From 3407a1622f94cf0621b7b792ab7511614264ccd5 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Andreas=20M=C3=BCller?= Date: Fri, 8 Jun 2012 09:45:09 +0000 Subject: [PATCH] latest changes to Gabon and Guiana activators --- .../cdm/app/eflora/FloraGuianasActivator.java | 38 +++++++++++++++---- .../cdm/app/eflora/FloreGabonActivator.java | 23 ++++++++--- 2 files changed, 48 insertions(+), 13 deletions(-) diff --git a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.java b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.java index 8b0306e3..1c8f1e0b 100644 --- a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.java +++ b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.java @@ -27,8 +27,8 @@ import eu.etaxonomy.cdm.io.common.events.IIoObserver; import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver; import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; -import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer; import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator; +import eu.etaxonomy.cdm.io.markup.MarkupTransformer; import eu.etaxonomy.cdm.model.description.Feature; import eu.etaxonomy.cdm.model.description.FeatureNode; import eu.etaxonomy.cdm.model.description.FeatureTree; @@ -55,8 +55,8 @@ public class FloraGuianasActivator { // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_preview(); // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_production(); -// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); - static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); + static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); +// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); //feature tree uuid @@ -65,6 +65,9 @@ public class FloraGuianasActivator { //classification static final UUID classificationUuid = UUID.fromString("5e3a1b07-2609-4597-bbda-7b02dfe8c2b3"); + private static final String SOURCE_REFERENCE_TITLE = "Flora of the Guianas"; + private static final String FEATURE_TREE_TITLE = "Flora of the Guianas Feature Tree"; + //check - import private boolean h2ForCheck = true; static CHECK check = CHECK.IMPORT_WITHOUT_CHECK; @@ -80,7 +83,7 @@ public class FloraGuianasActivator { private boolean includeFgu4 = false; - private boolean replaceStandardKeyTitles = false; + private boolean replaceStandardKeyTitles = true; private IIoObserver observer = new LoggingIoObserver(); private Set observerList = new HashSet(); @@ -104,7 +107,7 @@ public class FloraGuianasActivator { markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles); - markupConfig.setSourceReference(getSourceReference("Flore du Gabon")); + markupConfig.setSourceReference(getSourceReference(SOURCE_REFERENCE_TITLE)); CdmDefaultImport myImport = new CdmDefaultImport(); @@ -167,10 +170,10 @@ public class FloraGuianasActivator { } private FeatureTree makeFeatureNode(ITermService service){ - FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); + MarkupTransformer transformer = new MarkupTransformer(); FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); - result.setTitleCache("Flore Gabon Presentation Feature Tree"); + result.setTitleCache(FEATURE_TREE_TITLE); FeatureNode root = result.getRoot(); FeatureNode newNode; @@ -192,6 +195,12 @@ public class FloraGuianasActivator { newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); root.addChild(newNode); + newNode = FeatureNode.NewInstance(Feature.COMMON_NAME()); + root.addChild(newNode); + + newNode = FeatureNode.NewInstance(Feature.PHENOLOGY()); + root.addChild(newNode); + newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); root.addChild(newNode); addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); @@ -204,6 +213,14 @@ public class FloraGuianasActivator { newNode = FeatureNode.NewInstance(Feature.CITATION()); root.addChild(newNode); + String sql = "\nSELECT feature.titleCache " + + " FROM DescriptionElementBase deb INNER JOIN DefinedTermBase feature ON deb.feature_id = feature.id " + + " GROUP BY feature.id " + + " HAVING feature.id NOT IN (SELECT DISTINCT fn.feature_id " + + " FROM FeatureNode fn " + + " WHERE fn.feature_id IS NOT NULL) "; + logger.warn("Check for missing features in feature tree: " + sql); + return result; } @@ -267,6 +284,7 @@ public class FloraGuianasActivator { private static String [] descriptionFeatureList = new String[]{ "lifeform", + "Juvenile parts", "Bark", //new "wood", @@ -283,10 +301,13 @@ public class FloraGuianasActivator { "Stems", "stem leaves", "Leaves", + "extraxylary sclerenchyma", "flower-bearing stems", "Petiole", "Petiolules", "Leaflets", + "Lamina", + "Veins", "Thyrsus", "Thyrses", "Inflorescences", @@ -294,8 +315,9 @@ public class FloraGuianasActivator { "Young inflorescences", "Male inflorescences", "Female inflorescences", - "Bracts", + "rachises", "Pedicels", + "Bracts", "flowering buds", "scales", "Buds", diff --git a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.java b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.java index 579a3790..d6149328 100644 --- a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.java +++ b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.java @@ -27,7 +27,6 @@ import eu.etaxonomy.cdm.io.common.events.IIoObserver; import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver; import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; -import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer; import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator; import eu.etaxonomy.cdm.io.markup.MarkupTransformer; import eu.etaxonomy.cdm.model.description.Feature; @@ -55,8 +54,8 @@ public class FloreGabonActivator { // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_preview(); - static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_production(); -// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); +// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_production(); + static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); @@ -189,6 +188,8 @@ public class FloreGabonActivator { newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service); + newNode = FeatureNode.NewInstance(Feature.COMMON_NAME()); + root.addChild(newNode); newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); root.addChild(newNode); @@ -268,11 +269,13 @@ public class FloreGabonActivator { private static String [] descriptionFeatureList = new String[]{ "lifeform", + "Juvenile parts", "Bark", //new "wood", "Indumentum", "endophytic body", + "apical buds", "flowering buds", "Branchlets", "Branches", @@ -284,10 +287,17 @@ public class FloreGabonActivator { "Stems", "stem leaves", "Leaves", + "extraxylary sclerenchyma", "flower-bearing stems", "Petiole", "Petiolules", "Leaflets", + "Lamina", + "Veins", + "Lateral veins", + "secondary veins", + "Intersecondary veins", + "veinlets", "Thyrsus", "Thyrses", "Inflorescences", @@ -295,6 +305,7 @@ public class FloreGabonActivator { "Young inflorescences", "Male inflorescences", "Female inflorescences", + "rachises", "Bracts", "Pedicels", "flowering buds", @@ -311,6 +322,7 @@ public class FloreGabonActivator { "Axillary", "cymes", "Calyx", + "Androgynophore", "Petal", "Petals", "perigone", @@ -332,7 +344,8 @@ public class FloreGabonActivator { "Style", "annulus", "female flowers", - "Male flowers", + "Male flowers", + "Androphore", "Female", "Infructescences", //order not consistent (sometimes before "Flowers") "Fruit", @@ -351,7 +364,7 @@ public class FloreGabonActivator { "figure", "fig", - "figs", + "figs", -- 2.34.1