should fix filtering of statuses (#2543)

* should fix filtering of statuses * udpated change log * cleaned up * added get recent * updated the rest apidoc
GMOD · Dec 9, 2020 · d0d5396 · d0d5396
1 parent 5db4e4d
commit d0d5396
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -8,6 +8,7 @@ Features
 - Added the ability to sync the gene and transcript name with the click of a button [2519](https://github.com/GMOD/Apollo/issues/2519).
 - Added organism and species to menus [2537](https://github.com/GMOD/Apollo/pull/2537).
 - Added UUID lookup and link [2539](https://github.com/GMOD/Apollo/pull/2539/).
+- Added status filter for recent annotations [2543](https://github.com/GMOD/Apollo/pull/2543/).
 
 Bug Fixes
 

diff --git a/docs/web_services/examples/shell/getRecent.sh b/docs/web_services/examples/shell/getRecent.sh
@@ -4,10 +4,13 @@ url=$1
 username=$2
 password=$3
 days=$4
+status=$5
 
 usage() {
     echo "Sample script for exporting features from organism as GFF3 via web services"
-    echo "Usage:    ./getRecent.sh <complete_apollo_URL> <username> <password> <days>"
+    echo "Usage:    ./getRecent.sh <complete_apollo_URL> <username> <password> <days> <status>"
+    echo "Example:  ./getRecent.sh http://localhost:8080/apollo demo demo Finished|InProgress"
+    echo "Example:  ./getRecent.sh http://localhost:8080/apollo demo demo None"
     echo "Example:  ./getRecent.sh http://localhost:8080/apollo demo demo "
 }
 
@@ -16,6 +19,6 @@ if [[ ! -n "$url" || ! -n "$username" || ! -n "$password" || ! -n "$days" ]]; th
     exit
 fi
 
-echo curl "${url}/annotationEditor/getRecentAnnotations" -H 'Content-Type: application/json' --data "{'days':${days},  'username': '${username}', 'password': '${password}'}"
-curl "${url}/annotationEditor/getRecentAnnotations" -H 'Content-Type: application/json' --data "{'days':${days}, 'username': '${username}', 'password': '${password}'}"
+echo curl "${url}/annotationEditor/getRecentAnnotations" -H 'Content-Type: application/json' --data "{'days':${days},  'username': '${username}', 'password': '${password}', 'status':'${status}'}"
+curl "${url}/annotationEditor/getRecentAnnotations" -H 'Content-Type: application/json' --data "{'days':${days}, 'username': '${username}', 'password': '${password}', 'status':'${status}'}"
 
diff --git a/grails-app/controllers/org/bbop/apollo/AnnotationEditorController.groovy b/grails-app/controllers/org/bbop/apollo/AnnotationEditorController.groovy
@@ -1222,10 +1222,10 @@ class AnnotationEditorController extends AbstractApolloController implements Ann
 
     @RestApiMethod(description = "Get genes created or updated in the past, Returns JSON hash gene_name:organism", path = "/annotationEditor/getRecentAnnotations", verb = RestApiVerb.POST)
     @RestApiParams(params = [
-            @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)
-            , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY)
-            , @RestApiParam(name = "days", type = "Integer", paramType = RestApiParamType.QUERY, description = "Number of past days to retrieve annotations from.")
-
+        @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)
+        , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY)
+        , @RestApiParam(name = "days", type = "Integer", paramType = RestApiParamType.QUERY, description = "(Required) Number of past days to retrieve annotations from.")
+        , @RestApiParam(name = "status", type = "String", paramType = RestApiParamType.QUERY, description = "(optional: default allow all) Pipe-separated list of filters (e.g., 'Finished|Published').  Use 'None' if you want annotations without a status. ")
     ])
 
     def getRecentAnnotations() {
@@ -1236,7 +1236,8 @@ class AnnotationEditorController extends AbstractApolloController implements Ann
         }
 
         if (inputObject.get('days') instanceof Integer) {
-            JsonBuilder updatedGenes = annotationEditorService.recentAnnotations(inputObject.get('days'))
+            String filterString = inputObject.containsKey(FeatureStringEnum.STATUS.value) ? inputObject.getString(FeatureStringEnum.STATUS.value) : null
+            JsonBuilder updatedGenes = annotationEditorService.recentAnnotations(inputObject.getInt('days'),filterString)
             render updatedGenes
         } else {
             def error = [error: inputObject.get('days') + ' Param days must be an Integer']

diff --git a/grails-app/services/org/bbop/apollo/AnnotationEditorService.groovy b/grails-app/services/org/bbop/apollo/AnnotationEditorService.groovy
@@ -2,37 +2,56 @@ package org.bbop.apollo
 
 import grails.transaction.NotTransactional
 import grails.transaction.Transactional
-import static java.util.Calendar.YEAR
 import groovy.json.JsonBuilder
 
 @Transactional
 class AnnotationEditorService {
 
 
-    @NotTransactional
-    String cleanJSONString(String inputString){
-        String outputString = new String(inputString)
-        // remove leading string
-        outputString = outputString.indexOf("\"")==0 ? outputString.substring(1) : outputString
-        outputString = outputString.lastIndexOf("\"")==outputString.length()-1 ? outputString.substring(0,outputString.length()-1) : outputString
-//        outputString = outputString.replaceAll("/\\\\/","")
-        outputString = outputString.replaceAll("\\\\\"","\"")
-        outputString = outputString.replaceAll("\\\\\"","'")
-        return outputString
+  @NotTransactional
+  String cleanJSONString(String inputString) {
+    String outputString = new String(inputString)
+    // remove leading string
+    outputString = outputString.indexOf("\"") == 0 ? outputString.substring(1) : outputString
+    outputString = outputString.lastIndexOf("\"") == outputString.length() - 1 ? outputString.substring(0, outputString.length() - 1) : outputString
+    outputString = outputString.replaceAll("\\\\\"", "\"")
+    outputString = outputString.replaceAll("\\\\\"", "'")
+    return outputString
+  }
+
+  JsonBuilder recentAnnotations(Integer days, String statusFilter = null) {
+    Date today = new Date()
+    Date fromDate = today - days
+    List updatedGenes
+    if (statusFilter == null) {
+      updatedGenes = Gene.findAllByLastUpdatedGreaterThan(fromDate)
+    }
+    else
+    if (statusFilter.toLowerCase() == "none") {
+      updatedGenes = Gene.findAllByLastUpdatedGreaterThanAndStatusIsNull(fromDate)
+    } else {
+      List<String> statusFilterStringList = statusFilter.split("\\|")
+      List<Status> statusList = []
+      for(def statusString in statusFilterStringList){
+        Status status = Status.findByValue(statusString)
+        if(status) {
+          statusList.add(status)
+        }
+        else{
+          throw new RuntimeException("Status ${statusString} not found.")
+        }
+      }
+      updatedGenes = Gene.findAllByLastUpdatedGreaterThanAndStatusInList(fromDate, statusList)
+    }
+
+
+    Map geneToSpecies = [:]
+    updatedGenes.each { gene ->
+      geneToSpecies[gene.uniqueName] = gene.getFeatureLocation().sequence.organism.commonName
     }
 
-    JsonBuilder recentAnnotations(Integer days=1){
-    	Date today = new Date()
-    	Date fromDate = today - days
-    	List updatedGenes = Gene.findAllByLastUpdatedGreaterThan(fromDate)
-
-    	Map geneToSpecies = [ : ]    	
-    	updatedGenes.each { gene ->
-    		geneToSpecies[gene.uniqueName] = gene.getFeatureLocation().sequence.organism.commonName
-    	}
-
-    	JsonBuilder toJson = new JsonBuilder()
-    	toJson(geneToSpecies)
-    	return toJson
-    }        
+    JsonBuilder toJson = new JsonBuilder()
+    toJson(geneToSpecies)
+    return toJson
+  }
 }
diff --git a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java
@@ -359,11 +359,11 @@ public void onResponseReceived(Request request, Response response) {
                             statusListBox.setSelectedIndex(i + 1);
                         }
                     }
-                    statusLabelField.setVisible(true);
-                    statusListBox.setVisible(true);
+                  statusLabelField.setText("Status");
+                  statusListBox.setEnabled(true);
                 } else {
-                    statusLabelField.setVisible(false);
-                    statusListBox.setVisible(false);
+                  statusLabelField.setText("No status created");
+                  statusListBox.setEnabled(false);
                 }
             }
 

diff --git a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml
@@ -25,7 +25,7 @@
         .bolder {
             font-size: larger;
             font-weight: bolder;
-            width: 100px;
+            width: 50px;
         }
 
         .selectBox {
@@ -141,4 +141,4 @@
             </b:Column>
         </b:Row>
     </b:Container>
-</ui:UiBinder>
+</ui:UiBinder>