Fix 1134 go refactor v1

docs/Setup.md

@@ -27,9 +27,9 @@ Other possible [build settings for JBrowse](http://gmod.org/wiki/JBrowse_Configu
 
 Node versions 6+ have been tested.   I would recommend using [nvm](https://github.com/creationix/nvm) and ``nvm install 8```
 
-### Install python
+### Install python, make 
 
-Node has a python dependency. `sudo apt-get install python`
+Node has a python dependency. `sudo apt-get install python make`
 
 ### Install jdk
 

grails-app/controllers/org/bbop/apollo/go/GoAnnotationController.groovy

@@ -3,7 +3,6 @@ package org.bbop.apollo.go
 import grails.converters.JSON
 import grails.transaction.Transactional
 import org.bbop.apollo.Feature
-import org.bbop.apollo.Organism
 import org.bbop.apollo.User
 import org.codehaus.groovy.grails.web.json.JSONObject
 import org.restapidoc.annotation.RestApiMethod
@@ -83,7 +82,7 @@ class GoAnnotationController {
         goAnnotation.evidenceRef = dataObject.evidenceCode
         goAnnotation.negate = dataObject.negate ?: false
         goAnnotation.withOrFromArray = dataObject.withOrFrom
-        goAnnotation.referenceArray = dataObject.references
+        goAnnotation.notesArray = dataObject.references
         goAnnotation.lastUpdated = new Date()
         goAnnotation.dateCreated = new Date()
         goAnnotation.addToOwners(user)
@@ -118,7 +117,7 @@ class GoAnnotationController {
         goAnnotation.evidenceRef = dataObject.evidenceCode
         goAnnotation.negate = dataObject.negate ?: false
         goAnnotation.withOrFromArray = dataObject.withOrFrom
-        goAnnotation.referenceArray = dataObject.references
+        goAnnotation.notesArray = dataObject.references
         goAnnotation.lastUpdated = new Date()
         goAnnotation.addToOwners(user)
         goAnnotation.save(flush: true, failOnError: true,insert: false)

grails-app/domain/org/bbop/apollo/go/GoAnnotation.groovy

@@ -13,9 +13,10 @@ class GoAnnotation {
         geneProductRelationshipRef nullable: true, blank: false
         negate nullable: false
         withOrFromArray nullable: true, blank: true
-        referenceArray nullable: true, blank: true
+        notesArray nullable: true, blank: true
         dateCreated nullable: false
         lastUpdated nullable: false
+        reference nullable: false, blank: false
     }
 
     static hasMany = [
@@ -28,7 +29,8 @@ class GoAnnotation {
     String geneProductRelationshipRef
     Boolean negate
     String withOrFromArray
-    String referenceArray
+    String notesArray
+    String reference
     Date lastUpdated
     Date dateCreated
 

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

@@ -56,9 +56,9 @@ class GpadHandlerService {
         writeObject.out.write(goAnnotation.goRef)
         writeObject.out.write("\t")
         //5	Reference ::= ID		1	PMID:30695063
-//        writeObject.out.write(goAnnotation.referenceArray)
-        if (goAnnotation.referenceArray) {
-            JSONArray referenceArray = new JsonSlurper().parseText(goAnnotation.referenceArray) as JSONArray
+//        writeObject.out.write(goAnnotation.notesArray)
+        if (goAnnotation.notesArray) {
+            JSONArray referenceArray = new JsonSlurper().parseText(goAnnotation.notesArray) as JSONArray
             List<String> referenceList = referenceArray.collect()
             writeObject.out.write(referenceList.join("|"))
         }

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

@@ -248,23 +248,56 @@ class SequenceService {
         crc.update(sequence.name.getBytes());
         String hex = String.format("%08x", crc.getValue())
         String[] dirs = splitStringByNumberOfCharacters(hex, 3)
-        String seqDir = String.format("%s/seq/%s/%s/%s", sequence.organism.directory, dirs[0], dirs[1], dirs[2]);
-        String filePath = seqDir + "/" + sequence.name + "-" + chunkNumber + ".txt"
-        File file = new File(filePath)
-        if (file.exists()) {
-            return new File(filePath).text.toUpperCase()
+
+        Organism organism = sequence.organism
+        File trackListFile = new File(organism.trackList)
+        JSONObject trackListJsonObject = JSON.parse(trackListFile.text) as JSONObject
+        JSONArray tracksArray = trackListJsonObject.getJSONArray("tracks")
+
+        // support http://agrjbrowse2.s3-website-us-east-1.amazonaws.com/FlyBase/fruitfly/seq/{refseq_dirpath}/{refseq}-/seq/d3c/34b/35/2L-0.txtz
+        // convert to: http://agrjbrowse2.s3-website-us-east-1.amazonaws.com/FlyBase/fruitfly/seq/d3c/34b/35/2L-0.txtz
+        // support  "seq/{refseq_dirpath}/{refseq}-",
+        String urlTemplate = sequence.organism.directory
+        Boolean isCompressed = false
+        for (def track in tracksArray) {
+            if (track.label == "DNA") {
+                urlTemplate = track.urlTemplate
+                isCompressed = track.compress == 1
+            }
         }
-        // attempt with gzip
-        filePath = seqDir + "/" + sequence.name + "-" + chunkNumber + ".txtz"
-        file = new File(filePath)
-        if (file.exists()) {
-            def inflaterStream = new GZIPInputStream(new ByteArrayInputStream(file.bytes))
-            def uncompressedStr = inflaterStream.getText('UTF-8')
-            return uncompressedStr.toUpperCase()
+        // this will be automatically replaced correctly
+        urlTemplate = urlTemplate.replaceAll("\\{refseq\\}",sequence.name)
+        String seqPath = String.format("%s/%s/%s", dirs[0], dirs[1], dirs[2])
+        urlTemplate = urlTemplate.replaceAll("\\{refseq_dirpath\\}",seqPath)
+        String filePath = urlTemplate + chunkNumber + ".txt${isCompressed ? 'z' : ''}"
+        /**
+         * handle remote data
+         */
+        if (filePath.startsWith("http")) {
+            def url = new URL(filePath)
+            if (isCompressed) {
+                def inflaterStream = new GZIPInputStream(new ByteArrayInputStream(url.bytes))
+                def uncompressedStr = inflaterStream.getText('UTF-8')
+                return uncompressedStr.toUpperCase()
+            } else {
+                return url.text
+            }
         }
 
+        if(!filePath.startsWith("\\/")){
+            filePath = sequence.organism.directory + "/" + filePath
+        }
+        File file = new File(filePath)
+        if(file.exists()){
+            if (isCompressed) {
+                def inflaterStream = new GZIPInputStream(new ByteArrayInputStream(file.bytes))
+                def uncompressedStr = inflaterStream.getText('UTF-8')
+                return uncompressedStr.toUpperCase()
+            } else {
+                return file.text.toUpperCase()
+            }
+        }
         throw new RuntimeException("File not found on server: " + filePath)
-
     }
 
     String[] splitStringByNumberOfCharacters(String label, int size) {

grails-app/services/org/bbop/apollo/go/GoAnnotationService.groovy

@@ -35,7 +35,7 @@ class GoAnnotationService {
             goObject.put("evidenceCode",goAnnotation.evidenceRef)
             goObject.put("negate",goAnnotation.negate)
             goObject.put("withOrFrom",goAnnotation.withOrFromArray)
-            goObject.put("references",goAnnotation.referenceArray)
+            goObject.put("references",goAnnotation.notesArray)
             annotations.add(goObject)
         }