modelmatcher changes

pom.xml

@@ -205,4 +205,4 @@
         </plugins>
     </build>
 
-</project>
+</project>

src/main/java/ubc/pavlab/rdp/model/enums/ResearcherCategory.java

@@ -6,11 +6,11 @@
 @Getter
 @AllArgsConstructor
 public enum ResearcherCategory {
-    IN_SILICO( "in-silico" ),
-    IN_VITRO_BIOCHEMICAL( "in-vitro" ),
+    IN_VIVO( "in-vivo" ),
     IN_VITRO_CELLS( "in-vitro-cells" ),
+    IN_VITRO_BIOCHEMICAL( "in-vitro" ),
     IN_VITRO_STRUCTURAL( "in-vitro-structural" ),
-    IN_VIVO( "in-vivo" ),
+    IN_SILICO( "in-silico" ),
     OTHER( "other" );
     private final String id;
 }

src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java

@@ -112,7 +112,7 @@ public void sendResetTokenMessage( User user, PasswordResetToken token, Locale l
 
         // password reset always go through the primary email
         InternetAddress to = new InternetAddress( user.getEmail() );
-        String subject = "Reset your password";
+        String subject = "Reset your ModelMatcher password";
         String content =
                 "Hello " + user.getProfile().getName() + ",\r\n\r\n" +
                         "We recently received a request that you want to reset your password. " +
@@ -131,7 +131,7 @@ public void sendRegistrationMessage( User user, VerificationToken token ) throws
         String registrationEnding = messageSource.getMessage( "rdp.site.email.registration-ending", new String[]{ siteSettings.getContactEmail() }, Locale.getDefault() );
         // registration always go through the primary email
         InternetAddress recipientAddress = new InternetAddress( user.getEmail() );
-        String subject = "Confirm your registration";
+        String subject = "Confirm your ModelMatcher registration";
         String confirmationUrl = UriComponentsBuilder.fromUri( siteSettings.getHostUri() )
                 .path( "registrationConfirm" )
                 .queryParam( "token", token.getToken() )

src/main/java/ubc/pavlab/rdp/services/GeneInfoServiceImpl.java

@@ -102,7 +102,12 @@ public void updateGenes() {
                 } else {
                     log.info( MessageFormat.format( "Loading genes for {0} from {1}.",
                             taxon, taxon.getGeneUrl() ) );
+if(taxon.getId()==8364){
                     data = geneInfoParser.parse( taxon, taxon.getGeneUrl() );
+}
+else{
+data=new HashSet<>();
+}
                 }
                 log.info( MessageFormat.format( "Done parsing genes for {0}.", taxon ) );
                 geneInfoRepository.save( data );
@@ -173,4 +178,4 @@ private <T> boolean addAll( Collection<SearchResult<T>> container, Collection<T>
 
         return false;
     }
-}
+} 

src/main/java/ubc/pavlab/rdp/services/OrganInfoServiceImpl.java

@@ -50,11 +50,12 @@ public void updateOrganInfos() {
                 OrganInfo organInfo = organInfoRepository.findByUberonId( term.getId() );
                 if ( organInfo == null ) {
                     organInfo = new OrganInfo();
+	            organInfo.setName( term.getName() );
                     organInfo.setUberonId( term.getId() );
                     // only show organs that have been explicitly activated
                     organInfo.setActive( false );
                 }
-                organInfo.setName( term.getName() );
+
                 organInfo.setDescription( term.getDefinition() );
                 organInfoRepository.save( organInfo );
             }

src/main/java/ubc/pavlab/rdp/services/RemoteResourceServiceImpl.java

@@ -105,7 +105,15 @@ public Collection<User> findUsersByDescription( String descriptionLike, Set<Rese
     @PreAuthorize("hasPermission(null, 'international-search')")
     public Collection<UserGene> findGenesBySymbol( String symbol, Taxon taxon, Set<TierType> tiers, Integer orthologTaxonId, Set<ResearcherPosition> researcherPositions, Set<ResearcherCategory> researcherCategories, Set<String> organUberonIds ) {
         List<UserGene> intlUsergenes = new LinkedList<>();
-        for ( TierType tier : restrictTiers( tiers ) ) {
+        if(taxon.getId()==8364){
+return new LinkedList<>();
+}
+
+        if(orthologTaxonId==null){
+orthologTaxonId=-99;
+}
+
+	for ( TierType tier : restrictTiers( tiers ) ) {
             MultiValueMap<String, String> params = new LinkedMultiValueMap<>();
             params.add( "symbol", symbol );
             params.putAll( UserGeneSearchParams.builder()

src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java

@@ -94,8 +94,9 @@ public Set<GeneInfo> parse( Taxon taxon, InputStream input ) throws ParseExcepti
 
             return br.lines()
                     .map( line -> line.split( "\t" ) )
-                    .filter( values -> Integer.valueOf( values[0] ).equals( taxon.getId() ) )
                     .map( values -> {
+try{
+
                         GeneInfo gene = geneInfoRepository.findByGeneIdAndTaxon( Integer.valueOf( values[1] ), taxon );
                         if ( gene == null ) {
                             gene = new GeneInfo();
@@ -107,15 +108,19 @@ public Set<GeneInfo> parse( Taxon taxon, InputStream input ) throws ParseExcepti
                         gene.setName( values[8] );
                         SimpleDateFormat ncbiDateFormat = new SimpleDateFormat( "yyyyMMdd" );
                         try {
-                            gene.setModificationDate( ncbiDateFormat.parse( values[14] ) );
+                            gene.setModificationDate( ncbiDateFormat.parse( "20200926" ) );
                         } catch ( ParseException e ) {
                             log.warn( MessageFormat.format( "Could not parse date {0} for gene {1}.", values[14], values[1] ), e );
                         }
                         return gene;
+}
+catch(Exception e){
+return new GeneInfo();
+}
                     } ).collect( Collectors.toSet() );
         } catch ( IOException e ) {
             throw new ParseException( e.getMessage(), 0 );
         }
     }
 
-}
+}

src/main/resources/static/css/common.css

@@ -1,3 +1,6 @@
+a{
+	color: teal;
+}
 html {
     position: relative;
     min-height: 100%;

src/main/resources/static/css/login.css

@@ -1,3 +1,9 @@
+a{
+	color:teal
+}
+.btn{
+background-color:teal
+}
 html, body {
     margin: 0;
     height: 100%;

src/main/resources/static/js/model.js → src/main/resources/static/js/model1.js

@@ -61,6 +61,26 @@
                 row.push('');
                 if (customizableGeneLevel) {
                     row.push('');
+                } else {
+                    row.push('<span class="align-middle"><i class="delete-row align-middle"></i><a href="https://www.ncbi.nlm.nih.gov/gene/' + gene.geneId + '" target="_blank" class="align-middle" rel="noopener">' + gene.symbol + '</a></span>');
+                    row.push(gene.geneId);
+                    row.push('<span class="align-middle">' + gene.name + '</span>');
+                    row.push('<input name="primary" class="align-middle" type="checkbox"/>');
+                    if (customizableGeneLevel) {
+                        var privacyOptions = enabledGenePrivacyLevels.map(function (k) {
+                            var privacyLevel = privacyLevels[k];
+                            if (privacyLevel.ordinal!=1) {
+                                return '<option' +
+                                    ' value="' + privacyLevel.ordinal + '"' +
+                                    (privacyLevel.ordinal === userPrivacyLevel.ordinal ? ' selected' : '') + '>' +
+                                    privacyLevel.label +
+                                    '</option>';
+                            } else {
+                                return '';
+                            }
+                        }).join('');
+                        row.push('<select class="form-control">' + privacyOptions + '</select>');
+                    }
                 }
             } else {
                 /* gene is already in the table */

src/main/resources/templates/forgotPassword.html

@@ -14,8 +14,8 @@
     <div class="container py-4">
         <div class="row">
             <div class="col-md-10 offset-1">
-                <h4 class="form-signin-heading"><a th:href="@{/login}" th:text="#{rdp.site.fullname}"></a></h4>
-                <h6 class="form-signin-subheading">Researcher Registry</h6>
+                <h4 class="form-signin-heading">Forgot Password</h4>
+                <h6 class="form-signin-subheading">ModelMatcher</h6>
             </div>
         </div>
 

src/main/resources/templates/fragments/gene-table.html

@@ -14,22 +14,22 @@
             class="text-center"
             scope="col"
             data-toggle="tooltip"
-            th:title="${viewOnly} == null ? 'Primary genes constitute your TIER1 genes whereas non-primary genes will be part of your TIER2 genes.' : 'Tier determines the degree of involvment of a researcher with a gene.'">
+            th:title="${viewOnly} == null ? 'Primary genes are genes that your lab is actively working on, or genes where you have assays and reagents ready for immediately study.' : 'Tier determines the degree of involvment of a researcher with a gene.'">
             <span th:text="${viewOnly == null} ? 'Primary' : 'Tier'"></span>
             <i class="tip oi oi-question-mark"></i>
         </th>
         <th th:if="${viewOnly == null} and ${@applicationSettings.privacy.isCustomizableGeneLevel()}"
             class="text-center"
             scope="col"
             data-toggle="tooltip"
-            title="Privacy level determines who can see this gene in a search result.">
+            title="Public genes can be searched by all users. Restricted genes require a match request to be submitted.">
             Privacy Level
             <i class="tip oi oi-question-mark"></i>
         </th>
     </tr>
     </thead>
     <tbody>
-    <tr th:each="gene : ${genes}">
+    <tr th:if="${gene.effectivePrivacyLevel != T(ubc.pavlab.rdp.model.enums.PrivacyLevelType).PRIVATE or viewOnly == null}" th:each="gene : ${genes}">
         <td class="align-middle">
             <i th:if="${viewOnly == null}" class="delete-row align-middle"></i>
             <a th:href="@{https://www.ncbi.nlm.nih.gov/gene/{geneId}(geneId=${gene.geneId})}"
@@ -49,7 +49,7 @@
                        th:checked="${gene.tier == T(ubc.pavlab.rdp.model.enums.TierType).TIER1}"/>
             </td>
             <td th:if="${viewOnly != null}"
-                th:text="${gene.tier}"
+                th:text="${gene.tier==T(ubc.pavlab.rdp.model.enums.TierType).TIER1}?'Primary':'Secondary'"
                 class="text-center"></td>
         </th:block>
         <td th:if="${viewOnly == null} and ${@applicationSettings.privacy.isCustomizableGeneLevel()}"
@@ -63,12 +63,15 @@
             </select>
         </td>
     </tr>
+
     </tbody>
+<!--
     <tfoot th:if="${viewOnly != null}">
     <tr>
         <td colspan="3"></td>
     </tr>
     </tfoot>
+-->
 </table>
 </body>
 </html>

src/main/resources/templates/fragments/organ.html

@@ -18,7 +18,7 @@
                        class="form-check-input"/>
                 <label th:for="${#ids.prev('organUberonIds')}"
                        class="form-check-label">
-                    <img th:src="@{/images/organs/{uberonId}.svg(uberonId=${organInfo.uberonId})}"
+                    <img style="opacity:0.7" th:src="@{/images/organs/{uberonId}.svg(uberonId=${organInfo.uberonId})}"
                          th:alt="${#strings.capitalize(organInfo.name)}"
                          class="img-fluid"/>
                 </label>
@@ -29,10 +29,10 @@
 <div th:fragment="organs" class="row">
     <div th:each="organInfo, iter : ${@organInfoService.findByActiveTrueOrderByOrdering()}"
          th:if="${#lists.contains(checkedOrganUberonIds, organInfo.uberonId)}"
-         class="col-3 col-md-2 col-lg-1"
+         class="col-3 col-md-2 col-lg-2"
          data-toggle="tooltip"
          th:title="${#strings.capitalize(organInfo.name)}">
-        <img th:src="@{/images/organs/{uberonId}.svg(uberonId=${organInfo.uberonId})}"
+        <img style="opacity:0.7" th:src="@{/images/organs/{uberonId}.svg(uberonId=${organInfo.uberonId})}"
              th:alt="${#strings.capitalize(organInfo.name)}"
              class="img-fluid"/>
     </div>

src/main/resources/templates/fragments/term-table.html

@@ -11,7 +11,7 @@
         <th scope="col">Aspect</th>
         <th scope="col"
             data-toggle="tooltip"
-            title="Number of times genes associated to a term appear in your TIER1 or TIER2 genes.">
+            title="Number of times genes associated to a term appear in your Primary or Secondary genes.">
             Overlap
             <i class="tip oi oi-question-mark"></i>
         </th>

src/main/resources/templates/fragments/user-table.html

@@ -9,7 +9,6 @@
     <thead class="thead-light">
     <tr>
         <th scope="col"></th>
-        <th th:if="${remote}" scope="col">Origin</th>
         <th scope="col">Full Name</th>
         <th scope="col">
             <span th:unless="${@applicationSettings.profile.enabledResearcherPositions.isEmpty()}">Position and</span>
@@ -34,7 +33,6 @@
                 View User Profile
             </a>
         </td>
-        <td th:if="${remote}" th:text="${u.origin}"></td>
         <td th:text="${u.profile.fullName}"></td>
         <td>
             <span th:if="${u.profile.researcherPosition}"
@@ -61,12 +59,10 @@
     <thead class="thead-light">
     <tr>
         <th scope="col"></th>
-        <th th:if="${remote}" scope="col">Origin</th>
         <th scope="col">Full Name</th>
-        <th scope="col">
-            <span th:unless="${@applicationSettings.profile.enabledResearcherPositions.isEmpty()}">Position and</span>
-            Organization
-        </th>
+        <th th:if="not ${remote}" scope="col">Principal Investigator</th>
+        <th scope="col">Organization</th>
+
         <th scope="col">Gene</th>
         <th scope="col"
             data-toggle="tooltip"
@@ -93,32 +89,35 @@
                 <i class="oi oi-person"></i>
                 View User Profile
             </a>
-            <a th:if="${ug.anonymousId} and ${remote}"
-               th:href="@{/search/gene/by-anonymous-id/{anonymousId}/request-access(anonymousId=${ug.anonymousId},remoteHost=${ug.user.originUrl})}"
-               th:attr="data-anonymous-user-id=${ug.user.anonymousId},data-remote-host=${ug.user.originUrl}"
-               class="btn btn-primary btn-sm btn-block user-preview-popover">
-                <i class="oi oi-lock-locked"></i>
-                Request Access
-            </a>
-            <a th:if="${ug.anonymousId} and not ${remote}"
-               th:href="@{/search/gene/by-anonymous-id/{anonymousId}/request-access(anonymousId=${ug.anonymousId})}"
-               th:attr="data-anonymous-user-id=${ug.user.anonymousId}"
-               class="btn btn-primary btn-sm btn-block user-preview-popover">
+
+
+            <a th:if="${ug.anonymousId}"
+                             th:attr="data-anonymous-user-id=${ug.user.anonymousId}"
+               class="btn btn-primary btn-sm btn-block">
                 <i class="oi oi-lock-locked"></i>
-                Request Access
+                Restricted Gene
             </a>
+
         </td>
-        <td th:if="${remote}" th:text="${ug.user.origin}"></td>
-        <td th:text="${ug.user.profile.fullName}"></td>
         <td>
+<span th:if="${ug.anonymousId}">MM User</span>
+<span th:unless="${ug.anonymousId}" th:text="${ug.user.profile.fullName}"></span>
+
+</td>
+	<td th:if="not ${remote}">
             <span th:if="${ug.user.profile.researcherPosition}"
-                  th:text="#{'ResearcherPosition.' + ${ug.user.profile.researcherPosition}}">...</span>
-            <span th:if="${ug.user.profile.researcherPosition} != null and ${ug.user.profile.organization} != ''">at</span>
-            <span th:text="${ug.user.profile.organization}"></span>
-        </td>
+                  th:text="Yes">...</span>
+            <span th:unless="${ug.user.profile.researcherPosition}"
+                  th:text="${ug.anonymousId}?'?':'No'">...</span>
+	</td>
+        <td th:text="${ug.user.profile.organization}"></td>
         <td th:text="${ug.symbol}"></td>
-        <td th:text="${ug.tier}"></td>
-        <td th:text="${#strings.capitalizeWords(ug.taxon.commonName)}"></td>
+        <td th:text="${ug.tier==T(ubc.pavlab.rdp.model.enums.TierType).TIER1}?'Primary':'Secondary'"></td>
+        <td>
+            <span th:if="${ug.taxon.commonName=='e. coli'}"><i>E. coli</i></span>
+            <span th:unless="${ug.taxon.commonName=='e. coli'}" th:text="${#strings.capitalizeWords(ug.taxon.commonName)}">...</span>
+
+	</td>
     </tr>
     <tr th:if="${#lists.isEmpty(usergenes)}" class="table-warning">
         <td class="text-center warning" th:colspan="100">No user genes found matching the provided search criteria.</td>