From: Patrick Plitzner <p.plitzner@bgbm.org>
Date: Fri, 7 Dec 2018 14:01:31 +0000 (+0100)
Subject: Fix db connection
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib-apps.git/commitdiff_plain/43c3f7df27b6474f5bf327149a29c8bb250a803e

Fix db connection
---

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/plantglossary/PlantGlossaryActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/plantglossary/PlantGlossaryActivator.java
index 2dca5c4a..e8795834 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/plantglossary/PlantGlossaryActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/plantglossary/PlantGlossaryActivator.java
@@ -7,7 +7,6 @@ import java.io.InputStreamReader;
 import org.apache.log4j.Logger;
 
 import eu.etaxonomy.cdm.app.common.CdmDestinations;
-import eu.etaxonomy.cdm.app.util.TestDatabase;
 import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
 import eu.etaxonomy.cdm.database.DbSchemaValidation;
 import eu.etaxonomy.cdm.database.ICdmDataSource;
@@ -20,11 +19,20 @@ public class PlantGlossaryActivator {
 
 	private void doImport(ICdmDataSource cdmDestination) throws FileNotFoundException{
 
+	    /*
+	     * Source file:
+	     * https://github.com/biosemantics/glossaries/blob/925f2c1691ed00bf2b9a9cd7f83609cffae47145/Plant/0.11/Plant_glossary_term_category.csv
+	     *
+	     * Cleaning data:
+	     *  - remove all comments in csv file
+	     *  - fix "coetaneouser" by adding missing paramater for "remarks" -> "active"
+	     */
         FileInputStream inStream = new FileInputStream("/home/pplitzner/plantglossary.csv");
 		PlantGlossaryCsvImportConfigurator config = PlantGlossaryCsvImportConfigurator.NewInstance(new InputStreamReader(inStream), cdmDestination);
 		config.setCheck(CHECK.IMPORT_WITHOUT_CHECK);
+		config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
 
-		CdmDefaultImport<PlantGlossaryCsvImportConfigurator> myImport = new CdmDefaultImport<PlantGlossaryCsvImportConfigurator>();
+		CdmDefaultImport<PlantGlossaryCsvImportConfigurator> myImport = new CdmDefaultImport<>();
 
 		System.out.println("Start import from ("+ cdmDestination.toString() + ") ...");
 		myImport.invoke(config);
@@ -32,11 +40,10 @@ public class PlantGlossaryActivator {
 	}
 
 	public static void main(String[] args) {
-		PlantGlossaryActivator me = new PlantGlossaryActivator();
+		PlantGlossaryActivator activator = new PlantGlossaryActivator();
 		try {
-	        ICdmDataSource dataSource = CdmDestinations.makeDestination(DatabaseTypeEnum.MySQL, "127.0.0.1", "additivity", 3306, "root", "root");
-	        TestDatabase.initDb(dataSource, DbSchemaValidation.VALIDATE, true);
-            me.doImport(dataSource);
+	        ICdmDataSource dataSource = CdmDestinations.makeDestination(DatabaseTypeEnum.MySQL, "127.0.0.1", "empty", 3306, "root", null);
+            activator.doImport(dataSource);
         } catch (FileNotFoundException e) {
             e.printStackTrace();
         }