\r
package eu.etaxonomy.cdm.io.common;\r
\r
+import java.net.MalformedURLException;\r
+import java.net.URI;\r
+import java.net.URISyntaxException;\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
+import java.util.Arrays;\r
+import java.util.HashSet;\r
+import java.util.List;\r
+import java.util.Set;\r
import java.util.UUID;\r
\r
import org.apache.log4j.Logger;\r
\r
+import eu.etaxonomy.cdm.api.service.pager.Pager;\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
+import eu.etaxonomy.cdm.common.media.ImageInfo;\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.io.markup.MarkupTransformer;\r
import eu.etaxonomy.cdm.model.common.AnnotationType;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
import eu.etaxonomy.cdm.model.common.DescriptionElementSource;\r
import eu.etaxonomy.cdm.model.common.ExtensionType;\r
+import eu.etaxonomy.cdm.model.common.Figure;\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.Marker;\r
import eu.etaxonomy.cdm.model.common.MarkerType;\r
+import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\r
import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
+import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
+import eu.etaxonomy.cdm.model.description.PresenceTerm;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.description.TextData;\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.location.ReferenceSystem;\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.reference.Reference;\r
+import eu.etaxonomy.cdm.model.taxon.Classification;\r
+import eu.etaxonomy.cdm.model.taxon.Synonym;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
\r
/**\r
* @author a.mueller\r
*/\r
public abstract class CdmImportBase<CONFIG extends IImportConfigurator, STATE extends ImportStateBase> extends CdmIoBase<STATE> implements ICdmImport<CONFIG, STATE>{\r
private static Logger logger = Logger.getLogger(CdmImportBase.class);\r
+ \r
+ protected static final boolean CREATE = true;\r
+ protected static final boolean IMAGE_GALLERY = true;\r
+ protected static final boolean READ_MEDIA_DATA = true;\r
\r
- protected TaxonomicTree makeTree(STATE state, ReferenceBase reference){\r
- ReferenceBase ref = CdmBase.deproxy(reference, ReferenceBase.class);\r
- String treeName = "TaxonTree (Import)";\r
+ public static final UUID uuidUserDefinedNamedAreaLevelVocabulary = UUID.fromString("255144da-8d95-457e-a327-9752a8f85e5a");\r
+ public static final UUID uuidUserDefinedNamedAreaVocabulary = UUID.fromString("b2238399-a3af-4f6d-b7eb-ff5d0899bf1b");\r
+ public static final UUID uuidUserDefinedExtensionTypeVocabulary = UUID.fromString("e28c1394-1be8-4847-8b81-ab44eb6d5bc8");\r
+ public static final UUID uuidUserDefinedReferenceSystemVocabulary = UUID.fromString("467591a3-10b4-4bf1-9239-f06ece33e90a");\r
+ public static final UUID uuidUserDefinedFeatureVocabulary = UUID.fromString("fe5fccb3-a2f2-4b97-b199-6e2743cf1627");\r
+ public static final UUID uuidUserDefinedAnnotationTypeVocabulary = UUID.fromString("cd9ecdd2-9cae-4890-9032-ad83293ae883");\r
+ public static final UUID uuidUserDefinedMarkerTypeVocabulary = UUID.fromString("5f02a261-fd7d-4fce-bbe4-21472de8cd51");\r
+ \r
+ \r
+ private static final String UuidOnly = "UUIDOnly";\r
+ private static final String UuidLabel = "UUID or label";\r
+ private static final String UuidLabelAbbrev = "UUID, label or abbreviation";\r
+ private static final String UuidAbbrev = "UUID or abbreviation";\r
+ \r
+ public enum TermMatchMode{\r
+ UUID_ONLY(0, UuidOnly)\r
+ ,UUID_LABEL(1, UuidLabel)\r
+ ,UUID_LABEL_ABBREVLABEL(2, UuidLabelAbbrev)\r
+ ,UUID_ABBREVLABEL(3, UuidAbbrev)\r
+ ;\r
+ \r
+ \r
+ private int id;\r
+ private String representation;\r
+ private TermMatchMode(int id, String representation){\r
+ this.id = id;\r
+ this.representation = representation;\r
+ }\r
+ public int getId() {\r
+ return id;\r
+ }\r
+ public String getRepresentation() {\r
+ return representation;\r
+ }\r
+ public TermMatchMode valueOf(int id){\r
+ switch (id){\r
+ case 0: return UUID_ONLY;\r
+ case 1: return UUID_LABEL;\r
+ case 2: return UUID_LABEL_ABBREVLABEL;\r
+ case 3: return UUID_ABBREVLABEL;\r
+ default: return UUID_ONLY;\r
+ }\r
+ }\r
+ \r
+ \r
+ }\r
+ \r
+ protected Classification makeTree(STATE state, Reference reference){\r
+ Reference ref = CdmBase.deproxy(reference, Reference.class);\r
+ String treeName = "Classification (Import)";\r
if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){\r
treeName = ref.getTitleCache();\r
}\r
- TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);\r
+ Classification tree = Classification.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
+ tree.setUuid(config.getClassificationUuid());\r
}\r
- getTaxonTreeService().save(tree);\r
+ getClassificationService().save(tree);\r
state.putTree(ref, tree);\r
return tree;\r
}\r
\r
/**\r
* Alternative memory saving method variant of\r
- * {@link #makeTree(STATE state, ReferenceBase ref)} which stores only the\r
+ * {@link #makeTree(STATE state, Reference 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 ref\r
* @return\r
*/\r
- protected TaxonomicTree makeTreeMemSave(STATE state, ReferenceBase ref){\r
- String treeName = "TaxonTree (Import)";\r
+ protected Classification makeTreeMemSave(STATE state, Reference ref){\r
+ String treeName = "Classification (Import)";\r
if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){\r
treeName = ref.getTitleCache();\r
}\r
- TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);\r
+ Classification tree = Classification.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
+ tree.setUuid(config.getClassificationUuid());\r
}\r
- getTaxonTreeService().save(tree);\r
+ getClassificationService().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
+ return getExtensionType(state, uuid, label, text, labelAbbrev, null);\r
+ }\r
+ protected ExtensionType getExtensionType(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<ExtensionType> voc){\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ }\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
+ if (voc == null){\r
+ boolean isOrdered = false;\r
+ voc = getVocabulary(uuidUserDefinedExtensionTypeVocabulary, "User defined vocabulary for extension types", "User Defined Extension Types", null, null, isOrdered, extensionType);\r
+ }\r
+ voc.addTerm(extensionType);\r
+ getTermService().saveOrUpdate(extensionType);\r
}\r
state.putExtensionType(extensionType);\r
}\r
}\r
\r
protected MarkerType getMarkerType(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ return getMarkerType(state, uuid, label, text, labelAbbrev, null);\r
+ }\r
+\r
+ \r
+ protected MarkerType getMarkerType(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<MarkerType> voc){\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ }\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
+ if (voc == null){\r
+ boolean isOrdered = false;\r
+ voc = getVocabulary(uuidUserDefinedMarkerTypeVocabulary, "User defined vocabulary for marker types", "User Defined Marker Types", null, null, isOrdered, markerType);\r
+ }\r
+ voc.addTerm(markerType);\r
getTermService().save(markerType);\r
}\r
state.putMarkerType(markerType);\r
return markerType;\r
}\r
\r
- protected AnnotationType getAnnotationType(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ protected AnnotationType getAnnotationType(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<AnnotationType> voc){\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ }\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
+ if (voc == null){\r
+ boolean isOrdered = false;\r
+ voc = getVocabulary(uuidUserDefinedAnnotationTypeVocabulary, "User defined vocabulary for annotation types", "User Defined Annotation Types", null, null, isOrdered, annotationType);\r
+ }\r
+ \r
+ voc.addTerm(annotationType);\r
getTermService().save(annotationType);\r
}\r
state.putAnnotationType(annotationType);\r
return annotationType;\r
}\r
\r
+ \r
+ protected ReferenceSystem getReferenceSystem(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary voc){\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ }\r
+ ReferenceSystem refSystem = state.getReferenceSystem(uuid);\r
+ if (refSystem == null){\r
+ refSystem = (ReferenceSystem)getTermService().find(uuid);\r
+ if (refSystem == null){\r
+ refSystem = ReferenceSystem.NewInstance(text, label, labelAbbrev);\r
+ if (voc == null){\r
+ boolean isOrdered = false;\r
+ voc = getVocabulary(uuidUserDefinedReferenceSystemVocabulary, "User defined vocabulary for named areas", "User Defined Reference System", null, null, isOrdered, refSystem);\r
+ }\r
+ voc.addTerm(refSystem);\r
+ refSystem.setUuid(uuid);\r
+ getTermService().save(refSystem);\r
+ }\r
+ state.putReferenceSystem(refSystem);\r
+ }\r
+ return refSystem;\r
+ \r
+ }\r
+ \r
/**\r
* Returns a named area for a given uuid by first . If the named area does not\r
* @param state\r
* @return\r
*/\r
protected NamedArea getNamedArea(STATE state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level){\r
+ return getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level, null, null);\r
+ }\r
+\r
+ protected NamedArea getNamedArea(STATE state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc, TermMatchMode matchMode){\r
+ Class<NamedArea> clazz = NamedArea.class;\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ }\r
+ if (matchMode == null){\r
+ matchMode = TermMatchMode.UUID_ONLY;\r
+ }\r
NamedArea namedArea = state.getNamedArea(uuid);\r
if (namedArea == null){\r
- namedArea = (NamedArea)getTermService().find(uuid);\r
+ //TODO matching still experimental\r
+ namedArea = CdmBase.deproxy(getTermService().find(uuid),NamedArea.class);\r
+ if (namedArea == null && (matchMode.equals(TermMatchMode.UUID_LABEL) || matchMode.equals(TermMatchMode.UUID_LABEL_ABBREVLABEL ))){\r
+ //TODO test\r
+ Pager<NamedArea> areaPager = (Pager)getTermService().findByTitle(clazz, label, null, null, null, null, null, null);\r
+ namedArea = findBestMatchingArea(areaPager, uuid, label, text, labelAbbrev, areaType, level, voc);\r
+ }\r
+ if (namedArea == null && (matchMode.equals(TermMatchMode.UUID_ABBREVLABEL) || matchMode.equals(TermMatchMode.UUID_LABEL_ABBREVLABEL))){\r
+ Pager<NamedArea> areaPager = getTermService().findByRepresentationAbbreviation(labelAbbrev, clazz, null, null);\r
+ namedArea = findBestMatchingArea(areaPager, uuid, label, text, labelAbbrev, areaType, level, voc);\r
+ }\r
+ \r
if (namedArea == null){\r
namedArea = NamedArea.NewInstance(text, label, labelAbbrev);\r
+ if (voc == null){\r
+ boolean isOrdered = true;\r
+ voc = getVocabulary(uuidUserDefinedNamedAreaVocabulary, "User defined vocabulary for named areas", "User Defined Named Areas", null, null, isOrdered, namedArea);\r
+ }\r
+ voc.addTerm(namedArea);\r
namedArea.setType(areaType);\r
namedArea.setLevel(level);\r
namedArea.setUuid(uuid);\r
return namedArea;\r
}\r
\r
+ \r
+ private NamedArea findBestMatchingArea(Pager<NamedArea> areaPager, UUID uuid, String label, String text, String abbrev,\r
+ NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc) {\r
+ // TODO preliminary implementation\r
+ List<NamedArea> list = areaPager.getRecords();\r
+ if (list.size() == 0){\r
+ return null;\r
+ }else if (list.size() == 1){\r
+ return list.get(0);\r
+ }else if (list.size() > 1){\r
+ String message = "There is more than 1 matching area for %s, %s, %s. As a preliminary implementation I take the first";\r
+ message = String.format(message, label, abbrev, text);\r
+ logger.warn(message);\r
+ return list.get(0);\r
+ }\r
+ return null;\r
+ }\r
+\r
+\r
+ protected NamedAreaLevel getNamedAreaLevel(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<NamedAreaLevel> voc){\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ }\r
+ NamedAreaLevel namedAreaLevel = state.getNamedAreaLevel(uuid);\r
+ if (namedAreaLevel == null){\r
+ namedAreaLevel = CdmBase.deproxy(getTermService().find(uuid), NamedAreaLevel.class);\r
+ if (namedAreaLevel == null){\r
+ namedAreaLevel = NamedAreaLevel.NewInstance(text, label, labelAbbrev);\r
+ if (voc == null){\r
+ boolean isOrdered = true;\r
+ voc = getVocabulary(uuidUserDefinedNamedAreaLevelVocabulary, "User defined vocabulary for named area levels", "User Defined Named Area Levels", null, null, isOrdered, namedAreaLevel);\r
+ }\r
+ voc.addTerm(namedAreaLevel);\r
+ namedAreaLevel.setUuid(uuid);\r
+ getTermService().save(namedAreaLevel);\r
+ }\r
+ state.putNamedAreaLevel(namedAreaLevel);\r
+ }\r
+ return namedAreaLevel;\r
+ }\r
+ \r
+ \r
/**\r
- * Returns a feature for a given uuid by first ...\r
+ * Returns a feature if it exists, null otherwise.\r
+ * @see #getFeature(ImportStateBase, UUID, String, String, String, TermVocabulary)\r
+ * @param state\r
+ * @param uuid\r
+ * @return\r
+ */\r
+ protected Feature getFeature(STATE state, UUID uuid){\r
+ return getFeature(state, uuid, null, null, null, null);\r
+ }\r
+ \r
+ /**\r
+ * Returns a feature for a given uuid by first checking if the uuid has already been used in this import, if not\r
+ * checking if the feature exists in the database, if not creating it anew (with vocabulary etc.).\r
+ * If label, text and labelAbbrev are all <code>null</code> no feature is created.\r
* @param state\r
* @param uuid\r
* @param label\r
* @param labelAbbrev\r
* @return\r
*/\r
- protected Feature getFeature(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ protected Feature getFeature(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<Feature> voc){\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
+ if (feature == null && ! hasNoLabel(label, text, labelAbbrev)){\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
+// UUID uuidFeatureVoc = UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8"); \r
+ if (voc == null){\r
+ boolean isOrdered = false;\r
+ voc = getVocabulary(uuidUserDefinedFeatureVocabulary, "User defined vocabulary for features", "User Defined Features", null, null, isOrdered, feature);\r
+ }\r
voc.addTerm(feature);\r
getTermService().save(feature);\r
}\r
}\r
return feature;\r
}\r
+ \r
+ private boolean hasNoLabel(String label, String text, String labelAbbrev) {\r
+ return label == null && text == null && labelAbbrev == null;\r
+ }\r
+\r
+\r
+ /**\r
+ * Returns a presence term 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 PresenceTerm getPresenceTerm(STATE state, UUID uuid, String label, String text, String labelAbbrev){\r
+ if (uuid == null){\r
+ return null;\r
+ }\r
+ PresenceTerm presenceTerm = state.getPresenceTerm(uuid);\r
+ if (presenceTerm == null){\r
+ presenceTerm = (PresenceTerm)getTermService().find(uuid);\r
+ if (presenceTerm == null){\r
+ presenceTerm = PresenceTerm.NewInstance(text, label, labelAbbrev);\r
+ presenceTerm.setUuid(uuid);\r
+ //set vocabulary ; FIXME use another user-defined vocabulary\r
+ UUID uuidPresenceVoc = UUID.fromString("adbbbe15-c4d3-47b7-80a8-c7d104e53a05"); \r
+ TermVocabulary<PresenceTerm> voc = getVocabularyService().find(uuidPresenceVoc);\r
+ voc.addTerm(presenceTerm);\r
+ getTermService().save(presenceTerm);\r
+ }\r
+ state.putPresenceTerm(presenceTerm);\r
+ }\r
+ return presenceTerm;\r
+ }\r
\r
/**\r
* Returns a language for a given uuid by first ...\r
return language;\r
}\r
\r
+\r
+ /**\r
+ * @param uuid \r
+ * @return\r
+ * \r
+ */\r
+ protected <T extends DefinedTermBase> TermVocabulary<T> getVocabulary(UUID uuid, String text, String label, String abbrev, URI termSourceUri, boolean isOrdered, T type) {\r
+ List<String> propPath = Arrays.asList(new String[]{"terms"});\r
+ TermVocabulary<T> voc = getVocabularyService().load(uuid, propPath);\r
+ if (voc == null){\r
+ if (isOrdered){\r
+ voc = OrderedTermVocabulary.NewInstance(text, label, abbrev, termSourceUri);\r
+ }else{\r
+ voc = TermVocabulary.NewInstance(text, label, abbrev, termSourceUri);\r
+ }\r
+ voc.setUuid(uuid);\r
+ getVocabularyService().save(voc);\r
+ }\r
+ return voc;\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
* @param citation\r
* @throws SQLException\r
*/\r
- public void addOriginalSource(CdmBase cdmBase, Object idAttributeValue, String namespace, ReferenceBase citation) throws SQLException {\r
+ public void addOriginalSource(CdmBase cdmBase, Object idAttributeValue, String namespace, Reference citation) {\r
if (cdmBase instanceof ISourceable ){\r
IOriginalSource source;\r
ISourceable sourceable = (ISourceable)cdmBase;\r
return;\r
}\r
sourceable.addSource(source);\r
+ }else if (cdmBase != null){\r
+ logger.warn("Sourced object does not implement ISourceable: " + cdmBase.getClass() + "," + cdmBase.getUuid());\r
+ }else{\r
+ logger.warn("Sourced object is null");\r
}\r
}\r
\r
/**\r
- * @see #addOriginalSource(CdmBase, Object, String, ReferenceBase)\r
+ * @see #addOriginalSource(CdmBase, Object, String, Reference)\r
* @param rs\r
* @param cdmBase\r
* @param dbIdAttribute\r
* @param citation\r
* @throws SQLException\r
*/\r
- public void addOriginalSource(ResultSet rs, CdmBase cdmBase, String dbIdAttribute, String namespace, ReferenceBase citation) throws SQLException {\r
+ public void addOriginalSource(ResultSet rs, CdmBase cdmBase, String dbIdAttribute, String namespace, Reference citation) throws SQLException {\r
Object id = rs.getObject(dbIdAttribute);\r
addOriginalSource(cdmBase, id, namespace, citation);\r
}\r
} \r
}\r
\r
+ /**\r
+ * Returns the taxon description for a taxon. If there are multiple taxon descriptions\r
+ * an arbitrary one is chosen.\r
+ * If no taxon description exists, a new one is created if <code>createNewIfNotExists</code>\r
+ * is <code>true</code>.\r
+ * @param createNewIfNotExists\r
+ * @param isImageGallery if true only taxon description being image galleries are considered.\r
+ * If false only taxon description being no image galleries are considered.\r
+ * @return\r
+ */\r
+ public TaxonDescription getTaxonDescription(Taxon taxon, boolean isImageGallery, boolean createNewIfNotExists) {\r
+ Reference ref = null;\r
+ return getTaxonDescription(taxon, ref, isImageGallery, createNewIfNotExists);\r
+ }\r
+ \r
+ /**\r
+ * Like {@link #getTaxonDescription(Taxon, boolean, boolean)}\r
+ * Only matches a description if the given reference is a source of the description.<BR>\r
+ * If a new description is created the given reference will be added as a source.\r
+ * \r
+ * @see #getTaxonDescription(Taxon, boolean, boolean)\r
+ */\r
+ public TaxonDescription getTaxonDescription(Taxon taxon, Reference ref, 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
+ if (hasCorrespondingSource(ref, description)){\r
+ result = description;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (result == null && createNewIfNotExists){\r
+ result = TaxonDescription.NewInstance(taxon);\r
+ result.setImageGallery(isImageGallery);\r
+ if (ref != null){\r
+ result.addSource(null, null, ref, null);\r
+ }\r
+ }\r
+ return result;\r
+ }\r
+ \r
+\r
+ /**\r
+ * Returns the textdata that holds general information about a feature for a taxon description.\r
+ * This is mainly necessary for descriptions that have more than one description element for\r
+ * a given feature such as 'distribution', 'description' or 'common name'. It may also hold\r
+ * for hierarchical features where no description element exists for a higher hierarchie level.\r
+ * Example: the description feature has subfeatures. But some information like authorship, figures,\r
+ * sources need to be added to the description itself.\r
+ * Currently a feature placeholder is marked by a marker of type 'feature placeholder'. Maybe in future\r
+ * there will be a boolean marker in the TextData class itself.\r
+ * @param state \r
+ * @param feature \r
+ * @param taxon\r
+ * @param ref\r
+ * @param createIfNotExists\r
+ * @return\r
+ */\r
+ protected TextData getFeaturePlaceholder(STATE state, DescriptionBase<?> description, Feature feature, boolean createIfNotExists) {\r
+ UUID featurePlaceholderUuid = MarkupTransformer.uuidFeaturePlaceholder;\r
+ for (DescriptionElementBase element : description.getElements()){\r
+ if (element.isInstanceOf(TextData.class)){\r
+ TextData textData = CdmBase.deproxy(element, TextData.class);\r
+ if (textData.getFeature() == null || ! textData.getFeature().equals(feature)){\r
+ continue;\r
+ }\r
+ for (Marker marker : textData.getMarkers()){\r
+ MarkerType markerType = marker.getMarkerType();\r
+ if (markerType != null && \r
+ markerType.getUuid().equals(featurePlaceholderUuid) && \r
+ marker.getValue() == true){\r
+ return textData;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (createIfNotExists){\r
+ TextData newPlaceholder = TextData.NewInstance(feature);\r
+ MarkerType placeholderMarkerType = getMarkerType(state, featurePlaceholderUuid, "Feature Placeholder", "Feature Placeholder", null);\r
+ Marker marker = Marker.NewInstance(placeholderMarkerType, true);\r
+ newPlaceholder.addMarker(marker);\r
+ description.addElement(newPlaceholder);\r
+ return newPlaceholder;\r
+ }else{\r
+ return null;\r
+ }\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * Returns true, if this description has a source with a citation equal to the given reference.\r
+ * Returns true if the given reference is null.\r
+ * @param ref\r
+ * @param description\r
+ */\r
+ private boolean hasCorrespondingSource(Reference ref, TaxonDescription description) {\r
+ if (ref != null){\r
+ for (IdentifiableSource source : description.getSources()){\r
+ if (ref.equals(source.getCitation())){\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+ return true;\r
+ \r
+ }\r
+ \r
+ \r
+ /**\r
+ * Returns the accepted taxon of a {@link TaxonBase taxon base}. <BR>\r
+ * If taxonBase is of type taxon the same object is returned. If taxonBase is of type\r
+ * synonym the accepted taxon is returned if one exists. If no accepted taxon exists\r
+ * <code>null</code> is returned. If multiple accepted taxa exist the one taxon with the \r
+ * same secundum reference is returned. If no such single taxon exists an \r
+ * {@link IllegalStateException illegal state exception} is thrown. \r
+ * @param taxonBase\r
+ * @return\r
+ */\r
+ protected Taxon getAcceptedTaxon(TaxonBase<?> taxonBase) {\r
+ if (taxonBase == null){\r
+ return null;\r
+ }else if(taxonBase.isInstanceOf(Taxon.class)){\r
+ return CdmBase.deproxy(taxonBase, Taxon.class);\r
+ }else if(taxonBase.isInstanceOf(Synonym.class)){\r
+ Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);\r
+ Set<Taxon> acceptedTaxa = synonym.getAcceptedTaxa();\r
+ if (acceptedTaxa.size() == 0){\r
+ return null;\r
+ }else if (acceptedTaxa.size() == 1){\r
+ return acceptedTaxa.iterator().next();\r
+ }else{\r
+ Reference sec = synonym.getSec();\r
+ if (sec != null){\r
+ Set<Taxon> taxaWithSameSec = new HashSet<Taxon>();\r
+ for (Taxon taxon: acceptedTaxa){\r
+ if (sec.equals(taxon.getSec())){\r
+ taxaWithSameSec.add(taxon);\r
+ }\r
+ }\r
+ if (taxaWithSameSec.size() == 1){\r
+ return taxaWithSameSec.iterator().next();\r
+ }\r
+ }\r
+ throw new IllegalStateException("Can't define the one accepted taxon for a synonym out of multiple accept taxa");\r
+ }\r
+ }else{\r
+ throw new IllegalStateException("Unknown TaxonBase subclass: " + taxonBase.getClass().getName());\r
+ }\r
+ }\r
+\r
+ \r
+\r
+ /**\r
+ * Creates \r
+ * @param uriString\r
+ * @param readDataFromUrl\r
+ * @see #READ_MEDIA_DATA\r
+ * @return\r
+ * @throws MalformedURLException\r
+ */\r
+ protected Media getImageMedia(String uriString, boolean readMediaData, boolean isFigure) throws MalformedURLException {\r
+ if( uriString == null){\r
+ return null;\r
+ } else {\r
+ ImageInfo imageInfo = null;\r
+ URI uri;\r
+ try {\r
+ uri = new URI(uriString);\r
+ try {\r
+ if (readMediaData){\r
+ imageInfo = ImageInfo.NewInstance(uri, 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
+ fireWarningEvent(message, "unknown location", 2, 0);\r
+ }\r
+ ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInfo);\r
+ MediaRepresentation representation = MediaRepresentation.NewInstance();\r
+ if(imageInfo != null){\r
+ representation.setMimeType(imageInfo.getMimeType());\r
+ representation.setSuffix(imageInfo.getSuffix());\r
+ }\r
+ representation.addRepresentationPart(imageFile);\r
+ Media media = isFigure ? Figure.NewInstance() : Media.NewInstance();\r
+ media.addRepresentation(representation);\r
+ return media;\r
+ } catch (URISyntaxException e1) {\r
+ String message = "An URISyntaxException occurred when trying to create uri from multimedia objcet string: " + uriString;\r
+ logger.warn(message);\r
+ fireWarningEvent(message, "unknown location", 4, 0);\r
+ return null;\r
+ }\r
+ }\r
+ }\r
+\r
+ \r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff