Add geneFamily workflow

Author: Yan Xu

webapp/client/src/_nav.js

@@ -43,7 +43,7 @@ const _nav = [
         to: '/workflow/metagenomics',
         badge: {
           color: 'info',
-          text: '8',
+          text: '9',
         },
       },
     ],

webapp/client/src/components/OrcidLoginHelp.js

@@ -10,23 +10,23 @@ const OrcidLoginHelp = (props) => {
             ORCID Account Integration
           </CardTitle>
           <CardText className="edge-header-orcid-login-help-text">
-            <p>
-              EDGE requires an ORCID iD to log in. When logged in you have access to features such
-              as uploading files and the ability to create and manage workflow runs.
-            </p>
-            <p>
-              Click the &quot;ORCID Login&quot; button, to either register for an ORCID iD or, if
-              you already have one, to sign into your ORCID account, then grant permission for EDGE
-              to access your ORCID iD. This allows us to verify your identity and securely connect
-              to your ORCID iD. Additionally, we may use information, such as your name and id, to
-              associate your ORCID record with your EDGE workflow runs.
-            </p>
-            <p>
-              Learn more about{' '}
-              <a href="https://orcid.org/blog/2017/02/20/whats-so-special-about-signing">
-                what&apos;s so special about signing in.
-              </a>
-            </p>
+            EDGE requires an ORCID iD to log in. When logged in you have access to features such as
+            uploading files and the ability to create and manage workflow runs.
+            <br></br>
+            <br></br>
+            Click the &quot;ORCID Login&quot; button, to either register for an ORCID iD or, if you
+            already have one, to sign into your ORCID account, then grant permission for EDGE to
+            access your ORCID iD. This allows us to verify your identity and securely connect to
+            your ORCID iD. Additionally, we may use information, such as your name and id, to
+            associate your ORCID record with your EDGE workflow runs.
+            <br></br>
+            <br></br>
+            Learn more about{' '}
+            <a href="https://orcid.org/blog/2017/02/20/whats-so-special-about-signing">
+              what&apos;s so special about signing in.
+            </a>
+            <br></br>
+            <br></br>
           </CardText>
         </CardBody>
       </Card>

webapp/client/src/edge/um/user/UploadFiles.js

@@ -190,7 +190,7 @@ const UploadFiles = (props) => {
     <>
       <LoaderDialog
         loading={submitting}
-        text={'Uploading...' + Math.round((filesUploaded / files2upload) * 100) + '%'}
+        text={`Uploading... ${files2upload > 5 ? Math.round((filesUploaded / files2upload) * 100) + '%' : ''}`}
       />
       <ToastContainer />
       <div className="clearfix">

webapp/client/src/util.js

@@ -48,4 +48,9 @@ export const workflowList = {
     category: 'metagenomics',
     info: 'Reference-Based Analysis workflow ',
   },
+  geneFamily: {
+    label: 'Gene Family Analysis',
+    category: 'metagenomics',
+    info: 'Gene Family Analysis workflow ',
+  },
 }

webapp/client/src/workflows/metagenomics/Main.js

@@ -20,6 +20,7 @@ import { AntiSmash } from './forms/AntiSmash'
 import { Taxonomy } from './forms/Taxonomy'
 import { Phylogeny } from './forms/Phylogeny'
 import { RefBased } from './forms/RefBased'
+import { GeneFamily } from './forms/GeneFamily'
 
 const Main = (props) => {
   const navigate = useNavigate()
@@ -161,6 +162,25 @@ const Main = (props) => {
           : {}),
       }
     }
+    //add optional inputs to main inputs
+    if (workflow === 'geneFamily') {
+      // eslint-disable-next-line prettier/prettier
+      if (selectedWorkflows[workflow].inputs['readsGeneFamily'].value) {
+        // eslint-disable-next-line prettier/prettier
+        selectedWorkflows[workflow].inputs = {
+          ...selectedWorkflows[workflow].inputs,
+          // eslint-disable-next-line prettier/prettier
+          ...selectedWorkflows[workflow].readsInputs
+        }
+      } else {
+        // eslint-disable-next-line prettier/prettier
+        selectedWorkflows[workflow].inputs = {
+          ...selectedWorkflows[workflow].inputs,
+          // eslint-disable-next-line prettier/prettier
+          ...selectedWorkflows[workflow].contigsInputs
+        }
+      }
+    }
 
     Object.keys(selectedWorkflows[workflow].inputs).forEach((key) => {
       myWorkflow.input[key] = selectedWorkflows[workflow].inputs[key].value
@@ -283,7 +303,6 @@ const Main = (props) => {
           <h4 className="pt-3">Run a Single Workflow</h4>
           <hr />
           <Project setParams={setProject} />
-
           <br></br>
           <b>Workflow</b>
           <MySelect
@@ -537,7 +556,6 @@ const Main = (props) => {
               />
             </>
           )}
-          <br></br>
           {workflow === 'phylogeny' && (
             <>
               <InputRawReads
@@ -574,7 +592,6 @@ const Main = (props) => {
               />
             </>
           )}
-          <br></br>
           {workflow === 'refBased' && (
             <>
               <InputRawReads
@@ -611,9 +628,43 @@ const Main = (props) => {
               />
             </>
           )}
-          <br></br>
+          {workflow === 'geneFamily' && (
+            <>
+              <InputRawReads
+                setParams={setRawData}
+                isValidFileInput={isValidFileInput}
+                source={workflows[workflow]['rawReadsInput'].source}
+                sourceDisplay={workflows[workflow]['rawReadsInput'].text}
+                sourceOptionsOn={true}
+                text={workflows[workflow]['rawReadsInput'].text}
+                tooltip={workflows[workflow]['rawReadsInput'].tooltip}
+                title={'Input Raw Reads'}
+                fastqSettings={workflows[workflow]['rawReadsInput'].fastq}
+                fastaSettings={workflows[workflow]['rawReadsInput'].fasta}
+                isValid={rawDataParams ? rawDataParams.validForm : false}
+                errMessage={rawDataParams ? rawDataParams.errMessage : null}
+                allExpand={allExpand}
+                allClosed={allClosed}
+              />
+              <GeneFamily
+                name={workflow}
+                full_name={workflow}
+                title={workflowList[workflow].label}
+                setParams={setWorkflowParams}
+                isValid={
+                  selectedWorkflows[workflow] ? selectedWorkflows[workflow].validForm : false
+                }
+                errMessage={
+                  selectedWorkflows[workflow] ? selectedWorkflows[workflow].errMessage : null
+                }
+                source={rawDataParams.inputs.source.value}
+                pairedReads={rawDataParams.inputs.paired.value}
+                allExpand={allExpand}
+                allClosed={allClosed}
+              />
+            </>
+          )}
         </div>
-
         <div className="edge-center">
           <Button
             color="primary"

webapp/client/src/workflows/metagenomics/defaults.js

@@ -9,6 +9,7 @@ export const workflowOptions = [
   { value: 'taxonomy', label: workflowList['taxonomy'].label },
   { value: 'phylogeny', label: workflowList['phylogeny'].label },
   { value: 'refBased', label: workflowList['refBased'].label },
+  { value: 'geneFamily', label: workflowList['geneFamily'].label },
 ]
 
 export const taxClassificationOptions = {
@@ -1861,4 +1862,122 @@ export const workflows = {
       },
     },
   },
+  geneFamily: {
+    validForm: true,
+    errMessage: 'input error',
+    paramsOn: true,
+    files: [],
+    rawReadsInput: {
+      source: 'fastq',
+      fastq: {
+        enableInput: true,
+        placeholder: 'Select a file or enter a file http(s) url',
+        dataSources: ['upload', 'public', 'project'],
+        fileTypes: ['fastq', 'fq', 'fastq.gz', 'fq.gz'],
+        projectTypes: ['runFaQCs'],
+        projectScope: ['self+shared'],
+        viewFile: false,
+        isOptional: false,
+        cleanupInput: true,
+        maxInput: 1000,
+      },
+      fasta: {
+        enableInput: true,
+        placeholder: 'Select a file or enter a file http(s) url',
+        dataSources: ['upload', 'public', 'project'],
+        fileTypes: ['fasta', 'fa', 'fna', 'contigs'],
+        projectTypes: ['assembly', 'annotation'],
+        projectScope: ['self+shared'],
+        viewFile: false,
+        isOptional: false,
+        cleanupInput: true,
+        maxInput: 1,
+      },
+    },
+    inputs: {
+      readsGeneFamily: {
+        text: 'Reads Gene Family Analysis',
+        value: true,
+        switcher: {
+          trueText: 'Yes',
+          falseText: 'No',
+          defaultValue: true,
+        },
+      },
+      contigsGeneFamily: {
+        text: 'Contigs Gene Family Analysis',
+        value: false,
+        switcher: {
+          trueText: 'Yes',
+          falseText: 'No',
+          defaultValue: false,
+        },
+      },
+    },
+    readsInputs: {
+      virulenceFactorTool: {
+        text: 'Virulence Factor (VF) Detection Tool',
+        tooltip: `MetaVF Toolkit will identify VFs in PE reads through sequence similarity search using
+        VFDB 2.0 <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11402979/" target="_blank" rel="noopener noreferrer"><span style="color:yellow;">[here]</span></a>`,
+        value: 'MetaVF Toolkit',
+        display: 'MetaVF Toolkit',
+        options: [
+          { text: 'MetaVF Toolkit', value: 'MetaVF Toolkit' },
+          { text: 'PathoFact2', value: 'PathoFact2', disabled: true },
+        ],
+      },
+    },
+    contigsInputs: {
+      inputFAA: {
+        text: 'Input FAA File',
+        value: null,
+        display: null,
+        fileInput: {
+          enableInput: true,
+          placeholder: '(Required) Select a file or enter a file http(s) url',
+          dataSources: ['upload', 'public', 'project'],
+          fileTypes: ['faa'],
+          projectTypes: ['annotation'],
+          projectScope: ['self+shared'],
+          viewFile: false,
+          isOptional: false,
+          cleanupInput: true,
+        },
+      },
+      inputGFF: {
+        text: 'Input GFF File',
+        value: null,
+        display: null,
+        fileInput: {
+          enableInput: true,
+          placeholder: '(Required) Select a file or enter a file http(s) url',
+          dataSources: ['upload', 'public', 'project'],
+          fileTypes: ['gff'],
+          projectTypes: ['annotation'],
+          projectScope: ['self+shared'],
+          viewFile: false,
+          isOptional: false,
+          cleanupInput: true,
+        },
+      },
+      virulenceFactorTool: {
+        text: 'Virulence Factor (VF) Detection Tool',
+        tooltip: `MetaVF Toolkit will identify VFs in contigs through sequence similarity search using
+        VFDB 2.0 <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11402979/" target="_blank" rel="noopener noreferrer"><span style="color:yellow;">[here]</span></a>; PathoFact2.`,
+        value: 'MetaVF Toolkit',
+        display: 'MetaVF Toolkit',
+        options: [
+          { text: 'MetaVF Toolkit', value: 'MetaVF Toolkit' },
+          { text: 'PathoFact2', value: 'PathoFact2' },
+        ],
+      },
+    },
+    // only for input with validation method
+    validInputs: {
+      contigsInputs: {
+        inputFAA: { isValid: false, error: 'Input FAA File error. Required' },
+        inputGFF: { isValid: false, error: 'Input GFF File error. Required' },
+      },
+    },
+  },
 }