Merge pull request #192 from wtsi-npg/devel

pull from devel to master to create release 1.5.1

CHANGELOG.md

@@ -3,6 +3,30 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+
+## [1.5.1] - 2024-01-25
+
+### Changed
+
+* The 'Unknown' UI tab no longer displays the wells that have any
+  sequencing QC state associated with it. This feature was requested
+  by the users.
+
+* To increase code readability, renamed qc_state_for_product_exists
+  method in lang_qc::db::helper::qc to product_has_qc_state.
+
+* Added method products_have_qc_state to lang_qc::db::helper::qc,
+  used it to optimise (reduce the number of database queries) some
+  of the existing back-end code.
+
+### Fixed
+
+* The client side JavaScript dependency, element-plus, is pinned
+  to version 2.4.4. In mid-January 2024 this was the highest version
+  that worked with our code. The version expression we had "^2.3.7"
+  allowed for fetching the latest available version of this library. 
+
 ## [1.5.0]
 
 ### Added

frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "npg-longue-vue",
-  "version": "1.5.0",
+  "version": "1.5.1",
   "description": "UI for LangQC",
   "author": "Kieron Taylor <[email protected]>",
   "license": "GPL-3.0-or-later",
@@ -19,7 +19,7 @@
   },
   "dependencies": {
     "@element-plus/icons-vue": "^2.0.10",
-    "element-plus": "^2.3.7",
+    "element-plus": "2.4.4",
     "lodash": "^4.17.21",
     "pinia": "^2.0.23",
     "vue": "^3.2.37",

lang_qc/__init__.py

@@ -1 +1 @@
-__version__ = "1.5.0"
+__version__ = "1.5.1"

lang_qc/db/helper/qc.py

@@ -40,6 +40,7 @@
 
 APPLICATION_NAME = "LangQC"
 DEFAULT_QC_TYPE = "sequencing"
+SEQUENCING_QC_TYPE = DEFAULT_QC_TYPE
 CLAIMED_QC_STATE = "Claimed"
 DEFAULT_FINALITY = False
 ONLY_PRELIM_STATES = (CLAIMED_QC_STATE, "On hold")
@@ -78,7 +79,7 @@ def get_qc_states_by_id_product_list(
 
     If only sequencing type QC states are required, an optional
     argument, sequencing_outcomes_only, should be set to True.
-    If this case it is guaranteed that the list of QcState objects
+    In this case it is guaranteed that the list of QcState objects
     has only one member.
 
     Product IDs for which no QC states are found are omitted
@@ -100,7 +101,7 @@ def get_qc_states_by_id_product_list(
     )
 
 
-def qc_state_for_product_exists(
+def product_has_qc_state(
     session: Session, id_product: ChecksumSHA256, qc_type: str = None
 ) -> bool:
     """
@@ -132,6 +133,36 @@ def qc_state_for_product_exists(
     return bool(session.execute(query).scalar_one())
 
 
+def products_have_qc_state(
+    session: Session, ids: list[ChecksumSHA256], sequencing_outcomes_only: bool = False
+) -> set[ChecksumSHA256]:
+    """
+    Given a list of product IDs, returns a potentially empty subset of this list
+    as a Set object. Each product, identified by the product ID in the returned
+    set, has some QC state associated with it. If `sequencing_outcome_only`
+    boolean flag is true, the product must have sequencing QC state associated
+    with it; `library` QC state is excluded.
+
+    Arguments:
+        `session` - `sqlalchemy.orm.Session`, a connection for LangQC database.
+        `ids` - a list of string product IDs.
+        `sequencing_outcome_only` - a boolean flag indicating whether the caller
+        is interested in `sequencing` QC states only
+    """
+
+    query = select(SeqProduct.id_product).where(SeqProduct.id_product.in_(ids))
+    if sequencing_outcomes_only is True:
+        query = query.join(SeqProduct.qc_state).where(
+            QcStateDb.qc_type == _get_qc_type_row(session, SEQUENCING_QC_TYPE)
+        )
+
+    # We asked to retrieve data for one column only. The return value for
+    # each row is an array with a single value from this column.
+    product_ids = [row[0] for row in session.execute(query).all()]
+
+    return set(product_ids)
+
+
 def get_seq_product(session: Session, id_product: ChecksumSHA256) -> SeqProduct:
     """
     Given a product ID, returns a SeqProduct row for a database entity with
@@ -149,7 +180,7 @@ def get_seq_product(session: Session, id_product: ChecksumSHA256) -> SeqProduct:
 
 
 def get_qc_state_for_product(
-    session: Session, id_product: ChecksumSHA256, qc_type: str = "sequencing"
+    session: Session, id_product: ChecksumSHA256, qc_type: str = DEFAULT_QC_TYPE
 ) -> QcStateDb:
     """
     Returns a QcState database row associated with the product with the

lang_qc/db/helper/wells.py

@@ -29,7 +29,7 @@
 
 from lang_qc.db.helper.qc import (
     get_qc_states_by_id_product_list,
-    qc_state_for_product_exists,
+    products_have_qc_state,
 )
 from lang_qc.db.mlwh_schema import PacBioRunWellMetrics
 from lang_qc.db.qc_schema import QcState, QcStateDict, QcType
@@ -365,15 +365,11 @@ def _upcoming_wells(self):
             )
         )
 
-        wells = []
-        for w in self.session.execute(query).scalars().all():
-            if (
-                qc_state_for_product_exists(
-                    session=self.qcdb_session, id_product=w.id_pac_bio_product
-                )
-                is False
-            ):
-                wells.append(w)
+        wells = self.session.execute(query).scalars().all()
+        ids_with_qc_state = products_have_qc_state(
+            session=self.qcdb_session, ids=[w.id_pac_bio_product for w in wells]
+        )
+        wells = [w for w in wells if w.id_pac_bio_product not in ids_with_qc_state]
 
         self.total_number_of_items = len(wells)  # Save the number of retrieved wells.
 
@@ -420,10 +416,21 @@ def _aborted_and_unknown_wells(self, qc_flow_status: QcFlowStatusEnum):
             .all()
         )
 
+        qc_state_applicable = True
+        if qc_flow_status == QcFlowStatusEnum.UNKNOWN:
+            # Remove the wells that the QC team has dealt with.
+            ids_with_qc_state = products_have_qc_state(
+                session=self.qcdb_session,
+                ids=[w.id_pac_bio_product for w in wells],
+                sequencing_outcomes_only=True,
+            )
+            wells = [w for w in wells if w.id_pac_bio_product not in ids_with_qc_state]
+            qc_state_applicable = False
+
         # Save the number of retrieved rows.
         self.total_number_of_items = len(wells)
 
-        return self._well_models(self.slice_data(wells), True)
+        return self._well_models(self.slice_data(wells), qc_state_applicable)
 
     def _well_models(
         self,
@@ -454,7 +461,7 @@ def _well_models(
                     sequencing_outcomes_only=True,
                 ).get(id_product)
                 # A well can have only one or zero current sequencing outcomes.
-                if qced_products is not None:
+                if qced_products is not None and (len(qced_products) > 0):
                     attrs["qc_state"] = qced_products[0]
             pb_well = PacBioWell.model_validate(attrs)
             pb_well.copy_run_tracking_info(db_well)

lang_qc/endpoints/pacbio_well.py

@@ -29,7 +29,7 @@
 from lang_qc.db.helper.qc import (
     assign_qc_state_to_product,
     claim_qc_for_product,
-    qc_state_for_product_exists,
+    product_has_qc_state,
 )
 from lang_qc.db.helper.well import well_seq_product_find_or_create
 from lang_qc.db.helper.wells import PacBioPagedWellsFactory, WellWh
@@ -216,7 +216,7 @@ def claim_qc(
     mlwh_well = _find_well_product_or_error(id_product, mlwhdb_session)
 
     # Checking for any type of QC state
-    if qc_state_for_product_exists(qcdb_session, id_product):
+    if product_has_qc_state(qcdb_session, id_product):
         raise HTTPException(
             status_code=status.HTTP_409_CONFLICT,
             detail=f"Well for product {id_product} has QC state assigned",
@@ -261,10 +261,7 @@ def assign_qc_state(
 
     mlwh_well = _find_well_product_or_error(id_product, mlwhdb_session)
 
-    if (
-        qc_state_for_product_exists(qcdb_session, id_product, request_body.qc_type)
-        is False
-    ):
+    if product_has_qc_state(qcdb_session, id_product, request_body.qc_type) is False:
         raise HTTPException(
             status_code=status.HTTP_409_CONFLICT,
             detail="QC state of an unclaimed well cannot be updated",

pyproject.toml

@@ -3,7 +3,7 @@ name = "npg_langqc"
 packages = [
   { include = "lang_qc" },
 ]
-version = "1.5.0"
+version = "1.5.1"
 description = "FastAPI application for Long Read QC"
 authors = ["Adam Blanchet", "Marina Gourtovaia <[email protected]>", "Kieron Taylor <[email protected]>"]
 license = "GPL-3.0-or-later"

tests/test_pb_wells_factory.py

@@ -1,8 +1,9 @@
 import pytest
 from npg_id_generation.pac_bio import PacBioEntity
+from sqlalchemy import select
 
 from lang_qc.db.helper.wells import PacBioPagedWellsFactory, RunNotFoundError
-from lang_qc.db.qc_schema import QcState
+from lang_qc.db.qc_schema import QcState, QcType, SeqProduct
 from lang_qc.models.pacbio.well import PacBioPagedWells, PacBioWell
 from lang_qc.models.qc_flow_status import QcFlowStatusEnum
 from lang_qc.models.qc_state import QcState as QcStateModel
@@ -175,13 +176,15 @@ def test_paged_retrieval_for_statuses(
         QcFlowStatusEnum.ON_HOLD.name: 2,
         QcFlowStatusEnum.QC_COMPLETE.name: 4,
         QcFlowStatusEnum.UPCOMING.name: 4,
+        QcFlowStatusEnum.UNKNOWN.name: 2,
     }
 
     for status in [
         QcFlowStatusEnum.IN_PROGRESS,
         QcFlowStatusEnum.ON_HOLD,
         QcFlowStatusEnum.QC_COMPLETE,
         QcFlowStatusEnum.UPCOMING,
+        QcFlowStatusEnum.UNKNOWN,
     ]:
 
         factory = PacBioPagedWellsFactory(
@@ -425,3 +428,74 @@ def test_known_run_names_input(
     qc_state_objs = [well.qc_state for well in wells]
     assert qc_state_objs[0] is None
     assert qc_state_objs[1] is None
+
+
+def test_retrieval_for_unknown_status(
+    qcdb_test_session, mlwhdb_test_session, load_data4well_retrieval
+):
+    # SUBTRACTION_RUN_15:A1
+    # TRACTION_RUN_14:B1
+
+    factory = PacBioPagedWellsFactory(
+        qcdb_session=qcdb_test_session,
+        mlwh_session=mlwhdb_test_session,
+        page_size=10,
+        page_number=1,
+    )
+    paged_wells = factory.create_for_qc_status(QcFlowStatusEnum.UNKNOWN)
+    assert (
+        paged_wells.total_number_of_items == 2
+    ), "two wells with unknown status, no qc state"
+
+    # Create seq QC states for these wells and test that they are gone
+    # from the Unknown status.
+
+    id = PacBioEntity(run_name="TRACTION_RUN_14", well_label="B1").hash_product_id()
+
+    seq_product = SeqProduct(id_product=id, id_seq_platform=1, has_seq_data=1)
+    qcdb_test_session.add(seq_product)
+    qcdb_test_session.commit()
+
+    qc_type_row = (
+        qcdb_test_session.execute(select(QcType).where(QcType.qc_type == "library"))
+        .scalars()
+        .one()
+    )
+    qc_state = QcState(
+        created_by="LangQC",
+        is_preliminary=1,
+        id_qc_state_dict=2,
+        qc_type=qc_type_row,
+        seq_product=seq_product,
+        id_user=1,
+    )
+    qcdb_test_session.add(qc_state)
+    qcdb_test_session.commit()
+
+    paged_wells = factory.create_for_qc_status(QcFlowStatusEnum.UNKNOWN)
+    assert (
+        paged_wells.total_number_of_items == 2
+    ), """assigning library qc state to a well does not affect
+          its selection for the unknown status"""
+
+    qc_type_row = (
+        qcdb_test_session.execute(select(QcType).where(QcType.qc_type == "sequencing"))
+        .scalars()
+        .one()
+    )
+    qc_state = QcState(
+        created_by="LangQC",
+        is_preliminary=1,
+        id_qc_state_dict=3,
+        qc_type=qc_type_row,
+        seq_product=seq_product,
+        id_user=1,
+    )
+    qcdb_test_session.add(qc_state)
+    qcdb_test_session.commit()
+
+    paged_wells = factory.create_for_qc_status(QcFlowStatusEnum.UNKNOWN)
+    assert (
+        paged_wells.total_number_of_items == 1
+    ), """assigning sequencing qc state to a well removes it
+          from the selection for the unknown status"""