Fix #355 and #356

pegr/.gitignore

@@ -1,6 +1,7 @@
 Thumbs.db
 .DS_Store
 .gradle
+bin/
 build/
 out/
 .idea

pegr/grails-app/controllers/pegr/ApiController.groovy

@@ -794,12 +794,15 @@ class ApiController {
                         case "status":
                             sampleService.updateSampleStatus(sample.id, sampleDict.newValue)
                             break
+                        case "geoAccession":
+                            sampleService.update(sample.id, "geoAccession", sampleDict.newValue)
+                            break
                         default:
                             messages.push("Error: Sample ${sample.id}. Field ${sampleDict.field} cannot be edited.")
                             break
                     }
                 } catch(Exception e) {
-                    messages.push("Error: sample=${sampleDict.sampleID} and field=${sampleDict.field}. ${e.message}")
+                    messages.push("Error: sample=${sampleDict.sampleID} and field=${sampleDict.field}. ")
                 }
             }    
 

pegr/grails-app/domain/pegr/Sample.groovy

@@ -27,6 +27,7 @@ class Sample {
     String recommend
     GrowthMedia growthMedia
     String naturalId 
+    String geoAccession
 
     List getRuns() {
         return SequencingExperiment.where{sample == this}.collect{it.sequenceRun}
@@ -87,6 +88,7 @@ class Sample {
         recommend nullable: true
         growthMedia nullable: true
         naturalId nullable: true
+        geoAccession nullable: true, blank: true,unique: true
     }
 
     static mapping = {

pegr/grails-app/migrations/add_geo.groovy

@@ -0,0 +1,9 @@
+databaseChangeLog = {
+
+    changeSet(author: "danyingshao (generated)", id: "1620671544575-3") {
+        addColumn(tableName: "sample") {
+            column(name: "geo_accession", type: "varchar(255)")
+        }
+    }
+
+}

pegr/grails-app/migrations/changelog.groovy

@@ -2506,4 +2506,5 @@ databaseChangeLog = {
     include file: 'add_default_pipeline.groovy'
     include file: 'add_quality_control_file.groovy'
     include file: 'remove_index_version.groovy'
+    include file: 'add_geo.groovy'
 }

pegr/grails-app/services/pegr/AlignmentStatsService.groovy

@@ -244,7 +244,7 @@ class AlignmentStatsService {
     }
 
    /**
-    * Get the motif count from meme file
+    * Get the motif count from meme file. Obsolete.
     * @param datasets a list of maps
     * @return motifCount
     */

pegr/grails-app/services/pegr/SampleService.groovy

@@ -229,8 +229,14 @@ class SampleService {
 
     @Transactional
     def updateOther(Sample sample, String indexType, String indices) {
-        try {
-            sample.save()
+        try {    
+            sample.save(flush: true, failOnError: true)
+        } catch (grails.validation.ValidationException e) {
+            def errorMsg = sample.errors.fieldErrors
+                .collect { it.field  }
+                .join("; ")
+
+            throw new SampleException(message: "Error in " + errorMsg)
         } catch (Exception e) {
             throw new SampleException(message: "Error saving the sample!")
         }
@@ -509,6 +515,10 @@ class SampleService {
                 sample.assay = getAssay(value)
                 sample.save(faileOnError: true)
                 break
+            case "geoAccession" :
+                sample.geoAccession = value
+                sample.save(failOnError: true)
+                break
             default:
                 sample[field] = utilityService.getFloat(value)
                 sample.save(failOnError: true)

pegr/grails-app/views/help/bioinformaticsApiHelp.gsp

@@ -437,6 +437,7 @@ https://vesta.vmhost.psu.edu/pegr/api/updateSampleData?apiKey=
               <li>requestedGenomes (if multiple genomes are requested, use comma "," to deliminate the strings, e.g. "hg19,hg38")</li>
               <li>requestedPipelines (if multiple pipelines are requested, use comma "," to deliminate the strings, e.g. "paired-004,fastq-001")</li>
               <li>status</li>
+              <li>geoAccession</li>
             </ol>
 
             <p>After a request is posted, PEGR will return the status code and a message as below</p>

pegr/grails-app/views/report/_moduleFiles.gsp

@@ -1,6 +1,7 @@
 <h3>Files</h3>
 <table class="table table-bordered">
     <thead>
+        <th>Sample ID</th>
         <th>Sequence Run</th>
         <th>Fastq Files</th>
         <th>Fastqc Reports</th>
@@ -12,6 +13,7 @@
     <g:each in="${sampleDTOs}" var="sample">
         <g:each in="${sample.experiments}" var="experiment">
             <tr>
+                <td rowspan="${Math.max(1,experiment.alignments.size())}"><g:link controller="sample" action="show" id="${sample.id}">${sample.id}</g:link> ${sample.naturalId}</td>
                 <td rowspan="${Math.max(1,experiment.alignments.size())}">Run${experiment.runId}</td>
                 <td rowspan="${Math.max(1,experiment.alignments.size())}">
                 <g:if test="${experiment.fastq?.read1}">

pegr/grails-app/views/sample/_details.gsp

@@ -238,27 +238,28 @@
         </h4>
         <table class="table table-bordered">
             <tbody>
-            <tr><td>Sample Natural ID</td><td> ${sample.naturalId}</td></tr>
+            <tr><td>Sample natural ID</td><td> ${sample.naturalId}</td></tr>
             <tr><td>Index</td><td> ${sample.sequenceIndicesString} (${sample.sequenceIndicesIdString})</td></tr>
 
             <tr><td>Chromatin (ug)</td><td> <g:if test="${sample?.chromosomeAmount}">${sample.chromosomeAmount}</g:if></td></tr>
 
-            <tr><td>Avail. Cell# per aliquot (M)</td><td> <g:if test="${sample?.cellNumber}">${sample.cellNumber}</g:if></td></tr>
+            <tr><td>Avail. cell# per aliquot (M)</td><td> <g:if test="${sample?.cellNumber}">${sample.cellNumber}</g:if></td></tr>
 
             <tr><td>Volume per aliquot (ul)</td><td> <g:if test="${sample?.volume}">${sample.volume}</g:if></td></tr>
 
-            <tr><td>Requested Tags (M)</td><td> <g:if test="${sample?.requestedTagNumber}">${sample.requestedTagNumber}</g:if></td></tr>
+            <tr><td>Requested tags (M)</td><td> <g:if test="${sample?.requestedTagNumber}">${sample.requestedTagNumber}</g:if></td></tr>
 
             <tr><td>Requested genomes</td><td> ${sample?.requestedGenomes}</td></tr>
 
             <tr><td>Send data to</td><td> ${sample?.sendDataTo}</td></tr>
 
             <g:if test="${sample?.publicationReference}">
-            <tr><td>Publication Reference</td><td> ${sample.publicationReference}</td></tr>
+            <tr><td>Publication reference</td><td> ${sample?.publicationReference}</td></tr>
             </g:if>
 
             <g:if test="${sample.note}">
             <tr><td>Notes</td><td> ${sample.note}</td></tr>
+            <tr><td>GEO accession</td><td> ${sample?.geoAccession}</td></tr>
             </g:if>
             </tbody>
         </table>

pegr/grails-app/views/sample/editOther.gsp

@@ -12,7 +12,7 @@
         <g:form action="updateOther" class="fields">
             <g:hiddenField name="sampleId" value="${sample.id}"></g:hiddenField>
             <div>
-                <label>Sample Natural ID</label>
+                <label>Sample natural ID</label>
                 <input name="naturalId" size="40" value="${sample.naturalId}">
             </div>
             <div>
@@ -33,7 +33,7 @@
                 <input name="volume" class="isnumber" value="${sample.volume}">
             </div>
             <div>
-                <label>Requested Tags (M)</label>
+                <label>Requested tags (M)</label>
                 <input name="requestedTagNumber" class="isnumber" value="${sample.requestedTagNumber}">
             </div>
             <div>
@@ -46,13 +46,17 @@
                 <g:select class="sendTo no-tag-select2" name="sendToId" from="${pegr.User.list()}" optionKey="id" style="width: 150px" value="${sample.sendDataTo}"></g:select>
             </div>
             <div>
-                <label>Publication Reference</label>
+                <label>Publication reference</label>
                 <input name="publicationReference" value="${sample.publicationReference}">
             </div>
             <div>
                 <label>Notes</label>
                 <textarea name="note" cols="60" rows="4">${sample.note}</textarea>
             </div>
+            <div>
+                <label>GEO Accession</label>
+                <input name="geoAccession" value="${sample.geoAccession}">
+            </div>
             <div>
                 <g:submitButton name="save" value="Save" class="btn btn-primary"></g:submitButton>
                 <g:link action="edit" params="[sampleId: sample.id]" class="btn btn-default">Cancel</g:link>