Enabled progress and result view KANBAN-509

.github/workflows/PR-validation.yml

@@ -958,8 +958,18 @@ jobs:
       - webui-update-dependency-lock-files
       - webui-container-image-build
       - api-container-image-build
+    permissions:
+      id-token: write # Required for OIDC authentication to AWS (to perform AWS actions / access AGR AWS resources)
     runs-on: ubuntu-22.04
     steps:
+      # Configure environment variables used for AWS interaction,
+      # required for API container interactions with pipeline resources
+      - name: AWS credentials configuration
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: ${{ secrets.GH_ACTIONS_AWS_ROLE }}
+          role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-e2e-testing
+          aws-region: us-east-1
       - name: Check out repository code
         uses: actions/checkout@v4
       - name: Download API image artifact
@@ -999,13 +1009,23 @@ jobs:
         uses: cypress-io/github-action@v6
         with:
           working-directory: webui/
-          wait-on: 'http://localhost:3000, http://localhost:8080/api/health'
+          wait-on: 'http://localhost:8080/api/health, http://localhost:3000/submit'
           env: 'API_BASE_URL=http://localhost:8080'
+      - name: Report API container logs on E2E test failure
+        if: failure()
+        run: |
+          docker logs agr.pavi.dev-local.api.server
+      - name: Report webUI container logs on E2E test failure
+        if: failure()
+        run: |
+          docker logs agr.pavi.dev-local.webui.server
       - name: Cleanup webUI server (running container)
+        if: success() || failure()
         working-directory: webui/
         run: |
           make stop-container-dev
       - name: Cleanup API server (running container)
+        if: success() || failure()
         working-directory: api/
         run: |
           make stop-container-dev

webui/cypress/e2e/submit-workflow.cy.ts

@@ -72,11 +72,49 @@ describe('submit form behaviour', () => {
             }
         }
 
+        // Delete any records that had the delete flag set.
+        // Those records are deemed useful for submission form testing
+        // but require datasets too large for automated testing (too slow).
+        for(let i = 0, len = formInput.length; i < len; ++i){
+            if(formInput[i].delete){
+                cy.get('.p-inputgroup').eq(i).parents('tr').find('button#remove-record').click()
+            }
+        }
+
         // Submit button should become active after completing all input
         cy.get('@submitBtn').should('be.enabled')
 
-        // Submitting the analysis should report a UUID
+        // Submitting the analysis should route to the progress page
+        let jobUuid: string
+
         cy.get('@submitBtn').click()
-        cy.contains('div#display-message', /^job .+ is now pending\.$/)
+        cy.location().should((loc: Location) => {
+            expect(loc.pathname).to.eq('/progress')
+
+            //queryparams should contain the job UUID
+            const uuidCaptureRegex = /^\?uuid=([A-Za-z0-9-]+)$/
+            expect(loc.search).to.match(uuidCaptureRegex)
+
+            jobUuid = uuidCaptureRegex.exec(loc.search)![1]
+        })
+
+        // Progress page should indicate job progress
+        cy.contains('p#progress-msg', /^Job .+ is running\.$/)
+
+        // Successful job completion should route to the results page (wait max 5 minutes)
+        cy.location({timeout: 300000}).should((loc: Location) => {
+            expect(loc.pathname).to.eq('/result')
+
+            //queryparams should contain the same UUID as progress page did
+            expect(loc.search).to.eq(`?uuid=${jobUuid}`)
+        })
+
+        // Result page should display the expected alignment results
+        cy.readFile('cypress/fixtures/test-submit-success-output.txt').then(function(txt){
+            expect(txt).to.be.a('string')
+
+            cy.get('textarea#alignment-result-text').should('have.text', txt)
+        });
+
     })
 })

webui/cypress/fixtures/test-submit-success-input.json

@@ -4,19 +4,21 @@
         "transcripts": [
             "ENST00000346798.8",
             "ENST00000357903.7"
-        ]
+        ],
+        "delete": true
     },
     {
-        "gene": "RGD:2139",
+        "gene": "WB:WBGene00000149",
         "transcripts": [
-            "NM_019288.2"
+            "C42D8.8a.1",
+            "C42D8.8b.1"
         ]
     },
     {
-        "gene": "WB:WBGene00000149",
+        "gene": "FB:FBgn0000108",
         "transcripts": [
-            "C42D8.8a.1",
-            "C42D8.8b.1"
+            "Appl-RA",
+            "Appl-RB"
         ]
     }
 ]

webui/cypress/fixtures/test-submit-success-output.txt

@@ -0,0 +1,98 @@
+CLUSTAL O(1.2.4) multiple sequence alignment
+
+
+Appl_Appl-RA          -MCAALRRNLLLRSL-WVVLAIGTAQVQAASPRWEPQIAVLCEAGQIYQPQYLSEEGRWV	58
+Appl_Appl-RB          -MCAALRRNLLLRSL-WVVLAIGTAQVQAASPRWEPQIAVLCEAGQIYQPQYLSEEGRWV	58
+apl-1_C42D8.8a.1      MTVGKLMIGLLIPILVATVYAEGSPAGSKRHEKFIPMVAFSC----GYRNQYMTEEGSWK	56
+apl-1_C42D8.8b.1      MTVGKLMIGLLIPILVATVYAEGSPAGSKRHEKFIPMVAFSC----GYRNQYMTEEGSWK	56
+                         . *  .**:  *  .* * *:   .    :: * :*. *     *: **::*** * 
+
+Appl_Appl-RA          TDLSKKTTGPTCLRDKMDLLDYCKKAYPNRDITNIVESSHYQKIGGWCRQGALNAAKCKG	118
+Appl_Appl-RB          TDLSKKTTGPTCLRDKMDLLDYCKKAYPNRDITNIVESSHYQKIGGWCRQGALNAAKCKG	118
+apl-1_C42D8.8a.1      TDDER---YATCFSGKLDILKYCRKAYPSMNITNIVEYSHEVSISDWCREEGS---PCKW	110
+apl-1_C42D8.8b.1      TDDER---YATCFSGKLDILKYCRKAYPSMNITNIVEYSHEVSISDWCREEGS---PCKW	110
+                      ** .:     **: .*:*:*.**:****. :****** **  .*..***: .     ** 
+
+Appl_Appl-RA          SHRWIKPFRCL-GPFQSDALLVPEGCLFDHIHNASRCWPFVRWNQTGAAACQE------R	171
+Appl_Appl-RB          SHRWIKPFRCL-GPFQSDALLVPEGCLFDHIHNASRCWPFVRWNQTGAAACQE------R	171
+apl-1_C42D8.8a.1      TH-SVRPYHCIDGEFHSEALQVPHDCQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNK	169
+apl-1_C42D8.8b.1      TH-SVRPYHCIDGEFHSEALQVPHDCQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNK	169
+                      :*  ::*::*: * *:*:** **..* *.*::. .:*  : :*:: ..  *:       :
+
+Appl_Appl-RA          GMQMRSFAMLLPCGISVFSGVEFVCCPKHFKTDEIHVKKTDLPVMPAAQINSANDELVMN	231
+Appl_Appl-RB          GMQMRSFAMLLPCGISVFSGVEFVCCPKHFKTDEIHVKKTDLPVMPAAQINSANDELVMN	231
+apl-1_C42D8.8a.1      DMIVRSFAVLEPCALDMFTGVEFVCCPNDQTNKTD-VQKT------------------KE	210
+apl-1_C42D8.8b.1      DMIVRSFAVLEPCALDMFTGVEFVCCPNDQTNKTD-VQKT------------------KE	210
+                      .* :****:* **.:.:*:********:. ...   *:**                   :
+
+Appl_Appl-RA          DEDDSNDSNYSKDANEDDLDDEDDLMGDDEEDDMVADEAATAGGSPNTGSSGDSNSGSLD	291
+Appl_Appl-RB          DEDDSNDSNYSKDANEDDLDDEDDLMGDDEEDDMVADEAATAGGSPNTGSSGDSNSGSLD	291
+apl-1_C42D8.8a.1      --------------DEDDDDDEDDAYED--------------------------------	224
+apl-1_C42D8.8b.1      --------------DEDDDDDEDDAYED--------------------------------	224
+                                    :*** *****   *                                
+
+Appl_Appl-RA          DINAEYDSGEEGDNYEEDGAGSESEAEVEASWDQSGGAKVVSLKSDSSSPSSAPVAPAPE	351
+Appl_Appl-RB          DINAEYDSGEEGDNYEEDGAGSESEAEVEASWDQSGGAKVVSLKSDSSSPSSAPVAPAPE	351
+apl-1_C42D8.8a.1      -------------DYSEESDE---------------------------------------	232
+apl-1_C42D8.8b.1      -------------DYSEESDE---------------------------------------	232
+                                   :*.*:.                                         
+
+Appl_Appl-RA          KAPVKSESVTSTPQLSASAAAFVAANSGNSGTGAGAPPSTAQPTSDPYFTHFDPHYEHQS	411
+Appl_Appl-RB          KAPVKSESVTSTPQLSASAAAFVAANSGNSGTGAGAPPSTAQPTSDPYFTHFDPHYEHQS	411
+apl-1_C42D8.8a.1      ------------------------------------KDEEEPSSQDPYFKIANWTNEHDD	256
+apl-1_C42D8.8b.1      ------------------------------------KDEEEPSSQDPYFKIANWTNEHDD	256
+                                                            .    :.****.  :   **:.
+
+Appl_Appl-RA          YKVSQKRLEESHREKVTRVMKDWSDLEEKYQDMRLADPKAAQSFKQRMTARFQTSVQALE	471
+Appl_Appl-RB          YKVSQKRLEESHREKVTRVMKDWSDLEEKYQDMRLADPKAAQSFKQRMTARFQTSVQALE	471
+apl-1_C42D8.8a.1      FKKAEMRMDEKHRKKVDKVMKEWGDLETRYNEQKAKDPKGAEKFKSQMNARFQKTVSSLE	316
+apl-1_C42D8.8b.1      FKKAEMRMDEKHRKKVDKVMKEWGDLETRYNEQKAKDPKGAEKFKSQMNARFQKTVSSLE	316
+                      :* :: *::*.**:** :***:*.*** :*:: :  ***.*:.**.:*.****.:*.:**
+
+Appl_Appl-RA          EEGNAEKHQLAAMHQQRVLAHINQRKREAMTCYTQALTE--QPPNAHHVEKCLQKLLRAL	529
+Appl_Appl-RB          EEGNAEKHQLAAMHQQRVLAHINQRKREAMTCYTQALTE--QPPNAHHVEKCLQKLLRAL	529
+apl-1_C42D8.8a.1      EEHKRMRKEIEAVHEERVQAMLNEKKRDATHDYRQALATHVNKPNKHSVLQSLKAYIRAE	376
+apl-1_C42D8.8b.1      EEHKRMRKEIEAVHEERVQAMLNEKKRDATHDYRQALATHVNKPNKHSVLQSLKAYIRAE	376
+                      ** :  :::: *:*::** * :*::**:*   * ***:   : ** * * :.*:  :** 
+
+Appl_Appl-RA          HKDRAHALAHYRHLLNSGGPGGLEAAASERPRTLERLIDIDRAVNQSMTMLKRYPELSAK	589
+Appl_Appl-RB          HKDRAHALAHYRHLLNSGGPGGLEAAASERPRTLERLIDIDRAVNQSMTMLKRYPELSAK	589
+apl-1_C42D8.8a.1      EKDRMHTLNRYRHLLKADSK----EAAAYKPTVIHRLRYIDLRINGTLAMLRDFPDLEKY	432
+apl-1_C42D8.8b.1      EKDRMHTLNRYRHLLKADSK----EAAAYKPTVIHRLRYIDLRINGTLAMLRDFPDLEKY	432
+                      .*** *:* :*****::..      **: :* .:.**  **  :* :::**: :*:*.  
+
+Appl_Appl-RA          IAQLMNDYILALRSKDDIPGSSLGMSEEAEAGILDKYRVEIERKVAEKERLRLAEKQRKE	649
+Appl_Appl-RB          IAQLMNDYILALRSKDDIPGSSLGMSEEAEAGILDKYRVEIERKVAEKERLRLAEKQRKE	649
+apl-1_C42D8.8a.1      VRPIAVTYWKDYRDEVS-PDISVE--DSELTPIIHDDEFSKNAKLDVKAPTTTA-KPVKE	488
+apl-1_C42D8.8b.1      VRPIAVTYWKDYRDEVS-PDISVE--DSELTPIIHDDEFSKNAKLDVKAPTTTA-KPVKE	488
+                      :  :   *    *.: . *. *:   :.  : *:.. ... : *:  *     * *  **
+
+Appl_Appl-RA          QRAAEREKLREEKLRLEAKKVDDMLKSQVAEQQSQPTQSSTQSQAQQQQQEKSLPGKELG	709
+Appl_Appl-RB          QRAAEREKLREEKLRLEAKKVDDMLKSQVAEQQSQPTQSSTQSQAQQQQQEKSLPGKELG	709
+apl-1_C42D8.8a.1      ---TDNAKVLPTEASDSEEEADEYYEDEDDEQVKK-----------TPDMKKKVKVVDIK	534
+apl-1_C42D8.8b.1      ---TDNAKVLPTEASDSEEEADEYYEDEDDEQVKK-----------TPDMKKKVKVVDIK	534
+                         ::. *:   :   . ::.*:  :.:  ** .:             : :*.:   :: 
+
+Appl_Appl-RA          PDAALVTAA----NPNLETTKSEKDLSDTEYGEATVSSTKVQTVLPTVDDDAVQRAVEDV	765
+Appl_Appl-RB          PDAALVTAA----NPNLETTKSEKDLSDTEYGEATVS-TKVQTVLPTVDDDAVQRAVEDV	764
+apl-1_C42D8.8a.1      PKEIKVTIEEEKKAPKLVETSVQTDDEDD--DEDSSSSTSS------ESDEDEDKNIKEL	586
+apl-1_C42D8.8b.1      PKEV--TIEEEKKAPKLVETSVQTDDEDD--DEDSSSSTSS------ESDEDEDKNIKEL	584
+                      *.    *       *:*  *. :.* .*   .* : * *.        .*:  :: ::::
+
+Appl_Appl-RA          AAAVAHQEAEPQVQHFMTHDLGHRESSFSLRREFAQHAHAAKEGRNVYFTLSFAGIALMA	825
+Appl_Appl-RB          AAAVAHQEAEPQVQHFMTHDLGHRESSFSLRREFAQHAHAAKEGRNVYFTLSFAGIALMA	824
+apl-1_C42D8.8a.1      RV-----DIEPII---------DEPASFYRHDKLIQSPEVERSASSVFQPYVLASAMFIT	632
+apl-1_C42D8.8b.1      RV-----DIEPII---------DEPASFYRHDKLIQSPEVERSASSVFQPYVLASAMFIT	630
+                       .     : ** :         .. :**  : :: *  .. :.. .*:    :*.  :::
+
+Appl_Appl-RA          AVFVGVAVAKWRTSRSPHAQGFIEVDQ----NVTTHHPIVREEKIVPNMQINGYENPTYK	881
+Appl_Appl-RB          AVFVGVAVAKWRTSRSPHAQGFIEVDQVGCQNVTTHHPIVREEKIVPNMQINGYENPTYK	884
+apl-1_C42D8.8a.1      AI-CIIAFAITNARRRRAMRGFIEVDVY-----------TPEERHVAGMQVNGYENPTYS	680
+apl-1_C42D8.8b.1      AI-CIIAFAITNARRRRAMRGFIEVDVY-----------TPEERHVAGMQVNGYENPTYS	678
+                      *:   :*.*  .: *    :******             . **: * .**:********.
+
+Appl_Appl-RA          YFEVKE	887
+Appl_Appl-RB          YFEVKE	890
+apl-1_C42D8.8a.1      FFDSKA	686
+apl-1_C42D8.8b.1      FFDSKA	684
+                      :*: * 

webui/package.json

@@ -21,7 +21,8 @@
         "primeicons": "^7.0.0",
         "primereact": "~10.8.2",
         "react": "^18",
-        "react-dom": "^18"
+        "react-dom": "^18",
+        "uuid": "^10.0.0"
     },
     "devDependencies": {
         "@jest/globals": "^29.7.0",
@@ -31,14 +32,15 @@
         "@tsconfig/next": "~2.0.3",
         "@types/jest": "^29.5.12",
         "@types/node": "^20",
-        "@types/react-dom": "^18",
         "@types/react": "^18",
+        "@types/react-dom": "^18",
+        "@types/uuid": "^10.0.0",
         "cypress": "^13.14.1",
         "eslint-config-next": "14.2.7",
         "eslint-plugin-cypress": "^3.5.0",
         "eslint-plugin-jest": "^28.6.0",
-        "jest-environment-jsdom": "^29.7.0",
         "jest": "^29.7.0",
+        "jest-environment-jsdom": "^29.7.0",
         "postcss": "^8",
         "ts-node": "^10.9.2",
         "typescript": "~5.5"

webui/src/app/components/client/AlignmentEntry/AlignmentEntry.tsx

@@ -311,5 +311,6 @@ export const AlignmentEntry: FunctionComponent<AlignmentEntryProps> = (props: Al
                         } ))} />
                 <label htmlFor="transcripts">Transcripts</label>
             </FloatLabel><br />
-        </div>)
+        </div>
+    )
 }