Added an end point for well library data.

lang_qc/endpoints/pacbio_well.py

@@ -37,13 +37,18 @@
 from lang_qc.db.mlwh_connection import get_mlwh_db
 from lang_qc.db.qc_connection import get_qc_db
 from lang_qc.db.qc_schema import User
-from lang_qc.models.pacbio.well import PacBioPagedWells, PacBioWellFull
+from lang_qc.models.pacbio.well import (
+    PacBioPagedWells,
+    PacBioWellFull,
+    PacBioWellLibraries,
+)
 from lang_qc.models.qc_flow_status import QcFlowStatusEnum
 from lang_qc.models.qc_state import QcState, QcStateBasic
 from lang_qc.util.auth import check_user
 from lang_qc.util.errors import (
     InconsistentInputError,
     InvalidDictValueError,
+    MissingLimsDataError,
     RunNotFoundError,
 )
 from lang_qc.util.type_checksum import ChecksumSHA256
@@ -163,6 +168,32 @@ def get_wells_in_run(
     return response
 
 
+@router.get(
+    "/wells/{id_product}/libraries",
+    summary="Get well summary and LIMS data for all libraries",
+    responses={
+        status.HTTP_404_NOT_FOUND: {"description": "Well product does not exist"},
+        status.HTTP_422_UNPROCESSABLE_ENTITY: {"description": "Invalid product ID"},
+        status.HTTP_409_CONFLICT: {"description": "Missing or incomplete LIMS data"},
+    },
+    response_model=PacBioWellLibraries,
+)
+def get_well_lims_info(
+    id_product: ChecksumSHA256,
+    mlwhdb_session: Session = Depends(get_mlwh_db),
+) -> PacBioWellLibraries:
+
+    db_well = _find_well_product_or_error(id_product, mlwhdb_session)
+    well_libraries: PacBioWellLibraries
+    try:
+        well_libraries = PacBioWellLibraries(db_well=db_well)
+    except MissingLimsDataError as err:
+        # 409 - Request conflicts with the current state of the server.
+        raise HTTPException(409, detail=str(err))
+
+    return well_libraries
+
+
 @router.get(
     "/products/{id_product}/seq_level",
     summary="Get full sequencing QC metrics and state for a product",

lang_qc/models/pacbio/well.py

@@ -31,6 +31,7 @@
 from lang_qc.models.pacbio.qc_data import QCDataWell
 from lang_qc.models.pager import PagedResponse
 from lang_qc.models.qc_state import QcState
+from lang_qc.util.errors import MissingLimsDataError
 
 
 def get_field_names(cls):
@@ -199,7 +200,7 @@ def pre_root(cls, values: dict[str, Any]) -> dict[str, Any]:
         mlwh_db_row: PacBioRunWellMetrics = values.kwargs["db_well"]
         lims_data = mlwh_db_row.get_experiment_info()
         if len(lims_data) == 0:
-            raise ValueError(
+            raise MissingLimsDataError(
                 f"No LIMS data retrieved for {mlwh_db_row.__repr__()} "
                 "on account of partially linked or unlinked product data."
             )

lang_qc/util/errors.py

@@ -25,3 +25,10 @@ class EmptyListOfRunNamesError(Exception):
 
 class RunNotFoundError(Exception):
     """Exception to be used when no well metrics data for a run is found."""
+
+
+class MissingLimsDataError(Exception):
+    """
+    Exception to be used when product LIMS data is not available
+    or partially missing.
+    """

tests/endpoints/test_well_libraries.py

@@ -0,0 +1,70 @@
+from fastapi.testclient import TestClient
+from sqlalchemy import select
+
+# from lang_qc.db.mlwh_schema import PacBioRunWellMetrics
+
+
+def test_well_libraries(test_client: TestClient, mlwhdb_load_runs):
+    """Test retrieval of LIMS library data for a well."""
+
+    response = test_client.get(f"/pacbio/wells/malformed/libraries")
+    assert response.status_code == 422
+
+    id_product = "aaa8bd66e0f0895ea728c1d08103c62d3de8a57a5f879cee45f7b0acc028aa61"
+    response = test_client.get(f"/pacbio/wells/{id_product}/libraries")
+    assert response.status_code == 404
+
+    # Partially linked well
+    id_product = "26928ba6ec2a00c04dd6c7c68008ec9436e3979a384b9f708dc371c99f272e17"
+    response = test_client.get(f"/pacbio/wells/{id_product}/libraries")
+    assert response.status_code == 409
+    assert response.json()["detail"] == "".join(
+        [
+            "No LIMS data retrieved for lang_qc.db.mlwh_schema.PacBioRunWellMetrics:",
+            " pac_bio_run_name=TRACTION-RUN-1140, well_label=C1, plate_number=2,",
+            " id_pac_bio_product=26928ba6ec2a00c04dd6c7c68008ec9436e3979a384b9f708dc371c99f272e17",
+            " on account of partially linked or unlinked product data.",
+        ]
+    )
+
+    # Fully linked well
+    id_product = "513c674f489b106c6af716dd0d210826ff03b7648d50888839c3722ca1b10dbf"
+    response = test_client.get(f"/pacbio/wells/{id_product}/libraries")
+    assert response.status_code == 200
+    expected_response = {
+        "id_product": "513c674f489b106c6af716dd0d210826ff03b7648d50888839c3722ca1b10dbf",
+        "label": "A1",
+        "plate_number": 2,
+        "run_name": "TRACTION-RUN-1140",
+        "run_start_time": "2024-02-23T10:28:12",
+        "run_complete_time": "2024-02-25T20:53:05",
+        "well_start_time": "2024-02-24T14:25:12",
+        "well_complete_time": "2024-02-26T00:27:52",
+        "run_status": "Complete",
+        "well_status": "Complete",
+        "instrument_name": "84093",
+        "instrument_type": "Revio",
+        "qc_state": None,
+        "libraries": [
+            {
+                "study_id": "5901",
+                "study_name": "DTOL_Darwin Tree of Life",
+                "sample_id": "9478726",
+                "sample_name": "DTOL14523243",
+                "tag_sequence": ["ATCTGCACGTGAGTAT"],
+                "library_type": "Pacbio_HiFi",
+                "pool_name": "TRAC-2-7677",
+            },
+            {
+                "study_id": "5901",
+                "study_name": "DTOL_Darwin Tree of Life",
+                "sample_id": "9518398",
+                "sample_name": "DTOL14180244",
+                "tag_sequence": ["ATGTACTAGTGAGTAT"],
+                "library_type": "Pacbio_HiFi",
+                "pool_name": "TRAC-2-7677",
+            },
+        ],
+    }
+
+    assert response.json() == expected_response

tests/test_pb_well_models.py

@@ -11,6 +11,7 @@
     PacBioWellLibraries,
     PacBioWellSummary,
 )
+from lang_qc.util.errors import MissingLimsDataError
 from tests.conftest import compare_dates
 from tests.fixtures.well_data import load_data4well_retrieval, load_dicts_and_users
 
@@ -163,7 +164,7 @@ def test_create_summary_and_library_models_lims_info(
     pb_well = PacBioWellSummary(db_well=well_row)
     assert pb_well.study_names == []
 
-    with pytest.raises(ValueError, match=r"No LIMS data retrieved"):
+    with pytest.raises(MissingLimsDataError, match=r"No LIMS data retrieved"):
         PacBioWellLibraries(db_well=well_row)
 
     # Fully linked wells with one sample
@@ -242,5 +243,5 @@ def test_create_summary_and_library_models_lims_info(
     pb_well = PacBioWellSummary(db_well=well_row)
     assert pb_well.study_names == []
 
-    with pytest.raises(ValueError, match=r"No LIMS data retrieved"):
+    with pytest.raises(MissingLimsDataError, match=r"No LIMS data retrieved"):
         PacBioWellLibraries(db_well=well_row)