Merge pull request #216 from mgcam/on_hold_external

Introduced 'On hold external' QC state.

alembic/versions/2.1.0_extend_qc_state_dict.py

@@ -0,0 +1,22 @@
+"""extend_qc_state_dict
+
+Revision ID: 2.1.0
+Revises: 2.0.0
+Create Date: 2024-03-19 12:31:26.359652
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "2.1.0"
+down_revision = "2.0.0"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.execute("INSERT INTO qc_state_dict VALUES ('On hold external', NULL)")
+
+
+def downgrade() -> None:
+    op.execute("DELETE FROM qc_state_dict WHERE state='On hold external'")

lang_qc/db/helper/wells.py

@@ -169,10 +169,10 @@ class PacBioPagedWellsFactory(WellWh, PagedResponse):
     # For MySQL it's OK to use case-sensitive comparison operators since
     # its string comparisons for the collation we use are case-insensitive.
     FILTERS: ClassVar = {
-        QcFlowStatusEnum.ON_HOLD.name: (QcStateDict.state == "On hold"),
+        QcFlowStatusEnum.ON_HOLD.name: (QcStateDict.state.ilike("On hold%")),
         QcFlowStatusEnum.QC_COMPLETE.name: (QcState.is_preliminary == 0),
         QcFlowStatusEnum.IN_PROGRESS.name: and_(
-            QcState.is_preliminary == 1, QcStateDict.state != "On hold"
+            QcState.is_preliminary == 1, QcStateDict.state.notilike("On hold%")
         ),
         QcFlowStatusEnum.ABORTED.name: or_(
             PacBioRunWellMetrics.well_status.like("Abort%"),

lang_qc/endpoints/config.py

@@ -65,6 +65,8 @@ def _states_for_update(session) -> List:
     states = []
     for (name, row) in qc_state_dict(session).items():
         if name not in ["Aborted", "Claimed"]:
-            states.append({"description": name, "only_prelim": row.state == "On hold"})
+            states.append(
+                {"description": name, "only_prelim": "on hold" in row.state.lower()}
+            )
 
     return states

tests/endpoints/test_config.py

@@ -23,6 +23,7 @@ def test_get_config(test_client: TestClient, load_dicts_and_users):
             {"description": "Failed, Instrument", "only_prelim": False},
             {"description": "Failed, SMRT cell", "only_prelim": False},
             {"description": "On hold", "only_prelim": True},
+            {"description": "On hold external", "only_prelim": True},
             {"description": "Undecided", "only_prelim": False},
         ],
     }

tests/endpoints/test_dump_qc_states.py

@@ -41,7 +41,7 @@ def test_get_qc_by_product_id(test_client: TestClient, load_data4well_retrieval)
     assert SECOND_GOOD_CHECKSUM in response_data
     list_1 = response_data[FIRST_GOOD_CHECKSUM]
     list_2 = response_data[SECOND_GOOD_CHECKSUM]
-    qc_states = ["On hold", "Failed, Instrument"]
+    qc_states = ["On hold external", "Failed, Instrument"]
     for index, l in enumerate([list_1, list_2]):
         assert len(l) == 2
         # The list of QC state objects contains QC states

tests/endpoints/test_filtered_wells.py

@@ -81,7 +81,10 @@ def test_on_hold_filter(test_client: TestClient, load_data4well_retrieval):
     """Test passing `on_hold` filter."""
 
     status = "on_hold"
-    expected_data = [{"TRACTION_RUN_1:D1": "On hold"}, {"TRACTION_RUN_1:B1": "On hold"}]
+    expected_data = [
+        {"TRACTION_RUN_1:D1": "On hold external"},
+        {"TRACTION_RUN_1:B1": "On hold"},
+    ]
     num_total = len(expected_data)
 
     response = test_client.get(

tests/endpoints/test_wells4run.py

@@ -26,7 +26,7 @@ def test_existing_run(test_client: TestClient, load_data4well_retrieval):
     label_list = [well["label"] for well in resp["wells"]]
     assert label_list == ["A1", "B1", "C1", "D1"]
     qc_states = [well["qc_state"]["qc_state"] for well in resp["wells"]]
-    assert qc_states == ["Claimed", "On hold", "Claimed", "On hold"]
+    assert qc_states == ["Claimed", "On hold", "Claimed", "On hold external"]
 
     assert (
         resp["wells"][0]["instrument_name"] == "64016"

tests/fixtures/well_data.py

@@ -30,6 +30,7 @@
     {"state": "Passed", "outcome": 1},
     {"state": "Claimed", "outcome": None},
     {"state": "On hold", "outcome": None},
+    {"state": "On hold external", "outcome": None},
 ]
 
 PLATFORMS = [
@@ -66,7 +67,7 @@
     ["TRACTION_RUN_1", "A1", "Claimed", True, "2022-12-07 07:15:19", None],
     ["TRACTION_RUN_1", "B1", "On hold", True, "2022-12-08 07:15:19", None],
     ["TRACTION_RUN_1", "C1", "Claimed", True, "2022-12-08 08:15:19", None],
-    ["TRACTION_RUN_1", "D1", "On hold", True, "2022-12-08 09:15:19", None],
+    ["TRACTION_RUN_1", "D1", "On hold external", True, "2022-12-08 09:15:19", None],
     ["TRACTION_RUN_1", "E1", "Claimed", True, "2022-12-07 09:15:19", None],
     ["TRACTION_RUN_2", "A1", "Failed, Instrument", True, "2022-12-07 15:13:56", 1],
     ["TRACTION_RUN_2", "B1", "Failed, Instrument", False, "2022-12-08 15:18:56", 1],

tests/test_pb_wells_factory.py

@@ -31,7 +31,7 @@ def test_query_for_status(
         assert isinstance(state, QcState)
         assert state.is_preliminary == 1
         assert state.qc_type.qc_type == "sequencing"
-        assert state.qc_state_dict.state == "On hold"
+        assert state.qc_state_dict.state in ("On hold", "On hold external")
         compare_dates(state.date_updated, update_dates[index])
 
     factory = PacBioPagedWellsFactory(
@@ -400,8 +400,13 @@ def test_known_run_names_input(
     label_list = [well.label for well in wells]
     assert label_list == ["A1", "B1", "C1", "D1"]
 
-    qc_states = [well.qc_state.qc_state for well in wells]
-    expected_qc_states = ["Claimed", "On hold", "Claimed", "On hold"]
+    qc_states = sorted([well.qc_state.qc_state for well in wells])
+    expected_qc_states = [
+        "Claimed",
+        "Claimed",
+        "On hold",
+        "On hold external",
+    ]
     assert qc_states == expected_qc_states
 
     factory = PacBioPagedWellsFactory(

tests/test_qc_state_retrieval.py

@@ -30,7 +30,7 @@ def test_bulk_retrieval(qcdb_test_session, load_data4well_retrieval):
     # product IDs is performed.
     assert get_qc_states_by_id_product_list(qcdb_test_session, ["dodo"]) == {}
 
-    qc_state_descriptions = ["On hold", "Failed, Instrument"]
+    qc_state_descriptions = ["On hold external", "Failed, Instrument"]
 
     qc_states = get_qc_states_by_id_product_list(qcdb_test_session, two_good_ids_list)
     assert len(qc_states) == 2
@@ -140,23 +140,23 @@ def test_product_qc_state_retrieval(qcdb_test_session, load_data4well_retrieval)
     assert qc_state is not None
     assert qc_state.seq_product.id_product == FIRST_GOOD_CHECKSUM
     assert qc_state.qc_type.qc_type == "sequencing"
-    assert qc_state.qc_state_dict.state == "On hold"
+    assert qc_state.qc_state_dict.state == "On hold external"
 
     qc_state = get_qc_state_for_product(
         session=qcdb_test_session, id_product=FIRST_GOOD_CHECKSUM, qc_type="sequencing"
     )
     assert qc_state is not None
     assert qc_state.seq_product.id_product == FIRST_GOOD_CHECKSUM
     assert qc_state.qc_type.qc_type == "sequencing"
-    assert qc_state.qc_state_dict.state == "On hold"
+    assert qc_state.qc_state_dict.state == "On hold external"
 
     qc_state = get_qc_state_for_product(
         session=qcdb_test_session, id_product=FIRST_GOOD_CHECKSUM, qc_type="library"
     )
     assert qc_state is not None
     assert qc_state.seq_product.id_product == FIRST_GOOD_CHECKSUM
     assert qc_state.qc_type.qc_type == "library"
-    assert qc_state.qc_state_dict.state == "On hold"
+    assert qc_state.qc_state_dict.state == "On hold external"
 
     qc_state = get_qc_state_for_product(qcdb_test_session, SECOND_GOOD_CHECKSUM)
     assert qc_state is not None
@@ -183,6 +183,7 @@ def test_dict_helper(qcdb_test_session, load_dicts_and_users):
         "Failed, SMRT cell",
         "Claimed",
         "On hold",
+        "On hold external",
         "Undecided",
     ]
     assert list(qc_state_dict(qcdb_test_session).keys()) == expected_sorted_states