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 2dca5c4a14304a6c9d28bf1398a740a749643b8f..e87958347e1bc721671e737809f18ef9974fdba4 100644 (file)
--- 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();
         }