Merge branch 'main' into dialog-valadation-required-fields

.github/workflows/build-and-publish-docker-images.yml

@@ -11,7 +11,7 @@ env:
 
 jobs:
   build-and-push-image:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3

.github/workflows/common-static-analysis.yml

@@ -1,5 +1,4 @@
 name: Markdown, Docker, and Shell Static Analysis
-
 on: [push, pull_request, workflow_dispatch]
 
 env:
@@ -10,7 +9,8 @@ env:
 
 jobs:
   docker-shell-markdown-static-analysis:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/draft-paper.yml

@@ -11,7 +11,7 @@ on:
 
 jobs:
   paper:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     name: JOSS pandoc paper draft
     steps:
       - name: Checkout

.github/workflows/nodejs.yml

@@ -9,7 +9,8 @@ defaults:
 jobs:
   nodejs-ci:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
 
     strategy:
       matrix:

.github/workflows/python.yml

@@ -10,7 +10,9 @@ env:
 jobs:
   python-ci:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+
     strategy:
       fail-fast: false
       matrix:

.github/workflows/system-tests.yml

@@ -4,7 +4,8 @@ on: [push, pull_request, workflow_dispatch]
 
 jobs:
   system-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
 
     steps:
     - uses: actions/checkout@v3

backend/README.md

@@ -187,21 +187,26 @@ docker run -v <absolute_path_to_backend>/:/app/ -p 127.0.0.1:8000:8000 <image_id
 The backend service uses `pytest` as a testing framework for the Python code. The tests are broken out into unit,
 integration, and system tests.
 
-Note: The `-s` flag for the pytest routes the standard out to the console. It allows the `print()` statement to log
+Pytest notes:
+
+- In order for Rosalution to work, it requires a ROSALUTION_KEY environment variable to be set. Since the tests are not
+actually running Rosalution, this needs to be manually done each time when running pytest.
+
+- The `-s` flag for the pytest routes the standard out to the console. It allows the `print()` statement to log
 output of variables for development purposes.
 
 From the root `./` directory of the project:
 
 Unit Tests:
 
 ```bash
-pytest -s tests/unit
+ROSALUTION_KEY="fake-rosalution-key-used-in-pytest" pytest -s tests/unit
 ```
 
 Integration Tests:
 
 ```bash
-pytest -s tests/integration
+ROSALUTION_KEY="fake-rosalution-key-used-in-pytest" pytest -s tests/integration
 ```
 
 ### Code Coverage
@@ -218,5 +223,5 @@ Read <https://pytest-cov.readthedocs.io/en/latest/config.html> to learn more abo
 tool configuration.
 
 ```bash
-pytest --cov=src --cov-fail-under=80 --cov-branch --cov-report=term tests/unit/
+ROSALUTION_KEY="fake-rosalution-key-used-in-pytest" pytest --cov=src --cov-fail-under=80 --cov-branch --cov-report=term tests/unit/
 ```

backend/tests/unit/core/test_annotation_task.py

@@ -1,4 +1,5 @@
 """Tests Annotation Tasks and the creation of them"""
+from unittest.mock import patch
 import pytest
 
 from src.core.annotation_task import AnnotationTaskFactory, ForgeAnnotationTask, HttpAnnotationTask
@@ -88,7 +89,14 @@ def test_annotation_extraction_for_genomic_unit(http_annotation_task_gene, hpo_a
     } in actual_extractions
 
 
-def test_annotation_extraction_value_error_exception(http_annotation_task_gene, hpo_annotation_response):
+# Patching the temporary helper method that is writing to a file, this will be
+# removed once that helper method is no longer needed for the development
+
+
+@patch("src.core.annotation_task.log_to_file")
+def test_annotation_extraction_value_error_exception(
+    log_to_file_mock, http_annotation_task_gene, hpo_annotation_response
+):  # pylint: disable=unused-argument
     """Verifying annotation failure does not cause crash in application during extraction"""
 
     # Removing the expected value in the json to force a jq parse error to more closely

frontend/src/components/AnalysisListing/AnalysisListingLegend.vue

@@ -1,44 +1,88 @@
 <template>
   <div class="legend">
-    <font-awesome-icon icon="asterisk" size="lg" style="color: var(--rosalution-status-annotation);"/>
-    <p>Annotating</p>
-    <font-awesome-icon icon="clipboard-check" size="lg" style="color: var(--rosalution-status-ready);"/>
-    <p>Ready</p>
-    <font-awesome-icon icon="book-open" size="lg" style="color: var(--rosalution-status-active)"/>
-    <p>Active</p>
-    <font-awesome-icon icon="pause" size="lg" style="color: var(--rosalution-status-on-hold)"/>
-    <p>On Hold</p>
-    <font-awesome-icon icon="check" size="lg" style="color: var(--rosalution-status-approved)"/>
-    <p>Approved</p>
-    <font-awesome-icon icon="x" size="lg" style="color: var(--rosalution-status-declined)"/>
-    <p>Declined</p>
+    <div v-for="status in statuses" :key="status.name" class="status" @click="toggleFilter(status.name)">
+      <font-awesome-icon :icon="status.icon" size="lg" :style="{
+        color: isFiltered(status.name)
+          ? `var(--rosalution-status-${status.name})`
+          : 'var(--rosalution-grey-300)',
+      }" />
+      <p :style="{
+        color: isFiltered(status.name)
+          ? ''
+          : 'var(--rosalution-grey-300)',
+      }">
+        {{ status.displayName }}
+      </p>
+    </div>
   </div>
 </template>
 
-<style scoped>
+<script>
+import {FontAwesomeIcon} from '@fortawesome/vue-fontawesome';
+
+export default {
+  name: 'analysis-listing-legend',
+  emits: ['filtered-changed'],
+  components: {
+    'font-awesome-icon': FontAwesomeIcon,
+  },
+  data() {
+    return {
+      activeFilters: [],
+      statuses: [
+        {name: 'annotation', displayName: 'Annotating', icon: 'asterisk'},
+        {name: 'ready', displayName: 'Ready', icon: 'clipboard-check'},
+        {name: 'active', displayName: 'Active', icon: 'book-open'},
+        {name: 'on-hold', displayName: 'On Hold', icon: 'pause'},
+        {name: 'approved', displayName: 'Approved', icon: 'check'},
+        {name: 'declined', displayName: 'Declined', icon: 'times'},
+      ],
+    };
+  },
+  methods: {
+    toggleFilter(status) {
+      const index = this.activeFilters.indexOf(status);
+
+      if (index !== -1) {
+        this.activeFilters.splice(index, 1);
+      } else {
+        this.activeFilters.push(status);
+      }
 
+      if (this.activeFilters.length === this.statuses.length) {
+        this.activeFilters = [];
+      }
+
+      this.$emit('filtered-changed', this.activeFilters);
+    },
+    isFiltered(status) {
+      return this.activeFilters.includes(status) || this.activeFilters.length === 0;
+    },
+  },
+};
+</script>
+
+<style scoped>
 .legend {
   display: flex;
   flex-grow: 0;
   flex-direction: row;
   justify-content: center;
   align-items: center;
-  gap: 10px;
+  gap: var(--p-10);
   border-radius: var(--content-border-radius);
   padding: var(--p-8);
   background-color: var(--secondary-background-color);
 }
 
+.status {
+  display: flex;
+  align-items: center;
+  user-select: none;
+}
+
 .legend p {
   line-height: .245rem;
-  padding-right: var(--p-10);
+  padding-left: var(--p-10);
 }
-
 </style>
-
-
-<script>
-export default {
-  name: 'analysis-listing-legend',
-};
-</script>

frontend/src/views/AnalysisListingView.vue

@@ -27,7 +27,7 @@
   <app-footer>
     <InputDialog data-test="phenotips-import-dialog"/>
     <NotificationDialog data-test="notification-dialog" />
-    <AnalysisListingLegend/>
+    <AnalysisListingLegend @filtered-changed="filteredUpdated"/>
   </app-footer>
 </div>
 </template>
@@ -62,34 +62,44 @@ export default {
       store: authStore,
       searchText: '',
       analysisList: [],
+      filteredChanged: [],
     };
   },
   computed: {
     username() {
       return this.store.state.username;
     },
+    filteredAnalysisListing() {
+      return this.analysisList.filter((analysis) => {
+        return this.filteredChanged.length === 0 ||
+          this.filteredChanged.includes(analysis.latest_status.toLowerCase());
+      });
+    },
     searchedAnalysisListing() {
       const lowerCaseSearchText = this.searchText.toLowerCase();
 
-      return this.searchText === '' ? this.analysisList : this.analysisList.filter( (analysis) => {
+      return this.searchText === '' ? this.filteredAnalysisListing : this.filteredAnalysisListing.filter((analysis) => {
         return [analysis.name,
           analysis.created_date,
           analysis.last_modified_date,
           analysis.nominated_by,
         ].some((content) => content.toLowerCase().includes(lowerCaseSearchText)) ||
           analysis.genomic_units.some((unit) => {
             return (unit.gene && unit.gene.toLowerCase().includes(lowerCaseSearchText)) ||
-                (unit.transcripts &&
-                    unit.transcripts.some((transcript) => transcript.toLowerCase().includes(lowerCaseSearchText))) ||
-                (unit.variants && unit.variants.some((variant) => variant.toLowerCase().includes(lowerCaseSearchText)));
+              (unit.transcripts &&
+                unit.transcripts.some((transcript) => transcript.toLowerCase().includes(lowerCaseSearchText))) ||
+              (unit.variants && unit.variants.some((variant) => variant.toLowerCase().includes(lowerCaseSearchText)));
           });
-      } );
+      });
     },
   },
   created() {
     this.getListing();
   },
   methods: {
+    filteredUpdated(filteredChanged) {
+      this.filteredChanged = filteredChanged;
+    },
     async getListing() {
       this.analysisList.length = 0;
       const analyses = await Analyses.all();

frontend/test/components/AnalysisListing/AnalysisListingLegend.spec.js

@@ -5,13 +5,23 @@ import AnalysisListingLegend from '@/components/AnalysisListing/AnalysisListingL
 
 import {FontAwesomeIcon} from '@fortawesome/vue-fontawesome';
 
+const statuses = [
+  {name: 'annotation', displayName: 'Annotating', icon: 'asterisk'},
+  {name: 'ready', displayName: 'Ready', icon: 'clipboard-check'},
+  {name: 'active', displayName: 'Active', icon: 'book-open'},
+  {name: 'on-hold', displayName: 'On Hold', icon: 'pause'},
+  {name: 'approved', displayName: 'Approved', icon: 'check'},
+  {name: 'declined', displayName: 'Declined', icon: 'times'},
+];
+
 /**
- * helper function that shadllow mounts and returns the rendered component
+ * helper function that shallow mounts and returns the rendered component
  * @param {props} props props for testing to overwrite default props
  * @return {VueWrapper} returns a shallow mounted using props
  */
 function getMountedComponent(props) {
   const defaultProps = {
+    statuses,
   };
 
   return shallowMount(AnalysisListingLegend, {
@@ -30,4 +40,55 @@ describe('AnalysisListingLegend.vue', () => {
     expect(wrapper.html()).to.contains('Ready');
     expect(wrapper.html()).to.contains('Active');
   });
+
+  it('should all be colored when no statuses are being filtered for', () => {
+    const wrapper = getMountedComponent();
+    statuses.forEach((status) => {
+      expect(wrapper.html()).to.contains(`color: var(--rosalution-status-${status.name})`);
+    });
+  });
+
+  it('should only color the filtered status', async () => {
+    const wrapper = getMountedComponent();
+    const statusElements = wrapper.findAll('.status');
+    let readyStatus;
+
+    for (let i = 0; i < statusElements.length; i++) {
+      if (statusElements[i].text() === 'Ready') {
+        readyStatus = statusElements[i];
+      }
+    }
+
+    if (readyStatus) {
+      await readyStatus.trigger('click');
+      expect(wrapper.html()).to.contains('color: var(--rosalution-status-ready)');
+      statuses.forEach((status) => {
+        if (status.name !== 'ready') {
+          expect(wrapper.html()).to.contains(`color: var(--rosalution-grey-300)`);
+        }
+      });
+    } else {
+      throw new Error('Ready status not found');
+    }
+  });
+
+  it('should emit a filtered-changed event when a status is clicked', async () => {
+    const wrapper = getMountedComponent();
+    const statusElements = wrapper.findAll('.status');
+    let readyStatus;
+
+    for (let i = 0; i < statusElements.length; i++) {
+      if (statusElements[i].text() === 'Ready') {
+        readyStatus = statusElements[i];
+      }
+    }
+
+    if (readyStatus) {
+      await readyStatus.trigger('click');
+      expect(wrapper.emitted()).to.have.property('filtered-changed');
+      expect(wrapper.emitted()['filtered-changed'][0][0]).to.contains('ready');
+    } else {
+      throw new Error('Ready status not found');
+    }
+  });
 });

frontend/test/views/AnalysisListingView.spec.js

@@ -7,6 +7,7 @@ import Analyses from '@/models/analyses.js';
 import AnalysisCard from '@/components/AnalysisListing/AnalysisCard.vue';
 import AnalysisCreateCard from '@/components/AnalysisListing/AnalysisCreateCard.vue';
 import AnalysisListingHeader from '@/components/AnalysisListing/AnalysisListingHeader.vue';
+import AnalysisListingLegend from '@/components/AnalysisListing/AnalysisListingLegend.vue';
 import AnalysisListingView from '@/views/AnalysisListingView.vue';
 
 import NotificationDialog from '@/components/Dialogs/NotificationDialog.vue';
@@ -135,6 +136,14 @@ describe('AnalysisListingView', () => {
 
     expect(wrapper.vm.$router.push.called).to.be.true;
   });
+
+  it('should update the filter when the analysis listing header emits the update event', async () => {
+    const legend = wrapper.findComponent(AnalysisListingLegend);
+    legend.vm.$emit('filtered-changed', ['Approved']);
+    await legend.vm.$nextTick();
+
+    expect(wrapper.vm.filteredChanged).to.contain('Approved');
+  });
 });
 
 /**