 1, page_size: int = 100
+    ) -> Tuple[List[str], int]:
+        """
+        Returns (list_of_sample_ids, total_records) for a single experiment_result_id.
+        """
+        count_query = """
+                SELECT COUNT(DISTINCT sample_id)
+                FROM gene_expressions
+                WHERE experiment_result_id = $1
+            """
+        base_query = """
+                SELECT DISTINCT sample_id
+                FROM gene_expressions
+                WHERE experiment_result_id = $1
+                ORDER BY sample_id
+            """
+
+        async with self.connect() as conn:
+            total_records = await conn.fetchval(count_query, experiment_result_id)
+            if paginate:
+                offset = (page - 1) * page_size
+                query = base_query + " LIMIT $2 OFFSET $3"
+                rows = await conn.fetch(query, experiment_result_id, page_size, offset)
+            else:
+                rows = await conn.fetch(base_query, experiment_result_id)
+
+        items = [r["sample_id"] for r in rows]
+        return items, total_records
+
+    async def fetch_experiment_features(
+        self, experiment_result_id: str, paginate: bool = True, page: int = 1, page_size: int = 100
+    ) -> Tuple[List[str], int]:
+        """
+        Returns (list_of_features, total_records) for a single experiment_result_id.
+        """
+        count_query = """
+            SELECT COUNT(DISTINCT gene_code)
+            FROM gene_expressions
+            WHERE experiment_result_id = $1
+        """
+        base_query = """
+            SELECT DISTINCT gene_code
+            FROM gene_expressions
+            WHERE experiment_result_id = $1
+            ORDER BY gene_code
+        """
+
+        async with self.connect() as conn:
+            total_records = await conn.fetchval(count_query, experiment_result_id)
+            if paginate:
+                offset = (page - 1) * page_size
+                query = base_query + " LIMIT $2 OFFSET $3"
+                rows = await conn.fetch(query, experiment_result_id, page_size, offset)
+            else:
+                rows = await conn.fetch(base_query, experiment_result_id)
+
+        items = [r["gene_code"] for r in rows]
+        return items, total_records
+
     ########################
     # CRUD: gene_expressions
     ########################

transcriptomics_data_service/models.py

@@ -9,6 +9,11 @@
     "GeneExpressionResponse",
     "NormalizationMethodEnum",
     "ExpressionQueryBody",
+    "CountTypesEnum",
+    "PaginatedRequest",
+    "PaginatedResponse",
+    "FeaturesResponse",
+    "SamplesResponse",
 ]
 
 
@@ -32,6 +37,9 @@ class CountTypesEnum(str, Enum):
     getmm = GETMM
 
 
+#####################################
+# PAGINATION MODELS
+#####################################
 class PaginatedRequest(BaseModel):
     page: int = Field(1, ge=1, description="Current page number")
     page_size: int = Field(100, ge=1, le=1000, description="Number of records per page")
@@ -42,12 +50,26 @@ class PaginatedResponse(PaginatedRequest):
     total_pages: int = Field(..., ge=1, description="Total number of pages")
 
 
+#####################################
+# EXPERIMENTS
+#####################################
 class ExperimentResult(BaseModel):
     experiment_result_id: str = Field(..., min_length=1, max_length=255)
     assembly_id: Optional[str] = Field(None, max_length=255)
     assembly_name: Optional[str] = Field(None, max_length=255)
 
 
+class SamplesResponse(PaginatedResponse):
+    samples: List[str]
+
+
+class FeaturesResponse(PaginatedResponse):
+    features: List[str]
+
+
+#####################################
+# GENE EXPRESSIONS
+#####################################
 class GeneExpression(BaseModel):
     gene_code: str = Field(..., min_length=1, max_length=255, description="Feature identifier")
     sample_id: str = Field(..., min_length=1, max_length=255, description="Sample identifier")

transcriptomics_data_service/routers/experiment_results.py

@@ -1,17 +1,123 @@
-from fastapi import APIRouter
+from fastapi import APIRouter, HTTPException, status
 
 from transcriptomics_data_service.db import DatabaseDependency
+from transcriptomics_data_service.logger import LoggerDependency
+from transcriptomics_data_service.models import (
+    PaginatedRequest,
+    SamplesResponse,
+    FeaturesResponse,
+)
 
 __all__ = ["experiment_router"]
 
 experiment_router = APIRouter(prefix="/experiment")
 
 
-@experiment_router.delete("/{experiment_result_id}")
-async def delete_experiment_result(db: DatabaseDependency, experiment_result_id: str):
-    await db.delete_experiment_result(experiment_result_id)
+async def get_experiment_samples_handler(
+    experiment_result_id: str,
+    params: PaginatedRequest,
+    db: DatabaseDependency,
+    logger: LoggerDependency,
+) -> SamplesResponse:
+    """
+    Handler for fetching and returning samples for a experiment_result_id.
+    """
+    logger.info(f"Received query parameters for samples: {params}")
+
+    samples, total_records = await db.fetch_experiment_samples(
+        experiment_result_id=experiment_result_id,
+        paginate=True,
+        page=params.page,
+        page_size=params.page_size,
+    )
+
+    if not samples:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"No samples found for experiment '{experiment_result_id}'.",
+        )
+
+    total_pages = (total_records + params.page_size - 1) // params.page_size
+
+    return SamplesResponse(
+        page=params.page,
+        page_size=params.page_size,
+        total_records=total_records,
+        total_pages=total_pages,
+        samples=samples,
+    )
+
+
+async def get_experiment_features_handler(
+    experiment_result_id: str,
+    params: PaginatedRequest,
+    db: DatabaseDependency,
+    logger: LoggerDependency,
+) -> FeaturesResponse:
+    """
+    Handler for fetching and returning features for a experiment_result_id.
+    """
+    logger.info(f"Received query parameters for features: {params}")
+
+    features, total_records = await db.fetch_experiment_features(
+        experiment_result_id=experiment_result_id,
+        paginate=True,
+        page=params.page,
+        page_size=params.page_size,
+    )
+
+    if not features:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"No features found for experiment '{experiment_result_id}'.",
+        )
+
+    total_pages = (total_records + params.page_size - 1) // params.page_size
+
+    return FeaturesResponse(
+        page=params.page,
+        page_size=params.page_size,
+        total_records=total_records,
+        total_pages=total_pages,
+        features=features,
+    )
+
+
+@experiment_router.get("")
+async def get_all_experiments(db: DatabaseDependency):
+    experiments, _ = await db.fetch_experiment_results(paginate=False)
+    return experiments
 
 
 @experiment_router.get("/{experiment_result_id}")
 async def get_experiment_result(db: DatabaseDependency, experiment_result_id: str):
     return await db.read_experiment_result(experiment_result_id)
+
+
+@experiment_router.post(
+    "/{experiment_result_id}/samples", status_code=status.HTTP_200_OK, response_model=SamplesResponse
+)
+async def post_experiment_samples(
+    experiment_result_id: str,
+    params: PaginatedRequest,
+    db: DatabaseDependency,
+    logger: LoggerDependency,
+):
+    return await get_experiment_samples_handler(experiment_result_id, params, db, logger)
+
+
+@experiment_router.post(
+    "/{experiment_result_id}/features", status_code=status.HTTP_200_OK, response_model=FeaturesResponse
+)
+async def post_experiment_features(
+    experiment_result_id: str,
+    params: PaginatedRequest,
+    db: DatabaseDependency,
+    logger: LoggerDependency,
+):
+    return await get_experiment_features_handler(experiment_result_id, params, db, logger)
+
+
+@experiment_router.delete("/{experiment_result_id}")
+async def delete_experiment_result(db: DatabaseDependency, experiment_result_id: str):
+    await db.delete_experiment_result(experiment_result_id)