Merge branch 'update_toolchain' of https://github.com/nerdstrike/npg_…

…langqc into update_toolchain

CHANGELOG.md

@@ -3,6 +3,38 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+
+### Changed
+
+* To simplify object instantiation and fields' assignment for some
+  of the response models, converted `PacBioWell` and `PacBioWellFull`
+  models to pydantic dataclasses.
+* Changed the response model for filtered by either QC status or run wells from
+  `PacBioWell` to `PacBioWellSummary`, the latter initially being identical
+  the former. In order to propagate information about a study to the tabbed
+  well summary view, added a new field, study_names, to the `PacBioWellSummary`
+  model.
+* Added a new event to the tabbed well summary view, to the button with the well
+  name. Mouse hover over this button displays study names associated with the
+  well.
+* Changed the colour scheme of the above mentioned button from grey to orange
+  if one of the studies associated with the well is the BIOSCAN study, which
+  the QC team needs to deal with slightly differently.
+* Added a new QC state 'On hold external'. Semantically the new state is similar
+  to the existing 'On hold' state. The intended purpose of the new QC state - to
+  highlight the wells, which are waiting for a completion of some off-site
+  process (example - deplexing at http://mbrave.net/).
+
+### Added
+
+* A new response model `PacBioWellSummary`, which replaces `PacBioWell`
+  in the latest's capacity of the response model for a PacBio well
+  summary.
+* A new field, `study_names`, a potentially empty sorted array of
+  unique study names, is added to the response model for a PacBio
+  well summary.
+
 ## [2.0.0] - 2024-02-20
 
 ### Changed

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'")

frontend/src/components/QcView.vue

@@ -5,7 +5,7 @@
 
     import { computed } from "vue";
     import groupMetrics from "../utils/metrics.js";
-    import combineLabelWithPlate from "../utils/text.js"
+    import { combineLabelWithPlate } from "../utils/text.js"
 
     const props = defineProps({
         // Well object representing one prepared input for the instrument

frontend/src/components/WellTable.vue

@@ -2,7 +2,11 @@
 /*
 * Renders a table for a list of wells and generates buttons for selecting wells
 */
-import combineLabelWithPlate from "../utils/text.js"
+import { combineLabelWithPlate, listStudiesForTooltip } from "../utils/text.js"
+import { ElTooltip, ElButton } from "element-plus";
+
+const tooltipDelay = 500
+const studyNameHighlight = 'BIOSCAN UK for flying insects'
 
 defineProps({
   wellCollection: Object
@@ -28,9 +32,17 @@ defineEmits(['wellSelected'])
     <tr :key="wellObj.id_product" v-for="wellObj in wellCollection">
       <td>{{ wellObj.run_name }}</td>
       <td class="well_selector">
-        <button v-on:click="$emit('wellSelected', { idProduct: wellObj.id_product })">
-          {{ combineLabelWithPlate(wellObj.label, wellObj.plate_number) }}
-        </button>
+        <el-tooltip placement="top" effect="light" :show-after="tooltipDelay"
+          :content="'<span>'.concat(listStudiesForTooltip(wellObj.study_names)).concat('</span>')"
+          raw-content
+        >
+          <el-button
+            :type="wellObj.study_names.includes(studyNameHighlight) ? 'warning' : 'info'"
+            v-on:click="$emit('wellSelected', { idProduct: wellObj.id_product })"
+          >
+            {{ combineLabelWithPlate(wellObj.label, wellObj.plate_number) }}
+          </el-button>
+        </el-tooltip>
       </td>
       <td>{{ wellObj.instrument_type }} {{ wellObj.instrument_name }}</td>
       <td>{{ wellObj.qc_state ? wellObj.qc_state.qc_state : '&nbsp;' }}</td>

frontend/src/components/__tests__/WellTable.spec.js

@@ -7,9 +7,33 @@ describe('Rows of data give rows in the table', () => {
   const table = mount(WellTable, {
     props: {
       wellCollection: [
-        {run_name: 'TEST1', label: 'A1', plate_number: null, instrument_name: '1234', instrument_type: 'Revio', id_product: 'ABCDEF'},
-        {run_name: 'TEST1', label: 'B1', plate_number: null, instrument_name: '1234', instrument_type: 'Revio', id_product: '123456'},
-        {run_name: 'TEST2', label: 'A1', plate_number: 1, instrument_name: '1234', instrument_type: 'Revio', id_product: '123457'},
+        {
+          run_name: 'TEST1',
+          label: 'A1',
+          plate_number: null,
+          instrument_name: '1234',
+          instrument_type: 'Revio',
+          id_product: 'ABCDEF',
+          study_names: []
+        },
+        {
+          run_name: 'TEST1',
+          label: 'B1',
+          plate_number: null,
+          instrument_name: '1234',
+          instrument_type: 'Revio',
+          id_product: '123456',
+          study_names: ['Study name 1', 'Study name 2']
+        },
+        {
+          run_name: 'TEST2',
+          label: 'A1',
+          plate_number: 1,
+          instrument_name: '1234',
+          instrument_type: 'Revio',
+          id_product: '123457',
+          study_names: ['BIOSCAN UK for flying insects']
+        },
       ]
     }
   })
@@ -40,7 +64,14 @@ describe('Rows of data give rows in the table', () => {
     expect(table.emitted().wellSelected[0][0]).toHaveProperty('idProduct')
     expect(table.emitted().wellSelected[0][0].idProduct).toEqual('ABCDEF')
 
-    await rows[2].find('button').trigger('click')
+    let wellButton = rows[2].find('button')
+    await wellButton.trigger('click')
     expect(table.emitted().wellSelected[1][0].idProduct).toEqual('123456')
+    expect(wellButton.classes('el-tooltip__trigger')).toBeTruthy()
+    expect(wellButton.classes('el-button--info')).toBeTruthy()
+
+    wellButton = rows[3].find('button')
+    expect(wellButton.classes('el-tooltip__trigger')).toBeTruthy()
+    expect(wellButton.classes('el-button--warning')).toBeTruthy()
   })
 })

frontend/src/utils/__tests__/text.spec.js

@@ -1,7 +1,7 @@
 import { describe, test, expect } from 'vitest'
-import combineLabelWithPlate from '../text'
+import { combineLabelWithPlate, listStudiesForTooltip } from '../text'
 
-describe('Text processing', () => {
+describe('Well label and plate display', () => {
   test('Print well label without plate number', () => {
     expect(combineLabelWithPlate('A1', undefined)).toEqual('A1')
     expect(combineLabelWithPlate('A1', null)).toEqual('A1')
@@ -11,3 +11,18 @@ describe('Text processing', () => {
     expect(combineLabelWithPlate('A1', 1)).toEqual('1-A1')
   })
 })
+
+describe('Study names tooltip', () => {
+  test('Display a warning in case of an empty study array', () => {
+    expect(listStudiesForTooltip([])).toEqual('No study info')
+  })
+
+  test('Display a single study name for an array of one study', () => {
+    expect(listStudiesForTooltip(['My single study'])).toEqual('My single study')
+  })
+
+  test('Display multiple lines for multiple studies', () => {
+    expect(listStudiesForTooltip(['Study One', 'Study two', 'Study 3'])).toEqual(
+      'Study One<br />Study two<br />Study 3')
+  })
+})

frontend/src/utils/text.js

@@ -1,9 +1,16 @@
 // Reusable text-mangling for the interface
 
-export default function combineLabelWithPlate(well, plate) {
+export { combineLabelWithPlate, listStudiesForTooltip }
+
+function combineLabelWithPlate(well, plate) {
   if (!plate) {
     return well
   } else {
     return `${plate}-${well}`
   }
 }
+
+function listStudiesForTooltip(study_names) {
+  let names = study_names.length == 0 ? ['No study info'] : study_names
+  return names.join('<br />')
+}

frontend/src/views/__tests__/WellsByRun.spec.js

@@ -38,6 +38,7 @@ for (let index = 0; index < 2; index++) {
     instrument_name: "1234",
     instrument_type: "Revio",
     id_product: `${index}23456`,
+    study_names: [`Study ${index}`, 'Another study'],
     ...someLinkGeneration
   })
 }
@@ -48,6 +49,7 @@ const secondaryRun = {
   instrument_name: '1234',
   instrument_type: 'Revio',
   id_product: 'ABCDEF',
+  study_names: [],
   ...someLinkGeneration
 }
 
@@ -141,7 +143,6 @@ describe('Does it work?', async () => {
     let buttons = wrapper.findAll('button')
     buttons[1].trigger('click')
     await flushPromises()
-
     expect(wrapper.get('#well_summary').exists()).toBe(true)
   })
 

frontend/src/views/__tests__/WellsByStatus.spec.js

@@ -31,7 +31,8 @@ for (let index = 0; index < 10; index++) {
     well_status: "Complete",
     qc_state: null,
     instrument_name: 1234,
-    instrument_type: 'Revio'
+    instrument_type: 'Revio',
+    study_names: ['Some study'],
   })
 }
 
@@ -140,6 +141,7 @@ describe('View loads configuration on mount', async () => {
           qc_state: null,
           instrument_name: '1234',
           instrument_type: 'Revio',
+          study_names: [],
         }]
       })
     )

lang_qc/db/helper/wells.py

@@ -33,7 +33,7 @@
 )
 from lang_qc.db.mlwh_schema import PacBioRunWellMetrics
 from lang_qc.db.qc_schema import QcState, QcStateDict, QcType
-from lang_qc.models.pacbio.well import PacBioPagedWells, PacBioWell
+from lang_qc.models.pacbio.well import PacBioPagedWells, PacBioWellSummary
 from lang_qc.models.pager import PagedResponse
 from lang_qc.models.qc_flow_status import QcFlowStatusEnum
 from lang_qc.models.qc_state import QcState as QcStateModel
@@ -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%"),
@@ -195,7 +195,7 @@ def create_for_qc_status(
         specified by the `page_size`, `page_number` object's attributes and
         `qc_flow_status` argument of this function..
 
-        The `PacBioWell` objects in `wells` attribute of the returned object
+        The `PacBioWellPacBioWell` objects in `wells` attribute of the returned object
         are sorted in a way appropriate for the requested `qc_flow_status`.
         For the 'in progress' and 'on hold' requests the wells with most recently
         assigned QC states come first. For inbox requests the wells with least
@@ -230,7 +230,7 @@ def create_for_run(self, run_name: str) -> PacBioPagedWells:
         """
         Returns `PacBioPagedWells` object that corresponds to the criteria
         specified by the `page_size` and `page_number` attributes.
-        The `PacBioWell` objects in `wells` attribute of the returned object
+        The `PacBioWellSummary` objects in `wells` attribute of the returned object
         belong to runs specified by the `run_name` argument and are sorted
         by the run name and well label.
         """
@@ -281,7 +281,7 @@ def _retrieve_paged_qc_states(
 
     def _get_wells_for_status(
         self, qc_flow_status: QcFlowStatusEnum
-    ) -> List[PacBioWell]:
+    ) -> List[PacBioWellSummary]:
 
         wells = []
 
@@ -290,7 +290,7 @@ def _get_wells_for_status(
             id_product = qc_state_model.id_product
             mlwh_well = self.get_mlwh_well_by_product_id(id_product=id_product)
             if mlwh_well is not None:
-                pbw = PacBioWell(db_well=mlwh_well, qc_state=qc_state_model)
+                pbw = PacBioWellSummary(db_well=mlwh_well, qc_state=qc_state_model)
                 wells.append(pbw)
             else:
                 """
@@ -394,7 +394,7 @@ def _well_models(
             qc_state = None
             if id_product in qced_products:
                 qc_state = qced_products[id_product][0]
-            pb_well = PacBioWell(db_well=db_well, qc_state=qc_state)
+            pb_well = PacBioWellSummary(db_well=db_well, qc_state=qc_state)
             pb_wells.append(pb_well)
 
         return pb_wells

lang_qc/db/mlwh_schema.py

@@ -538,6 +538,27 @@ class PacBioRunWellMetrics(Base):
         "PacBioProductMetrics", back_populates="pac_bio_run_well_metrics"
     )
 
+    def get_experiment_info(self):
+        """Returns a list of PacBioRun mlwh database rows.
+
+        Returns LIMS information about the PacBio experiment
+        for this well, one pac_bio_run table row per sample
+        (product) in the well.
+
+        If any or all of the pac_bio_product_metrics rows linked
+        to this well record are not linked to the pac_bio_run
+        table, and empty array is returned, thus preventing incomplete
+        data being supplied to the client.
+        """
+        product_metrics = self.pac_bio_product_metrics
+        experiment_info = [
+            pbr for pbr in [pm.pac_bio_run for pm in product_metrics] if pbr is not None
+        ]
+        if len(experiment_info) != len(product_metrics):
+            experiment_info = []
+
+        return experiment_info
+
 
 class PacBioProductMetrics(Base):
     __tablename__ = "pac_bio_product_metrics"

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