Merge branch 'devel' into render_product_metrics

CHANGELOG.md

@@ -5,6 +5,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+## [2.2.0] - 2024-06-11
+
+### Added
+
+* New endpoint added to support potential email notifications when QC states are finalised. `/products/qc?weeks={n}&seq_level={bool}&final={bool}`. It returns recent QC events
+
+### Fixed
+
+* Warehouse schema updated to match breaking change in pac_bio_product_metrics table
+
 ## [2.1.0] - 2024-04-15
 
 ### Changed
@@ -77,7 +87,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 * 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. 
+  allowed for fetching the latest available version of this library.
 
 ## [1.5.0]
 

frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "npg-longue-vue",
-  "version": "2.1.0",
+  "version": "2.2.0",
   "description": "UI for LangQC",
   "author": "Kieron Taylor <[email protected]>",
   "license": "GPL-3.0-or-later",

lang_qc/__init__.py

@@ -1 +1 @@
-__version__ = "2.1.0"
+__version__ = "2.2.0"

lang_qc/db/helper/qc.py

@@ -20,7 +20,7 @@
 # this program. If not, see <http://www.gnu.org/licenses/>.
 
 from collections import defaultdict
-from datetime import datetime
+from datetime import date, datetime, timedelta
 
 from sqlalchemy import and_, func, select
 from sqlalchemy.exc import NoResultFound
@@ -105,6 +105,62 @@ def get_qc_states_by_id_product_list(
     return dict(response)
 
 
+def get_qc_states(
+    session: Session,
+    num_weeks: int,
+    sequencing_outcomes_only: bool = False,
+    final_only: bool = False,
+) -> dict[ChecksumSHA256, list[QcState]]:
+    """
+    Returns a dictionary where keys are the product IDs, and the values are
+    lists of QcState records of any type for the same product.
+
+    The num_weeks argument limits the look-back time window.
+
+    If only sequencing type QC states are required, an optional
+    argument, sequencing_outcomes_only, should be set to True.
+    In this case it is guaranteed that the list of QcState objects
+    has only one member.
+
+    If only final QC states are required, an optional argument final_only
+    should be set to True.
+    """
+
+    if num_weeks < 1:
+        raise ValueError("num_weeks should be a positive number")
+
+    query = (
+        select(QcStateDb)
+        .join(QcStateDb.seq_product)
+        .join(QcType)
+        .join(QcStateDict)
+        .join(User)
+        .where(QcStateDb.date_updated > date.today() - timedelta(weeks=num_weeks))
+        .options(
+            selectinload(QcStateDb.seq_product),
+            selectinload(QcStateDb.qc_type),
+            selectinload(QcStateDb.user),
+            selectinload(QcStateDb.qc_state_dict),
+        )
+    )
+    if sequencing_outcomes_only is True:
+        query = query.where(QcType.qc_type == SEQUENCING_QC_TYPE)
+    if final_only is True:
+        query = query.where(QcStateDb.is_preliminary == 0)
+
+    qc_states_dict = dict()
+    for qc_state in [
+        QcState.from_orm(row) for row in session.execute(query).scalars().all()
+    ]:
+        id = qc_state.id_product
+        if id in qc_states_dict:
+            qc_states_dict[id].append(qc_state)
+        else:
+            qc_states_dict[id] = [qc_state]
+
+    return qc_states_dict
+
+
 def product_has_qc_state(
     session: Session, id_product: ChecksumSHA256, qc_type: str = None
 ) -> bool:

lang_qc/db/mlwh_schema.py

@@ -25,9 +25,30 @@
 from sqlalchemy.dialects.mysql import SMALLINT as mysqlSMALLINT
 from sqlalchemy.dialects.mysql import TINYINT as mysqlTINYINT
 from sqlalchemy.dialects.mysql import VARCHAR as mysqlVARCHAR
-from sqlalchemy.orm import declarative_base, relationship
+from sqlalchemy.orm import DeclarativeBase, relationship
 
-Base = declarative_base()
+
+class Base(DeclarativeBase):
+    """
+    A base class for declarative class definitions for the ml warehouse database.
+    """
+
+    def _get_row_description(self, fields: list[str]) -> str:
+        """
+        Returns a printable representation of the database table row. Interprets
+        a list of strings given as the `fields` argument as a list of column
+        names. Combines the name of the class, names of the given columns
+        and respective values into a row description. The columns for which
+        the row has a NULL value are omitted from the description.
+        """
+
+        pairs = []
+        for name in fields:
+            value = self.__getattribute__(name)
+            if value is not None:
+                pairs.append(f"{name}={value}")
+        description = ", ".join(pairs)
+        return f"{self.__module__}.{self.__class__.__name__}: {description}"
 
 
 class Sample(Base):
@@ -538,7 +559,16 @@ class PacBioRunWellMetrics(Base):
         "PacBioProductMetrics", back_populates="pac_bio_run_well_metrics"
     )
 
-    def get_experiment_info(self):
+    """Custom or customised methods are added below"""
+
+    def __repr__(self):
+        """Returns a printable representation of the database row"""
+
+        return self._get_row_description(
+            ["pac_bio_run_name", "well_label", "plate_number", "id_pac_bio_product"]
+        )
+
+    def get_experiment_info(self) -> list[PacBioRun]:
         """Returns a list of PacBioRun mlwh database rows.
 
         Returns LIMS information about the PacBio experiment

lang_qc/endpoints/pacbio_well.py

@@ -38,13 +38,18 @@
 from lang_qc.db.qc_connection import get_qc_db
 from lang_qc.db.qc_schema import User
 from lang_qc.models.pacbio.qc_data import QCPoolMetrics
-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, PacBioWellSHA256
@@ -164,6 +169,32 @@ 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/endpoints/product.py

@@ -18,15 +18,19 @@
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <http://www.gnu.org/licenses/>.
 
-from fastapi import APIRouter, Depends
+from typing import Annotated
+
+from fastapi import APIRouter, Depends, Query
 from sqlalchemy.orm import Session
 from starlette import status
 
-from lang_qc.db.helper.qc import get_qc_states_by_id_product_list
+from lang_qc.db.helper.qc import get_qc_states, get_qc_states_by_id_product_list
 from lang_qc.db.qc_connection import get_qc_db
 from lang_qc.models.qc_state import QcState
 from lang_qc.util.type_checksum import ChecksumSHA256
 
+RECENTLY_QCED_NUM_WEEKS = 4
+
 router = APIRouter(
     prefix="/products",
     tags=["product"],
@@ -62,3 +66,39 @@ def bulk_qc_fetch(
 ):
 
     return get_qc_states_by_id_product_list(session=qcdb_session, ids=request_body)
+
+
+@router.get(
+    "/qc",
+    summary="Returns a dictionary of QC states",
+    description="""
+    The response is a dictionary of lists of QcState models hashed on product IDs.
+    Multiple QC states for the same product might be returned if the query is not
+    constrained to a single QC type.
+
+    Query parameters constrain the semantics of the response.
+        `weeks`  - number of weeks to look back, defaults to four.
+        `seq_level` - a boolean option. If `True`, only `sequencing` type QC states
+            are returned. If `False` (the default), all types of QC states are
+            returned.
+        `final` - a boolean option. If `True`, only final QC states are returned.
+            If `False` (the default), both final and preliminary QC states are
+            returned.
+    """,
+    responses={
+        status.HTTP_422_UNPROCESSABLE_ENTITY: {"description": "Invalid number of weeks"}
+    },
+    response_model=dict[ChecksumSHA256, list[QcState]],
+)
+def qc_fetch(
+    weeks: Annotated[int, Query(gt=0)] = RECENTLY_QCED_NUM_WEEKS,
+    seq_level: bool = False,
+    final: bool = False,
+    qcdb_session: Session = Depends(get_qc_db),
+) -> dict[ChecksumSHA256, list[QcState]]:
+    return get_qc_states(
+        session=qcdb_session,
+        num_weeks=weeks,
+        sequencing_outcomes_only=seq_level,
+        final_only=final,
+    )