import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;\r
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
-import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;\r
import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;\r
+import eu.etaxonomy.cdm.io.markup.MarkupTransformer;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
import eu.etaxonomy.cdm.model.description.FeatureNode;\r
import eu.etaxonomy.cdm.model.description.FeatureTree;\r
\r
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_preview();\r
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_production();\r
-// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();\r
- static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();\r
+ static final ICdmDataSource cdmDestination = CdmDestinations.localH2();\r
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();\r
\r
\r
//feature tree uuid\r
//classification\r
static final UUID classificationUuid = UUID.fromString("5e3a1b07-2609-4597-bbda-7b02dfe8c2b3");\r
\r
+ private static final String SOURCE_REFERENCE_TITLE = "Flora of the Guianas";\r
+ private static final String FEATURE_TREE_TITLE = "Flora of the Guianas Feature Tree";\r
+\r
//check - import\r
private boolean h2ForCheck = true;\r
static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;\r
private boolean includeFgu4 = false;\r
\r
\r
- private boolean replaceStandardKeyTitles = false;\r
+ private boolean replaceStandardKeyTitles = true;\r
\r
private IIoObserver observer = new LoggingIoObserver();\r
private Set<IIoObserver> observerList = new HashSet<IIoObserver>();\r
markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);\r
\r
\r
- markupConfig.setSourceReference(getSourceReference("Flore du Gabon"));\r
+ markupConfig.setSourceReference(getSourceReference(SOURCE_REFERENCE_TITLE));\r
\r
CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>(); \r
\r
}\r
\r
private FeatureTree makeFeatureNode(ITermService service){\r
- FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();\r
+ MarkupTransformer transformer = new MarkupTransformer();\r
\r
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);\r
- result.setTitleCache("Flore Gabon Presentation Feature Tree");\r
+ result.setTitleCache(FEATURE_TREE_TITLE);\r
FeatureNode root = result.getRoot();\r
FeatureNode newNode;\r
\r
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());\r
root.addChild(newNode);\r
\r
+ newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());\r
+ root.addChild(newNode);\r
+\r
+ newNode = FeatureNode.NewInstance(Feature.PHENOLOGY());\r
+ root.addChild(newNode);\r
+ \r
newNode = FeatureNode.NewInstance(Feature.ECOLOGY());\r
root.addChild(newNode);\r
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);\r
newNode = FeatureNode.NewInstance(Feature.CITATION());\r
root.addChild(newNode);\r
\r
+ String sql = "\nSELECT feature.titleCache " +\r
+ " FROM DescriptionElementBase deb INNER JOIN DefinedTermBase feature ON deb.feature_id = feature.id " + \r
+ " GROUP BY feature.id " + \r
+ " HAVING feature.id NOT IN (SELECT DISTINCT fn.feature_id " +\r
+ " FROM FeatureNode fn " +\r
+ " WHERE fn.feature_id IS NOT NULL) ";\r
+ logger.warn("Check for missing features in feature tree: " + sql);\r
+ \r
return result;\r
}\r
\r
\r
private static String [] descriptionFeatureList = new String[]{\r
"lifeform", \r
+ "Juvenile parts",\r
"Bark",\r
//new\r
"wood",\r
"Stems", \r
"stem leaves", \r
"Leaves",\r
+ "extraxylary sclerenchyma",\r
"flower-bearing stems", \r
"Petiole", \r
"Petiolules", \r
"Leaflets", \r
+ "Lamina",\r
+ "Veins",\r
"Thyrsus", \r
"Thyrses", \r
"Inflorescences", \r
"Young inflorescences", \r
"Male inflorescences", \r
"Female inflorescences", \r
- "Bracts", \r
+ "rachises",\r
"Pedicels", \r
+ "Bracts", \r
"flowering buds", \r
"scales", \r
"Buds", \r
import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;\r
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
-import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;\r
import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;\r
import eu.etaxonomy.cdm.io.markup.MarkupTransformer;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
\r
\r
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_preview();\r
- static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_production();\r
-// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();\r
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_production();\r
+ static final ICdmDataSource cdmDestination = CdmDestinations.localH2();\r
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();\r
\r
\r
\r
newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);\r
\r
+ newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());\r
+ root.addChild(newNode);\r
\r
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());\r
root.addChild(newNode);\r
\r
private static String [] descriptionFeatureList = new String[]{\r
"lifeform", \r
+ "Juvenile parts",\r
"Bark",\r
//new\r
"wood",\r
"Indumentum", \r
"endophytic body", \r
+ "apical buds",\r
"flowering buds", \r
"Branchlets", \r
"Branches", \r
"Stems", \r
"stem leaves", \r
"Leaves",\r
+ "extraxylary sclerenchyma",\r
"flower-bearing stems", \r
"Petiole", \r
"Petiolules", \r
"Leaflets", \r
+ "Lamina",\r
+ "Veins",\r
+ "Lateral veins",\r
+ "secondary veins",\r
+ "Intersecondary veins",\r
+ "veinlets",\r
"Thyrsus", \r
"Thyrses", \r
"Inflorescences", \r
"Young inflorescences", \r
"Male inflorescences", \r
"Female inflorescences", \r
+ "rachises",\r
"Bracts", \r
"Pedicels", \r
"flowering buds", \r
"Axillary", \r
"cymes", \r
"Calyx", \r
+ "Androgynophore",\r
"Petal", \r
"Petals",\r
"perigone",\r
"Style", \r
"annulus", \r
"female flowers", \r
- "Male flowers", \r
+ "Male flowers", \r
+ "Androphore",\r
"Female", \r
"Infructescences", //order not consistent (sometimes before "Flowers") \r
"Fruit", \r
\r
"figure", \r
"fig", \r
- "figs", \r
+ "figs", \r
\r
\r
\r