small adjustments for functional tests (#2610)

* fixed return types for functional tests * redid the image * reverted * added support for annotator tests * removed error if no organisms found * fixed organism service tests * removed adding owner to a deleted exon * fixed update * redid REST docs
GMOD · Apr 21, 2021 · 1a24955 · 1a24955
1 parent 2f54601
commit 1a24955
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Showing 7 changed files with 1,411 additions and 1,263 deletions.
diff --git a/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy b/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy
@@ -846,23 +846,66 @@ class AnnotatorController {
         render annotatorService.getAppState(params.get(FeatureStringEnum.CLIENT_TOKEN.value).toString()) as JSON
     }
 
+    @RestApiMethod(description = "Update common path and return system info", path = "/updateCommonPath", verb = RestApiVerb.POST)
+    @RestApiParams(params =[
+            @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)
+            , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY)
+            , @RestApiParam(name = "directory", type = "string",  paramType = RestApiParamType.QUERY, description = "Relative or absolute common path directory")
+    ])
     @Transactional
-    String updateCommonPath(String directory) {
-        log.debug "Updating the common path for ${directory}"
+    String updateCommonPath() {
+        JSONObject dataObject = permissionService.handleInput(request, params)
         JSONObject returnObject = new JSONObject()
+        String directory = dataObject.directory
 
         try {
+            if (!permissionService.hasGlobalPermissions(dataObject, GlobalPermissionEnum.ADMIN)) {
+                render status: HttpStatus.UNAUTHORIZED
+                return
+            }
             String returnString = trackService.updateCommonDataDirectory(directory) as String
-            log.info "Returning common data directory ${returnString}"
             if (returnString) {
                 returnObject.error = returnString
             }
+            render getSystemInfo()
+            return
         } catch (e) {
             returnObject.error = e.getMessage()
         }
         render returnObject as JSON
     }
 
+    @RestApiMethod(description = "Get system info", path = "/getSystemInfo", verb = RestApiVerb.POST)
+    @Transactional(readOnly  = true )
+    String getSystemInfo() {
+        log.debug "Getting the common data path"
+        JSONObject returnObject = new JSONObject()
+
+        try {
+            String returnString = trackService.getCommonDataDirectory()
+            log.debug "Returning common data directory ${returnString}"
+            if (returnString) {
+                returnObject.error = returnString
+            }
+            File file = new File(returnString)
+            returnObject.put("relativePath",returnString)
+            returnObject.put("absolutePath",file.absolutePath)
+            returnObject.put("absolute",file.absolute)
+            returnObject.put("exists",file.exists())
+            returnObject.put("writable",file.canWrite())
+            returnObject.put("readable",file.canRead())
+            returnObject.put("directory",file.isDirectory())
+            returnObject.put("executable",file.canExecute())
+            returnObject.put("freeSpace",file.getFreeSpace())
+            returnObject.put("totalSpace",file.getTotalSpace())
+            returnObject.put("usableSpace",file.getUsableSpace())
+            returnObject.put("root",new File("").absolutePath)
+            returnObject.put("realPath",servletContext.getRealPath("/"))
+        } catch (e) {
+            returnObject.error = e.getMessage()
+        }
+        render returnObject as JSON
+    }
 /**
  */
     @Transactional

diff --git a/grails-app/controllers/org/bbop/apollo/OrganismController.groovy b/grails-app/controllers/org/bbop/apollo/OrganismController.groovy
@@ -365,11 +365,11 @@ class OrganismController {
               File rawDirectory = new File(directory.absolutePath + "/seq")
               assert rawDirectory.mkdir()
               assert rawDirectory.setWritable(true)
-              File archiveFile = new File(rawDirectory.absolutePath + File.separator + organismName + "." + sequenceTypeEnum.suffix)
+              File archiveFile = new File(rawDirectory.absolutePath + File.separator + organismName + "." + sequenceTypeEnum.correctedSuffix)
               sequenceDataFile.transferTo(archiveFile)
               organism.directory = directory.absolutePath
 
-              String fastaPath = rawDirectory.absolutePath + File.separator + organismName + ".fa"
+              String fastaPath = rawDirectory.absolutePath + File.separator + organismName + "." + SequenceTypeEnum.FA.suffix
               // decompress if need be
               if (sequenceTypeEnum.compression != null) {
                 List<String> fileNames = fileService.decompress(archiveFile, rawDirectory.absolutePath)
@@ -380,10 +380,10 @@ class OrganismController {
                 oldFile.renameTo(newFile)
               }
 
-              log.info "search db file : ${searchDatabaseDataFile.name} ${searchDatabaseDataFile.size} ${searchDatabaseDataFile.originalFilename} ${searchDatabaseDataFile.contentType}"
 
 
               if (searchDatabaseDataFile != null && searchDatabaseDataFile.size > 0) {
+                log.info "search db file : ${searchDatabaseDataFile.name} ${searchDatabaseDataFile.size} ${searchDatabaseDataFile.originalFilename} ${searchDatabaseDataFile.contentType}"
                 File searchDirectory = new File(directory.absolutePath + "/search")
                 assert searchDirectory.mkdir()
                 assert searchDirectory.setWritable(true)
@@ -1565,11 +1565,12 @@ class OrganismController {
         organismList = organismList.findAll{ o -> o.publicMode }
       }
 
-      if (!organismList) {
-        def error = [error: 'Not authorized for any organisms']
-        render error as JSON
-        return
-      }
+      // should just return an empty array
+//      if (!organismList) {
+//        def error = [error: 'Not authorized for any organisms']
+//        render error as JSON
+//        return
+//      }
 
       UserOrganismPreference userOrganismPreference = UserOrganismPreference.findByUserAndCurrentOrganism(permissionService.getCurrentUser(requestObject), true, [max: 1, sort: "lastUpdated", order: "desc"])
       Long defaultOrganismId = userOrganismPreference ? userOrganismPreference.organism.id : null
@@ -1598,6 +1599,8 @@ class OrganismController {
           id                        : organism.id,
           commonName                : organism.commonName,
           blatdb                    : organism.blatdb,
+          genomeFasta               : organism.genomeFasta,
+          genomeFastaIndex          : organism.genomeFastaIndex,
           directory                 : organism.directory,
           annotationCount           : annotationCount,
           sequences                 : sequenceCount,

diff --git a/grails-app/controllers/org/bbop/apollo/UserController.groovy b/grails-app/controllers/org/bbop/apollo/UserController.groovy
@@ -2,7 +2,6 @@ package org.bbop.apollo
 
 import grails.converters.JSON
 import grails.transaction.Transactional
-import org.apache.shiro.authc.UsernamePasswordToken
 import org.apache.shiro.crypto.hash.Sha256Hash
 import org.bbop.apollo.gwt.shared.FeatureStringEnum
 import org.bbop.apollo.gwt.shared.GlobalPermissionEnum
@@ -414,7 +413,14 @@ class UserController {
 
             log.info "Added user ${user.username} with role ${role.name}"
 
-            render new JSONObject() as JSON
+            JSONObject jsonObject = user.properties
+            log.debug "json object ${jsonObject as JSON}"
+            jsonObject.email = user.username
+            jsonObject.username = user.username
+            jsonObject.id = user.id
+            jsonObject.userId = user.id
+            log.debug "rendering json object "
+            render jsonObject as JSON
         } catch (e) {
             log.error(e.fillInStackTrace())
             JSONObject jsonObject = new JSONObject()
@@ -588,11 +594,18 @@ class UserController {
             UserTrackPermission.deleteAll(UserTrackPermission.findAllByUser(user))
             UserOrganismPermission.deleteAll(UserOrganismPermission.findAllByUser(user))
             UserOrganismPreference.deleteAll(UserOrganismPreference.findAllByUser(user))
-            user.delete(flush: true)
 
             log.info "Removed user ${user.username}"
 
-            render new JSONObject() as JSON
+            JSONObject jsonObject = user.properties
+            log.debug "json object ${jsonObject as JSON}"
+            jsonObject.email = user.username
+            jsonObject.username = user.username
+            jsonObject.id = user.id
+            jsonObject.userId = user.id
+            log.debug "rendering json object "
+            render jsonObject as JSON
+            user.delete(flush: true)
         } catch (e) {
             log.error(e.fillInStackTrace())
             JSONObject jsonObject = new JSONObject()

diff --git a/grails-app/services/org/bbop/apollo/RequestHandlingService.groovy b/grails-app/services/org/bbop/apollo/RequestHandlingService.groovy
@@ -1979,9 +1979,7 @@ class RequestHandlingService {
             JSONObject jsonExon = features.getJSONObject(i)
             Exon exon = Exon.findByUniqueName(jsonExon.getString(FeatureStringEnum.UNIQUENAME.value));
             checkOwnersDelete(exon, inputObject)
-
             exonService.deleteExon(transcript, exon);
-            featureService.addOwnersByString(inputObject.username, exon)
         }
         def transcriptsToUpdate = featureService.handleDynamicIsoformOverlap(transcript)
         if (transcriptsToUpdate.size() > 0) {

diff --git a/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java b/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java
@@ -114,7 +114,7 @@ public enum FeatureStringEnum {
         SYNONYMS,
         STRUCTURAL_EDIT,
         HIGHLIGHTED_REGION("highlighted region"),
-        UNIQUENAME,
+        UNIQUENAME("uniquename"),
         // TODO: move these to a SequenceTypeEnum
         TYPE_PEPTIDE("peptide"),
         TYPE_CDS("cds"),

diff --git a/src/gwt/org/bbop/apollo/gwt/shared/track/SequenceTypeEnum.java b/src/gwt/org/bbop/apollo/gwt/shared/track/SequenceTypeEnum.java
@@ -4,18 +4,23 @@
 public enum SequenceTypeEnum {
 
     FA("fa"),
+    FASTA("fasta"),
     FNA("fna"),
     FA_GZ("fa.gz","gz"),
+    FASTA_GZ("fasta.gz","gz"),
     FNA_GZ("fna.gz","gz"),
     FA_ZIP("fa.zip","zip"),
+    FASTA_ZIP("fasta.zip","zip"),
     FNA_ZIP("fna.zip","zip"),
     FA_TGZ("fa.tgz","tar.gz"),
+    FASTA_TGZ("fasta.tgz","tar.gz"),
     FNA_TGZ("fna.tgz","tar.gz"),
     FA_TAR_GZ("fa.tar.gz","tar.gz"),
+    FASTA_TAR_GZ("fasta.tar.gz","tar.gz"),
     FNA_TAR_GZ("fna.tar.gz","tar.gz");
 
-    private String suffix ;
-    private String compression;
+    private final String suffix ;
+    private final String compression;
 
     SequenceTypeEnum(String suffix){
         this(suffix,null);
@@ -34,6 +39,10 @@ public String getCompression() {
         return compression;
     }
 
+    public String getCorrectedSuffix(){
+        return FA.suffix + (compression!=null ?  "." + compression : "") ;
+    }
+
     public static SequenceTypeEnum getSequenceTypeForFile(String fileName){
         for(SequenceTypeEnum sequenceTypeEnum : values()){
             if(fileName.endsWith(sequenceTypeEnum.suffix)){