possibly fixes #2290 (#2291)

* possibly fixes #2290 * two additional small fixes * fixed if a missing user id
GMOD · Oct 29, 2019 · 57a1f2e · 57a1f2e
1 parent 8b6eb2d
commit 57a1f2e
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Showing 3 changed files with 13 additions and 8 deletions.
diff --git a/grails-app/controllers/org/bbop/apollo/OrganismController.groovy b/grails-app/controllers/org/bbop/apollo/OrganismController.groovy
@@ -279,13 +279,20 @@ class OrganismController {
           obsolete: false,
           valid: true,
           species: requestObject.species ?: "",
-          metadata: requestObject.metadata ?: "",
+          metadata: requestObject.metadata ? requestObject.metadata.toString() : "",
           publicMode: requestObject.publicMode ?: false,
           nonDefaultTranslationTable: requestObject.nonDefaultTranslationTable ?: null,
           dataAddedViaWebServices: true
         ).save(failOnError: true, flush: true, insert: true)
         def currentUser = permissionService.currentUser
-        organism.addMetaData("creator", currentUser.id.toString())
+        String userId = null
+        if(currentUser){
+          userId = currentUser.id.toString()
+        }
+        else{
+          userId = requestObject.username as String
+        }
+        organism.addMetaData("creator", userId)
         File directory = trackService.getExtendedDataDirectory(organism)
 
         if (directory.mkdirs() && directory.setWritable(true)) {
@@ -1078,7 +1085,7 @@ class OrganismController {
         throw new Exception('empty fields detected')
       }
 
-      log.debug "Adding ${organismJson.publicMode}"
+      log.debug "Adding organsim json ${organismJson as JSON}"
       Organism organism = new Organism(
         commonName: organismJson.commonName
         , directory: organismJson.directory
@@ -1336,7 +1343,7 @@ class OrganismController {
       Organism organism = Organism.findById(organismJson.id)
       if (organism) {
         log.debug "Updating organism metadata ${organismJson as JSON}"
-        organism.metadata = organismJson.metadata
+        organism.metadata = organismJson.metadata?.toString()
         organism.save(flush: true, insert: false, failOnError: true)
       } else {
         throw new Exception('Organism not found')
@@ -1485,9 +1492,6 @@ class OrganismController {
 
     // global version
     OrganismSummary organismSummaryInstance = permissionService.currentUser.roles.first().rank == GlobalPermissionEnum.ADMIN.rank ? reportService.generateAllFeatureSummary() : new OrganismSummary()
-//        OrganismSummary organismSummaryInstance = reportService.generateAllFeatureSummary()
-
-//        def organismPermissions = permissionService.getOrganismsWithPermission(permissionService.currentUser)
     def organisms = permissionService.getOrganismsWithMinimumPermission(permissionService.currentUser, PermissionEnum.ADMINISTRATE)
 
 

diff --git a/grails-app/domain/org/bbop/apollo/Organism.groovy b/grails-app/domain/org/bbop/apollo/Organism.groovy
@@ -15,7 +15,6 @@ class Organism implements JsonMetadata {
         genus nullable: true
         valid nullable: true
         blatdb nullable: true
-        metadata nullable: true
         commonName nullable: false
         genomeFasta nullable: true
         obsolete nullable: true
@@ -76,6 +75,7 @@ class Organism implements JsonMetadata {
     static mapping = {
         publicMode defaultValue: true
         obsolete defaultValue: false
+        metadata type: 'text'
     }
 
 }
diff --git a/grails-app/services/org/bbop/apollo/DomainMarshallerService.groovy b/grails-app/services/org/bbop/apollo/DomainMarshallerService.groovy
@@ -27,6 +27,7 @@ class DomainMarshallerService {
             returnArray['genus'] = it?.genus
             returnArray['species'] = it?.species
             returnArray['directory'] = it.directory
+            returnArray['metadata'] = it?.metadata
             return returnArray
         }