Introduced 'On hold external' QC state.

This state will be assigned to wells when the outcome of the QC assessment depends on liasing with a third party. The existing 'On hold' state will be used for flagging internal investigations. As fas as QC statuses and workflow is concerned, the new state is handled in the same way as the existing 'On hold' state.
wtsi-npg · Mar 22, 2024 · 0577d55 · 0577d55
1 parent f599e37
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diff --git a/alembic/versions/2.1.0_extend_qc_state_dict.py b/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'")
diff --git a/lang_qc/db/helper/wells.py b/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%"),

diff --git a/lang_qc/endpoints/config.py b/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
diff --git a/tests/endpoints/test_config.py b/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},
         ],
     }

diff --git a/tests/endpoints/test_dump_qc_states.py b/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

diff --git a/tests/endpoints/test_filtered_wells.py b/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(

diff --git a/tests/endpoints/test_wells4run.py b/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"

diff --git a/tests/fixtures/well_data.py b/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],

diff --git a/tests/test_pb_wells_factory.py b/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(

diff --git a/tests/test_qc_state_retrieval.py b/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