Revision 20553b7e
Added by Katja Luther over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsFindIdenticalNamesActivator.java | ||
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| 85 | 85 |
private boolean writeSameNamesToCsvFile( |
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List<PesiMergeObject> mergingObjects, String string) {
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<<<<<<< HEAD |
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/** |
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* @param args |
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*/ |
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public static void main(String[] args) {
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FaunaEuErmsFindIdenticalNamesActivator sc = new FaunaEuErmsFindIdenticalNamesActivator(); |
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CdmApplicationController appCtrFaunaEu = sc.initDb(faunaEuropaeaSource); |
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String sFileName = "C:\\Users\\k.luther\\test"; |
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//CdmApplicationController appCtrErms = sc.initDb(ermsSource); |
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List<String> propertyPaths = new ArrayList<>(); |
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propertyPaths.add("sources.*");
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propertyPaths.add("sources.idInSource");
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propertyPaths.add("sources.idNamespace");
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propertyPaths.add("taxonBases.*");
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propertyPaths.add("taxonBases.relationsFromThisTaxon");
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propertyPaths.add("taxonBases.taxonNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.*");
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propertyPaths.add("taxonBases.taxonNodes.childNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.childNodes.classification.rootNode.childNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.childNodes.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.childNodes.classification.rootNode.childNodes.*");
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System.err.println("Start getIdenticalNames...");
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faunaSec = appCtrFaunaEu.getReferenceService().load(UUID.fromString("6786d863-75d4-4796-b916-c1c3dff4cb70"));
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ermsSec = appCtrFaunaEu.getReferenceService().load(UUID.fromString("7744bc26-f914-42c4-b54a-dd2a030a8bb7"));
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Map<String, List<TaxonName>> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(ermsSec, faunaSec, propertyPaths); |
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List<FaunaEuErmsMerging> mergingObjects = new ArrayList<>(); |
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FaunaEuErmsMerging mergeObject; |
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TaxonName faunaEuTaxName; |
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TaxonName ermsTaxName; |
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System.err.println("Start creating merging objects");
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mergingObjects= sc.createMergeObjects(namesOfIdenticalTaxa, appCtrFaunaEu); |
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boolean resultOK = true; |
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System.err.println("Start creating csv files");
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resultOK = resultOK && sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv"); |
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resultOK = resultOK &&sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv"); |
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resultOK = resultOK &&sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv"); |
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//do not create the phylum file, explanation inside the method writeSameNamesdifferentPhylumToCsv |
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//resultOK = resultOK &&sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv"); |
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resultOK = resultOK &&sc.writeSameNamesDifferentParentToCsv(mergingObjects, sFileName + "parent.csv"); |
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System.err.println("End merging Fauna Europaea and Erms" + resultOK);
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System.exit(0); |
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} |
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private boolean writeSameNamesToCsVFile( |
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List<FaunaEuErmsMerging> mergingObjects, String string) {
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======= |
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>>>>>>> 34743ac779cc3f8570bd9eae6109207adda534ea |
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try{
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FileWriter writer = new FileWriter(string); |
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|
| ... | ... | |
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} |
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} |
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<<<<<<< HEAD |
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private boolean writeSameNamesdifferentPhylumToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
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try |
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{
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//do we really need this?? it is a taxon needed merged like all others? for erms only one taxon has different phylum. (Valencia, but these are not the same taxa -> fish and ribbon worms) |
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======= |
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private boolean writeSameNamesDifferentPhylumToCsv( |
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List<PesiMergeObject> mergingObjects, String sfileName){
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try{
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>>>>>>> 34743ac779cc3f8570bd9eae6109207adda534ea |
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FileWriter writer = new FileWriter(sfileName); |
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//create Header |
| ... | ... | |
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createHeader(writer, firstLine); |
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//write data |
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<<<<<<< HEAD |
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for (FaunaEuErmsMerging merging : mergingObjects){
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//TODO the phyllum is always different doing it this way, maybe we need to merge the phylum taxa first and then |
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======= |
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for (PesiMergeObject merging : mergingObjects){
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//TODO |
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>>>>>>> 34743ac779cc3f8570bd9eae6109207adda534ea |
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if ((merging.getPhylumInErms()== null )^ (merging.getPhylumInFaunaEu()== null)){
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writeCsvLine(writer, merging) ; |
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}else if(!((merging.getPhylumInErms()==null) && (merging.getPhylumInFaunaEu()==null))){
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if(!merging.getPhylumInErms().getNameTitleCache().equals(merging.getPhylumInFaunaEu().getNameTitleCache())){
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if(!merging.getPhylumInErms().equals(merging.getPhylumInFaunaEu())){
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writeCsvLine(writer, merging) ; |
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} |
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} |
| ... | ... | |
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writer.append(';');
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writer.append("id in Fauna Europaea");
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writer.append(';');
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writer.append("name in FE");
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writer.append("name");
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writer.append(';');
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writer.append("author in FE");
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writer.append("author");
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writer.append(';');
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writer.append("rank in FE");
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writer.append("rank");
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writer.append(';');
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writer.append("state in FE");
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writer.append("state");
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writer.append(';');
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writer.append("phylum in FE");
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writer.append("phylum");
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writer.append(';');
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writer.append("parent in FE");
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writer.append("parent");
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writer.append(';');
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writer.append("parent rank in FE");
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writer.append("parent rank");
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writer.append(';');
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writer.append("uuid in Erms");
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writer.append(';');
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writer.append("id in Erms");
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writer.append(';');
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writer.append("name in Erms");
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writer.append("name");
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writer.append(';');
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writer.append("author in Erms");
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writer.append("author");
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writer.append(';');
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writer.append("rank in Erms");
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writer.append("rank");
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writer.append(';');
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writer.append("state in Erms");
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writer.append("state");
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writer.append(';');
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writer.append("phylum in Erms");
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writer.append("phylum");
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writer.append(';');
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writer.append("parent in Erms");
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writer.append("parent");
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writer.append(';');
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writer.append("parent rank in Erms");
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writer.append("parent rank");
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writer.append('\n');
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} |
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| ... | ... | |
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} |
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writer.append(';');
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writer.append(merging.getPhylumInErms() != null? merging.getPhylumInErms().getTitleCache():""); |
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writer.append(merging.getPhylumInErms() != null? merging.getPhylumInErms().getTaxonTitleCache():"");
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writer.append(';');
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writer.append(merging.getParentStringInErms()); |
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writer.append(';');
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| ... | ... | |
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Classification classification1 = appCtr.getClassificationService().load(uuidClassification1); |
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Classification classification2 = appCtr.getClassificationService().load(uuidClassification2); |
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<<<<<<< HEAD |
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} |
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}else{
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mergeObject.setStatInFaunaEu(false); |
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TaxonNode parentNode = getAcceptedNode(faunaEuName); |
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//TODO: ändern mit erweitertem Initializer.. |
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if (parentNode != null){
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TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName()); |
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String parentNameCache = parentName.getNameCache(); |
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mergeObject.setParentStringInFaunaEu(parentNameCache); |
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mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel()); |
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} |
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} |
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mergeObject.setRankInErms(ermsName.getRank().getLabel()); |
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mergeObject.setRankInFaunaEu(faunaEuName.getRank().getLabel()); |
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merge.add(mergeObject); |
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} |
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======= |
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List<PesiMergeObject> merge = new ArrayList<>(); |
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for (String nameCache: names.keySet()){
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createSingleMergeObject(appCtr, merge, nameCache, names.get(nameCache),classification1, classification2); |
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} |
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>>>>>>> 34743ac779cc3f8570bd9eae6109207adda534ea |
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return merge; |
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} |
Also available in: Unified diff
revert wrong merge changes on findIdenticalNameActivator