Merge pull request rousakis#1 from rousakis/master

Merged Commits from rousakis project
WydD · Nov 19, 2015 · 7ef370c · 7ef370c
2 parents 252e681 + 2774f52
commit 7ef370c
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Showing 70 changed files with 208 additions and 130 deletions.
diff --git a/...ions/ontological/ChangesOntologySchema.n3 → ...ontological/EMBL/ChangesOntologySchema.n3 b/...ions/ontological/ChangesOntologySchema.n3 → ...ontological/EMBL/ChangesOntologySchema.n3
diff --git a/Change Definitions/ontological/EMBL/JSON definitions/Add Definition b/Change Definitions/ontological/EMBL/JSON definitions/Add Definition
@@ -0,0 +1,22 @@
+{
+  "Complex_Change": "Add Definition",
+  "Priority": 11.0,
+  "Complex_Change_Parameters": [
+    {
+      "subject": "1:ADD_PROPERTY_INSTANCE:-subject"
+    },
+	{
+      "definition": "1:ADD_PROPERTY_INSTANCE:-object"
+    }
+  ],
+  "Simple_Changes": [
+    {
+      "Simple_Change": "ADD_PROPERTY_INSTANCE",
+      "Simple_Change_Uri": "1:ADD_PROPERTY_INSTANCE",
+      "Is_Optional": false,
+      "Selection_Filter": "1:ADD_PROPERTY_INSTANCE:-property = <http://www.ebi.ac.uk/efo/definition>",
+      "Mapping_Filter": "",
+      "Join_Filter": ""
+    }
+  ]
+}
diff --git a/Change Definitions/ontological/EMBL/JSON definitions/Add Synonym b/Change Definitions/ontological/EMBL/JSON definitions/Add Synonym
@@ -0,0 +1,22 @@
+{
+  "Complex_Change": "Add Synonym",
+  "Priority": 13.0,
+  "Complex_Change_Parameters": [
+    {
+      "subject": "1:ADD_PROPERTY_INSTANCE:-subject"
+    },
+	{
+      "synonym": "1:ADD_PROPERTY_INSTANCE:-object"
+    }
+  ],
+  "Simple_Changes": [
+    {
+      "Simple_Change": "ADD_PROPERTY_INSTANCE",
+      "Simple_Change_Uri": "1:ADD_PROPERTY_INSTANCE",
+      "Is_Optional": false,
+      "Selection_Filter": "1:ADD_PROPERTY_INSTANCE:-property = <http://www.ebi.ac.uk/efo/alternative_term>",
+      "Mapping_Filter": "",
+      "Join_Filter": ""
+    }
+  ]
+}
diff --git a/Change Definitions/ontological/EMBL/JSON definitions/Delete Definition b/Change Definitions/ontological/EMBL/JSON definitions/Delete Definition
@@ -0,0 +1,22 @@
+{
+  "Complex_Change": "Delete Definition",
+  "Priority": 12.0,
+  "Complex_Change_Parameters": [
+    {
+      "subject": "1:DELETE_PROPERTY_INSTANCE:-subject"
+    },
+	{
+      "definition": "1:DELETE_PROPERTY_INSTANCE:-object"
+    }
+  ],
+  "Simple_Changes": [
+    {
+      "Simple_Change": "DELETE_PROPERTY_INSTANCE",
+      "Simple_Change_Uri": "1:DELETE_PROPERTY_INSTANCE",
+      "Is_Optional": false,
+      "Selection_Filter": "1:DELETE_PROPERTY_INSTANCE:-property = <http://www.ebi.ac.uk/efo/definition>",
+      "Mapping_Filter": "",
+      "Join_Filter": ""
+    }
+  ]
+}
diff --git a/Change Definitions/ontological/EMBL/JSON definitions/Delete Synonym b/Change Definitions/ontological/EMBL/JSON definitions/Delete Synonym
@@ -0,0 +1,22 @@
+{
+  "Complex_Change": "Delete Synonym",
+  "Priority": 14.0,
+  "Complex_Change_Parameters": [
+    {
+      "subject": "1:DELETE_PROPERTY_INSTANCE:-subject"
+    },
+	{
+      "synonym": "1:DELETE_PROPERTY_INSTANCE:-object"
+    }
+  ],
+  "Simple_Changes": [
+    {
+      "Simple_Change": "DELETE_PROPERTY_INSTANCE",
+      "Simple_Change_Uri": "1:DELETE_PROPERTY_INSTANCE",
+      "Is_Optional": false,
+      "Selection_Filter": "1:DELETE_PROPERTY_INSTANCE:-property = <http://www.ebi.ac.uk/efo/alternative_term>",
+      "Mapping_Filter": "",
+      "Join_Filter": ""
+    }
+  ]
+}
diff --git a/Change Definitions/ontological/EMBL/JSON definitions/Mark as Obsolete b/Change Definitions/ontological/EMBL/JSON definitions/Mark as Obsolete
@@ -0,0 +1,30 @@
+{
+  "Complex_Change": "Mark as Obsolete",
+  "Priority": 15.0,
+  "Complex_Change_Parameters": [
+    {
+      "obs_class": "1:ADD_SUPERCLASS:-subclass"
+    },
+	{
+      "reason": "2:ADD_PROPERTY_INSTANCE:-object"
+    }
+  ],
+  "Simple_Changes": [
+	{
+      "Simple_Change": "ADD_SUPERCLASS",
+      "Simple_Change_Uri": "1:ADD_SUPERCLASS",
+      "Is_Optional": false,
+      "Selection_Filter": "1:ADD_SUPERCLASS:-superclass = <http://www.geneontology.org/formats/oboInOwl#ObsoleteClass>",
+      "Mapping_Filter": "",
+      "Join_Filter": ""
+    },
+    {
+      "Simple_Change": "ADD_PROPERTY_INSTANCE",
+      "Simple_Change_Uri": "2:ADD_PROPERTY_INSTANCE",
+      "Is_Optional": false,
+      "Selection_Filter": "2:ADD_PROPERTY_INSTANCE:-property = <http://www.ebi.ac.uk/efo/reason_for_obsolescence>",
+      "Mapping_Filter": "",
+      "Join_Filter": "2:ADD_PROPERTY_INSTANCE:-subject = 1:ADD_SUPERCLASS:-subclass"
+    }
+  ]
+}
diff --git a/pom.xml b/pom.xml
@@ -16,21 +16,11 @@
     </properties>
 
     <dependencies>
-        <dependency>
-            <groupId>com.sun.jersey</groupId>
-            <artifactId>jersey-json</artifactId>
-            <version>1.3</version>
-        </dependency>
         <dependency>
             <groupId>com.sun.jersey</groupId>
             <artifactId>jersey-server</artifactId>
             <version>1.3</version>
         </dependency>
-        <dependency>
-            <groupId>com.sun.jersey</groupId>
-            <artifactId>jersey-client</artifactId>
-            <version>1.3</version>
-        </dependency>
         <dependency>
             <groupId>com.sun.jersey.contribs</groupId>
             <artifactId>jersey-multipart</artifactId>

diff --git a/src/main/java/clients/TestChangeDetection.java b/src/main/java/clients/TestChangeDetection.java
@@ -8,6 +8,8 @@
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
 import javax.ws.rs.core.MediaType;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
 
 /**
  *
@@ -23,13 +25,14 @@ public static void main(String[] args) {
         String ip = "139.91.183.48";
         ip = "localhost";
         WebResource r = c.resource("http://" + ip + ":8181/ForthMaven-1.0/diachron/change_detection");
-        String input = "{ \"Old_Version\" : \"" + v1 + "\", "
-                + "\"New_Version\" : \"" + v2 + "\", "
-                + "\"Ingest\" : " + ingest + ", "
-                + "\"Complex_Changes\" : [ ], "
-                + "\"Associations\" : null"
-                + "}";
-        ClientResponse response = r.type(MediaType.APPLICATION_JSON).accept(MediaType.APPLICATION_JSON).post(ClientResponse.class, input);
+        JSONObject input = new JSONObject();
+        input.put("Dataset_URI", "http://www.ebi.ac.uk/efo/");
+        input.put("Old_Version", v1);
+        input.put("New_Version", v2);
+        input.put("Ingest", ingest);
+        input.put("Complex_Changes", new JSONArray());
+        input.put("Associations", null);
+        ClientResponse response = r.type(MediaType.APPLICATION_JSON).accept(MediaType.APPLICATION_JSON).post(ClientResponse.class, input.toJSONString());
         System.out.println(response.getEntity(String.class));
         System.out.println(response.getStatus());
     }

diff --git a/src/main/java/clients/TestDefineCC.java b/src/main/java/clients/TestDefineCC.java
@@ -8,6 +8,7 @@
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
 import javax.ws.rs.core.MediaType;
+import org.json.simple.JSONObject;
 
 /**
  *
@@ -19,10 +20,11 @@ public static void main(String[] args) {
         Client c = Client.create();
         System.out.println("Testing Define CC Service...");
         String ip = "139.91.183.48";
-        ip = "localhost";
+//        ip = "localhost";
         String url = "http://" + ip + ":8181/ForthMaven-1.0/diachron/complex_change";
         WebResource r = c.resource(url);
-        String input = "{ "
+
+        String ccDef = "{ "
                 + "\"Complex_Change\" : \"Mark_as_Obsolete_v2\", "
                 + "\"Priority\" : 1.0, "
                 + "\"Complex_Change_Parameters\": ["
@@ -50,7 +52,11 @@ public static void main(String[] args) {
                 + " ]"
                 + "}";
 
-        ClientResponse response = r.type(MediaType.APPLICATION_JSON).accept(MediaType.APPLICATION_JSON).post(ClientResponse.class, input);
+        JSONObject input = new JSONObject();
+        input.put("Dataset_URI", "http://www.ebi.ac.uk/efo/");
+        input.put("CC_Definition", ccDef);
+
+        ClientResponse response = r.type(MediaType.APPLICATION_JSON).accept(MediaType.APPLICATION_JSON).post(ClientResponse.class, input.toJSONString());
         System.out.println(response.getEntity(String.class));
         System.out.println(response.getStatus());
         System.out.println("-----\n");

diff --git a/src/main/java/clients/TestDeleteCC.java b/src/main/java/clients/TestDeleteCC.java
@@ -7,7 +7,9 @@
 import com.sun.jersey.api.client.Client;
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.core.util.MultivaluedMapImpl;
 import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.MultivaluedMap;
 
 /**
  *
@@ -21,11 +23,14 @@ public static void main(String[] args) {
         // test delete cc service
         System.out.println("Testing Delete Service...");
         String ip = "139.91.183.48";
-        ip = "localhost";
+//        ip = "localhost";
         String url = "http://" + ip + ":8181/ForthMaven-1.0/diachron/complex_change";
         String ccName = "Mark_as_Obsolete_v2";
+        MultivaluedMap<String, String> params = new MultivaluedMapImpl();
+        params.putSingle("name", ccName);
+        params.putSingle("dataset_uri", "http://www.ebi.ac.uk/efo/");
         WebResource r = c.resource(url);
-        ClientResponse response = r.path(ccName).accept(MediaType.APPLICATION_JSON).delete(ClientResponse.class);
+        ClientResponse response = r.queryParams(params).accept(MediaType.APPLICATION_JSON).delete(ClientResponse.class);
         System.out.println(response.getEntity(String.class));
         System.out.println(response.getStatus());
         System.out.println("-----\n");

diff --git a/src/main/java/clients/TestInfoCC.java b/src/main/java/clients/TestInfoCC.java
@@ -7,8 +7,9 @@
 import com.sun.jersey.api.client.Client;
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.core.util.MultivaluedMapImpl;
 import javax.ws.rs.core.MediaType;
-
+import javax.ws.rs.core.MultivaluedMap;
 /**
  *
  * @author rousakis
@@ -23,9 +24,13 @@ public static void main(String[] args) {
         String url = "http://" + ip + "/ForthMaven-1.0/diachron/complex_change";
         WebResource r = c.resource(url);
         String ccName = "Add Synonym";
-        ClientResponse response = r.path(ccName).accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
+        MultivaluedMap<String, String> params = new MultivaluedMapImpl();
+        params.putSingle("name", ccName);
+        params.putSingle("dataset_uri", "http://www.ebi.ac.uk/efo/");
+        ClientResponse response = r.queryParams(params).accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
         System.out.println(response.getEntity(String.class));
         System.out.println(response.getStatus());
         System.out.println("-----\n");
+
     }
 }
diff --git a/src/main/java/clients/TestQuery.java b/src/main/java/clients/TestQuery.java
@@ -18,7 +18,7 @@ public class TestQuery {
     public static void main(String[] args) {
         Client c = Client.create();
         String ip = "139.91.183.48:8181";
-        ip = "139.91.183.65:8080";
+//        ip = "139.91.183.65:8080";
         System.out.println("Testing Query Service...");
         String query = "select ?sc ?param_name ?param_value ?v1 ?v2 where { "
                 + "?sc a co:Add_Label; "

diff --git a/src/main/java/services/change_detection/ChangeDetectionImpl.java b/src/main/java/services/change_detection/ChangeDetectionImpl.java
@@ -4,11 +4,8 @@
  */
 package services.change_detection;
 
-import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.OutputStream;
-import java.util.Properties;
-import javax.servlet.ServletContext;
 import javax.ws.rs.Consumes;
 import javax.ws.rs.GET;
 import javax.ws.rs.POST;
@@ -35,7 +32,6 @@
 import org.diachron.detection.repositories.SesameVirtRep;
 import org.diachron.detection.utils.ChangesDetector;
 import org.diachron.detection.utils.ChangesManager;
-import org.diachron.detection.utils.SCDUtils;
 import utils.PropertiesManager;
 import utils.Utils;
 
@@ -61,6 +57,7 @@ public ChangeDetectionImpl() {
      * @param <b>inputMessage</b> : A JSON-encoded string which has the
      * following form: <br>
      * { <br>
+     * "Dataset_Uri" : "http://dataset", <br>
      * "Old_Version" : "v1", <br>
      * "New_Version" : "v2", <br>
      * "Ingest" : true, <br>
@@ -69,6 +66,9 @@ public ChangeDetectionImpl() {
      * } <br>
      * where
      * <ul>
+     * <li>Dataset_Uri - The URI of the dataset whose versions will be compared.
+     * If this parameter is missing from the JSON input message, then the URI
+     * will be taken from the properties file. <br>
      * <li>Old_Version - The old version URI of a DIACHRON entity.<br>
      * <li>New_Version - The old version URI of a DIACHRON entity.<br>
      * <li>Ingest - A flag which denotes whether the service is called due to a
@@ -106,12 +106,16 @@ public Response changeDetectJSON(String inputMessage) {
         JSONParser jsonParser = new JSONParser();
         try {
             JSONObject jsonObject = (JSONObject) jsonParser.parse(inputMessage);
-            if (jsonObject.size() != 5) {
-                String message = "JSON input message should have exactly 5 arguments.";
+            if (jsonObject.size() != 5 && jsonObject.size() != 6) {
+                String message = "JSON input message should have 5 or 6 arguments.";
                 String json = "{ \"Success\" : false, "
                         + "\"Message\" : \"" + message + "\" }";
                 return Response.status(400).entity(json).build();
             } else {
+                String datasetUri = (String) jsonObject.get("Dataset_URI");
+                if (datasetUri == null) {
+                    datasetUri = propertiesManager.getPropertyValue("Dataset_URI");
+                }
                 String oldVersion = (String) jsonObject.get("Old_Version");
                 String newVersion = (String) jsonObject.get("New_Version");
                 boolean ingest = (Boolean) jsonObject.get("Ingest");
@@ -120,9 +124,7 @@ public Response changeDetectJSON(String inputMessage) {
                 if (oldVersion == null || newVersion == null || ccs == null) {
                     throw new ParseException(-1);
                 }
-                ///
-                String datasetUri = propertiesManager.getPropertyValue("Dataset_URI");
-                String changesOntologySchema = propertiesManager.getPropertyValue("Changes_Ontology_Schema");
+                String changesOntologySchema = Utils.getDatasetSchema(datasetUri);
                 ChangesDetector detector = null;
                 try {
                     ChangesManager cManager = new ChangesManager(propertiesManager.getProperties(), datasetUri, oldVersion, newVersion, false);
@@ -135,6 +137,7 @@ public Response changeDetectJSON(String inputMessage) {
                     return Response.status(400).entity(json).build();
                 }
                 if (ingest) {
+                    detector.detectAssociations(oldVersion, newVersion);
                     detector.detectSimpleChanges(oldVersion, newVersion, null);
                 }
                 String[] cChanges = {};
@@ -185,10 +188,8 @@ public Response changeDetectJSON(String inputMessage) {
     @Produces(MediaType.APPLICATION_JSON)
     public Response queryChangesOntologyGet(@QueryParam("query") String query,
             @QueryParam("format") String format) {
-        Properties prop = new Properties();
         OutputStream output = null;
         try {
-//            prop.load(this.getClass().getResourceAsStream(propFile));
             String ip = propertiesManager.getPropertyValue("Repository_IP");
             String username = propertiesManager.getPropertyValue("Repository_Username");
             String password = propertiesManager.getPropertyValue("Repository_Password");
@@ -198,7 +199,6 @@ public Response queryChangesOntologyGet(@QueryParam("query") String query,
             query = query.replace(" where ", " from <" + changesOntol + "> ");
             TupleQuery tupleQuery = sesame.getCon().prepareTupleQuery(QueryLanguage.SPARQL, query);
             output = new OutputStream() {
-
                 private StringBuilder string = new StringBuilder();
 
                 @Override
@@ -292,8 +292,6 @@ public Response queryChangesOntologyPost(String inputMessage) {
                 if (format == null || query == null) {
                     throw new ParseException(-1);
                 }
-                ///
-//                prop.load(this.getClass().getResourceAsStream(propFile));
                 String ip = propertiesManager.getPropertyValue("Repository_IP");
                 String username = propertiesManager.getPropertyValue("Repository_Username");
                 String password = propertiesManager.getPropertyValue("Repository_Password");