Code refactoring

cumbof · Aug 25, 2020 · ba669f1 · ba669f1
1 parent eae87ed
commit ba669f1
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Showing 5 changed files with 24 additions and 20 deletions.
diff --git a/src/opengdc/Settings.java b/src/opengdc/Settings.java
@@ -1,6 +1,8 @@
 package opengdc;
 
 import java.io.File;
+import java.net.URISyntaxException;
+import java.nio.file.Paths;
 
 /**
  *

diff --git a/src/opengdc/UpdateScheduler.java b/src/opengdc/UpdateScheduler.java
@@ -41,7 +41,7 @@ public static void main(String[] args) {
         //String inputDiseaseAbbreviation = "ACC";
         //String inputDisease = (inputProgram+"-"+inputDiseaseAbbreviation).toLowerCase();
 
-        files_datetime = Settings.getFilesDatetime();
+        String files_datetime = Settings.getFilesDatetime();
         if (args.length == 2) {
             //args[0];
             files_datetime = args[1];

diff --git a/src/opengdc/UpdateTask.java b/src/opengdc/UpdateTask.java
@@ -44,7 +44,7 @@ public void run() {
         System.out.println("----------------------------------------");
         System.out.println("Timer task started at: " + new Date());
         //updateTask();
-	Settings.setFilesDatetime(files_datetime)
+	Settings.setFilesDatetime(files_datetime);
 	Main.runMain();
         System.out.println("Timer task finished at: " + new Date());
         System.out.println("----------------------------------------");

diff --git a/src/opengdc/test/FilterAttributesTest.java b/src/opengdc/test/FilterAttributesTest.java
@@ -19,15 +19,17 @@ public static void main(String[] args) {
         attributes.add("manually_curated__associated_entities__case_id");
         attributes.add("manually_curated__cases__case_id");
 
-        String selected_attribute = MetadataHandler.selectAttribute(attributes);
-        System.err.println(selected_attribute);
+        ArrayList<String> selected_attributes = MetadataHandler.selectAttributes(attributes);
+        for (String attr: selected_attributes)
+            System.err.println(attr);
 
         attributes = new ArrayList<>();
         attributes.add("manually_curated__associated_entities__entity_id");
         attributes.add("manually_curated__annotations__entity_id");
 
-        selected_attribute = MetadataHandler.selectAttribute(attributes);
-        System.err.println(selected_attribute);
+        selected_attributes = MetadataHandler.selectAttributes(attributes);
+        for (String attr: selected_attributes)
+            System.err.println(attr);
     }
 
 }
diff --git a/src/opengdc/util/GDCQuery.java b/src/opengdc/util/GDCQuery.java
@@ -56,7 +56,7 @@ public class GDCQuery {
 
 	public static String query(String disease, String dataType, int recursive_iteration) {
 		try {
-			String files_datetime = Settings.getFilesDatetime()
+			String files_datetime = Settings.getFilesDatetime();
 			String payload_top = "{" +
 						"\"filters\":{" +
 							"\"op\":\"and\"," +
@@ -89,15 +89,15 @@ public static String query(String disease, String dataType, int recursive_iterat
 									"}" +
 								"}";
 
-			payload_datetime = ",{" +
-						"\"op\":\">=\"," +
-						"\"content\":{" +
+			String payload_datetime = ",{" +
+                                                    "\"op\":\">=\"," +
+                                                    "\"content\":{" +
 							"\"field\":\"files.created_datetime\"," +
 							"\"value\":[" +
 								"\""+files_datetime+"\"" +
 							"]" + 
-						"}" +
-					   "}";
+                                                    "}" +
+                                                  "}";
 
 			if (dataType.toLowerCase().contains("clinical") || dataType.toLowerCase().contains("biospecimen")) {
 				payload_datetime = ",{" +
@@ -122,17 +122,17 @@ public static String query(String disease, String dataType, int recursive_iterat
 									"}" +
 								   "}" +
 							"]" +
-						    "}"
+						    "}";
 			}
 
-			payload_bottom = "]" +
-				"}," +
-				"\"format\":\"json\"," +
-				"\"size\":\""+SIZE_LIMIT+"\"," +
-				"\"pretty\":\"true\"" +
-			"}";
+			String payload_bottom = "]" +
+                                            "}," +
+                                            "\"format\":\"json\"," +
+                                            "\"size\":\""+SIZE_LIMIT+"\"," +
+                                            "\"pretty\":\"true\"" +
+                                        "}";
 
-			payload = payload_top + payload_datetime + payload_bottom;
+			String payload = payload_top + payload_datetime + payload_bottom;
 
 			String url = BASE_SEARCH_URL;
 			URL obj = new URL(url);