latest Vibrant Activator DwcA import changes

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/DwcaScratchpadImportActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/DwcaScratchpadImportActivator.java
index bbafe50c7a3badbf3497afeaf66108f1cae515a6..21e765ef74e71c69199f7dd8535baeac14c172b4 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/DwcaScratchpadImportActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/DwcaScratchpadImportActivator.java
@@ -10,6 +10,7 @@
 package eu.etaxonomy.cdm.app.vibrant;\r
 \r
 import java.net.URI;\r
+import java.util.UUID;\r
 \r
 import org.apache.log4j.Logger;\r
 \r
@@ -37,45 +38,75 @@ public class DwcaScratchpadImportActivator {
        \r
        //database validation status (create, update, validate ...)\r
        static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;\r
-       static final URI source = dwca_test_scratch_test();\r
-       \r
+\r
+       //      static final URI source =  dwca_emonocots_dioscoreaceae();\r
+       static final URI source =  dwca_emonocots_zingiberaceae();\r
+//     static final URI source =  dwca_emonocots_cypripedioideae();\r
        \r
 //     static final ICdmDataSource cdmDestination = CdmDestinations.localH2();\r
-       static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_dwca();\r
+       static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();\r
 //     static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();\r
-\r
        \r
        //default nom code is ICZN as it allows adding publication year \r
-       static final NomenclaturalCode defaultNomCode = null;\r
+       static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICBN;\r
 \r
+       //title\r
+       static final String title = "Scratchpad test import";\r
        \r
        //check - import\r
        static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;\r
+       static int partitionSize = 1000;\r
        \r
        //config\r
        static DatasetUse datasetUse = DatasetUse.CLASSIFICATION;\r
        \r
        //validate\r
-       static boolean validateRankConsistency = true;\r
+       static boolean validateRankConsistency = false;\r
        \r
        \r
        //taxa\r
        static final boolean doTaxa = true;\r
+       static final boolean doDistribution = true;\r
        \r
        \r
        \r
        static final MappingType mappingType = MappingType.InMemoryMapping;\r
        \r
-       private void doImport(ICdmDataSource cdmDestination){\r
+       //classification\r
+       static final UUID classificationUuid = UUID.fromString("d9d199b6-eaf4-47c8-a732-0639bc445c56");\r
+       \r
+       \r
+       //config\r
+       static boolean scientificNameIdAsOriginalSourceId = true;\r
+       static boolean guessNomRef = false;\r
+       private boolean handleAllRefsAsCitation = false;\r
+       private static final boolean useSourceReferenceAsSec = true;\r
+       \r
+\r
+       //deduplicate\r
+       static final boolean doDeduplicate = false;\r
+\r
+       \r
+       \r
+       protected void doImport(URI source, ICdmDataSource cdmDestination, UUID classificationUuid, String title, DbSchemaValidation hbm2dll){\r
                \r
                //make Source\r
                DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);\r
                config.addObserver(new LoggingIoObserver());\r
+               config.setClassificationUuid(classificationUuid);\r
                config.setCheck(check);\r
                config.setDbSchemaValidation(hbm2dll);\r
                config.setMappingType(mappingType);\r
+               \r
+               config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);\r
                config.setValidateRankConsistency(validateRankConsistency);\r
+               config.setDefaultPartitionSize(partitionSize);\r
                config.setNomenclaturalCode(defaultNomCode);\r
+               config.setDatasetUse(datasetUse);\r
+               config.setGuessNomenclaturalReferences(guessNomRef);\r
+               config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);\r
+               config.setUseSourceReferenceAsSec(useSourceReferenceAsSec);\r
+               config.setSourceReferenceTitle(title);\r
                \r
                CdmDefaultImport myImport = new CdmDefaultImport();\r
 \r
@@ -97,10 +128,26 @@ public class DwcaScratchpadImportActivator {
                return result;\r
        }\r
 \r
+       //Dwca\r
+       public static URI dwca_emonocots_local() {\r
+               URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");\r
+               return sourceUrl;\r
+       }\r
        \r
-       //Scratchpads test\r
-       public static URI dwca_test_scratch_test() {\r
-               URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_export_scratchpads_test.zip");\r
+       //emonocots_dioscoreaceae\r
+       public static URI dwca_emonocots_dioscoreaceae() {\r
+               URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");\r
+               return sourceUrl;\r
+       }\r
+       \r
+       //emonocots_zingiberaceae\r
+       public static URI dwca_emonocots_zingiberaceae() {\r
+               URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");\r
+               return sourceUrl;\r
+       }\r
+       //emonocots_cypripedioideae\r
+       public static URI dwca_emonocots_cypripedioideae() {\r
+               URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_cypripedioideae.zip");\r
                return sourceUrl;\r
        }\r
        \r
@@ -110,7 +157,7 @@ public class DwcaScratchpadImportActivator {
         */\r
        public static void main(String[] args) {\r
                DwcaScratchpadImportActivator me = new DwcaScratchpadImportActivator();\r
-               me.doImport(cdmDestination);\r
+               me.doImport(source, cdmDestination, classificationUuid, title, hbm2dll);\r
        }\r
        \r
 }\r

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.java
index 8ba60557b014ff85e789efe1b3275e47b105a506..7494b1eab9778800419ecdf42c897adc5d929827 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.java
@@ -9,6 +9,9 @@
 \r
 package eu.etaxonomy.cdm.app.vibrant;\r
 \r
+import java.net.URI;\r
+import java.util.UUID;\r
+\r
 import org.apache.log4j.Logger;\r
 \r
 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;\r
@@ -32,17 +35,28 @@ public class VibrantActivator {
        private static final Logger logger = Logger.getLogger(VibrantActivator.class);\r
 \r
        //database validation status (create, update, validate ...)\r
-       static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;\r
+//     static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;\r
+       static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;\r
+       \r
        static final Source iopiSource = BerlinModelSources.iopi();\r
        static final Source mclSource = BerlinModelSources.mcl();\r
        static final Source emSource = BerlinModelSources.PESI3_euroMed();\r
+       static final URI dioscoreaceaeSource = DwcaScratchpadImportActivator.dwca_emonocots_dioscoreaceae();\r
+       static final URI cypripedioideaeSource = DwcaScratchpadImportActivator.dwca_emonocots_cypripedioideae();\r
+       static final URI zingiberaceaeSource = DwcaScratchpadImportActivator.dwca_emonocots_zingiberaceae();\r
        \r
 //     static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();\r
-       static final ICdmDataSource cdmDestination = cdm_test_local_vibrant();\r
+//     static final ICdmDataSource cdmDestination = cdm_test_local_vibrant();\r
+//     static final ICdmDataSource cdmDestination = cdm_vibrant_dev();\r
+       static final ICdmDataSource cdmDestination = cdm_vibrant_emonoctos_dev();\r
+       \r
 \r
-       static final boolean doMcl = true;\r
-       static final boolean doEuroMed = true;\r
+       static final boolean doMcl = false;\r
+       static final boolean doEuroMed = false;\r
        static final boolean doIopi = false;\r
+       static final boolean doDioscoreaceae = true;\r
+       static final boolean doZingiberaceae = false;\r
+       static final boolean doCypripedioideae = false;\r
        \r
        \r
        /**\r
@@ -69,6 +83,27 @@ public class VibrantActivator {
                        hbm2dll = DbSchemaValidation.NONE;\r
                }\r
                \r
+               if (doDioscoreaceae){\r
+                       DwcaScratchpadImportActivator scratchpadActivator = new DwcaScratchpadImportActivator();\r
+                       UUID uuid = UUID.fromString("3bf59b32-9269-4225-944f-570256d40a9b");\r
+                       scratchpadActivator.doImport(dioscoreaceaeSource, cdmRepository,uuid , "Dioscoreaceae (Scratchpads)", hbm2dll);\r
+                       hbm2dll = DbSchemaValidation.NONE;\r
+               }\r
+               \r
+               if (doZingiberaceae){\r
+                       DwcaScratchpadImportActivator scratchpadActivator = new DwcaScratchpadImportActivator();\r
+                       UUID uuid = UUID.fromString("8fb0f951-ccd8-41c4-8d0b-99ba1fbd2dc2");\r
+                       scratchpadActivator.doImport(zingiberaceaeSource, cdmRepository, uuid, " (Scratchpads)", hbm2dll);\r
+                       hbm2dll = DbSchemaValidation.NONE;\r
+               }\r
+               \r
+               if (doCypripedioideae){\r
+                       DwcaScratchpadImportActivator scratchpadActivator = new DwcaScratchpadImportActivator();\r
+                       UUID uuid = UUID.fromString("a2b0ecf5-1a9d-4d94-a9ef-f57717a49bfd");\r
+                       scratchpadActivator.doImport(cypripedioideaeSource, cdmRepository, uuid, " (Scratchpads)", hbm2dll);\r
+                       hbm2dll = DbSchemaValidation.NONE;\r
+               }\r
+               \r
                if (doEuroMed){\r
                        logger.warn("DON'T FORGET to reset E+M filter");\r
                        System.out.println("DON'T FORGET to reset E+M filter");\r
@@ -83,5 +118,21 @@ public class VibrantActivator {
                String cdmUserName = "root";\r
                return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);\r
        }\r
+       \r
+       public static ICdmDataSource cdm_vibrant_dev(){\r
+               DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;\r
+               String cdmServer = "160.45.63.201";\r
+               String cdmDB = "cdm_vibrant_index"; \r
+               String cdmUserName = "edit";\r
+               return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);\r
+       }\r
+       \r
+       public static ICdmDataSource cdm_vibrant_emonoctos_dev(){\r
+               DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;\r
+               String cdmServer = "160.45.63.201";\r
+               String cdmDB = "cdm_vibrant_index_emonocots"; \r
+               String cdmUserName = "edit";\r
+               return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);\r
+       }\r
 \r
 }\r