From ac5fb7afc03929649c9345e054de5a043f411f1c Mon Sep 17 00:00:00 2001 From: =?utf8?q?Andreas=20M=C3=BCller?= Date: Thu, 26 Jan 2017 17:02:01 +0100 Subject: [PATCH] ref #6369 adapt existing occurrences of interface to removed generics in cdmlib-app --- .../cdm/io/cyprus/CyprusExcelImport.java | 12 ++-- .../cdm/io/eflora/EfloraTaxonImport.java | 69 +++++++++---------- .../CentralAfricaEricaceaeTaxonImport.java | 28 ++++---- .../ferns/CentralAfricaFernsTaxonImport.java | 10 +-- ...CentralAfricaFernsTaxonRelationImport.java | 14 ++-- 5 files changed, 64 insertions(+), 69 deletions(-) diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java index fc0d62d6..ac46f71b 100644 --- a/app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java +++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusExcelImport.java @@ -32,9 +32,8 @@ import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm; import eu.etaxonomy.cdm.model.description.TaxonDescription; import eu.etaxonomy.cdm.model.description.TextData; import eu.etaxonomy.cdm.model.location.NamedArea; -import eu.etaxonomy.cdm.model.name.BotanicalName; +import eu.etaxonomy.cdm.model.name.INonViralName; import eu.etaxonomy.cdm.model.name.NomenclaturalCode; -import eu.etaxonomy.cdm.model.name.NonViralName; import eu.etaxonomy.cdm.model.name.Rank; import eu.etaxonomy.cdm.model.reference.Reference; import eu.etaxonomy.cdm.model.taxon.Classification; @@ -517,15 +516,14 @@ public class CyprusExcelImport extends ExcelImporterBase { private TaxonBase createTaxon(CyprusImportState state, Rank rank, String taxonNameStr, Class statusClass, NomenclaturalCode nc) { TaxonBase taxonBase; - NonViralName taxonNameBase = null; + INonViralName taxonNameBase = null; if (nc == NomenclaturalCode.ICVCN){ logger.warn("ICVCN not yet supported"); }else{ - taxonNameBase =(NonViralName) nc.getNewTaxonNameInstance(rank); - //NonViralName nonViralName = (NonViralName)taxonNameBase; - INonViralNameParser parser = nameParser;//NonViralNameParserImpl.NewInstance(); - taxonNameBase = (NonViralName)parser.parseFullName(taxonNameStr, nc, rank); + taxonNameBase = nc.getNewTaxonNameInstance(rank); + INonViralNameParser parser = nameParser;//NonViralNameParserImpl.NewInstance(); + taxonNameBase = parser.parseFullName(taxonNameStr, nc, rank); //taxonNameBase.setNameCache(taxonNameStr); diff --git a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java index a6d1cd35..7a1e24ed 100644 --- a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java +++ b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java @@ -58,10 +58,10 @@ import eu.etaxonomy.cdm.model.description.TaxonDescription; import eu.etaxonomy.cdm.model.description.TextData; import eu.etaxonomy.cdm.model.name.BotanicalName; import eu.etaxonomy.cdm.model.name.HomotypicalGroup; +import eu.etaxonomy.cdm.model.name.INonViralName; import eu.etaxonomy.cdm.model.name.NameRelationshipType; import eu.etaxonomy.cdm.model.name.NameTypeDesignation; import eu.etaxonomy.cdm.model.name.NomenclaturalCode; -import eu.etaxonomy.cdm.model.name.NonViralName; import eu.etaxonomy.cdm.model.name.Rank; import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; @@ -610,7 +610,7 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO name = TaxonNameBase.castAndDeproxy(nvn); + String num = null; boolean hasGenusInfo = false; - TeamOrPersonBase lastTeam = null; + TeamOrPersonBase lastTeam = null; //genus List elGenus = XmlHelp.getAttributedChildListWithValue(elNom, "name", "class", "genus"); @@ -1262,19 +1263,19 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO name, String referenceTitle, TeamOrPersonBase lastTeam) { + protected TeamOrPersonBase handleNameUsage(Taxon taxon, INonViralName name, String referenceTitle, TeamOrPersonBase lastTeam) { Reference ref = ReferenceFactory.newGeneric(); referenceTitle = removeStartingSymbols(referenceTitle, ref); @@ -1374,7 +1374,7 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO team = name.getCombinationAuthorship(); if (team == null){ logger.warn("Name has nom. ref. but no author team. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value); }else{ @@ -1575,7 +1575,7 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO elInfraRank, Rank infraRank) { + private Rank handleInfRank(INonViralName name, List elInfraRank, Rank infraRank) { if (elInfraRank.size() == 1){ String strRank = elInfraRank.get(0).getTextNormalize(); try { @@ -1622,7 +1622,7 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO name, Rank infraRank, String value) { + private void handleInfrEpi(INonViralName name, Rank infraRank, String value) { if (infraRank != null && infraRank.isInfraSpecific()){ name.setInfraSpecificEpithet(value); if (CdmUtils.isCapital(value)){ @@ -1647,8 +1647,8 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO name; if (isSynonym){ name = BotanicalName.NewInstance(Rank.SPECIES(), homotypicalGroup); SynonymType synonymType = SynonymType.HETEROTYPIC_SYNONYM_OF(); @@ -1657,7 +1657,7 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO name) { + private void handleInfraspecificEpithet(Element element, String attrValue, INonViralName name) { String value = element.getTextNormalize(); if (value.indexOf("subsp.") != -1){ //TODO genus and species epi @@ -1690,7 +1690,7 @@ public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class); + TeamOrPersonBase refTeam = nomRef.getAuthorship(); if (nameTeam == null ){ logger.warn("Name has nom. ref. but no author team. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value); }else if (refTeam == null ){ @@ -167,7 +163,9 @@ public class CentralAfricaEricaceaeTaxonImport extends EfloraTaxonImport { * @param value */ @Override - protected TeamOrPersonBase handleNameUsage(Taxon taxon, NonViralName name, String referenceTitle, TeamOrPersonBase lastTeam) { + protected TeamOrPersonBase handleNameUsage(Taxon taxon, INonViralName name, + String referenceTitle, TeamOrPersonBase lastTeam) { + Reference ref = ReferenceFactory.newGeneric(); ref.setTitleCache(referenceTitle, true); @@ -190,7 +188,7 @@ public class CentralAfricaEricaceaeTaxonImport extends EfloraTaxonImport { // parseReferenceType(ref); TextData textData = TextData.NewInstance(Feature.CITATION()); - textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, singleRef, microReference, name, null); + textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, singleRef, microReference, (TaxonNameBase) name, null); description.addElement(textData); } return team; @@ -229,7 +227,7 @@ public class CentralAfricaEricaceaeTaxonImport extends EfloraTaxonImport { } - protected TeamOrPersonBase getReferenceAuthor (Reference ref, NonViralName name) { + protected TeamOrPersonBase getReferenceAuthor (Reference ref, INonViralName name) { String titleString = ref.getTitleCache(); String re = "\\(.*\\)"; Pattern pattern = Pattern.compile(re); @@ -248,7 +246,7 @@ public class CentralAfricaEricaceaeTaxonImport extends EfloraTaxonImport { } - private TeamOrPersonBase getAuthorTeam(String authorString, NonViralName name) { + private TeamOrPersonBase getAuthorTeam(String authorString, INonViralName name) { //TODO atomize // TeamOrPersonBase nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class); // String nameTeamTitle = nameTeam == null ? "" : nameTeam.getNomenclaturalTitle(); @@ -367,7 +365,7 @@ public class CentralAfricaEricaceaeTaxonImport extends EfloraTaxonImport { } @Override - protected void handleGenus(String value, TaxonNameBase taxonName) { + protected void handleGenus(String value, INonViralName taxonName) { // do nothing } diff --git a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java index 16b10970..c8954ba2 100644 --- a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java +++ b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java @@ -45,12 +45,12 @@ import eu.etaxonomy.cdm.model.common.CdmBase; import eu.etaxonomy.cdm.model.common.ExtensionType; import eu.etaxonomy.cdm.model.common.TimePeriod; import eu.etaxonomy.cdm.model.name.BotanicalName; +import eu.etaxonomy.cdm.model.name.INonViralName; import eu.etaxonomy.cdm.model.name.NameTypeDesignation; import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; import eu.etaxonomy.cdm.model.name.NomenclaturalCode; import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; -import eu.etaxonomy.cdm.model.name.NonViralName; import eu.etaxonomy.cdm.model.name.Rank; import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; @@ -647,13 +647,13 @@ public class CentralAfricaFernsTaxonImport extends CentralAfricaFernsImportBase if (StringUtils.isNotBlank(referenceString) || StringUtils.isNotBlank(volume) || StringUtils.isNotBlank(pages) || StringUtils.isNotBlank(illustrations) || StringUtils.isNotBlank(datePublishedString) || StringUtils.isNotBlank(paperTitle)){ - NonViralName name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class); + INonViralName name = taxonBase.getName(); Reference reference = ReferenceFactory.newGeneric(); reference.setAuthorship(name.getCombinationAuthorship()); reference.setTitle(referenceString); reference.setVolume(volume); reference.setEdition(part); - Reference inrefernce = null; + Reference inreference = null; //TODO parser TimePeriod datePublished = TimePeriodParser.parseString(datePublishedString); reference.setDatePublished(datePublished); @@ -697,7 +697,7 @@ public class CentralAfricaFernsTaxonImport extends CentralAfricaFernsImportBase TaxonBase taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class); if (StringUtils.isNotBlank(nomRemarksString)){ - NonViralName name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class); + INonViralName name = taxonBase.getName(); parseNomRemark(state, name, nomRemarksString.trim(),taxonStatus, taxonNumber); } return taxonBase; @@ -707,7 +707,7 @@ public class CentralAfricaFernsTaxonImport extends CentralAfricaFernsImportBase } - private void parseNomRemark(CentralAfricaFernsImportState state, NonViralName name, String nomRemarksString, String taxonStatus, String taxonNumber) { + private void parseNomRemark(CentralAfricaFernsImportState state, INonViralName name, String nomRemarksString, String taxonStatus, String taxonNumber) { if (nomRemarksString.equalsIgnoreCase("comb. illeg.")){ name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.COMBINATION_ILLEGITIMATE())); diff --git a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java index 3ba95072..c2b6f168 100644 --- a/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java +++ b/cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java @@ -48,7 +48,7 @@ import eu.etaxonomy.cdm.model.location.NamedArea; import eu.etaxonomy.cdm.model.location.NamedAreaLevel; import eu.etaxonomy.cdm.model.location.NamedAreaType; import eu.etaxonomy.cdm.model.name.BotanicalName; -import eu.etaxonomy.cdm.model.name.NonViralName; +import eu.etaxonomy.cdm.model.name.INonViralName; import eu.etaxonomy.cdm.model.name.Rank; import eu.etaxonomy.cdm.model.name.TaxonNameBase; import eu.etaxonomy.cdm.model.reference.Reference; @@ -142,7 +142,7 @@ public class CentralAfricaFernsTaxonRelationImport extends CentralAfricaFernsIm List taxonList = getTaxonService().list(Taxon.class, null, null, null, propPath ); for (Taxon taxon : taxonList){ - NonViralName nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class); + INonViralName nvn = taxon.getName(); UUID uuid = taxon.getUuid(); String nameCache = nvn.getNameCache(); String titleCache = nvn.getTitleCache(); @@ -401,8 +401,8 @@ public class CentralAfricaFernsTaxonRelationImport extends CentralAfricaFernsIm * @param constructedHigherTaxon */ private Taxon mergeExistingAndConstructedTaxon(CentralAfricaFernsImportState state, Taxon existingTaxon, Taxon constructedTaxon) { - NonViralName constructedName = CdmBase.deproxy(constructedTaxon.getName(), NonViralName.class); - NonViralName existingName = CdmBase.deproxy(existingTaxon.getName(), NonViralName.class); + INonViralName constructedName = constructedTaxon.getName(); + INonViralName existingName = existingTaxon.getName(); if (constructedName.hasAuthors()){ if (! existingName.hasAuthors()){ logger.warn(state.getTaxonNumber() + " - Constrcucted name ("+constructedName.getTitleCache()+") has authors but existing name ("+existingName.getTitleCache()+") has no authors"); @@ -574,7 +574,7 @@ public class CentralAfricaFernsTaxonRelationImport extends CentralAfricaFernsIm * @param name2 * @return */ - private boolean authorsMatch(NonViralName name1, NonViralName name2) { + private boolean authorsMatch(INonViralName name1, INonViralName name2) { String combinationAuthor1 = name1.computeCombinationAuthorNomenclaturalTitle(); String combinationAuthor2 = name2.computeCombinationAuthorNomenclaturalTitle(); String basionymAuthor1 = name1.computeBasionymAuthorNomenclaturalTitle(); @@ -1187,8 +1187,8 @@ public class CentralAfricaFernsTaxonRelationImport extends CentralAfricaFernsIm * @param existingHigherTaxon */ private boolean mergeAuthors_old(Taxon higherTaxon, Taxon existingHigherTaxon) { - NonViralName existingName = CdmBase.deproxy(higherTaxon.getName(), NonViralName.class); - NonViralName newName = CdmBase.deproxy(existingHigherTaxon.getName(), NonViralName.class); + INonViralName existingName = higherTaxon.getName(); + INonViralName newName = existingHigherTaxon.getName(); if (existingName == newName){ return true; } -- 2.34.1