wired stuff through to the end

grails-app/controllers/org/bbop/apollo/IOServiceController.groovy

@@ -26,6 +26,7 @@ class IOServiceController extends AbstractApolloController {
     def featureService
     def gff3HandlerService
     def fastaHandlerService
+    def jbrowseHandlerService
     def chadoHandlerService
     def preferenceService
     def permissionService
@@ -63,6 +64,8 @@ class IOServiceController extends AbstractApolloController {
             , @RestApiParam(name = "output", type = "string", paramType = RestApiParamType.QUERY, description = "Output method 'file','text'")
             , @RestApiParam(name = "exportAllSequences", type = "boolean", paramType = RestApiParamType.QUERY, description = "Export all reference sequences for an organism (over-rides 'sequences')")
             , @RestApiParam(name = "exportGff3Fasta", type = "boolean", paramType = RestApiParamType.QUERY, description = "Export reference sequence when exporting GFF3 annotations.")
+            , @RestApiParam(name = "exportFullJBrowse", type = "boolean", paramType = RestApiParamType.QUERY, description = "Export Full JBrowse installation when exporting as track (default false).")
+            , @RestApiParam(name = "exportJBrowseSequence", type = "boolean", paramType = RestApiParamType.QUERY, description = "Export JBrowse sequence when exporting JBrowse track (default false).")
             , @RestApiParam(name = "region", type = "String", paramType = RestApiParamType.QUERY, description = "Highlighted genomic region to export in form sequence:min..max  e.g., chr3:1001..1034")
     ]
     )
@@ -79,6 +82,13 @@ class IOServiceController extends AbstractApolloController {
             String typeOfExport = dataObject.type
             String sequenceType = dataObject.seqType
             Boolean exportAllSequences = dataObject.exportAllSequences ? Boolean.valueOf(dataObject.exportAllSequences) : false
+//            // always export all
+//            if(typeOfExport == FeatureStringEnum.TYPE_JBROWSE.value){
+//                exportAllSequences = true
+//            }
+
+            Boolean exportFullJBrowse = dataObject.exportFullJBrowse ?  Boolean.valueOf(dataObject.exportFullJBrowse) : false
+            Boolean exportJBrowseSequence = dataObject.exportJBrowseSequence ?  Boolean.valueOf(dataObject.exportJBrowseSequence) : false
             Boolean exportGff3Fasta = dataObject.exportGff3Fasta ? Boolean.valueOf(dataObject.exportGff3Fasta) : false
             String output = dataObject.output
             String adapter = dataObject.adapter
@@ -203,6 +213,19 @@ class IOServiceController extends AbstractApolloController {
                 }
                  return // ??
             }
+            else if (typeOfExport == FeatureStringEnum.TYPE_JBROWSE.getValue()) {
+                if(exportFullJBrowse){
+                    render jbrowseHandlerService.writeFullJBrowse(organism)
+                }
+                else
+                if(exportJBrowseSequence){
+                    render jbrowseHandlerService.writeJBrowseDirectory(organism)
+                }
+                else{
+                    render jbrowseHandlerService.writeTrackOnly(organism)
+                }
+                return // ??
+            }
 
             //generating a html fragment with the link for download that can be rendered on client side
             String uuidString = UUID.randomUUID().toString()

grails-app/services/org/bbop/apollo/JbrowseHandlerService.groovy

@@ -0,0 +1,68 @@
+package org.bbop.apollo
+
+import grails.transaction.Transactional
+import org.codehaus.groovy.grails.web.json.JSONObject
+
+import java.security.MessageDigest
+import java.sql.Timestamp
+
+/**
+ *
+ * Chado Compliance Layers
+ * Level 0: Relational schema - this basically means that the schema is adhered to
+ * Level 1: Ontologies - this means that all features in the feature table are of a type represented in SO and
+ * all feature relationships in feature_relationship table must be SO relationship types
+ * Level 2: Graph - all features relationships between a feature of type X and Y must correspond to relationship of
+ * that type in SO.
+ *
+ * Relevant Chado modules:
+ * Chado General Module
+ * Chado CV Module
+ * Chado Organism Module
+ * Chado Sequence Module
+ * Chado Publication Module
+ *
+ */
+
+@Transactional
+class JbrowseHandlerService {
+
+    def configWrapperService
+    def sequenceService
+    def featureRelationshipService
+    def transcriptService
+    def cdsService
+
+    /**
+     * Track only
+     * @param organism
+     * @return
+     */
+    def writeTrackOnly(Organism organism) {
+        JSONObject returnObject = new JSONObject()
+        println "writing track only"
+        return returnObject
+    }
+
+    /**
+     * Directory only
+     * @param organism
+     * @return
+     */
+    def writeJBrowseDirectory(Organism organism) {
+        JSONObject returnObject = new JSONObject()
+        println "writing track only"
+        return returnObject
+    }
+
+    /**
+     * Full JBrowse
+     * @param organism
+     * @return
+     */
+    def writeFullJBrowse(Organism organism) {
+        JSONObject returnObject = new JSONObject()
+        return returnObject
+    }
+
+}

src/gwt/org/bbop/apollo/gwt/client/ExportPanel.java

@@ -34,6 +34,8 @@ public class ExportPanel extends Modal {
     private Boolean exportAll = false;
     private OrganismInfo currentOrganismInfo;
     private Boolean exportAllSequencesToChado = false;
+    private Boolean exportFullJBrowse = false;
+    private Boolean exportJBrowseSequence = false;
     HTML sequenceInfoLabel = new HTML();
     HTML typeLabel = new HTML();
     HTML sequenceTypeLabel = new HTML();
@@ -181,13 +183,16 @@ public void onClick(ClickEvent clickEvent) {
         jbrowseExportButton2.addClickHandler(new ClickHandler() {
             @Override
             public void onClick(ClickEvent clickEvent) {
+                exportJBrowseSequence = true ;
                 exportButton.setEnabled(true);
             }
         });
 
         jbrowseExportButton3.addClickHandler(new ClickHandler() {
             @Override
             public void onClick(ClickEvent clickEvent) {
+                exportJBrowseSequence = true ;
+                exportFullJBrowse = true ;
                 exportButton.setEnabled(true);
             }
         });
@@ -333,4 +338,12 @@ public Boolean getExportAllSequencesToChado() {
     public void setExportAllSequencesToChado(Boolean value) {
         this.exportAllSequencesToChado = value;
     }
+
+    public Boolean getExportFullJBrowse() {
+        return exportFullJBrowse;
+    }
+
+    public Boolean getExportJBrowseSequence() {
+        return exportJBrowseSequence;
+    }
 }

src/gwt/org/bbop/apollo/gwt/client/rest/SequenceRestService.java

@@ -4,10 +4,7 @@
 import com.google.gwt.http.client.Request;
 import com.google.gwt.http.client.RequestCallback;
 import com.google.gwt.http.client.Response;
-import com.google.gwt.json.client.JSONArray;
-import com.google.gwt.json.client.JSONObject;
-import com.google.gwt.json.client.JSONParser;
-import com.google.gwt.json.client.JSONString;
+import com.google.gwt.json.client.*;
 import org.bbop.apollo.gwt.client.Annotator;
 import org.bbop.apollo.gwt.client.ExportPanel;
 import org.bbop.apollo.gwt.client.SequencePanel;
@@ -57,6 +54,8 @@ else if (type.equals(FeatureStringEnum.TYPE_JBROWSE.getValue())) {
             jsonObject.put("seqType", new JSONString(""));
             jsonObject.put("exportGff3Fasta", new JSONString(""));
             jsonObject.put("chadoExportType", new JSONString(""));
+            jsonObject.put("exportJBrowseSequence", JSONBoolean.getInstance(exportPanel.getExportJBrowseSequence()));
+            jsonObject.put("exportFullJBrowse", JSONBoolean.getInstance(exportPanel.getExportFullJBrowse()));
         }
         else {
             jsonObject.put("chadoExportType", new JSONString(""));