Fix bug

Author: Yan Xu

webapp/client/src/edge/project/forms/FastqInput.js

@@ -67,6 +67,7 @@ export const FastqInput = (props) => {
       {!props.disableSwitcher && (
         <>
           <Switcher
+            id={'interleaved'}
             name={'interleaved'}
             setParams={setSwitcher}
             text={components[componentName].params['interleaved'].text}

webapp/client/src/edge/project/forms/Switcher.js

@@ -6,7 +6,7 @@ import { components } from './defaults'
 
 export const Switcher = (props) => {
   const componentName = 'switcher'
-  const [form, setState] = useState({ ...components[componentName] })
+  const [form, setState] = useState({ ...components[componentName], isTrue: props.defaultValue })
   const [doValidation, setDoValidation] = useState(0)
 
   const setNewState2 = (name, value) => {
@@ -18,11 +18,7 @@ export const Switcher = (props) => {
   }
 
   useEffect(() => {
-    form.isTrue = props.defaultValue
-  }, []) // eslint-disable-line react-hooks/exhaustive-deps
-
-  useEffect(() => {
-    setState({ ...components[componentName] })
+    setState({ ...components[componentName], isTrue: props.defaultValue })
   }, [props.reset]) // eslint-disable-line react-hooks/exhaustive-deps
 
   useEffect(() => {

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

@@ -32,7 +32,7 @@ const Main = (props) => {
     setDoValidation(doValidation + 1)
   }
   const setWorkflowParams = (params, workflowName) => {
-    console.log(workflowName, params)
+    //console.log(workflowName, params)
     setSelectedWorkflows({ ...selectedWorkflows, [workflowName]: params })
     setDoValidation(doValidation + 1)
   }
@@ -63,6 +63,9 @@ const Main = (props) => {
           selectedWorkflows[workflow].inputs[key].value
       }
     })
+    // set pairedFile flag
+    myWorkflow.input['pairedFile'] = !myWorkflow.input['interleaved']
+
     //update input for nextflow
     if (!myWorkflow.input['artifactFile']) {
       myWorkflow.input['artifactFile'] = '${projectDir}/nf_assets/NO_FILE3'

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

@@ -7,7 +7,7 @@ export const workflows = {
     validForm: false,
     errMessage: 'input error',
     inputs: {
-      pairedFile: {
+      interleaved: {
         text: 'Is interleaved',
         value: true,
       },

webapp/client/src/edge/workflows/metagenomics/forms/RunFaQCs.js

@@ -26,7 +26,7 @@ export const RunFaQCs = (props) => {
   }
 
   const setIntegerInput = (inForm, name) => {
-    console.log(inForm, name)
+    //console.log(inForm, name)
     if (inForm.validForm) {
       form.inputs[name].value = inForm.integerInput
       if (validInputs[name]) {
@@ -65,7 +65,7 @@ export const RunFaQCs = (props) => {
 
   const setFastqInput = (inForm, name) => {
     if (inForm.validForm) {
-      form.inputs['pairedFile'].value = !inForm.interleaved
+      form.inputs['interleaved'].value = inForm.interleaved
       if (inForm.interleaved) {
         form.inputs[name].value = inForm.fileInput
         form.inputs[name].display = inForm.fileInput_display
@@ -77,7 +77,8 @@ export const RunFaQCs = (props) => {
         validInputs[name].isValid = true
       }
     } else {
-      form.inputs['pairedFile'].value = inForm.interleaved
+      // reset values
+      form.inputs['interleaved'].value = true
       form.inputs[name].value = []
       form.inputs[name].display = []
       if (validInputs[name]) {
@@ -172,6 +173,7 @@ export const RunFaQCs = (props) => {
           />
           <br></br>
           <Switcher
+            id={'trimAdapter'}
             name={'trimAdapter'}
             setParams={setSwitcher}
             text={workflows[workflowName].inputs['trimAdapter'].text}
@@ -193,6 +195,7 @@ export const RunFaQCs = (props) => {
           />
           <br></br>
           <Switcher
+            id={'trimPolyA'}
             name={'trimPolyA'}
             setParams={setSwitcher}
             text={workflows[workflowName].inputs['trimPolyA'].text}
@@ -261,6 +264,7 @@ export const RunFaQCs = (props) => {
           />
           <br></br>
           <Switcher
+            id={'filtPhiX'}
             name={'filtPhiX'}
             setParams={setSwitcher}
             text={workflows[workflowName].inputs['filtPhiX'].text}

webapp/docs/EDGE-v3-readsQC-ui.xlsx

@@ -166,6 +166,9 @@ const getProjectRunStats = async (code, type, req) => {
     if (proj) {
       // get associated job
       const job = await Job.findOne({ 'project': { $eq: code } });
+      if (!job) {
+        return {};
+      }
       const projHome = `${config.IO.PROJECT_BASE_DIR}/${code}`;
       const statsJson = `${projHome}/run_stats.json`;
       if (job.queue === 'nextflow') {

webapp/server/edge-api/utils/project.js

@@ -66,13 +66,15 @@ const abortJob = async (proj) => {
   // If is local, find pid in .nextflow.pid and kill process and all descendant processes: pkill -TERM -P <pid>
   // If is slurm, delete slurm job?
   const pidFile = `${config.IO.PROJECT_BASE_DIR}/${proj.code}/nextflow/.nextflow.pid`;
-  let all = fs.readFileSync(pidFile, 'utf8');
-  all = all.trim();  // final crlf in file
-  const lines = all.split('\n');
-  const pid = parseInt(lines[0], 10);
-  const cmd = `pkill -TERM -P ${pid}`;
-  // Don't need to wait for the deletion, the process may already complete
-  execCmd(cmd);
+  if (fs.existsSync(pidFile)) {
+    let all = fs.readFileSync(pidFile, 'utf8');
+    all = all.trim();  // final crlf in file
+    const lines = all.split('\n');
+    const pid = parseInt(lines[0], 10);
+    const cmd = `pkill -TERM -P ${pid}`;
+    // Don't need to wait for the deletion, the process may already complete
+    execCmd(cmd);
+  }
   // delete job
   Job.deleteOne({ project: proj.code }, (err) => {
     if (err) {