removed depcrecation and cleaned up code (#2619)

* removed depcrecation and cleaned up code * updated changelog * updated documentation
GMOD · May 12, 2021 · 180a5b1 · 180a5b1
1 parent 5eae7d8
commit 180a5b1
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -5,6 +5,10 @@ Features
 
 - Added method to upload bulk functional annotations from JSON in the interface [2617](https://github.com/GMOD/Apollo/pull/2617),[2618](https://github.com/GMOD/Apollo/pull/2618).
 
+Bug Fix
+
+- Removed deprecation from SequenceController.sequenceByName [2619](https://github.com/GMOD/Apollo/pull/2619).
+
 
 ## 2.6.4 
 

diff --git a/grails-app/conf/UrlMappings.groovy b/grails-app/conf/UrlMappings.groovy
@@ -41,7 +41,8 @@ class UrlMappings {
 
         "/sequence/${organismString}/?loc=${sequenceName}:${fmin}..${fmax}"(controller: "sequence", action: "sequenceByLocation",[params:params])
         "/sequence/${organismString}/${sequenceName}:${fmin}..${fmax}"(controller: "sequence", action: "sequenceByLocation",[params:params])
-        "/sequence/${organismString}/${sequenceName}/${featureName}.${type}"(controller: "sequence", action: "sequenceByName",[params:params])
+        // mapping not found
+//        "/sequence/sequenceByName/${organismString}/${sequenceName}/${featureName}.${type}"(controller: "sequence", action: "sequenceByName",[params:params])
         "/sequence/cache/clear/${organismName}/${sequenceName}"(controller: "sequence", action: "clearSequenceCache")
         "/sequence/cache/clear/${organismName}"(controller: "sequence", action: "clearOrganismCache")
 

diff --git a/grails-app/controllers/org/bbop/apollo/SequenceController.groovy b/grails-app/controllers/org/bbop/apollo/SequenceController.groovy
@@ -250,7 +250,7 @@ class SequenceController {
         render view: "report", model: [sequenceInstanceList: sequenceInstanceList, organisms: organisms, organism: organism, sequenceInstanceCount: sequenceInstanceCount]
     }
 
-    @RestApiMethod(description = "Get sequence data within a range (also works as post)", path = "/sequence/<organism name>/<sequence name>:<fmin>..<fmax>?ignoreCache=<ignoreCache>", verb = RestApiVerb.GET)
+    @RestApiMethod(description = "Get sequence data within a range (also works as post)", path = "GET /sequence/<organism name>/<sequence name>:<fmin>..<fmax>?ignoreCache=<ignoreCache>, POST /sequence/sequenceByLocation", verb = RestApiVerb.GET)
     @RestApiParams(params = [
             @RestApiParam(name = "organismString", type = "string", paramType = RestApiParamType.QUERY, description = "Organism common name or ID(required)")
             , @RestApiParam(name = "sequenceName", type = "string", paramType = RestApiParamType.QUERY, description = "Sequence name(required)")
@@ -261,6 +261,8 @@ class SequenceController {
     @Transactional
     String sequenceByLocation(String organismString, String sequenceName, int fmin, int fmax) {
 
+        println "sequence by location "
+
         // handle post data
         def inputJSON = request.JSON as JSONObject
         organismString = organismString ?: inputJSON.organismString
@@ -304,15 +306,14 @@ class SequenceController {
 
     }
 
-    @RestApiMethod(description = "Get sequence data as for a selected name (also works as post)", path = "/sequence/<organism name>/<sequence name>/<feature name>.<type>?ignoreCache=<ignoreCache>", verb = RestApiVerb.GET)
+    @RestApiMethod(description = "Get sequence data as for a selected name (also works as post)", path = "/sequence/sequenceByName", verb = RestApiVerb.GET)
     @RestApiParams(params = [
             @RestApiParam(name = "organismString", type = "string", paramType = RestApiParamType.QUERY, description = "Organism common name or ID (required)")
             , @RestApiParam(name = "sequenceName", type = "string", paramType = RestApiParamType.QUERY, description = "Sequence name (required)")
             , @RestApiParam(name = "featureName", type = "string", paramType = RestApiParamType.QUERY, description = "The uniqueName (UUID) or given name of the feature (typically transcript) of the element to retrieve sequence from")
             , @RestApiParam(name = "type", type = "string", paramType = RestApiParamType.QUERY, description = "(default genomic) Return type: genomic, cds, cdna, peptide")
             , @RestApiParam(name = "ignoreCache", type = "boolean", paramType = RestApiParamType.QUERY, description = "(default false).  Use cache for request if available.")
     ])
-    @Deprecated
     @Transactional
     String sequenceByName(String organismString, String sequenceName, String featureName, String type) {
 
@@ -351,7 +352,6 @@ class SequenceController {
         }
 
         Feature feature = Feature.findByUniqueName(featureName)
-        println "feature name: $featureName"
         if (!feature) {
             def features = Feature.findAllByName(featureName)
 
@@ -366,13 +366,9 @@ class SequenceController {
             }
         }
 
-        println "found a feature: $feature"
-
         if (feature) {
             String sequenceString = sequenceService.getSequenceForFeature(feature, type)
-            println "A: ${sequenceString?.trim()} .. $type"
             if(sequenceString?.trim()){
-                println "B"
                 render sequenceString
                 sequenceService.cacheRequest(sequenceString, organismString, sequenceName, featureName, type, paramMap)
                 return
@@ -393,7 +389,7 @@ class SequenceController {
         JSONObject organismJson = permissionService.handleInput(request, params)
         // if global admin
         Organism organism = Organism.findByCommonName(organismName) ?: Organism.findById(organismName as Long)
-        if (permissionService.hasGlobalPermissions(organismJson,GlobalPermissionEnum.ADMIN) || checkPermission(organismName)){
+        if (organism && permissionService.hasGlobalPermissions(organismJson,GlobalPermissionEnum.ADMIN) || checkPermission(organismName)){
             int removed = SequenceCache.countByOrganismNameAndSequenceName(organismName, sequenceName)
             SequenceCache.deleteAll(SequenceCache.findAllByOrganismNameAndSequenceName(organismName, sequenceName))
             render new JSONObject(removed: removed) as JSON