\r
package eu.etaxonomy.cdm.io.common;\r
\r
+import java.net.MalformedURLException;\r
+import java.net.URL;\r
+import java.sql.ResultSet;\r
+import java.sql.SQLException;\r
+import java.util.Set;\r
+import java.util.UUID;\r
+\r
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
+import eu.etaxonomy.cdm.common.mediaMetaData.ImageMetaData;\r
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
+import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
+import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
+import eu.etaxonomy.cdm.model.common.AnnotationType;\r
+import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.DescriptionElementSource;\r
+import eu.etaxonomy.cdm.model.common.ExtensionType;\r
+import eu.etaxonomy.cdm.model.common.IOriginalSource;\r
+import eu.etaxonomy.cdm.model.common.ISourceable;\r
+import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
+import eu.etaxonomy.cdm.model.common.IdentifiableSource;\r
+import eu.etaxonomy.cdm.model.common.Language;\r
+import eu.etaxonomy.cdm.model.common.MarkerType;\r
+import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
+import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
+import eu.etaxonomy.cdm.model.description.Feature;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.location.NamedArea;\r
+import eu.etaxonomy.cdm.model.location.NamedAreaLevel;\r
+import eu.etaxonomy.cdm.model.location.NamedAreaType;\r
+import eu.etaxonomy.cdm.model.media.ImageFile;\r
+import eu.etaxonomy.cdm.model.media.Media;\r
+import eu.etaxonomy.cdm.model.media.MediaRepresentation;\r
+import eu.etaxonomy.cdm.model.name.NonViralName;\r
+import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
+import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;\r
\r
/**\r
* @version 1.0\r
*/\r
public abstract class CdmImportBase<CONFIG extends IImportConfigurator, STATE extends ImportStateBase> extends CdmIoBase<STATE> implements ICdmImport<CONFIG, STATE>{\r
- @SuppressWarnings("unused")\r
private static Logger logger = Logger.getLogger(CdmImportBase.class);\r
\r
- protected TaxonomicTree makeTree(STATE state, ReferenceBase ref){\r
+ protected TaxonomicTree makeTree(STATE state, ReferenceBase reference){\r
+ ReferenceBase ref = CdmBase.deproxy(reference, ReferenceBase.class);\r
String treeName = "TaxonTree (Import)";\r
if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){\r
treeName = ref.getTitleCache();\r
TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);\r
tree.setReference(ref);\r
\r
- getTaxonService().saveTaxonomicTree(tree);\r
+\r
+ // use defined uuid for first tree\r
+ CONFIG config = (CONFIG)state.getConfig();\r
+ if (state.countTrees() < 1 ){\r
+ tree.setUuid(config.getTaxonomicTreeUuid());\r
+ }\r
+ getTaxonTreeService().save(tree);\r
state.putTree(ref, tree);\r
return tree;\r
}\r
\r
+ \r
+ /**\r
+ * Alternative memory saving method variant of\r
+ * {@link #makeTree(STATE state, ReferenceBase ref)} which stores only the\r
+ * UUID instead of the full tree in the <code>ImportStateBase</code> by \r
+ * using <code>state.putTreeUuid(ref, tree);</code>\r
+ * \r
+ * @param state\r
+ * @param ref\r
+ * @return\r
+ */\r
+ protected TaxonomicTree makeTreeMemSave(STATE state, ReferenceBase ref){\r
+ String treeName = "TaxonTree (Import)";\r
+ if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){\r
+ treeName = ref.getTitleCache();\r
+ }\r
+ TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);\r
+ tree.setReference(ref);\r
+ \r
+\r
+ // use defined uuid for first tree\r
+ CONFIG config = (CONFIG)state.getConfig();\r
+ if (state.countTrees() < 1 ){\r
+ tree.setUuid(config.getTaxonomicTreeUuid());\r
+ }\r
+ getTaxonTreeService().save(tree);\r
+ state.putTreeUuid(ref, tree);\r
+ return tree;\r
+ }\r
+ \r
+ \r
+ protected ExtensionType getExtensionType(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ ExtensionType extensionType = state.getExtensionType(uuid);\r
+ if (extensionType == null){\r
+ extensionType = (ExtensionType)getTermService().find(uuid);\r
+ if (extensionType == null){\r
+ extensionType = ExtensionType.NewInstance(text, label, labelAbbrev);\r
+ extensionType.setUuid(uuid);\r
+ ExtensionType.DOI().getVocabulary().addTerm(extensionType);\r
+ getTermService().save(extensionType);\r
+ }\r
+ state.putExtensionType(extensionType);\r
+ }\r
+ return extensionType;\r
+ }\r
+ \r
+ \r
+ protected MarkerType getMarkerType(STATE state, String keyString) {\r
+ IInputTransformer transformer = state.getTransformer();\r
+ MarkerType markerType = null;\r
+ try {\r
+ markerType = transformer.getMarkerTypeByKey(keyString);\r
+ } catch (UndefinedTransformerMethodException e) {\r
+ logger.info("getMarkerTypeByKey not yet implemented for this import");\r
+ }\r
+ if (markerType == null ){\r
+ UUID uuid;\r
+ try {\r
+ uuid = transformer.getMarkerTypeUuid(keyString);\r
+ return getMarkerType(state, uuid, keyString, keyString, keyString);\r
+ } catch (UndefinedTransformerMethodException e) {\r
+ logger.warn("getMarkerTypeUuid not yet implemented for this import");\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ \r
+ protected MarkerType getMarkerType(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ MarkerType markerType = state.getMarkerType(uuid);\r
+ if (markerType == null){\r
+ markerType = (MarkerType)getTermService().find(uuid);\r
+ if (markerType == null){\r
+ markerType = MarkerType.NewInstance(label, text, labelAbbrev);\r
+ markerType.setUuid(uuid);\r
+ MarkerType.COMPLETE().getVocabulary().addTerm(markerType);\r
+ getTermService().save(markerType);\r
+ }\r
+ state.putMarkerType(markerType);\r
+ }\r
+ return markerType;\r
+ }\r
+ \r
+ protected AnnotationType getAnnotationType(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ AnnotationType annotationType = state.getAnnotationType(uuid);\r
+ if (annotationType == null){\r
+ annotationType = (AnnotationType)getTermService().find(uuid);\r
+ if (annotationType == null){\r
+ annotationType = AnnotationType.NewInstance(label, text, labelAbbrev);\r
+ annotationType.setUuid(uuid);\r
+ AnnotationType.EDITORIAL().getVocabulary().addTerm(annotationType);\r
+ getTermService().save(annotationType);\r
+ }\r
+ state.putAnnotationType(annotationType);\r
+ }\r
+ return annotationType;\r
+ }\r
+ \r
+ /**\r
+ * Returns a named area for a given uuid by first . If the named area does not\r
+ * @param state\r
+ * @param uuid\r
+ * @param label\r
+ * @param text\r
+ * @param labelAbbrev\r
+ * @param areaType\r
+ * @param level\r
+ * @return\r
+ */\r
+ protected NamedArea getNamedArea(STATE state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level){\r
+ NamedArea namedArea = state.getNamedArea(uuid);\r
+ if (namedArea == null){\r
+ namedArea = (NamedArea)getTermService().find(uuid);\r
+ if (namedArea == null){\r
+ namedArea = NamedArea.NewInstance(text, label, labelAbbrev);\r
+ namedArea.setType(areaType);\r
+ namedArea.setLevel(level);\r
+ namedArea.setUuid(uuid);\r
+ getTermService().save(namedArea);\r
+ }\r
+ state.putNamedArea(namedArea);\r
+ }\r
+ return namedArea;\r
+ }\r
+ \r
+ /**\r
+ * Returns a feature for a given uuid by first ...\r
+ * @param state\r
+ * @param uuid\r
+ * @param label\r
+ * @param text\r
+ * @param labelAbbrev\r
+ * @return\r
+ */\r
+ protected Feature getFeature(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ if (uuid == null){\r
+ return null;\r
+ }\r
+ Feature feature = state.getFeature(uuid);\r
+ if (feature == null){\r
+ feature = (Feature)getTermService().find(uuid);\r
+ if (feature == null){\r
+ feature = Feature.NewInstance(text, label, labelAbbrev);\r
+ feature.setUuid(uuid);\r
+ feature.setSupportsTextData(true);\r
+ //set vocabulary ; FIXME use another user-defined vocabulary\r
+ UUID uuidFeatureVoc = UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8"); \r
+ TermVocabulary<Feature> voc = getVocabularyService().find(uuidFeatureVoc);\r
+ voc.addTerm(feature);\r
+ getTermService().save(feature);\r
+ }\r
+ state.putFeature(feature);\r
+ }\r
+ return feature;\r
+ }\r
+\r
+ /**\r
+ * Returns a language for a given uuid by first ...\r
+ * @param state\r
+ * @param uuid\r
+ * @param label\r
+ * @param text\r
+ * @param labelAbbrev\r
+ * @return\r
+ */\r
+ protected Language getLanguage(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ if (uuid == null){\r
+ return null;\r
+ }\r
+ Language language = state.getLanguage(uuid);\r
+ if (language == null){\r
+ language = (Language)getTermService().find(uuid);\r
+ if (language == null){\r
+ language = Language.NewInstance(text, label, labelAbbrev);\r
+ \r
+ language.setUuid(uuid);\r
+ //set vocabulary ; FIXME use another user-defined vocabulary\r
+ UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de"); \r
+ TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc);\r
+ voc.addTerm(language);\r
+ getTermService().save(language);\r
+ }\r
+ state.putLanguage(language);\r
+ }\r
+ return language;\r
+ }\r
+ \r
+ /**\r
+ * Adds an orginal source to a sourceable objects (implemented for Identifiable entity and description element.\r
+ * If cdmBase is not sourceable nothing happens.\r
+ * TODO Move to DbImportBase once this exists.\r
+ * TODO also implemented in DbImportObjectCreationMapper (reduce redundance)\r
+ * @param rs\r
+ * @param cdmBase\r
+ * @param dbIdAttribute\r
+ * @param namespace\r
+ * @param citation\r
+ * @throws SQLException\r
+ */\r
+ public void addOriginalSource(CdmBase cdmBase, Object idAttributeValue, String namespace, ReferenceBase citation) throws SQLException {\r
+ if (cdmBase instanceof ISourceable ){\r
+ IOriginalSource source;\r
+ ISourceable sourceable = (ISourceable)cdmBase;\r
+ Object id = idAttributeValue;\r
+ String strId = String.valueOf(id);\r
+ String microCitation = null;\r
+ if (cdmBase instanceof IdentifiableEntity){\r
+ source = IdentifiableSource.NewInstance(strId, namespace, citation, microCitation);\r
+ }else if (cdmBase instanceof DescriptionElementBase){\r
+ source = DescriptionElementSource.NewInstance(strId, namespace, citation, microCitation);\r
+ }else{\r
+ logger.warn("ISourceable not beeing identifiable entities or description element base are not yet supported. CdmBase is of type " + cdmBase.getClass().getName() + ". Original source not added.");\r
+ return;\r
+ }\r
+ sourceable.addSource(source);\r
+ }\r
+ }\r
+ \r
+ /**\r
+ * @see #addOriginalSource(CdmBase, Object, String, ReferenceBase)\r
+ * @param rs\r
+ * @param cdmBase\r
+ * @param dbIdAttribute\r
+ * @param namespace\r
+ * @param citation\r
+ * @throws SQLException\r
+ */\r
+ public void addOriginalSource(ResultSet rs, CdmBase cdmBase, String dbIdAttribute, String namespace, ReferenceBase citation) throws SQLException {\r
+ Object id = rs.getObject(dbIdAttribute);\r
+ addOriginalSource(cdmBase, id, namespace, citation);\r
+ }\r
+ \r
+\r
+ /**\r
+ * If the child taxon is missing genus or species epithet information and the rank is below <i>genus</i>\r
+ * or <i>species</i> respectively the according epithets are taken from the parent taxon.\r
+ * If the name is an autonym and has no combination author/basionym author the authors are taken from\r
+ * the parent.\r
+ * @param parentTaxon\r
+ * @param childTaxon\r
+ */\r
+ protected void fillMissingEpithetsForTaxa(Taxon parentTaxon, Taxon childTaxon) {\r
+ NonViralName parentName = HibernateProxyHelper.deproxy(parentTaxon.getName(), NonViralName.class);\r
+ NonViralName childName = HibernateProxyHelper.deproxy(childTaxon.getName(), NonViralName.class);\r
+ fillMissingEpithets(parentName, childName);\r
+ }\r
+ \r
+ /**\r
+ * If the child name is missing genus or species epithet information and the rank is below <i>genus</i>\r
+ * or <i>species</i> respectively the according epithets are taken from the parent name.\r
+ * If the name is an autonym and has no combination author/basionym author the authors are taken from\r
+ * the parent.\r
+ * @param parentTaxon\r
+ * @param childTaxon\r
+ */\r
+ protected void fillMissingEpithets(NonViralName parentName, NonViralName childName) {\r
+ if (CdmUtils.isEmpty(childName.getGenusOrUninomial()) && childName.getRank().isLower(Rank.GENUS()) ){\r
+ childName.setGenusOrUninomial(parentName.getGenusOrUninomial());\r
+ }\r
+ \r
+ if (CdmUtils.isEmpty(childName.getSpecificEpithet()) && childName.getRank().isLower(Rank.SPECIES()) ){\r
+ childName.setSpecificEpithet(parentName.getSpecificEpithet());\r
+ }\r
+ if (childName.isAutonym() && childName.getCombinationAuthorTeam() == null && childName.getBasionymAuthorTeam() == null ){\r
+ childName.setCombinationAuthorTeam(parentName.getCombinationAuthorTeam());\r
+ childName.setBasionymAuthorTeam(parentName.getBasionymAuthorTeam());\r
+ } \r
+ }\r
+ \r
+ /**\r
+ * Returns the image gallery for a taxon. If there are multiple taxon descriptions\r
+ * marked as image galleries an arbitrary one is chosen.\r
+ * If no image gallery exists, a new one is created if <code>createNewIfNotExists</code>\r
+ * is <code>true</code>.\r
+ * @param createNewIfNotExists\r
+ * @return\r
+ */\r
+ public TaxonDescription getTaxonDescription(Taxon taxon, boolean isImageGallery, boolean createNewIfNotExists) {\r
+ TaxonDescription result = null;\r
+ Set<TaxonDescription> descriptions= taxon.getDescriptions();\r
+ for (TaxonDescription description : descriptions){\r
+ if (description.isImageGallery() == isImageGallery){\r
+ result = description;\r
+ break;\r
+ }\r
+ }\r
+ if (result == null && createNewIfNotExists){\r
+ result = TaxonDescription.NewInstance(taxon);\r
+ result.setImageGallery(isImageGallery);\r
+ }\r
+ return result;\r
+ }\r
+ \r
+\r
+ /**\r
+ * @param derivedUnitFacade\r
+ * @param multimediaObject\r
+ * @throws MalformedURLException\r
+ */\r
+ protected Media getImageMedia(String multimediaObject, boolean readDataFromUrl) throws MalformedURLException {\r
+ if( multimediaObject == null){\r
+ return null;\r
+ } else {\r
+ ImageMetaData imd = ImageMetaData.newInstance();\r
+ try {\r
+ if (readDataFromUrl){\r
+ URL url = new URL(multimediaObject);\r
+ imd.readMetaData(url.toURI(), 0);\r
+ }\r
+ } catch (Exception e) {\r
+ String message = "An error occurred when trying to read image meta data: " + e.getMessage();\r
+ logger.warn(message);\r
+ }\r
+ ImageFile imf = ImageFile.NewInstance(multimediaObject, null, imd);\r
+ MediaRepresentation representation = MediaRepresentation.NewInstance();\r
+ representation.setMimeType(imd.getMimeType());\r
+ representation.addRepresentationPart(imf);\r
+ Media media = Media.NewInstance();\r
+ media.addRepresentation(representation);\r
+ \r
+ return media;\r
+ }\r
+ }\r
+\r
+ \r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff