diff --git a/.github/workflows/code-qa.yaml b/.github/workflows/code-qa-js.yaml similarity index 56% rename from .github/workflows/code-qa.yaml rename to .github/workflows/code-qa-js.yaml index 3de7e76..8417951 100644 --- a/.github/workflows/code-qa.yaml +++ b/.github/workflows/code-qa-js.yaml @@ -1,17 +1,40 @@ -# This workflow will do a clean install of node dependencies, build the source code and run tests across different versions of node -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions - -name: Code Quality Assurance +name: Code Quality Assurance - JavaScript/TypeScript on: push: branches: [master] - paths-ignore: - - "core/scripts/APIandLibraries/**" + paths: + - "**/*.js" + - "**/*.ts" + - "**/*.mjs" + - "**/*.html" + - "**/*.css" + - "**/*.json" + - "**/*.xml" + - "**/*.svg" + - "**/*.png" + - "**/*.webp" + - "**/*.ico" + - ".prettierrc" + - ".github/workflows/code-qa-js.yaml" + - "package*.json" pull_request: branches: [master] - paths-ignore: - - "core/scripts/APIandLibraries/**" + paths: + - "**/*.js" + - "**/*.ts" + - "**/*.mjs" + - "**/*.html" + - "**/*.css" + - "**/*.json" + - "**/*.xml" + - "**/*.svg" + - "**/*.png" + - "**/*.webp" + - "**/*.ico" + - ".prettierrc" + - ".github/workflows/code-qa-js.yaml" + - "package*.json" permissions: contents: read @@ -26,13 +49,13 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Use Node.js ${{ matrix.node-version }} uses: actions/setup-node@v6 with: node-version: ${{ matrix.node-version }} - name: Cache Node.js modules - uses: actions/cache@v4 + uses: actions/cache@v5 with: path: ~/.npm key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }} @@ -47,4 +70,4 @@ jobs: - name: Run tests run: npm run test:jest - name: Run Playwright tests - run: npx playwright install --with-deps && npm run test:playwright:headless + run: npx playwright install --with-deps && npm run test:e2e:headless diff --git a/.github/workflows/code-qa-markdown.yaml b/.github/workflows/code-qa-markdown.yaml new file mode 100644 index 0000000..d432e46 --- /dev/null +++ b/.github/workflows/code-qa-markdown.yaml @@ -0,0 +1,44 @@ +name: Code Quality Assurance - Markdown + +on: + push: + branches: [master] + paths: + - "**/*.md" + - ".markdownlint.json" + - ".markdownlintignore" + - ".github/workflows/code-qa-markdown.yaml" + - "package*.json" + pull_request: + branches: [master] + paths: + - "**/*.md" + - ".markdownlint.json" + - ".markdownlintignore" + - ".github/workflows/code-qa-markdown.yaml" + - "package*.json" + +permissions: + contents: read +jobs: + lint-markdown: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + - name: Use Node.js ${{ matrix.node-version }} + uses: actions/setup-node@v6 + with: + node-version: ${{ matrix.node-version }} + - name: Cache Node.js modules + uses: actions/cache@v5 + with: + path: ~/.npm + key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }} + restore-keys: | + ${{ runner.os }}-node- + - name: Run installs + run: npm ci + - name: Run markdownlint on Markdown files + run: npm run lint:markdown diff --git a/.github/workflows/codeql-analysis.yaml b/.github/workflows/codeql-analysis.yaml index feee28e..12fe0d0 100644 --- a/.github/workflows/codeql-analysis.yaml +++ b/.github/workflows/codeql-analysis.yaml @@ -50,7 +50,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 # Initializes the CodeQL tools for scanning. - name: Initialize CodeQL diff --git a/.markdownlint.json b/.markdownlint.json new file mode 100644 index 0000000..3a4eaee --- /dev/null +++ b/.markdownlint.json @@ -0,0 +1,6 @@ +{ + "MD007": false, + "MD010": false, + "MD013": false, + "MD060": false +} diff --git a/.markdownlintignore b/.markdownlintignore new file mode 100644 index 0000000..b73df77 --- /dev/null +++ b/.markdownlintignore @@ -0,0 +1,56 @@ +# Markdown to ignore +LICENSE.md + +# dependencies +**/node_modules +/.pnp +.pnp.js + +# VS code +.vscode/settings.json +.vscode/launch.json + +# System Files +.DS_Store + +# Coverage and testing +.coverage +/coverage +coverage.html +coverage.out +coverage.xml +cypress/screenshots +cypress/videos + +# Playwright +node_modules/ +test-results/ +playwright-report/ +blob-report/ +playwright/.cache/ +playwright/.auth/ +playwright-report/ +blob-report/ +test-results/ + +# Packages +core/scripts/APIandLibraries/**/* + +# workbox +workbox-config.cjs +core/scripts/serviceWorker + +# Visual Studio Code +.vscode/settings.json +.vscode/launch.json + +# Data files +.fasta +.xlsx +.csv + +# PDFs +.pdf + +# Ignore minified files +*.min.* diff --git a/.prettierignore b/.prettierignore index a156cc6..b9bfd68 100644 --- a/.prettierignore +++ b/.prettierignore @@ -3,31 +3,35 @@ /.pnp .pnp.js -# Build files -*.min.js -*.min.css -sw.js -*.js.map - -# Packages -core/scripts/APIandLibraries/**/* +# VS code +.vscode/settings.json +.vscode/launch.json -# R data files -.Rproj.user -.Rhistory -.RData -.Ruserdata +# System Files +.DS_Store -# Server files -.htaccess +# Coverage and testing +.coverage +/coverage +coverage.html +coverage.out +coverage.xml +cypress/screenshots +cypress/videos + +# Playwright +node_modules/ +test-results/ +playwright-report/ +blob-report/ +playwright/.cache/ +playwright/.auth/ +playwright-report/ +blob-report/ +test-results/ -# misc -.DS_Store -.env.local -.env.development.local -.env.test.local -.env.production.local -.vscode +# Packages +core/scripts/APIandLibraries/**/* # workbox workbox-config.cjs diff --git a/CHANGELOG.md b/CHANGELOG.md index 5366ff5..07f27ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -182,7 +182,7 @@ Bug fix: ## [1.0.0] - 2018-09-20 -The official release of SciGrade is here! You can visit it and see all of it in action at https://scigrade.com/ or learn how it works by looking through our EDIT.MD code. +The official release of SciGrade is here! You can visit it and see all of it in action at or learn how it works by looking through our EDIT.MD code. Enjoy learning with CRISPR on SciGrade! -Alex diff --git a/core/scripts/crispr_scripts.js b/core/scripts/crispr_scripts.js index 514bb7c..7b04e9a 100644 --- a/core/scripts/crispr_scripts.js +++ b/core/scripts/crispr_scripts.js @@ -308,28 +308,28 @@ function checkAnswers() { MARgRNAseq = false; MARgRNAseq_degree = 0; } else if ( - (correctNucleotidePosition >= possible_comparable_answers[i].Position - 1 + 1 && - correctNucleotidePosition <= possible_comparable_answers[i].Position - 1 + 10) || - (correctNucleotidePosition <= possible_comparable_answers[i].Position - 1 - 1 && - correctNucleotidePosition >= possible_comparable_answers[i].Position - 1 - 10) + (correctNucleotidePosition >= possibleAnswer.Position - 1 + 1 && + correctNucleotidePosition <= possibleAnswer.Position - 1 + 10) || + (correctNucleotidePosition <= possibleAnswer.Position - 1 - 1 && + correctNucleotidePosition >= possibleAnswer.Position - 1 - 10) ) { MARgRNAseq = true; MARgRNAseq_degree = 1; true_counts += 1; } else if ( - (correctNucleotidePosition >= possible_comparable_answers[i].Position - 1 && - correctNucleotidePosition <= possible_comparable_answers[i].Position - 1 + 20) || - (correctNucleotidePosition <= possible_comparable_answers[i].Position - 1 && - correctNucleotidePosition >= possible_comparable_answers[i].Position - 1 - 20) + (correctNucleotidePosition >= possibleAnswer.Position - 1 && + correctNucleotidePosition <= possibleAnswer.Position - 1 + 20) || + (correctNucleotidePosition <= possibleAnswer.Position - 1 && + correctNucleotidePosition >= possibleAnswer.Position - 1 - 20) ) { MARgRNAseq = true; MARgRNAseq_degree = 2; true_counts += 1; } else if ( - (correctNucleotidePosition >= possible_comparable_answers[i].Position - 1 && - correctNucleotidePosition <= possible_comparable_answers[i].Position - 1 + 30) || - (correctNucleotidePosition <= possible_comparable_answers[i].Position - 1 && - correctNucleotidePosition >= possible_comparable_answers[i].Position - 1 - 30) + (correctNucleotidePosition >= possibleAnswer.Position - 1 && + correctNucleotidePosition <= possibleAnswer.Position - 1 + 30) || + (correctNucleotidePosition <= possibleAnswer.Position - 1 && + correctNucleotidePosition >= possibleAnswer.Position - 1 - 30) ) { MARgRNAseq = true; MARgRNAseq_degree = 3; @@ -338,7 +338,7 @@ function checkAnswers() { // If the sequence if correct, check all other results: if (MARgRNAseq) { - const temp_answer = element; + const temp_answer = possibleAnswer; // Check if the cut position matches the answer's input if ( temp_answer.Position && diff --git a/core/scripts/crispr_scripts.min.js b/core/scripts/crispr_scripts.min.js index 791d708..719bb19 100644 --- a/core/scripts/crispr_scripts.min.js +++ b/core/scripts/crispr_scripts.min.js @@ -24,4 +24,4 @@ let selection_inMode="practice";const listOfGenes=["eBFP","ACTN3","HBB","CCR5"," - `,e+='
',e+='',e+='',e+='This would be your off-target score for your gRNA. NOTE: This input only takes numbers',e+="
",e+='
',e+='',e+='',e+='This would be your forward primer (F1) for your gRNA',e+="
",e+='
',e+='',e+='',e+='This would be your reverse primer (R1) for your gRNA',e+="
",e+='',e+='',e+="",e+="",$("#work").append(e)}else(gene_backgroundInfo===""||!gene_backgroundInfo||!backgroundInfo?.[0].gene_list[current_gene])&&alert("Error code lFS50-66 occurred. Please contact admin or TA!")}function isNumberOrDashKey(e){const n=e.which?e.which:e.keyCode;return!(n!==46&&n!==45&&n>31&&(n<48||n>57))}let MARgRNAseq=!1,MARgRNAseq_degree=0,MARPAMseq=!1,MARCutPos=!1,MARstrand=!1,MAROffTarget=!1,MAROffTarget_degree=0,MAROffTarget_aboveOpt=!1,MAROffTarget_above35=!1,MAROffTarget_onlyOption=!1,MARF1primers=!1,MARR1primers=!1,possible_comparable_answers=[],correctNucleotideIncluded=!1,true_counts=0,checkAnswers_executed=!1;function checkAnswers(){MARgRNAseq=!1,MARgRNAseq_degree=0,MARPAMseq=!1,MARCutPos=!1,MARstrand=!1,correctNucleotideIncluded=!1,true_counts=0;const e=gene_backgroundInfo.gene_list[current_gene]["Target position"]-1,n=document?.getElementById("sequence_input")?.value?.trim()||void 0;if(possible_comparable_answers=[],n)for(const t of benchling_gRNA_outputs.gene_list[current_gene])t.Sequence===n&&possible_comparable_answers.push(t);if(possible_comparable_answers.length>0)for(const t of possible_comparable_answers){if(true_counts=0,correctNucleotideIncluded=!1,t.Strand===1){const o=t.Position-1-1+3,a=t.Position-1-17;e>=a&&e<=o&&(correctNucleotideIncluded=!0)}else if(t.Strand===-1){const o=t.Position-1+17,a=t.Position-1-3;e>=a&&e<=o&&(correctNucleotideIncluded=!0)}if(correctNucleotideIncluded){let o,a;if(t.Strand===1?(o=t.Position-1+2,a=t.Position-1+4,document.getElementById("strand_input").value==="Sense (+)"&&(MARstrand=!0,true_counts+=1)):t.Strand===-1&&(o=t.Position-1-2,a=t.Position-1-4,document.getElementById("strand_input").value==="Antisense (-)"&&(MARstrand=!0,true_counts+=1)),e>=o&&e<=a?(MARgRNAseq=!1,MARgRNAseq_degree=0):e>=possible_comparable_answers[i].Position-1+1&&e<=possible_comparable_answers[i].Position-1+10||e<=possible_comparable_answers[i].Position-1-1&&e>=possible_comparable_answers[i].Position-1-10?(MARgRNAseq=!0,MARgRNAseq_degree=1,true_counts+=1):e>=possible_comparable_answers[i].Position-1&&e<=possible_comparable_answers[i].Position-1+20||e<=possible_comparable_answers[i].Position-1&&e>=possible_comparable_answers[i].Position-1-20?(MARgRNAseq=!0,MARgRNAseq_degree=2,true_counts+=1):(e>=possible_comparable_answers[i].Position-1&&e<=possible_comparable_answers[i].Position-1+30||e<=possible_comparable_answers[i].Position-1&&e>=possible_comparable_answers[i].Position-1-30)&&(MARgRNAseq=!0,MARgRNAseq_degree=3,true_counts+=1),MARgRNAseq){const r=element;r.Position&&parseInt(r.Position,10)===parseInt(document.getElementById("position_input").value,10)?(MARCutPos=!0,true_counts+=1):(r.Position===null||r.Position===void 0)&&alert("Error code cA302-307: retrieving server information on 'Position' answers occurred. Please contact admin or TA!"),(r.PAM||r.PAM)&&r.PAM===document.getElementById("pam_input").value.trim()?(MARPAMseq=!0,true_counts+=1):(r.PAM===null||r.PAM===void 0)&&alert("Error code cA311-317: retrieving server information on 'PAM' answers occurred. Please contact admin or TA!"),r["Specificity Score"]||r["Specificity Score"]?checkOffTarget(r["Specificity Score"]):(r["Specificity Score"]===null||r["Specificity Score"]===void 0)&&alert("Error code cA342-348: retrieving server information on 'Specificity Score' answers occurred. Please contact admin or TA!"),checkF1Primers(document?.getElementById("sequence_input")?.value?.trim()||""),checkR1Primers(document?.getElementById("sequence_input")?.value?.trim()||"")}}}checkAnswers_executed=!0}let offtarget_List=[],offtarget_dict={},offtarget_dictParse=[],offtarget_Use=[];function checkOffTarget(e){MAROffTarget=!1,MAROffTarget_degree=0,MAROffTarget_aboveOpt=!1,MAROffTarget_above35=!1,MAROffTarget_onlyOption=!1;const n=Math.floor(e),t=Math.ceil(e),o=parseInt(document.getElementById("offtarget_input").value,10);if(correctNucleotideIncluded&&MARgRNAseq&&o>=n&&o<=t&&(MAROffTarget=!0,true_counts+=1),MAROffTarget){const a=parseInt(document.getElementById("position_input").value,10)+35,r=parseInt(document.getElementById("position_input").value,10)-35;offtarget_List=[],offtarget_dict={},offtarget_dictParse=[],offtarget_Use=[];for(let s=0;s=r&&benchling_gRNA_outputs.gene_list[current_gene][s].Position<=a&&benchling_gRNA_outputs.gene_list[current_gene][s]["Specificity Score"]&&(offtarget_List.push(benchling_gRNA_outputs.gene_list[current_gene][s]["Specificity Score"]),offtarget_dict[s]=benchling_gRNA_outputs.gene_list[current_gene][s]["Specificity Score"],offtarget_dictParse.push(s));let c=!0;Math.max.apply(null,offtarget_List)<35&&(c=!1);const d=Math.max.apply(null,offtarget_List),u=getOffTargetOptimalValue(d);o>=u?(MAROffTarget_aboveOpt=!0,MAROffTarget_above35=!0,MAROffTarget_degree=1):o>=35?(MAROffTarget_above35=!0,Math.max.apply(null,offtarget_List)<80?MAROffTarget_degree=1:MAROffTarget_degree=2):c||(MAROffTarget_onlyOption=!0,MAROffTarget_degree=3)}}function getOffTargetOptimalValue(e){const n=e-e*.2;return n>80||n<35?80:n}let possible_F1_primers=[];function checkF1Primers(e){MARF1primers=!1,possible_F1_primers=[];const n="TAATACGACTCACTATAG";let t=!0;e[0]==="G"&&(t=!1);for(let o=16;o<=20;o+=1)possible_F1_primers.push(n+e.slice(0,o));if(!t)for(let o=16;o<=20;o+=1)possible_F1_primers.push(n+e.slice(1,o));possible_F1_primers.includes(document.getElementById("f1_input").value.trim())&&(MARF1primers=!0)}let possible_R1_primers=[];const complementary_nt_dict={A:"T",T:"A",C:"G",G:"C"};function checkR1Primers(e){MARR1primers=!1,possible_R1_primers=[];const n="TTCTAGCTCTAAAAC";let t="";for(const o of e)t=complementary_nt_dict[o]+t;for(let o=19;o<=20;o+=1)possible_R1_primers.push(n+t.slice(0,o));possible_R1_primers.includes(document.getElementById("r1_input").value.trim())&&(MARR1primers=!0)}function createComplementarySeq(e){let n="";for(const t of e)n=complementary_nt_dict[t]+n;return n}let studentMark=0,studentMarkPercentage=0;const markTotal=10;function markAnswers(){studentMark=0,checkAnswers_executed||checkAnswers(),checkAnswers_executed&&(MARgRNAseq&&(MARgRNAseq_degree===1?studentMark+=2:MARgRNAseq_degree===2?studentMark+=1:MARgRNAseq_degree===3&&(studentMark+=.5)),MARPAMseq&&(studentMark+=2),MAROffTarget&&(MAROffTarget_degree===1?studentMark+=2:MAROffTarget_degree===2?studentMark+=1:MAROffTarget_degree===3&&(studentMark+=.5)),MARF1primers&&(studentMark+=2),MARR1primers&&(studentMark+=2),studentMarkPercentage=(studentMark/markTotal*100).toFixed(2),studentMarkPercentage>100?studentMarkPercentage=100:studentMarkPercentage<0&&(studentMarkPercentage=0))}function showFeedback(){$("#mainContainer").empty();let e="

You would only receive feedback on your practice attempts and not your final assignments.

";e+="

The assignment itself is marked out of 10 marks with 2 marks for each input excluding gRNA strand direction, cut position and target region range (these three values are used to calculate if you have the right answer or not which means they are still crucial that they are still correct).

",e+="

The following is the breakdown of what marks you would have received and why you would have gotten them:

",e+=`

Mark: ${all_marks[0]}/10 (${all_marks[1]})

`;let n=0,t="Your gRNA sequence was wrong and not found in the Benchling gRNA outputs. Either you made a typo or this answer was not correct and did not contain the target cut site within an acceptable range.";MARgRNAseq&&(MARgRNAseq_degree===1?(n=2,t="This means your answer was correct and you received full marks."):MARgRNAseq_degree===2?(n=1,t="This means your sequence was partially correct as it contains the target sequence within a 20bp range but was not optimal. One mark."):MARgRNAseq_degree===3&&(n=.5,t="This means your sequence was not wrong (therefore was still correct) but there were better options out there. I recommend you try this practice assignment again. Still worth some marks though (half a mark)."));let o=0,a="Your PAM sequence was wrong and not found relative to your gRNA sequence. Either you made a typo or this answer was not correct. Either it contained the cut site within the PAM site or it was not an NGG or NAG PAM site (SciGrade only accepts either of those two PAM sites).";MARPAMseq&&(o=2,a="This means your answer was correct and you received full marks.");let r=0,c="Your off-target score was wrong. Either it was not above/within the optimal range (or above 35) or the last-resort option.";MAROffTarget&&(MAROffTarget_degree===1?(r=2,c="This means your answer was correct while above/within the optimal and you received full marks."):MAROffTarget_degree===2?(r=1,c="This means your answer was technically correct as its on-target value was above 35."):MAROffTarget_degree===3&&(r=.5,c="This means your answer was partially correct as it was found to be your only option is solely based on the target region range you selected."));let d=0,u="";for(let l=0;l For gRNA Strand Sequence, you put down "${all_answers[0]}" which gave you the mark ${n}.

`,e+=t,e+="",e+="",e+="",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For gRNA PAM Sequence, you put down "${all_answers[1]}" which gave you the mark ${o}.

`,e+=a,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For Off-Target Score, you put down "${all_answers[4]}" which gave you the mark ${r}.

`,e+=c,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For F1 Primer, you put down "${all_answers[5]}" which gave you the mark ${d}.

`,e+=s,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For R1 Primer, you put down "${all_answers[6]}" which gave you the mark ${p}.

`,e+=m,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="

If at any point you wish to dispute marks, please contact your TA or professor once you completed your assignment. If you have found a bug in our SciGrade marking system, please contact your professor or our admin.

",e+="
",e+='

',$("#mainContainer").append(e)}function showNewInput(e,n,t){document.getElementById(String(e)).value===String(n)?document.getElementById(String(t)).removeAttribute("hidden"):document.getElementById(String(t)).setAttribute("hidden",!0)}let completed_assignments=[],all_answers=[],all_outputs=[],all_marks=[];function submitAnswers(){all_answers=[],all_outputs=[],all_marks=[],checkAnswers(),setTimeout(()=>{markAnswers(),all_answers.push(document?.getElementById("sequence_input")?.value?.trim()||"",document.getElementById("pam_input").value.trim(),document.getElementById("position_input").value,document.getElementById("strand_input").value,document.getElementById("offtarget_input").value,document.getElementById("f1_input").value.trim(),document.getElementById("r1_input").value.trim()),all_outputs.push(MARstrand,MARgRNAseq,MARgRNAseq_degree,MARCutPos,MARPAMseq,MAROffTarget,MAROffTarget_degree,MAROffTarget_aboveOpt,MAROffTarget_above35,MAROffTarget_onlyOption,MARF1primers,MARR1primers),all_marks.push(studentMark,studentMarkPercentage),document.getElementById("options_label").innerHTML="Would you like to see feedback on your answers or start a new assignment?",document.getElementById("seeFeedback").removeAttribute("hidden"),showFeedback(),$("#feedbackButton").click()},750)}function IfPressEnter(e,n){(e.which===13||e.keyCode===13)&&$(`#${n}`).click()}function backToAssignments(){redirectCRISPR(),$("#practice").click()}$(()=>{$("form").submit(()=>!1)}),typeof module<"u"&&module.exports&&(module.exports={getOffTargetOptimalValue,isNumberOrDashKey,createComplementarySeq,checkOffTarget,checkF1Primers,checkR1Primers,fillGeneList,get MAROffTarget(){return MAROffTarget},get MAROffTarget_degree(){return MAROffTarget_degree},get MARF1primers(){return MARF1primers},get MARR1primers(){return MARR1primers},__setTestState(e={}){e.correctNucleotideIncluded!==void 0&&(correctNucleotideIncluded=e.correctNucleotideIncluded),e.MARgRNAseq!==void 0&&(MARgRNAseq=e.MARgRNAseq),e.benchling_gRNA_outputs!==void 0&&(benchling_gRNA_outputs=e.benchling_gRNA_outputs),e.current_gene!==void 0&&(current_gene=e.current_gene),e.gene_backgroundInfo!==void 0&&(gene_backgroundInfo=e.gene_backgroundInfo)},__resetState(){MAROffTarget=!1,MAROffTarget_degree=0,MARF1primers=!1,MARR1primers=!1,MAROffTarget_aboveOpt=!1,MAROffTarget_above35=!1,MAROffTarget_onlyOption=!1,correctNucleotideIncluded=!1,MARgRNAseq=!1}}); + `,e+='
',e+='',e+='',e+='This would be your off-target score for your gRNA. NOTE: This input only takes numbers',e+="
",e+='
',e+='',e+='',e+='This would be your forward primer (F1) for your gRNA',e+="
",e+='
',e+='',e+='',e+='This would be your reverse primer (R1) for your gRNA',e+="
",e+='',e+='',e+="",e+="",$("#work").append(e)}else(gene_backgroundInfo===""||!gene_backgroundInfo||!backgroundInfo?.[0].gene_list[current_gene])&&alert("Error code lFS50-66 occurred. Please contact admin or TA!")}function isNumberOrDashKey(e){const n=e.which?e.which:e.keyCode;return!(n!==46&&n!==45&&n>31&&(n<48||n>57))}let MARgRNAseq=!1,MARgRNAseq_degree=0,MARPAMseq=!1,MARCutPos=!1,MARstrand=!1,MAROffTarget=!1,MAROffTarget_degree=0,MAROffTarget_aboveOpt=!1,MAROffTarget_above35=!1,MAROffTarget_onlyOption=!1,MARF1primers=!1,MARR1primers=!1,possible_comparable_answers=[],correctNucleotideIncluded=!1,true_counts=0,checkAnswers_executed=!1;function checkAnswers(){MARgRNAseq=!1,MARgRNAseq_degree=0,MARPAMseq=!1,MARCutPos=!1,MARstrand=!1,correctNucleotideIncluded=!1,true_counts=0;const e=gene_backgroundInfo.gene_list[current_gene]["Target position"]-1,n=document?.getElementById("sequence_input")?.value?.trim()||void 0;if(possible_comparable_answers=[],n)for(const t of benchling_gRNA_outputs.gene_list[current_gene])t.Sequence===n&&possible_comparable_answers.push(t);if(possible_comparable_answers.length>0)for(const t of possible_comparable_answers){if(true_counts=0,correctNucleotideIncluded=!1,t.Strand===1){const i=t.Position-1-1+3,r=t.Position-1-17;e>=r&&e<=i&&(correctNucleotideIncluded=!0)}else if(t.Strand===-1){const i=t.Position-1+17,r=t.Position-1-3;e>=r&&e<=i&&(correctNucleotideIncluded=!0)}if(correctNucleotideIncluded){let i,r;if(t.Strand===1?(i=t.Position-1+2,r=t.Position-1+4,document.getElementById("strand_input").value==="Sense (+)"&&(MARstrand=!0,true_counts+=1)):t.Strand===-1&&(i=t.Position-1-2,r=t.Position-1-4,document.getElementById("strand_input").value==="Antisense (-)"&&(MARstrand=!0,true_counts+=1)),e>=i&&e<=r?(MARgRNAseq=!1,MARgRNAseq_degree=0):e>=t.Position-1+1&&e<=t.Position-1+10||e<=t.Position-1-1&&e>=t.Position-1-10?(MARgRNAseq=!0,MARgRNAseq_degree=1,true_counts+=1):e>=t.Position-1&&e<=t.Position-1+20||e<=t.Position-1&&e>=t.Position-1-20?(MARgRNAseq=!0,MARgRNAseq_degree=2,true_counts+=1):(e>=t.Position-1&&e<=t.Position-1+30||e<=t.Position-1&&e>=t.Position-1-30)&&(MARgRNAseq=!0,MARgRNAseq_degree=3,true_counts+=1),MARgRNAseq){const o=t;o.Position&&parseInt(o.Position,10)===parseInt(document.getElementById("position_input").value,10)?(MARCutPos=!0,true_counts+=1):(o.Position===null||o.Position===void 0)&&alert("Error code cA302-307: retrieving server information on 'Position' answers occurred. Please contact admin or TA!"),(o.PAM||o.PAM)&&o.PAM===document.getElementById("pam_input").value.trim()?(MARPAMseq=!0,true_counts+=1):(o.PAM===null||o.PAM===void 0)&&alert("Error code cA311-317: retrieving server information on 'PAM' answers occurred. Please contact admin or TA!"),o["Specificity Score"]||o["Specificity Score"]?checkOffTarget(o["Specificity Score"]):(o["Specificity Score"]===null||o["Specificity Score"]===void 0)&&alert("Error code cA342-348: retrieving server information on 'Specificity Score' answers occurred. Please contact admin or TA!"),checkF1Primers(document?.getElementById("sequence_input")?.value?.trim()||""),checkR1Primers(document?.getElementById("sequence_input")?.value?.trim()||"")}}}checkAnswers_executed=!0}let offtarget_List=[],offtarget_dict={},offtarget_dictParse=[],offtarget_Use=[];function checkOffTarget(e){MAROffTarget=!1,MAROffTarget_degree=0,MAROffTarget_aboveOpt=!1,MAROffTarget_above35=!1,MAROffTarget_onlyOption=!1;const n=Math.floor(e),t=Math.ceil(e),i=parseInt(document.getElementById("offtarget_input").value,10);if(correctNucleotideIncluded&&MARgRNAseq&&i>=n&&i<=t&&(MAROffTarget=!0,true_counts+=1),MAROffTarget){const r=parseInt(document.getElementById("position_input").value,10)+35,o=parseInt(document.getElementById("position_input").value,10)-35;offtarget_List=[],offtarget_dict={},offtarget_dictParse=[],offtarget_Use=[];for(let a=0;a=o&&benchling_gRNA_outputs.gene_list[current_gene][a].Position<=r&&benchling_gRNA_outputs.gene_list[current_gene][a]["Specificity Score"]&&(offtarget_List.push(benchling_gRNA_outputs.gene_list[current_gene][a]["Specificity Score"]),offtarget_dict[a]=benchling_gRNA_outputs.gene_list[current_gene][a]["Specificity Score"],offtarget_dictParse.push(a));let l=!0;Math.max.apply(null,offtarget_List)<35&&(l=!1);const u=Math.max.apply(null,offtarget_List),c=getOffTargetOptimalValue(u);i>=c?(MAROffTarget_aboveOpt=!0,MAROffTarget_above35=!0,MAROffTarget_degree=1):i>=35?(MAROffTarget_above35=!0,Math.max.apply(null,offtarget_List)<80?MAROffTarget_degree=1:MAROffTarget_degree=2):l||(MAROffTarget_onlyOption=!0,MAROffTarget_degree=3)}}function getOffTargetOptimalValue(e){const n=e-e*.2;return n>80||n<35?80:n}let possible_F1_primers=[];function checkF1Primers(e){MARF1primers=!1,possible_F1_primers=[];const n="TAATACGACTCACTATAG";let t=!0;e[0]==="G"&&(t=!1);for(let i=16;i<=20;i+=1)possible_F1_primers.push(n+e.slice(0,i));if(!t)for(let i=16;i<=20;i+=1)possible_F1_primers.push(n+e.slice(1,i));possible_F1_primers.includes(document.getElementById("f1_input").value.trim())&&(MARF1primers=!0)}let possible_R1_primers=[];const complementary_nt_dict={A:"T",T:"A",C:"G",G:"C"};function checkR1Primers(e){MARR1primers=!1,possible_R1_primers=[];const n="TTCTAGCTCTAAAAC";let t="";for(const i of e)t=complementary_nt_dict[i]+t;for(let i=19;i<=20;i+=1)possible_R1_primers.push(n+t.slice(0,i));possible_R1_primers.includes(document.getElementById("r1_input").value.trim())&&(MARR1primers=!0)}function createComplementarySeq(e){let n="";for(const t of e)n=complementary_nt_dict[t]+n;return n}let studentMark=0,studentMarkPercentage=0;const markTotal=10;function markAnswers(){studentMark=0,checkAnswers_executed||checkAnswers(),checkAnswers_executed&&(MARgRNAseq&&(MARgRNAseq_degree===1?studentMark+=2:MARgRNAseq_degree===2?studentMark+=1:MARgRNAseq_degree===3&&(studentMark+=.5)),MARPAMseq&&(studentMark+=2),MAROffTarget&&(MAROffTarget_degree===1?studentMark+=2:MAROffTarget_degree===2?studentMark+=1:MAROffTarget_degree===3&&(studentMark+=.5)),MARF1primers&&(studentMark+=2),MARR1primers&&(studentMark+=2),studentMarkPercentage=(studentMark/markTotal*100).toFixed(2),studentMarkPercentage>100?studentMarkPercentage=100:studentMarkPercentage<0&&(studentMarkPercentage=0))}function showFeedback(){$("#mainContainer").empty();let e="

You would only receive feedback on your practice attempts and not your final assignments.

";e+="

The assignment itself is marked out of 10 marks with 2 marks for each input excluding gRNA strand direction, cut position and target region range (these three values are used to calculate if you have the right answer or not which means they are still crucial that they are still correct).

",e+="

The following is the breakdown of what marks you would have received and why you would have gotten them:

",e+=`

Mark: ${all_marks[0]}/10 (${all_marks[1]})

`;let n=0,t="Your gRNA sequence was wrong and not found in the Benchling gRNA outputs. Either you made a typo or this answer was not correct and did not contain the target cut site within an acceptable range.";MARgRNAseq&&(MARgRNAseq_degree===1?(n=2,t="This means your answer was correct and you received full marks."):MARgRNAseq_degree===2?(n=1,t="This means your sequence was partially correct as it contains the target sequence within a 20bp range but was not optimal. One mark."):MARgRNAseq_degree===3&&(n=.5,t="This means your sequence was not wrong (therefore was still correct) but there were better options out there. I recommend you try this practice assignment again. Still worth some marks though (half a mark)."));let i=0,r="Your PAM sequence was wrong and not found relative to your gRNA sequence. Either you made a typo or this answer was not correct. Either it contained the cut site within the PAM site or it was not an NGG or NAG PAM site (SciGrade only accepts either of those two PAM sites).";MARPAMseq&&(i=2,r="This means your answer was correct and you received full marks.");let o=0,l="Your off-target score was wrong. Either it was not above/within the optimal range (or above 35) or the last-resort option.";MAROffTarget&&(MAROffTarget_degree===1?(o=2,l="This means your answer was correct while above/within the optimal and you received full marks."):MAROffTarget_degree===2?(o=1,l="This means your answer was technically correct as its on-target value was above 35."):MAROffTarget_degree===3&&(o=.5,l="This means your answer was partially correct as it was found to be your only option is solely based on the target region range you selected."));let u=0,c="";for(let s=0;s For gRNA Strand Sequence, you put down "${all_answers[0]}" which gave you the mark ${n}.

`,e+=t,e+="",e+="",e+="",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For gRNA PAM Sequence, you put down "${all_answers[1]}" which gave you the mark ${i}.

`,e+=r,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For Off-Target Score, you put down "${all_answers[4]}" which gave you the mark ${o}.

`,e+=l,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For F1 Primer, you put down "${all_answers[5]}" which gave you the mark ${u}.

`,e+=a,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="
",e+="
",e+="",e+="
",e+="
",e+="
",e+="
",e+=`

For R1 Primer, you put down "${all_answers[6]}" which gave you the mark ${f}.

`,e+=p,e+="
",e+="
",e+="
",$("#mainContainer").append(e),e="
",e+="

If at any point you wish to dispute marks, please contact your TA or professor once you completed your assignment. If you have found a bug in our SciGrade marking system, please contact your professor or our admin.

",e+="
",e+='

',$("#mainContainer").append(e)}function showNewInput(e,n,t){document.getElementById(String(e)).value===String(n)?document.getElementById(String(t)).removeAttribute("hidden"):document.getElementById(String(t)).setAttribute("hidden",!0)}let completed_assignments=[],all_answers=[],all_outputs=[],all_marks=[];function submitAnswers(){all_answers=[],all_outputs=[],all_marks=[],checkAnswers(),setTimeout(()=>{markAnswers(),all_answers.push(document?.getElementById("sequence_input")?.value?.trim()||"",document.getElementById("pam_input").value.trim(),document.getElementById("position_input").value,document.getElementById("strand_input").value,document.getElementById("offtarget_input").value,document.getElementById("f1_input").value.trim(),document.getElementById("r1_input").value.trim()),all_outputs.push(MARstrand,MARgRNAseq,MARgRNAseq_degree,MARCutPos,MARPAMseq,MAROffTarget,MAROffTarget_degree,MAROffTarget_aboveOpt,MAROffTarget_above35,MAROffTarget_onlyOption,MARF1primers,MARR1primers),all_marks.push(studentMark,studentMarkPercentage),document.getElementById("options_label").innerHTML="Would you like to see feedback on your answers or start a new assignment?",document.getElementById("seeFeedback").removeAttribute("hidden"),showFeedback(),$("#feedbackButton").click()},750)}function IfPressEnter(e,n){(e.which===13||e.keyCode===13)&&$(`#${n}`).click()}function backToAssignments(){redirectCRISPR(),$("#practice").click()}$(()=>{$("form").submit(()=>!1)}),typeof module<"u"&&module.exports&&(module.exports={getOffTargetOptimalValue,isNumberOrDashKey,createComplementarySeq,checkOffTarget,checkF1Primers,checkR1Primers,fillGeneList,get MAROffTarget(){return MAROffTarget},get MAROffTarget_degree(){return MAROffTarget_degree},get MARF1primers(){return MARF1primers},get MARR1primers(){return MARR1primers},__setTestState(e={}){e.correctNucleotideIncluded!==void 0&&(correctNucleotideIncluded=e.correctNucleotideIncluded),e.MARgRNAseq!==void 0&&(MARgRNAseq=e.MARgRNAseq),e.benchling_gRNA_outputs!==void 0&&(benchling_gRNA_outputs=e.benchling_gRNA_outputs),e.current_gene!==void 0&&(current_gene=e.current_gene),e.gene_backgroundInfo!==void 0&&(gene_backgroundInfo=e.gene_backgroundInfo)},__resetState(){MAROffTarget=!1,MAROffTarget_degree=0,MARF1primers=!1,MARR1primers=!1,MAROffTarget_aboveOpt=!1,MAROffTarget_above35=!1,MAROffTarget_onlyOption=!1,correctNucleotideIncluded=!1,MARgRNAseq=!1}}); diff --git a/core/scripts/crispr_scripts.test.js b/core/scripts/crispr_scripts.test.js index ff4325c..f880144 100644 --- a/core/scripts/crispr_scripts.test.js +++ b/core/scripts/crispr_scripts.test.js @@ -103,6 +103,11 @@ describe("crispr_scripts.js - Utility Functions", () => { const cases = [ { name: "short sequence ATCG", input: "ATCG", want: "CGAT" }, { name: "longer sequence", input: "GCTCGTGACCACCCTGACCT", want: "AGGTCAGGGTGGTCACGAGC" }, + { + name: "gRNA sequence from eBFP marking tests", + input: "AAGCACTGCACGCCGTGGGT", + want: "ACCCACGGCGTGCAGTGCTT", + }, { name: "empty sequence", input: "", want: "" }, { name: "single nucleotide A", input: "A", want: "T" }, { name: "single nucleotide T", input: "T", want: "A" }, diff --git a/core/scripts/runtime.test.js b/core/scripts/runtime.test.js index f55172b..2756bfe 100644 --- a/core/scripts/runtime.test.js +++ b/core/scripts/runtime.test.js @@ -113,25 +113,6 @@ describe("runtime.js - Runtime Flow Helpers", () => { }); describe("redirectCRISPR()", () => { - const cases = [ - { - name: "clears and repopulates main container", - }, - { - name: "calls loadCRISPRJSON_Files before fillGeneList", - }, - ]; - - it.each(cases)("$name", async ({ name }) => { - // Execute the ACTUAL imported function - await redirectCRISPR(); - - // Verify - expect(mockJQuery.empty).toHaveBeenCalled(); - expect(global.loadCRISPRJSON_Files).toHaveBeenCalledTimes(1); - expect(global.fillGeneList).toHaveBeenCalledTimes(1); - }); - it("ensures DOM elements are properly cleared before population", async () => { // Execute the ACTUAL imported function await redirectCRISPR(); @@ -177,23 +158,4 @@ describe("runtime.js - Runtime Flow Helpers", () => { expect(executionSequence).toEqual(["empty", "append", "loadCRISPRJSON_Files", "fillGeneList"]); }); }); - - describe("Integration: Runtime flow initialization", () => { - it("properly initializes runtime flow when both functions are called", async () => { - mockElement.value = "APOE"; - global.checkAnswers_executed = true; - global.document.getElementById.mockReturnValue(mockElement); - - // Execute ACTUAL imported functions - await redirectCRISPR(); - loadGeneContent(); - - // Verify complete state - expect(global.possible_gene).toBe("APOE"); - expect(global.checkAnswers_executed).toBe(false); - expect(mockJQuery.empty).toHaveBeenCalled(); - expect(global.loadCRISPRJSON_Files).toHaveBeenCalled(); - expect(global.fillGeneList).toHaveBeenCalled(); - }); - }); }); diff --git a/core/scripts/serviceWorker/sw.js b/core/scripts/serviceWorker/sw.js index 4006668..4a0009b 100644 --- a/core/scripts/serviceWorker/sw.js +++ b/core/scripts/serviceWorker/sw.js @@ -1,2 +1,2 @@ -if(!self.define){let e,r={};const c=(c,o)=>(c=new 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\ No newline at end of file diff --git a/core/systemrun.html b/core/systemrun.html index a71bc9f..867f2ff 100644 --- a/core/systemrun.html +++ b/core/systemrun.html @@ -85,14 +85,10 @@ release: "scigrade@1.2.0", integrations: [ - new Sentry.BrowserTracing(), - new Sentry.Integrations.CaptureConsole({ + Sentry.captureConsoleIntegration({ levels: ["error"], }), ], - - // We recommend adjusting this value in production, or using tracesSampler for finer control - tracesSampleRate: 1.0, }); Sentry.configureScope((scope) => { diff --git a/docs/guides/data-structures.md b/docs/guides/data-structures.md index 5e07e5f..f38ad63 100644 --- a/docs/guides/data-structures.md +++ b/docs/guides/data-structures.md @@ -12,8 +12,6 @@ SciGrade uses JSON as its primary data format for gene information and guide RNA **Purpose:** Store educational metadata and background information for each gene. -### Root Structure - ```json { "_id": "5a67577c01ac2022a0eb6f56", @@ -87,8 +85,6 @@ From actual data (HBB gene): **Purpose:** Reference data for validating student-submitted gRNA sequences and calculating off-target scores. -### Root Structure - ```json { "_id": "5a8deb6a547dd8319415ac3d", @@ -185,7 +181,7 @@ From actual data (HBB gene): **Format:** Standard FASTA format -``` +```fasta >ACTN3 ACGTACGTACGTACGTACGTACGTACGTACGT ``` diff --git a/docs/guides/setup.md b/docs/guides/setup.md index 5df4a35..bb8f48c 100644 --- a/docs/guides/setup.md +++ b/docs/guides/setup.md @@ -46,8 +46,8 @@ npm run prettier # Format code automatically # Testing npm run test # Run jest unit tests npm run test:jest # Run jest unit tests only -npm run test:playwright:headless # Run playwright tests headless -npm run test:playwright:ui # Run playwright tests in UI mode +npm run test:e2e:headless # Run E2E tests headless +npm run test:e2e:ui # Run E2E tests in UI mode # Validation npm run validate # Run prettier, eslint, jest, and playwright tests @@ -153,13 +153,14 @@ npm run test:jest Test files in [tests/playwright/](../../tests/playwright/): - [homepage.spec.js](../../tests/playwright/homepage.spec.js) - Main UI tests +- [submission.spec.js](../../tests/playwright/submission.spec.js) - Submission flow tests - [accessibility.js](../../tests/playwright/utils/accessibility.js) - Accessibility utilities Run tests: ```bash -npm run test:playwright:headless # CI mode -npm run test:playwright:ui # Interactive mode +npm run test:e2e:headless # CI mode +npm run test:e2e:ui # Interactive mode ``` ## Building for Production diff --git a/eslint.config.js b/eslint.config.js index 0bd6b06..23bdd6e 100644 --- a/eslint.config.js +++ b/eslint.config.js @@ -3,7 +3,13 @@ import globals from "globals"; export default [ { - ignores: ["node_modules/**/*", "core/scripts/APIandLibraries/**/*", "**/*.min.js"], + ignores: [ + "node_modules/**/*", + "core/scripts/APIandLibraries/**/*", + "**/*.min.js", + "**/playwright-report/**/*", + "**/test-results/**/*", + ], }, { languageOptions: { diff --git 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"version": "1.1.0", "resolved": "https://registry.npmjs.org/unbox-primitive/-/unbox-primitive-1.1.0.tgz", @@ -11343,9 +12357,9 @@ } }, "node_modules/undici-types": { - "version": "7.16.0", - "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz", - "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw==", + "version": "7.18.2", + "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.18.2.tgz", + "integrity": "sha512-AsuCzffGHJybSaRrmr5eHr81mwJU3kjw6M+uprWvCXiNeN9SOGwQ3Jn8jb8m3Z6izVgknn1R0FTCEAP2QrLY/w==", "dev": true, "license": "MIT" }, diff --git a/package.json b/package.json index 7e8b4cc..7ac965c 100644 --- a/package.json +++ b/package.json @@ -23,6 +23,7 @@ "audit:fix": "npm i && npm audit fix", "eslint:check": "eslint ./", "eslint": "eslint --fix ./", + "lint:markdown": "markdownlint \"**/*.md\"", "minify": "esbuild core/scripts/runtime.js --minify --outfile=core/scripts/runtime.min.js && esbuild core/scripts/crispr_scripts.js --minify --outfile=core/scripts/crispr_scripts.min.js", "prettier:check": "prettier --check ./", "prettier": "prettier --write ./", @@ -30,9 +31,9 @@ "start": "http-server . -p 3000", "test": "jest", "test:jest": "jest --passWithNoTests", - "test:playwright:headless": "npx playwright test --reporter=list", - "test:playwright:ui": "npx playwright test --ui", - "validate": "npm run prettier && npm run eslint && npm run minify && npm run test:jest && npm run test:playwright:headless", + "test:e2e:headless": "npx playwright test --reporter=list", + "test:e2e:ui": "npx playwright test --ui", + "validate": "npm run prettier && npm run eslint && npm run minify && npm run test:jest && npm run test:e2e:headless && npm run lint:markdown", "workbox": "workbox generateSW workbox-config.cjs" }, "bugs": { @@ -57,7 +58,7 @@ "devDependencies": { "@playwright/test": "^1.58.2", "@types/jest": "^30.0.0", - "@types/node": "^25.2.3", + "@types/node": "^25.3.0", "axe-playwright": "^2.2.2", "esbuild": "^0.27.3", "eslint": "^10.0.0", @@ -67,6 +68,7 @@ "http-server": "^14.1.1", "jest": "^30.2.0", "jest-environment-jsdom": "^30.2.0", + "markdownlint-cli": "^0.47.0", "prettier": "^3.8.1", "workbox-cli": "^7.4.0" } diff --git a/playwright.config.js b/playwright.config.js index 4622598..8bd1fce 100644 --- a/playwright.config.js +++ b/playwright.config.js @@ -10,18 +10,7 @@ import { defineConfig, devices } from "@playwright/test"; // dotenv.config({ path: path.resolve(__dirname, '.env') }); /** Android Devices to test on */ -const androidDeviceList = [ - "Galaxy A55", - "Galaxy A55 landscape", - "Nexus 6", - "Nexus 6 landscape", - "Nexus 6P", - "Nexus 6P landscape", - "Pixel 3", - "Pixel 3 landscape", - "Pixel 7", - "Pixel 7 landscape", -]; +const androidDeviceList = ["Galaxy A55", "Nexus 6P", "Pixel 3", "Pixel 7", "Pixel 7 landscape"]; /** * @see https://playwright.dev/docs/test-configuration @@ -33,9 +22,8 @@ export default defineConfig({ /* Fail the build on CI if you accidentally left test.only in the source code. */ forbidOnly: !!process.env.CI, /* Retry on CI only */ - retries: process.env.CI ? 2 : 0, - /* Opt out of parallel tests on CI. */ - workers: process.env.CI ? 1 : undefined, + retries: 2, + workers: 20, /* Reporter to use. See https://playwright.dev/docs/test-reporters */ reporter: [["list"], ["html"], ["json", { outputFile: "test-results/results.json" }]], /* Shared settings for all the projects below. See https://playwright.dev/docs/api/class-testoptions. */ diff --git a/tests/playwright/submission.spec.js b/tests/playwright/submission.spec.js new file mode 100644 index 0000000..62cfe80 --- /dev/null +++ b/tests/playwright/submission.spec.js @@ -0,0 +1,83 @@ +import { test, expect } from "@playwright/test"; + +// Test case table for score-based E2E tests +const scoreTestCases = [ + { + name: "seq input a bit off - partial credit", + inputs: { + sequence_input: "AAGCACTGCACGCCGTGGGT", + strand_input: "Antisense (-)", + pam_input: "CAG", + position_input: "381", + offtarget_input: "87", + f1_input: "TAATACGACTCACTATAGAAGCACTGCACGCCGT", + r1_input: "TTCTAGCTCTAAAACACCCACGGCGTGCAGTGCT", + }, + expectedScore: 9, + }, + { + name: "failing gRNA and primers - zero score", + inputs: { + sequence_input: "AAAAAAAAAAAAAAAAAAAA", + strand_input: "Sense (+)", + pam_input: "AAA", + position_input: "999", + offtarget_input: "1", + f1_input: "AAAAAAAAAAAAAAAAAAAA", + r1_input: "TTTTTTTTTTTTTTTTTTTT", + }, + expectedScore: 0, + }, +]; + +test.describe("SciGrade Submission Flow", () => { + test.beforeEach(async ({ page }) => { + // Navigate to the application page + await page.goto("http://localhost:3000/core/systemrun.html"); + + // Wait for the page to fully load (redirectCRISPR builds the UI) + await page.waitForSelector("#gene_dropdown_selection"); + + // Wait for gene list to be populated (fillGeneList runs after JSON load) + await page.waitForFunction(() => { + const sel = document.getElementById("gene_dropdown_selection"); + return sel && sel.options.length > 0; + }); + + // Select eBFP gene (default test gene) + await page.selectOption("#gene_dropdown_selection", "eBFP"); + + // Click Load Gene button + await page.getByRole("button", { name: "Load Gene" }).click(); + + // Wait for the form to be generated (loadWork appends form inputs into #work) + await page.waitForSelector("#sequence_input", { state: "visible" }); + }); + + // Data-driven tests using test case table + for (const testCase of scoreTestCases) { + test(`should submit ${testCase.name}`, async ({ page }) => { + // Fill in all form inputs from test case + await page.fill("#sequence_input", testCase.inputs.sequence_input); + await page.selectOption("#strand_input", testCase.inputs.strand_input); + await page.fill("#pam_input", testCase.inputs.pam_input); + await page.fill("#position_input", testCase.inputs.position_input); + await page.fill("#offtarget_input", testCase.inputs.offtarget_input); + await page.fill("#f1_input", testCase.inputs.f1_input); + await page.fill("#r1_input", testCase.inputs.r1_input); + + // Click Submit button + await page.click("#assignmentSubmitButton"); + + // Wait for feedback to render + await expect(page.locator("body")).toContainText(/Mark:/, { timeout: 15000 }); + + // Verify expected score + await expect(page.locator("body")).toContainText(`Mark: ${testCase.expectedScore}/10`); + + // Verify feedback sections are present + await expect(page.locator("body")).toContainText(/gRNA Strand Sequence/); + await expect(page.locator("body")).toContainText(/gRNA PAM Sequence/); + }); + } +});