add mongo script to merge dataset

Author: bridge2014

mongoScript/mongoscript.js

@@ -0,0 +1,114 @@
+// [feiqiao@tahsin191 ~]$ mongo < ~/script/mongoscript.js
+
+print("define local variables\n");
+
+var host="129.49.249.191";
+var port="27015";
+var dbname="u24_luad";
+var case_id="TCGA-55-7994-01Z-00-DX1";
+var subject_id = "TCGA-55-7994";
+var merge_execution_id="merge_seq_1";
+var user="tester"
+
+
+//show dbs;
+//use u24_luad  
+//show collections
+//db = connect("localhost:27020/myDatabase");
+
+db = connect(host+":"+ port+"/"+ dbname);
+
+//db.getCollectionNames();
+
+db.createCollection("newcollection");
+ 
+db.newcollection.remove({});
+
+print("get segmentations within irregular annotation ... \n");
+//get segmentations within irregular annotation 
+db.objects.find({"provenance.image.case_id":case_id,
+                    "provenance.image.subject_id":subject_id,
+                    "provenance.analysis.execution_id":"humantest",
+                    "geometry.type":null
+                  }).forEach( function(annotation)
+                   {db.objects.aggregate([ { $match: {"provenance.image.case_id":case_id,
+                                                      "provenance.image.subject_id":subject_id,
+                                                      "provenance.analysis.execution_id":annotation.algorithm,                                                      
+                                                      "geometry": {
+                                                                   $geoWithin: {
+                                                                                $geometry: {
+                                                                                            type : "Polygon" ,
+                                                                                            coordinates: annotation.geometry.coordinates
+                                                                                           }
+                                                                               }
+                                                                  }                                                       
+                                                      } }, { $out: "tmpCollection" } ]);  
+                    db.tmpCollection.copyTo("newcollection");                                                       
+                   } );  
+ 
+ db.newcollection.find().count();
+ 
+ print("get segmentations within rectangle annotation ... \n");
+//get segmentations within rectangle annotation 
+db.objects.find({"provenance.image.case_id":case_id,
+                    "provenance.image.subject_id":subject_id,
+                    "provenance.analysis.execution_id":"humantest",
+                    "geometry.type": {$exists : true, $ne : ""}
+                  }).forEach( function(annotation)
+                   {db.objects.aggregate([ { $match: {"provenance.image.case_id":case_id,
+                                                      "provenance.image.subject_id":subject_id,
+                                                      "provenance.analysis.execution_id":annotation.algorithm,                                                      
+                                                       x : { '$gte':annotation.geometry.coordinates[0][0][0], '$lte':annotation.geometry.coordinates[0][2][0]},
+                                                       y : { '$gte':annotation.geometry.coordinates[0][0][1], '$lte':annotation.geometry.coordinates[0][2][1]}                                                    
+                                                      } }, { $out: "tmpCollection" } ]);  
+                    db.tmpCollection.copyTo("newcollection");                                                       
+                   } ); 
+ 
+ print("composite dataset record count:");                                    
+db.newcollection.find().count();
+  
+ print("update execution_id for this new collection:");   
+// update execution_id for this new collection
+db.newcollection.update({},
+                        {$set : {"provenance.analysis.execution_id":merge_execution_id}},
+                        {upsert:false, multi:true});
+                        
+ 
+print("delete all old composite dataset of segmentations:");  
+// delete all merged segmentations
+ db.objects.deleteMany({"provenance.image.case_id":case_id,
+                         "provenance.image.subject_id":subject_id,
+                         "provenance.analysis.execution_id":merge_execution_id                                                     
+                       } );
+
+print("insert new dataset from newcollection as array:");  
+ //insert from newcollection as array
+ db.objects.insert( db.newcollection.find({ },{"_id":0}).toArray() ); 
+
+
+//print("insert new metadate document of merging dataset to the metadata collection:");
+// insert new metadate document of merging dataset to the metadata collection 
+var merge_execution_id_records= db.metadata.find({"image.case_id":case_id,"image.subject_id":subject_id,"provenance.analysis_execution_id":merge_execution_id}).count();
+		
+if(merge_execution_id_records == 0){
+ print("insert new metadate document of merging dataset to the metadata collection:");  
+   db.metadata.insertOne(
+   { 
+    "title" : "merge_seq_1", 
+     "user":user,
+     "provenance" : {
+        "analysis_execution_id" : merge_execution_id, 
+        "type" : "human"
+                   }, 
+    "image" : {
+        "case_id" : case_id, 
+        "subject_id" : subject_id
+     }
+  });
+}	
+
+
+exit;
+	
+
+