Fixed bug in creating tables introduced by last bug fix. Implemented …

…creation of schema.
OHDSI · Jul 16, 2017 · 6d2e6e7 · 6d2e6e7
1 parent 585c3c6
commit 6d2e6e7
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/src/org/ohdsi/databases/ConnectionWrapper.java b/src/org/ohdsi/databases/ConnectionWrapper.java
@@ -84,6 +84,10 @@ else if (dbType.equals(DbType.POSTGRESQL))
 			execute("USE " + database);
 	}
 
+	public void createDatabase(String database) {
+			execute("CREATE SCHEMA " + database);
+	}
+
 	/**
 	 * Execute the given SQL statement.
 	 * 
@@ -205,7 +209,7 @@ public void createTable(String table, List<String> fields, List<String> types, L
 			sql.append("  " + fields.get(i) + " " + types.get(i));
 		}
 		if (primaryKey != null && primaryKey.size() != 0)
-			sql.append("\n  PRIMARY KEY (" + StringUtilities.join(primaryKey, ",") + ")\n");
+			sql.append(",\n  PRIMARY KEY (" + StringUtilities.join(primaryKey, ",") + ")\n");
 		sql.append(");\n\n");
 		execute(Abbreviator.abbreviate(sql.toString()));
 	}

diff --git a/src/org/ohdsi/medlineXmlToDatabase/MedlineAnalyserMain.java b/src/org/ohdsi/medlineXmlToDatabase/MedlineAnalyserMain.java
@@ -43,7 +43,7 @@ public static void main(String[] args) {
 		MedlineAnalyserMain main = new MedlineAnalyserMain();
 		main.analyseFolder(iniFile.get("XML_FOLDER"));
 		main.createDatabase(iniFile.get("SERVER"), iniFile.get("SCHEMA"), iniFile.get("DOMAIN"), iniFile.get("USER"), iniFile.get("PASSWORD"),
-				iniFile.get("DATA_SOURCE_TYPE"));
+				iniFile.get("DATA_SOURCE_TYPE"), iniFile.get("CREATE_SCHEMA"));
 //		MedlineAnalyserMain main = new MedlineAnalyserMain();
 //		main.analyseFolder("S:/Data/MEDLINE/Unprocessed/test");
 	}
@@ -67,8 +67,10 @@ private void analyse(Document document) {
 		}
 	}
 
-	private void createDatabase(String server, String schema, String domain, String user, String password, String dateSourceType) {
+	private void createDatabase(String server, String schema, String domain, String user, String password, String dateSourceType, String createSchema) {
 		ConnectionWrapper connectionWrapper = new ConnectionWrapper(server, domain, user, password, new DbType(dateSourceType));
+		if (createSchema.toLowerCase().equals("true"))
+			connectionWrapper.createDatabase(schema);
 		connectionWrapper.use(schema);
 		System.out.println("Creating tables");
 		medlineCitationAnalyser.createTables(connectionWrapper);

diff --git a/src/org/ohdsi/medlineXmlToDatabase/MedlineCitationAnalyser.java b/src/org/ohdsi/medlineXmlToDatabase/MedlineCitationAnalyser.java
@@ -140,8 +140,6 @@ public void createTables(ConnectionWrapper connectionWrapper) {
 
 
 	private void analyseNode(Node node, String name, String tableName) {
-				 if (node.getNodeName().toLowerCase().equals("abstracttext"))
-				 System.out.println("asf");
 		// Add attributes:
 		NamedNodeMap attributes = node.getAttributes();
 		if (attributes != null)