Study and publication Learn details : External data links

resources/queries/cds/learn_publicationExternalLinks.sql

@@ -0,0 +1,6 @@
+SELECT
+    elm.protocol_id,
+    el.*
+FROM cds.external_link el
+         LEFT JOIN cds.external_link_map elm ON el.cds_link_id = elm.cds_link_id
+WHERE elm.type = 'publication'

resources/queries/cds/learn_publicationdata.sql

@@ -15,6 +15,7 @@
  */
 SELECT
     pd.publication_id,
+    pd.display_order,
     doc.*
 FROM cds.publicationDocument pd
     LEFT JOIN document doc ON pd.document_id = doc.document_id

resources/queries/cds/learn_studyExternalLinks.sql

@@ -0,0 +1,6 @@
+SELECT
+    elm.protocol_id,
+    el.*
+FROM cds.external_link el
+    LEFT JOIN cds.external_link_map elm ON el.cds_link_id = elm.cds_link_id
+    WHERE elm.type = 'study'

resources/schemas/cds.xml

@@ -729,6 +729,7 @@
             <column columnName="publication_id"/>
             <column columnName="document_id"/>
             <column columnName="container"/>
+            <column columnName="display_order"/>
         </columns>
     </table>
     <table tableName="document" tableDbType="TABLE">
@@ -1423,6 +1424,7 @@
             <column columnName="publication_id"/>
             <column columnName="document_id"/>
             <column columnName="container"/>
+            <column columnName="display_order"/>
         </columns>
     </table>
     <table tableName="import_studyReport" tableDbType="TABLE">
@@ -2267,4 +2269,23 @@
             <column columnName="container"/>
         </columns>
     </table>
+    <table tableName="external_link" tableDbType="TABLE">
+        <columns>
+            <column columnName="cds_link_id"/>
+            <column columnName="link_label"/>
+            <column columnName="link_url"/>
+            <column columnName="link_type"/>
+            <column columnName="link_description"/>
+            <column columnName="container"/>
+        </columns>
+    </table>
+    <table tableName="external_link_map" tableDbType="TABLE">
+        <columns>
+            <column columnName="row_id"/>
+            <column columnName="cds_link_id"/>
+            <column columnName="protocol_id"/>
+            <column columnName="type"/>
+            <column columnName="container"/>
+        </columns>
+    </table>
 </tables>

resources/schemas/dbscripts/postgresql/cds-24.002-24.003.sql

@@ -0,0 +1,29 @@
+ALTER TABLE cds.import_PublicationDocument ADD COLUMN display_order INT;
+ALTER TABLE cds.PublicationDocument ADD COLUMN display_order INT;
+
+CREATE TABLE cds.external_link
+(
+    cds_link_id     VARCHAR(250) NOT NULL,
+    link_label      VARCHAR(250) NOT NULL,
+    link_url        VARCHAR(250) NOT NULL,
+    link_type       VARCHAR(100),
+    link_description VARCHAR(250),
+    container       ENTITYID NOT NULL,
+
+    CONSTRAINT PK_external_links PRIMARY KEY (cds_link_id, container)
+);
+
+CREATE TABLE cds.external_link_map
+(
+    row_id          SERIAL,
+    cds_link_id     VARCHAR(250) NOT NULL,
+    protocol_id     VARCHAR(250) NOT NULL,
+    type            VARCHAR(100) NOT NULL,
+    container       ENTITYID NOT NULL,
+
+    CONSTRAINT PK_external_link_map PRIMARY KEY (row_id),
+    CONSTRAINT UQ_external_link_map UNIQUE (cds_link_id, protocol_id, type, container),
+    CONSTRAINT FK_external_link_map_cds_link_id FOREIGN KEY (cds_link_id, container) REFERENCES cds.external_link (cds_link_id, container)
+);
+CREATE INDEX IX_external_link_map_cds_link_id ON cds.external_link_map(cds_link_id);
+

src/org/labkey/cds/CDSManager.java

@@ -234,7 +234,10 @@ public void cleanContainer(Container c)
                     "alignment_run",
                     "allele_sequence",
                     "antibody_class",
-                    "header_source"
+                    "header_source",
+
+                    "external_link_map",
+                    "external_link"
             })
             {
                 TableInfo t = dbSchema.getTable(s);

src/org/labkey/cds/CDSModule.java

@@ -106,7 +106,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 24.002;
+        return 24.003;
     }
 
     @Override

src/org/labkey/cds/data/steps/CDSImportTask.java

@@ -98,6 +98,10 @@ public class CDSImportTask extends ImportTask
         new CDSImportCopyConfig("import_Virus_Metadata_All", "Virus_Metadata_All"),
         new CDSImportCopyConfig("import_Virus_Lab_Id", "Virus_Lab_Id"),
         new CDSImportCopyConfig("import_Virus_Synonym", "Virus_Synonym"),
+
+        // External repository links
+        new CDSImportCopyConfig("external_link"),
+        new CDSImportCopyConfig("external_link_map")
     };
 
     @Override

src/org/labkey/cds/view/template/ConnectorTemplate.jsp

@@ -356,6 +356,7 @@
             srcPath + "/app/view/module/StudyResources.js",
             srcPath + "/app/view/module/MabDetails.js",
             srcPath + "/app/view/module/PublicationDetails.js",
+            srcPath + "/app/view/module/PublicationResources.js",
             srcPath + "/app/view/module/ProductHeader.js",
             srcPath + "/app/view/module/ProductOtherProducts.js",
             srcPath + "/app/view/module/StudyHeader.js",

test/sampledata/dataspace/cdsimport/PublicationDocument.txt

@@ -1,4 +1,4 @@
-publication_id	document_id
-80	301
-136	300
-80	302
+publication_id	document_id	display_order
+80	301	2
+136	300	
+80	302	1

test/sampledata/dataspace/cdsimport/external_link.txt

@@ -0,0 +1,4 @@
+cds_link_id	link_label	link_url	link_type	link_description
+cds_link_001	Vivli Data Repository	http://vivli.com/data/CAVD725		
+cds_link_002	Test Data Repository	http://vivli.com/data/TEST	test link	not a real URL
+cds_link_003	GitHub	https://github.com/labkey		

test/sampledata/dataspace/cdsimport/external_link_map.txt

@@ -0,0 +1,7 @@
+cds_link_id	protocol_id	type
+cds_link_001	q2	study
+cds_link_002	q2	study
+cds_link_003	z117	study
+cds_link_001	136	publication
+cds_link_002	136	publication
+cds_link_003	80	publication

webapp/Connector/cube.js

@@ -815,7 +815,12 @@ Ext4.define('Connector.cube.Configuration', {
                         type: 'publicationnonintegrateddata',
                         staticData: {
                             title: 'Publication data',
-                            instructions: 'Download files'
+                            instructions: 'Download individual files'
+                        }
+                    },{
+                        type: 'publicationresources',
+                        staticData: {
+                            title: 'Other publication resources'
                         }
                     },{
                         type: 'interactivereports',

webapp/Connector/extapp.lib.xml

@@ -211,6 +211,7 @@
         <script path="Connector/src/app/view/module/StudyResources.js"/>
         <script path="Connector/src/app/view/module/MabDetails.js"/>
         <script path="Connector/src/app/view/module/PublicationDetails.js"/>
+        <script path="Connector/src/app/view/module/PublicationResources.js"/>
         <script path="Connector/src/app/view/module/ProductHeader.js"/>
         <script path="Connector/src/app/view/module/ProductOtherProducts.js"/>
         <script path="Connector/src/app/view/module/StudyHeader.js"/>

webapp/Connector/src/app/model/Publication.js

@@ -39,6 +39,7 @@ Ext.define('Connector.app.model.Publication', {
         {name: 'studies', convert : Connector.model.Filter.asArray},
         {name: 'interactive_reports', convert : Connector.model.Filter.asArray},
         {name: 'curated_groups', convert : Connector.model.Filter.asArray},
-        {name: 'data_types_available', convert : Connector.model.Filter.asArray}
+        {name: 'data_types_available', convert : Connector.model.Filter.asArray},
+        {name: 'external_links', convert : Connector.model.Filter.asArray}
     ]
 });

webapp/Connector/src/app/model/StudyOverview.js

@@ -123,6 +123,7 @@ Ext.define('Connector.app.model.StudyOverview', {
         {name: 'interactive_reports', convert : Connector.model.Filter.asArray},
         {name: 'curated_groups', convert : Connector.model.Filter.asArray},
         {name: 'data_types_available', convert : Connector.model.Filter.asArray},
-        {name: 'data_available'}
+        {name: 'data_available'},
+        {name: 'external_links', convert : Connector.model.Filter.asArray}
     ]
 });

webapp/Connector/src/app/store/Publication.js

@@ -29,6 +29,7 @@ Ext.define('Connector.app.store.Publication', {
         this.publicationDocuments = undefined;
         this.publicationReportsData = undefined;
         this.publicationCuratedGroupData = undefined;
+        this.external_links = undefined;
 
         this.loadAccessibleStudies(this._onLoadComplete, this); // populate this.accessibleStudies
 
@@ -71,6 +72,13 @@ Ext.define('Connector.app.store.Publication', {
             success: this.onLoadPublicationCuratedGroup,
             scope: this
         });
+
+        LABKEY.Query.selectRows({
+            schemaName: 'cds',
+            queryName: 'learn_publicationExternalLinks',
+            success: this.onLoadExternalLinks,
+            scope: this
+        });
     },
 
     onLoadPublications: function (data) {
@@ -103,6 +111,11 @@ Ext.define('Connector.app.store.Publication', {
         this._onLoadComplete();
     },
 
+    onLoadExternalLinks : function(externalLinks) {
+        this.external_links = externalLinks.rows;
+        this._onLoadComplete();
+    },
+
     _onLoadComplete : function() {
         if (Ext.isDefined(this.publicationData)
                 && Ext.isDefined(this.studyData)
@@ -111,6 +124,7 @@ Ext.define('Connector.app.store.Publication', {
                 && Ext.isDefined(this.publicationDocuments)
                 && Ext.isDefined(this.publicationReportsData)
                 && Ext.isDefined(this.publicationCuratedGroupData)
+                && Ext.isDefined(this.external_links)
                 && this.isLoadComplete()) {
 
             this.publicationData.sort(function(row1, row2) {
@@ -170,6 +184,7 @@ Ext.define('Connector.app.store.Publication', {
             }, this).map(function(doc) {
                 return {
                     publication_id: doc.publication_id,
+                    display_order : doc.display_order || 0,
                     document_id: doc.document_id,
                     label: doc.label,
                     fileName: doc.filename,
@@ -191,6 +206,20 @@ Ext.define('Connector.app.store.Publication', {
                 publicationMap[doc.publication_id].push(doc);
             }, this);
 
+            // sort the publication docs according to display order (ascending)
+            Ext.Object.each(publicationMap, function(key, publications){
+                publications.sort(function(a, b){
+                   return a.display_order - b.display_order;
+               });
+            });
+
+            // map any external links to each publication
+            var externalLinkMap = {};
+            Ext.each(this.external_links, function (link) {
+                externalLinkMap[link.protocol_id] = externalLinkMap[link.protocol_id] || [];
+                externalLinkMap[link.protocol_id].push(link);
+            }, this);
+
             var savedReports = [];
             for (var i=0; i < this.publicationReportsData.length; i++) {
                 var id = this.publicationReportsData[i].cds_report_id.toString();
@@ -243,6 +272,9 @@ Ext.define('Connector.app.store.Publication', {
                 publication.publication_data_count = publication.publication_data.length;
                 publication.data_availability = publication.publication_data.length > 0;
 
+                // external links
+                publication.external_links = externalLinkMap[publication.publication_id] || [];
+
                 //saved reports
                 var savedRep = savedReports.filter(function (value) {
                     return value.publication_id.toString() === publication.publication_id;
@@ -271,6 +303,7 @@ Ext.define('Connector.app.store.Publication', {
             this.publicationReportsData = undefined;
             this.savedReportsData = [];
             this.publicationCuratedGroupData = undefined;
+            this.external_links = [];
 
             this.loadRawData(publications);
             this.fireEvent('dataloaded');

webapp/Connector/src/app/store/StudyOverview.js

@@ -35,12 +35,16 @@ Ext.define('Connector.app.store.StudyOverview', {
         this.assayIdentifiers = undefined;
         this.studyReportsData = undefined;
         this.studyCuratedGroupData = undefined;
+        this.external_links = undefined;
 
         this.loadAccessibleStudies(this._onLoadComplete, this); // populate this.accessibleStudies
 
         LABKEY.Query.selectRows({
             schemaName: 'cds.metadata',
             queryName: 'study',
+            filterArray: [
+                LABKEY.Filter.create('study_name', id, LABKEY.Filter.Types.EQUALS)
+            ],
             success: this.onLoadStudies,
             scope: this
         });
@@ -135,6 +139,15 @@ Ext.define('Connector.app.store.StudyOverview', {
             success: this.onNILoadDocuments,
             scope: this
         });
+        LABKEY.Query.selectRows({
+            schemaName: 'cds',
+            queryName: 'learn_studyExternalLinks',
+            filterArray: [
+                LABKEY.Filter.create('protocol_id', id, LABKEY.Filter.Types.EQUALS)
+            ],
+            success: this.onLoadStudyExternalLinks,
+            scope: this
+        });
     },
 
     onLoadStudies : function(studyData) {
@@ -199,6 +212,11 @@ Ext.define('Connector.app.store.StudyOverview', {
         this._onLoadComplete();
     },
 
+    onLoadStudyExternalLinks : function(externalLinks) {
+        this.external_links = externalLinks.rows;
+        this._onLoadComplete();
+    },
+
     _onLoadComplete: function () {
         if (Ext.isDefined(this.studyData)
                 && Ext.isDefined(this.productData)
@@ -213,6 +231,7 @@ Ext.define('Connector.app.store.StudyOverview', {
                 && Ext.isDefined(this.assayIdentifiers)
                 && Ext.isDefined(this.studyReportsData)
                 && Ext.isDefined(this.studyCuratedGroupData)
+                && Ext.isDefined(this.external_links)
                 && this.isLoadComplete()) {
             var studies = [], products, productNames, productClasses;
             var relationshipOrderList = this.relationshipOrderData.map(function(relOrder) {
@@ -544,13 +563,11 @@ Ext.define('Connector.app.store.StudyOverview', {
                 study.data_types_available = this.getDataTypesAvailable(study);
                 study.data_available = (study.assays_added_count > 0 || study.ni_assays_added_count > 0 || study.pub_available_data_count > 0) ? 'Data added' : 'Data not added';
 
+                // additional data repositories
+                study.external_links = this.external_links;
                 studies.push(study);
             }, this);
 
-            studies.sort(function(studyA, studyB) {
-                return Connector.model.Filter.sorters.natural(studyA.label, studyB.label);
-            });
-
             this.studyData = undefined;
             this.assayData = undefined;
             this.productData = undefined;
@@ -563,6 +580,7 @@ Ext.define('Connector.app.store.StudyOverview', {
             this.studyReportsData = undefined;
             this.savedReportsData = [];
             this.studyCuratedGroupData = undefined;
+            this.external_links = [];
 
             this.loadRawData(studies);
             this.dataLoaded = true;

webapp/Connector/src/app/view/module/NonIntegratedDataAvailability.js

@@ -303,15 +303,18 @@ Ext.define('Connector.view.module.PublicationNonIntegratedData', {
         return new Ext4.XTemplate(
             '<tpl>',
                 '<table>',
-                    '<tr>',
-                        '<td class="non-integrated-data">',
-                            '<tpl if="isLinkValid">',
+                    '<tpl if="isLinkValid">',
+                        '<tr>',
+                            '<td>',
+                                '<img class="detail-has-data-small" src="' + Connector.resourceContext.path + '/images/learn/smallCheck.png"/>',
+                            '</td>',
+                            '<td class="non-integrated-data">',
                                 '<span>{label:htmlEncode}</span>',
                                 '&nbsp;{suffix}&nbsp;',
                                 '<a href="{filePath}" target="_blank"><img alt="{label}" src="' + LABKEY.contextPath + '/Connector/images/download-icon.svg' + '" height="13" width="13" align="right"/></a>',
-                            '</tpl>',
-                        '</td>',
-                    '</tr>',
+                            '</td>',
+                        '</tr>',
+                        '</tpl>',
                 '</table>',
             '</tpl>');
     }