List of usage examples for org.jdom2 Element getChildText
public String getChildText(final String cname)
From source file:com.bio4j.neo4jdb.programs.ImportUniprot.java
License:Open Source License
private static void importProteinFeatures(XMLElement entryXMLElem, BatchInserter inserter, BatchInserterIndexProvider indexProvider, long currentProteinId) { //-----------------create batch indexes---------------------------------- //---------------------------------------------------------------------- BatchInserterIndex featureTypeNameIndex = indexProvider.nodeIndex(FeatureTypeNode.FEATURE_TYPE_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex nodeTypeIndex = indexProvider.nodeIndex(Bio4jManager.NODE_TYPE_INDEX_NAME, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); //------------------------------------------------------------------------ //--------------------------------features---------------------------------------------------- List<Element> featuresList = entryXMLElem.asJDomElement().getChildren(UniprotStuff.FEATURE_TAG_NAME); for (Element featureElem : featuresList) { String featureTypeSt = featureElem.getAttributeValue(UniprotStuff.FEATURE_TYPE_ATTRIBUTE); //long featureTypeNodeId = indexService.getSingleNode(FeatureTypeNode.FEATURE_TYPE_NAME_INDEX, featureTypeSt); long featureTypeNodeId = -1; IndexHits<Long> featureTypeNameIndexHits = featureTypeNameIndex .get(FeatureTypeNode.FEATURE_TYPE_NAME_INDEX, featureTypeSt); if (featureTypeNameIndexHits.hasNext()) { featureTypeNodeId = featureTypeNameIndexHits.getSingle(); }//from ww w . jav a2s . com featureTypeNameIndexHits.close(); if (featureTypeNodeId < 0) { featureTypeProperties.put(FeatureTypeNode.NAME_PROPERTY, featureTypeSt); featureTypeNodeId = inserter.createNode(featureTypeProperties); //indexService.index(featureTypeNodeId, FeatureTypeNode.FEATURE_TYPE_NAME_INDEX, featureTypeSt); featureTypeNameIndex.add(featureTypeNodeId, MapUtil.map(FeatureTypeNode.FEATURE_TYPE_NAME_INDEX, featureTypeSt)); //---flushing feature type name index---- featureTypeNameIndex.flush(); //---adding feature type node to node_type index---- nodeTypeIndex.add(featureTypeNodeId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, FeatureTypeNode.NODE_TYPE)); } String featureDescSt = featureElem.getAttributeValue(UniprotStuff.FEATURE_DESCRIPTION_ATTRIBUTE); if (featureDescSt == null) { featureDescSt = ""; } String featureIdSt = featureElem.getAttributeValue(UniprotStuff.FEATURE_ID_ATTRIBUTE); if (featureIdSt == null) { featureIdSt = ""; } String featureStatusSt = featureElem.getAttributeValue(UniprotStuff.STATUS_ATTRIBUTE); if (featureStatusSt == null) { featureStatusSt = ""; } String featureEvidenceSt = featureElem.getAttributeValue(UniprotStuff.EVIDENCE_ATTRIBUTE); if (featureEvidenceSt == null) { featureEvidenceSt = ""; } Element locationElem = featureElem.getChild(UniprotStuff.FEATURE_LOCATION_TAG_NAME); Element positionElem = locationElem.getChild(UniprotStuff.FEATURE_POSITION_TAG_NAME); String beginFeatureSt; String endFeatureSt; if (positionElem != null) { beginFeatureSt = positionElem.getAttributeValue(UniprotStuff.FEATURE_POSITION_POSITION_ATTRIBUTE); endFeatureSt = beginFeatureSt; } else { beginFeatureSt = locationElem.getChild(UniprotStuff.FEATURE_LOCATION_BEGIN_TAG_NAME) .getAttributeValue(UniprotStuff.FEATURE_LOCATION_POSITION_ATTRIBUTE); endFeatureSt = locationElem.getChild(UniprotStuff.FEATURE_LOCATION_END_TAG_NAME) .getAttributeValue(UniprotStuff.FEATURE_LOCATION_POSITION_ATTRIBUTE); } if (beginFeatureSt == null) { beginFeatureSt = ""; } if (endFeatureSt == null) { endFeatureSt = ""; } String originalSt = featureElem.getChildText(UniprotStuff.FEATURE_ORIGINAL_TAG_NAME); String variationSt = featureElem.getChildText(UniprotStuff.FEATURE_VARIATION_TAG_NAME); if (originalSt == null) { originalSt = ""; } if (variationSt == null) { variationSt = ""; } String featureRefSt = featureElem.getAttributeValue(UniprotStuff.FEATURE_REF_ATTRIBUTE); if (featureRefSt == null) { featureRefSt = ""; } featureProperties.put(BasicFeatureRel.DESCRIPTION_PROPERTY, featureDescSt); featureProperties.put(BasicFeatureRel.ID_PROPERTY, featureIdSt); featureProperties.put(BasicFeatureRel.EVIDENCE_PROPERTY, featureEvidenceSt); featureProperties.put(BasicFeatureRel.STATUS_PROPERTY, featureStatusSt); featureProperties.put(BasicFeatureRel.BEGIN_PROPERTY, beginFeatureSt); featureProperties.put(BasicFeatureRel.END_PROPERTY, endFeatureSt); featureProperties.put(BasicFeatureRel.ORIGINAL_PROPERTY, originalSt); featureProperties.put(BasicFeatureRel.VARIATION_PROPERTY, variationSt); featureProperties.put(BasicFeatureRel.REF_PROPERTY, featureRefSt); switch (featureTypeSt) { case ActiveSiteFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, activeSiteFeatureRel, featureProperties); break; case BindingSiteFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, bindingSiteFeatureRel, featureProperties); break; case CrossLinkFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, crossLinkFeatureRel, featureProperties); break; case GlycosylationSiteFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, glycosylationSiteFeatureRel, featureProperties); break; case InitiatorMethionineFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, initiatorMethionineFeatureRel, featureProperties); break; case LipidMoietyBindingRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, lipidMoietyBindingRegionFeatureRel, featureProperties); break; case MetalIonBindingSiteFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, metalIonBindingSiteFeatureRel, featureProperties); break; case ModifiedResidueFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, modifiedResidueFeatureRel, featureProperties); break; case NonStandardAminoAcidFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, nonStandardAminoAcidFeatureRel, featureProperties); break; case NonTerminalResidueFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, nonTerminalResidueFeatureRel, featureProperties); break; case PeptideFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, peptideFeatureRel, featureProperties); break; case UnsureResidueFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, unsureResidueFeatureRel, featureProperties); break; case MutagenesisSiteFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, mutagenesisSiteFeatureRel, featureProperties); break; case SequenceVariantFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, sequenceVariantFeatureRel, featureProperties); break; case CalciumBindingRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, calciumBindingRegionFeatureRel, featureProperties); break; case ChainFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, chainFeatureRel, featureProperties); break; case CoiledCoilRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, coiledCoilRegionFeatureRel, featureProperties); break; case CompositionallyBiasedRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, compositionallyBiasedRegionFeatureRel, featureProperties); break; case DisulfideBondFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, disulfideBondFeatureRel, featureProperties); break; case DnaBindingRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, dnaBindingRegionFeatureRel, featureProperties); break; case DomainFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, domainFeatureRel, featureProperties); break; case HelixFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, helixFeatureRel, featureProperties); break; case IntramembraneRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, intramembraneRegionFeatureRel, featureProperties); break; case NonConsecutiveResiduesFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, nonConsecutiveResiduesFeatureRel, featureProperties); break; case NucleotidePhosphateBindingRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, nucleotidePhosphateBindingRegionFeatureRel, featureProperties); break; case PropeptideFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, propeptideFeatureRel, featureProperties); break; case RegionOfInterestFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, regionOfInterestFeatureRel, featureProperties); break; case RepeatFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, repeatFeatureRel, featureProperties); break; case ShortSequenceMotifFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, shortSequenceMotifFeatureRel, featureProperties); break; case SignalPeptideFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, signalPeptideFeatureRel, featureProperties); break; case SpliceVariantFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, spliceVariantFeatureRel, featureProperties); break; case StrandFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, strandFeatureRel, featureProperties); break; case TopologicalDomainFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, topologicalDomainFeatureRel, featureProperties); break; case TransitPeptideFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, transitPeptideFeatureRel, featureProperties); break; case TransmembraneRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, transmembraneRegionFeatureRel, featureProperties); break; case ZincFingerRegionFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, zincFingerRegionFeatureRel, featureProperties); break; case SiteFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, siteFeatureRel, featureProperties); break; case TurnFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, turnFeatureRel, featureProperties); break; case SequenceConflictFeatureRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, featureTypeNodeId, sequenceConflictFeatureRel, featureProperties); break; } } }
From source file:com.bio4j.neo4jdb.programs.ImportUniprot.java
License:Open Source License
private static void importProteinComments(XMLElement entryXMLElem, BatchInserter inserter, BatchInserterIndexProvider indexProvider, long currentProteinId, String proteinSequence, UniprotDataXML uniprotDataXML) { //---------------indexes declaration--------------------------- BatchInserterIndex commentTypeNameIndex = indexProvider.nodeIndex(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex subcellularLocationNameIndex = indexProvider.nodeIndex( SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex isoformIdIndex = indexProvider.nodeIndex(IsoformNode.ISOFORM_ID_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex nodeTypeIndex = indexProvider.nodeIndex(Bio4jManager.NODE_TYPE_INDEX_NAME, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); //----------------------------------------------------------- List<Element> comments = entryXMLElem.asJDomElement().getChildren(UniprotStuff.COMMENT_TAG_NAME); for (Element commentElem : comments) { String commentTypeSt = commentElem.getAttributeValue(UniprotStuff.COMMENT_TYPE_ATTRIBUTE); Element textElem = commentElem.getChild("text"); String commentTextSt = ""; String commentStatusSt = ""; String commentEvidenceSt = ""; if (textElem != null) { commentTextSt = textElem.getText(); commentStatusSt = textElem.getAttributeValue("status"); if (commentStatusSt == null) { commentStatusSt = ""; }//from w w w .j a va2 s . c om commentEvidenceSt = textElem.getAttributeValue("evidence"); if (commentEvidenceSt == null) { commentEvidenceSt = ""; } } commentProperties.put(BasicCommentRel.TEXT_PROPERTY, commentTextSt); commentProperties.put(BasicCommentRel.STATUS_PROPERTY, commentStatusSt); commentProperties.put(BasicCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt); //-----------------COMMENT TYPE NODE RETRIEVING/CREATION---------------------- //long commentTypeId = indexService.getSingleNode(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, commentTypeSt); IndexHits<Long> commentTypeNameIndexHits = commentTypeNameIndex .get(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, commentTypeSt); long commentTypeId = -1; if (commentTypeNameIndexHits.hasNext()) { commentTypeId = commentTypeNameIndexHits.getSingle(); } commentTypeNameIndexHits.close(); if (commentTypeId < 0) { commentTypeProperties.put(CommentTypeNode.NAME_PROPERTY, commentTypeSt); commentTypeId = inserter.createNode(commentTypeProperties); commentTypeNameIndex.add(commentTypeId, MapUtil.map(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, commentTypeSt)); //----flushing the indexation---- commentTypeNameIndex.flush(); //---adding comment type node to node_type index---- nodeTypeIndex.add(commentTypeId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, CommentTypeNode.NODE_TYPE)); } //-----toxic dose---------------- switch (commentTypeSt) { case ToxicDoseCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, toxicDoseCommentRel, commentProperties); break; case CautionCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, cautionCommentRel, commentProperties); break; case CofactorCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, cofactorCommentRel, commentProperties); break; case DiseaseCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, diseaseCommentRel, commentProperties); break; case OnlineInformationCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: onlineInformationCommentProperties.put(OnlineInformationCommentRel.STATUS_PROPERTY, commentStatusSt); onlineInformationCommentProperties.put(OnlineInformationCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt); onlineInformationCommentProperties.put(OnlineInformationCommentRel.TEXT_PROPERTY, commentTextSt); String nameSt = commentElem.getAttributeValue("name"); if (nameSt == null) { nameSt = ""; } String linkSt = ""; Element linkElem = commentElem.getChild("link"); if (linkElem != null) { String uriSt = linkElem.getAttributeValue("uri"); if (uriSt != null) { linkSt = uriSt; } } onlineInformationCommentProperties.put(OnlineInformationCommentRel.NAME_PROPERTY, nameSt); onlineInformationCommentProperties.put(OnlineInformationCommentRel.LINK_PROPERTY, linkSt); inserter.createRelationship(currentProteinId, commentTypeId, onlineInformationCommentRel, onlineInformationCommentProperties); break; case TissueSpecificityCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, tissueSpecificityCommentRel, commentProperties); break; case FunctionCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, functionCommentRel, commentProperties); break; case BiotechnologyCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, biotechnologyCommentRel, commentProperties); break; case SubunitCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, subunitCommentRel, commentProperties); break; case PolymorphismCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, polymorphismCommentRel, commentProperties); break; case DomainCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, domainCommentRel, commentProperties); break; case PostTranslationalModificationCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, postTranslationalModificationCommentRel, commentProperties); break; case CatalyticActivityCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, catalyticActivityCommentRel, commentProperties); break; case DisruptionPhenotypeCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, disruptionPhenotypeCommentRel, commentProperties); break; case BioPhysicoChemicalPropertiesCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: biophysicochemicalCommentProperties.put(BioPhysicoChemicalPropertiesCommentRel.STATUS_PROPERTY, commentStatusSt); biophysicochemicalCommentProperties.put(BioPhysicoChemicalPropertiesCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt); biophysicochemicalCommentProperties.put(BioPhysicoChemicalPropertiesCommentRel.TEXT_PROPERTY, commentTextSt); String phDependenceSt = commentElem.getChildText("phDependence"); String temperatureDependenceSt = commentElem.getChildText("temperatureDependence"); if (phDependenceSt == null) { phDependenceSt = ""; } if (temperatureDependenceSt == null) { temperatureDependenceSt = ""; } String absorptionMaxSt = ""; String absorptionTextSt = ""; Element absorptionElem = commentElem.getChild("absorption"); if (absorptionElem != null) { absorptionMaxSt = absorptionElem.getChildText("max"); absorptionTextSt = absorptionElem.getChildText("text"); if (absorptionMaxSt == null) { absorptionMaxSt = ""; } if (absorptionTextSt == null) { absorptionTextSt = ""; } } String kineticsSt = ""; Element kineticsElem = commentElem.getChild("kinetics"); if (kineticsElem != null) { kineticsSt = new XMLElement(kineticsElem).toString(); } String redoxPotentialSt = ""; String redoxPotentialEvidenceSt = ""; Element redoxPotentialElem = commentElem.getChild("redoxPotential"); if (redoxPotentialElem != null) { redoxPotentialSt = redoxPotentialElem.getText(); redoxPotentialEvidenceSt = redoxPotentialElem.getAttributeValue("evidence"); if (redoxPotentialSt == null) { redoxPotentialSt = ""; } if (redoxPotentialEvidenceSt == null) { redoxPotentialEvidenceSt = ""; } } biophysicochemicalCommentProperties.put( BioPhysicoChemicalPropertiesCommentRel.TEMPERATURE_DEPENDENCE_PROPERTY, temperatureDependenceSt); biophysicochemicalCommentProperties .put(BioPhysicoChemicalPropertiesCommentRel.PH_DEPENDENCE_PROPERTY, phDependenceSt); biophysicochemicalCommentProperties .put(BioPhysicoChemicalPropertiesCommentRel.KINETICS_XML_PROPERTY, kineticsSt); biophysicochemicalCommentProperties .put(BioPhysicoChemicalPropertiesCommentRel.ABSORPTION_MAX_PROPERTY, absorptionMaxSt); biophysicochemicalCommentProperties .put(BioPhysicoChemicalPropertiesCommentRel.ABSORPTION_TEXT_PROPERTY, absorptionTextSt); biophysicochemicalCommentProperties.put( BioPhysicoChemicalPropertiesCommentRel.REDOX_POTENTIAL_EVIDENCE_PROPERTY, redoxPotentialEvidenceSt); biophysicochemicalCommentProperties .put(BioPhysicoChemicalPropertiesCommentRel.REDOX_POTENTIAL_PROPERTY, redoxPotentialSt); inserter.createRelationship(currentProteinId, commentTypeId, bioPhysicoChemicalPropertiesCommentRel, biophysicochemicalCommentProperties); break; case AllergenCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, allergenCommentRel, commentProperties); break; case PathwayCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, pathwayCommentRel, commentProperties); break; case InductionCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, inductionCommentRel, commentProperties); break; case ProteinSubcellularLocationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getSubcellularLocations()) { List<Element> subcLocations = commentElem .getChildren(UniprotStuff.SUBCELLULAR_LOCATION_TAG_NAME); for (Element subcLocation : subcLocations) { List<Element> locations = subcLocation.getChildren(UniprotStuff.LOCATION_TAG_NAME); Element firstLocation = locations.get(0); //long firstLocationId = indexService.getSingleNode(SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX, firstLocation.getTextTrim()); long firstLocationId = -1; IndexHits<Long> firstLocationIndexHits = subcellularLocationNameIndex.get( SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX, firstLocation.getTextTrim()); if (firstLocationIndexHits.hasNext()) { firstLocationId = firstLocationIndexHits.getSingle(); } firstLocationIndexHits.close(); long lastLocationId = firstLocationId; if (firstLocationId < 0) { subcellularLocationProperties.put(SubcellularLocationNode.NAME_PROPERTY, firstLocation.getTextTrim()); lastLocationId = createSubcellularLocationNode(subcellularLocationProperties, inserter, subcellularLocationNameIndex, nodeTypeIndex); //---flushing subcellular location name index--- subcellularLocationNameIndex.flush(); } for (int i = 1; i < locations.size(); i++) { long tempLocationId; IndexHits<Long> tempLocationIndexHits = subcellularLocationNameIndex.get( SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX, locations.get(i).getTextTrim()); if (tempLocationIndexHits.hasNext()) { tempLocationId = tempLocationIndexHits.getSingle(); tempLocationIndexHits.close(); } else { subcellularLocationProperties.put(SubcellularLocationNode.NAME_PROPERTY, locations.get(i).getTextTrim()); tempLocationId = createSubcellularLocationNode(subcellularLocationProperties, inserter, subcellularLocationNameIndex, nodeTypeIndex); subcellularLocationNameIndex.flush(); } inserter.createRelationship(tempLocationId, lastLocationId, subcellularLocationParentRel, null); lastLocationId = tempLocationId; } Element lastLocation = locations.get(locations.size() - 1); String evidenceSt = lastLocation.getAttributeValue(UniprotStuff.EVIDENCE_ATTRIBUTE); String statusSt = lastLocation.getAttributeValue(UniprotStuff.STATUS_ATTRIBUTE); String topologyStatusSt = ""; String topologySt = ""; Element topologyElem = subcLocation.getChild("topology"); if (topologyElem != null) { topologySt = topologyElem.getText(); topologyStatusSt = topologyElem.getAttributeValue("status"); } if (topologyStatusSt == null) { topologyStatusSt = ""; } if (topologySt == null) { topologySt = ""; } if (evidenceSt == null) { evidenceSt = ""; } if (statusSt == null) { statusSt = ""; } proteinSubcellularLocationProperties.put(ProteinSubcellularLocationRel.EVIDENCE_PROPERTY, evidenceSt); proteinSubcellularLocationProperties.put(ProteinSubcellularLocationRel.STATUS_PROPERTY, statusSt); proteinSubcellularLocationProperties.put(ProteinSubcellularLocationRel.TOPOLOGY_PROPERTY, topologySt); proteinSubcellularLocationProperties .put(ProteinSubcellularLocationRel.TOPOLOGY_STATUS_PROPERTY, topologyStatusSt); inserter.createRelationship(currentProteinId, lastLocationId, proteinSubcellularLocationRel, proteinSubcellularLocationProperties); } } break; case UniprotStuff.COMMENT_ALTERNATIVE_PRODUCTS_TYPE: if (uniprotDataXML.getIsoforms()) { List<Element> eventList = commentElem.getChildren("event"); List<Element> isoformList = commentElem.getChildren("isoform"); for (Element isoformElem : isoformList) { String isoformIdSt = isoformElem.getChildText("id"); String isoformNoteSt = isoformElem.getChildText("note"); String isoformNameSt = isoformElem.getChildText("name"); String isoformSeqSt = ""; Element isoSeqElem = isoformElem.getChild("sequence"); if (isoSeqElem != null) { String isoSeqTypeSt = isoSeqElem.getAttributeValue("type"); if (isoSeqTypeSt.equals("displayed")) { isoformSeqSt = proteinSequence; } } if (isoformNoteSt == null) { isoformNoteSt = ""; } if (isoformNameSt == null) { isoformNameSt = ""; } isoformProperties.put(IsoformNode.ID_PROPERTY, isoformIdSt); isoformProperties.put(IsoformNode.NOTE_PROPERTY, isoformNoteSt); isoformProperties.put(IsoformNode.NAME_PROPERTY, isoformNameSt); isoformProperties.put(IsoformNode.SEQUENCE_PROPERTY, isoformSeqSt); //-------------------------------------------------------- //long isoformId = indexService.getSingleNode(IsoformNode.ISOFORM_ID_INDEX, isoformIdSt); long isoformId = -1; IndexHits<Long> isoformIdIndexHits = isoformIdIndex.get(IsoformNode.ISOFORM_ID_INDEX, isoformIdSt); if (isoformIdIndexHits.hasNext()) { isoformId = isoformIdIndexHits.getSingle(); } isoformIdIndexHits.close(); if (isoformId < 0) { isoformId = createIsoformNode(isoformProperties, inserter, isoformIdIndex, nodeTypeIndex); } for (Element eventElem : eventList) { String eventTypeSt = eventElem.getAttributeValue("type"); switch (eventTypeSt) { case AlternativeProductInitiationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(isoformId, alternativeProductInitiationId, isoformEventGeneratorRel, null); break; case AlternativeProductPromoterRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(isoformId, alternativeProductPromoterId, isoformEventGeneratorRel, null); break; case AlternativeProductRibosomalFrameshiftingRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(isoformId, alternativeProductRibosomalFrameshiftingId, isoformEventGeneratorRel, null); break; case AlternativeProductSplicingRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(isoformId, alternativeProductSplicingId, isoformEventGeneratorRel, null); break; } } //protein isoform relationship inserter.createRelationship(currentProteinId, isoformId, proteinIsoformRel, null); } } break; case UniprotStuff.COMMENT_SEQUENCE_CAUTION_TYPE: sequenceCautionProperties.put(BasicProteinSequenceCautionRel.EVIDENCE_PROPERTY, commentEvidenceSt); sequenceCautionProperties.put(BasicProteinSequenceCautionRel.STATUS_PROPERTY, commentStatusSt); sequenceCautionProperties.put(BasicProteinSequenceCautionRel.TEXT_PROPERTY, commentTextSt); Element conflictElem = commentElem.getChild("conflict"); if (conflictElem != null) { String conflictTypeSt = conflictElem.getAttributeValue("type"); String resourceSt = ""; String idSt = ""; String versionSt = ""; ArrayList<String> positionsList = new ArrayList<>(); Element sequenceElem = conflictElem.getChild("sequence"); if (sequenceElem != null) { resourceSt = sequenceElem.getAttributeValue("resource"); if (resourceSt == null) { resourceSt = ""; } idSt = sequenceElem.getAttributeValue("id"); if (idSt == null) { idSt = ""; } versionSt = sequenceElem.getAttributeValue("version"); if (versionSt == null) { versionSt = ""; } } Element locationElem = commentElem.getChild("location"); if (locationElem != null) { Element positionElem = locationElem.getChild("position"); if (positionElem != null) { String tempPos = positionElem.getAttributeValue("position"); if (tempPos != null) { positionsList.add(tempPos); } } } sequenceCautionProperties.put(BasicProteinSequenceCautionRel.RESOURCE_PROPERTY, resourceSt); sequenceCautionProperties.put(BasicProteinSequenceCautionRel.ID_PROPERTY, idSt); sequenceCautionProperties.put(BasicProteinSequenceCautionRel.VERSION_PROPERTY, versionSt); switch (conflictTypeSt) { case ProteinErroneousGeneModelPredictionRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (positionsList.size() > 0) { for (String tempPosition : positionsList) { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, tempPosition); inserter.createRelationship(currentProteinId, seqCautionErroneousGeneModelPredictionId, proteinErroneousGeneModelPredictionRel, sequenceCautionProperties); } } else { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, ""); inserter.createRelationship(currentProteinId, seqCautionErroneousGeneModelPredictionId, proteinErroneousGeneModelPredictionRel, sequenceCautionProperties); } break; case ProteinErroneousInitiationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (positionsList.size() > 0) { for (String tempPosition : positionsList) { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, tempPosition); inserter.createRelationship(currentProteinId, seqCautionErroneousInitiationId, proteinErroneousInitiationRel, sequenceCautionProperties); } } else { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, ""); inserter.createRelationship(currentProteinId, seqCautionErroneousInitiationId, proteinErroneousInitiationRel, sequenceCautionProperties); } break; case ProteinErroneousTranslationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (positionsList.size() > 0) { for (String tempPosition : positionsList) { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, tempPosition); inserter.createRelationship(currentProteinId, seqCautionErroneousTranslationId, proteinErroneousTranslationRel, sequenceCautionProperties); } } else { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, ""); inserter.createRelationship(currentProteinId, seqCautionErroneousTranslationId, proteinErroneousTranslationRel, sequenceCautionProperties); } break; case ProteinErroneousTerminationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (positionsList.size() > 0) { for (String tempPosition : positionsList) { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, tempPosition); inserter.createRelationship(currentProteinId, seqCautionErroneousTerminationId, proteinErroneousTerminationRel, sequenceCautionProperties); } } else { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, ""); inserter.createRelationship(currentProteinId, seqCautionErroneousTerminationId, proteinErroneousTerminationRel, sequenceCautionProperties); } break; case ProteinFrameshiftRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (positionsList.size() > 0) { for (String tempPosition : positionsList) { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, tempPosition); inserter.createRelationship(currentProteinId, seqCautionFrameshiftId, proteinFrameshiftRel, sequenceCautionProperties); } } else { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, ""); inserter.createRelationship(currentProteinId, seqCautionFrameshiftId, proteinFrameshiftRel, sequenceCautionProperties); } break; case ProteinMiscellaneousDiscrepancyRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (positionsList.size() > 0) { for (String tempPosition : positionsList) { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, tempPosition); inserter.createRelationship(currentProteinId, seqCautionMiscellaneousDiscrepancyId, proteinMiscellaneousDiscrepancyRel, sequenceCautionProperties); } } else { sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, ""); inserter.createRelationship(currentProteinId, seqCautionMiscellaneousDiscrepancyId, proteinMiscellaneousDiscrepancyRel, sequenceCautionProperties); } break; } } break; case DevelopmentalStageCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, developmentalStageCommentRel, commentProperties); break; case MiscellaneousCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, miscellaneousCommentRel, commentProperties); break; case SimilarityCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, similarityCommentRel, commentProperties); break; case RnaEditingCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: rnaEditingCommentProperties.put(RnaEditingCommentRel.STATUS_PROPERTY, commentStatusSt); rnaEditingCommentProperties.put(RnaEditingCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt); rnaEditingCommentProperties.put(RnaEditingCommentRel.TEXT_PROPERTY, commentTextSt); List<Element> locationsList = commentElem.getChildren("location"); for (Element tempLoc : locationsList) { String positionSt = tempLoc.getChild("position").getAttributeValue("position"); rnaEditingCommentProperties.put(RnaEditingCommentRel.POSITION_PROPERTY, positionSt); inserter.createRelationship(currentProteinId, commentTypeId, rnaEditingCommentRel, rnaEditingCommentProperties); } break; case PharmaceuticalCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, pharmaceuticalCommentRel, commentProperties); break; case EnzymeRegulationCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: inserter.createRelationship(currentProteinId, commentTypeId, enzymeRegulationCommentRel, commentProperties); break; case MassSpectrometryCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE: String methodSt = commentElem.getAttributeValue("method"); String massSt = commentElem.getAttributeValue("mass"); if (methodSt == null) { methodSt = ""; } if (massSt == null) { massSt = ""; } String beginSt = ""; String endSt = ""; Element locationElem = commentElem.getChild("location"); if (locationElem != null) { Element beginElem = commentElem.getChild("begin"); Element endElem = commentElem.getChild("end"); if (beginElem != null) { beginSt = beginElem.getAttributeValue("position"); } if (endElem != null) { endSt = endElem.getAttributeValue("position"); } } massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.STATUS_PROPERTY, commentStatusSt); massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt); massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.TEXT_PROPERTY, commentTextSt); massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.METHOD_PROPERTY, methodSt); massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.MASS_PROPERTY, massSt); massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.BEGIN_PROPERTY, beginSt); massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.END_PROPERTY, endSt); inserter.createRelationship(currentProteinId, commentTypeId, massSpectrometryCommentRel, massSpectrometryCommentProperties); break; } } }
From source file:com.bio4j.neo4jdb.programs.ImportUniprot.java
License:Open Source License
private static String getProteinFullName(Element proteinElement) { if (proteinElement == null) { return ""; } else {// www .j a v a 2 s .co m Element recElem = proteinElement.getChild(UniprotStuff.PROTEIN_RECOMMENDED_NAME_TAG_NAME); if (recElem == null) { return ""; } else { return recElem.getChildText(UniprotStuff.PROTEIN_FULL_NAME_TAG_NAME); } } }
From source file:com.bio4j.neo4jdb.programs.ImportUniprot.java
License:Open Source License
private static String getProteinShortName(Element proteinElement) { if (proteinElement == null) { return ""; } else {/*from w ww.j a v a2s. c om*/ Element recElem = proteinElement.getChild(UniprotStuff.PROTEIN_RECOMMENDED_NAME_TAG_NAME); if (recElem == null) { return ""; } else { return recElem.getChildText(UniprotStuff.PROTEIN_SHORT_NAME_TAG_NAME); } } }
From source file:com.bio4j.neo4jdb.programs.ImportUniprot.java
License:Open Source License
private static void importProteinCitations(XMLElement entryXMLElem, BatchInserter inserter, BatchInserterIndexProvider indexProvider, long currentProteinId, UniprotDataXML uniprotDataXML) { //-----------------create batch indexes---------------------------------- //---------------------------------------------------------------------- BatchInserterIndex personNameIndex = indexProvider.nodeIndex(PersonNode.PERSON_NAME_FULL_TEXT_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, FULL_TEXT_ST)); BatchInserterIndex consortiumNameIndex = indexProvider.nodeIndex(ConsortiumNode.CONSORTIUM_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex thesisTitleIndex = indexProvider.nodeIndex(ThesisNode.THESIS_TITLE_FULL_TEXT_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, FULL_TEXT_ST)); BatchInserterIndex instituteNameIndex = indexProvider.nodeIndex(InstituteNode.INSTITUTE_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex countryNameIndex = indexProvider.nodeIndex(CountryNode.COUNTRY_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex cityNameIndex = indexProvider.nodeIndex(CityNode.CITY_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex patentNumberIndex = indexProvider.nodeIndex(PatentNode.PATENT_NUMBER_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex bookNameIndex = indexProvider.nodeIndex(BookNode.BOOK_NAME_FULL_TEXT_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, FULL_TEXT_ST)); BatchInserterIndex publisherNameIndex = indexProvider.nodeIndex(PublisherNode.PUBLISHER_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex onlineArticleTitleIndex = indexProvider.nodeIndex( OnlineArticleNode.ONLINE_ARTICLE_TITLE_FULL_TEXT_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, FULL_TEXT_ST)); BatchInserterIndex onlineJournalNameIndex = indexProvider.nodeIndex( OnlineJournalNode.ONLINE_JOURNAL_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex submissionTitleIndex = indexProvider.nodeIndex(SubmissionNode.SUBMISSION_TITLE_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, FULL_TEXT_ST)); BatchInserterIndex articleTitleIndex = indexProvider.nodeIndex(ArticleNode.ARTICLE_TITLE_FULL_TEXT_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, FULL_TEXT_ST)); BatchInserterIndex articleDoiIdIndex = indexProvider.nodeIndex(ArticleNode.ARTICLE_DOI_ID_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex articlePubmedIdIndex = indexProvider.nodeIndex(ArticleNode.ARTICLE_PUBMED_ID_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex articleMedlineIdIndex = indexProvider.nodeIndex(ArticleNode.ARTICLE_MEDLINE_ID_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex journalNameIndex = indexProvider.nodeIndex(JournalNode.JOURNAL_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex nodeTypeIndex = indexProvider.nodeIndex(Bio4jManager.NODE_TYPE_INDEX_NAME, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); BatchInserterIndex dbNameIndex = indexProvider.nodeIndex(DBNode.DB_NAME_INDEX, MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST)); //---------------------------------------------------------------------- //---------------------------------------------------------------------- List<Element> referenceList = entryXMLElem.asJDomElement().getChildren(UniprotStuff.REFERENCE_TAG_NAME); for (Element reference : referenceList) { List<Element> citationsList = reference.getChildren(UniprotStuff.CITATION_TAG_NAME); for (Element citation : citationsList) { String citationType = citation.getAttributeValue(UniprotStuff.DB_REFERENCE_TYPE_ATTRIBUTE); List<Long> authorsPersonNodesIds = new ArrayList<>(); List<Long> authorsConsortiumNodesIds = new ArrayList<>(); List<Element> authorPersonElems = citation.getChild("authorList").getChildren("person"); List<Element> authorConsortiumElems = citation.getChild("authorList").getChildren("consortium"); for (Element person : authorPersonElems) { //long personId = indexService.getSingleNode(PersonNode.PERSON_NAME_INDEX, person.getAttributeValue("name")); long personId = -1; IndexHits<Long> personNameIndexHits = personNameIndex .get(PersonNode.PERSON_NAME_FULL_TEXT_INDEX, person.getAttributeValue("name")); if (personNameIndexHits.hasNext()) { personId = personNameIndexHits.getSingle(); }/*from w w w. j a v a 2 s. c om*/ personNameIndexHits.close(); if (personId < 0) { personProperties.put(PersonNode.NAME_PROPERTY, person.getAttributeValue("name")); personId = createPersonNode(personProperties, inserter, personNameIndex, nodeTypeIndex); //flushing person name index personNameIndex.flush(); } authorsPersonNodesIds.add(personId); } for (Element consortium : authorConsortiumElems) { long consortiumId = -1; IndexHits<Long> consortiumIdIndexHits = consortiumNameIndex .get(ConsortiumNode.CONSORTIUM_NAME_INDEX, consortium.getAttributeValue("name")); if (consortiumIdIndexHits.hasNext()) { consortiumId = consortiumIdIndexHits.getSingle(); } consortiumIdIndexHits.close(); if (consortiumId < 0) { consortiumProperties.put(ConsortiumNode.NAME_PROPERTY, consortium.getAttributeValue("name")); consortiumId = createConsortiumNode(consortiumProperties, inserter, consortiumNameIndex, nodeTypeIndex); //---flushing consortium name index-- consortiumNameIndex.flush(); } authorsConsortiumNodesIds.add(consortiumId); } //---------------------------------------------------------------------------- //-----------------------------THESIS----------------------------------------- switch (citationType) { case ThesisNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getThesis()) { String dateSt = citation.getAttributeValue("date"); String titleSt = citation.getChildText("title"); if (dateSt == null) { dateSt = ""; } if (titleSt == null) { titleSt = ""; } long thesisId = -1; IndexHits<Long> thesisTitleIndexHits = thesisTitleIndex .get(ThesisNode.THESIS_TITLE_FULL_TEXT_INDEX, titleSt); if (thesisTitleIndexHits.hasNext()) { thesisId = thesisTitleIndexHits.getSingle(); } thesisTitleIndexHits.close(); if (thesisId < 0) { thesisProperties.put(ThesisNode.DATE_PROPERTY, dateSt); thesisProperties.put(ThesisNode.TITLE_PROPERTY, titleSt); //---thesis node creation and indexing thesisId = inserter.createNode(thesisProperties); nodeTypeIndex.add(thesisId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, ThesisNode.NODE_TYPE)); thesisTitleIndex.add(thesisId, MapUtil.map(ThesisNode.THESIS_TITLE_FULL_TEXT_INDEX, titleSt)); //flushing thesis title index thesisTitleIndex.flush(); //---authors association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(thesisId, personId, thesisAuthorRel, null); } //-----------institute----------------------------- String instituteSt = citation.getAttributeValue("institute"); String countrySt = citation.getAttributeValue("country"); if (instituteSt != null) { long instituteId = -1; IndexHits<Long> instituteNameIndexHits = instituteNameIndex .get(InstituteNode.INSTITUTE_NAME_INDEX, instituteSt); if (instituteNameIndexHits.hasNext()) { instituteId = instituteNameIndexHits.getSingle(); } instituteNameIndexHits.close(); if (instituteId < 0) { instituteProperties.put(InstituteNode.NAME_PROPERTY, instituteSt); instituteId = createInstituteNode(instituteProperties, inserter, instituteNameIndex, nodeTypeIndex); //flushing institute name index instituteNameIndex.flush(); } if (countrySt != null) { //long countryId = indexService.getSingleNode(CountryNode.COUNTRY_NAME_INDEX, countrySt); long countryId = -1; IndexHits<Long> countryNameIndexHits = countryNameIndex .get(CountryNode.COUNTRY_NAME_INDEX, countrySt); if (countryNameIndexHits.hasNext()) { countryId = countryNameIndexHits.getSingle(); } countryNameIndexHits.close(); if (countryId < 0) { countryProperties.put(CountryNode.NAME_PROPERTY, countrySt); countryId = createCountryNode(countryProperties, inserter, countryNameIndex, nodeTypeIndex); //flushing country name index countryNameIndex.flush(); } inserter.createRelationship(instituteId, countryId, instituteCountryRel, null); } inserter.createRelationship(thesisId, instituteId, thesisInstituteRel, null); } } //--protein citation relationship inserter.createRelationship(thesisId, currentProteinId, thesisProteinCitationRel, null); } //---------------------------------------------------------------------------- //-----------------------------PATENT----------------------------------------- break; case PatentNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getPatents()) { String numberSt = citation.getAttributeValue("number"); String dateSt = citation.getAttributeValue("date"); String titleSt = citation.getChildText("title"); if (dateSt == null) { dateSt = ""; } if (titleSt == null) { titleSt = ""; } if (numberSt == null) { numberSt = ""; } if (!numberSt.equals("")) { long patentId = -1; IndexHits<Long> patentNumberIndexHits = patentNumberIndex .get(PatentNode.PATENT_NUMBER_INDEX, numberSt); if (patentNumberIndexHits.hasNext()) { patentId = patentNumberIndexHits.getSingle(); } patentNumberIndexHits.close(); if (patentId < 0) { patentProperties.put(PatentNode.NUMBER_PROPERTY, numberSt); patentProperties.put(PatentNode.DATE_PROPERTY, dateSt); patentProperties.put(PatentNode.TITLE_PROPERTY, titleSt); //---patent node creation and indexing patentId = inserter.createNode(patentProperties); patentNumberIndex.add(patentId, MapUtil.map(PatentNode.PATENT_NUMBER_INDEX, numberSt)); nodeTypeIndex.add(patentId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, PatentNode.NODE_TYPE)); //---flushing patent number index--- patentNumberIndex.flush(); //---authors association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(patentId, personId, patentAuthorRel, null); } } //--protein citation relationship inserter.createRelationship(patentId, currentProteinId, patentProteinCitationRel, null); } } //---------------------------------------------------------------------------- //-----------------------------SUBMISSION----------------------------------------- break; case SubmissionNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getSubmissions()) { String dateSt = citation.getAttributeValue("date"); String titleSt = citation.getChildText("title"); String dbSt = citation.getAttributeValue("db"); if (dateSt == null) { dateSt = ""; } if (titleSt == null) { titleSt = ""; } submissionProperties.put(SubmissionNode.DATE_PROPERTY, dateSt); submissionProperties.put(SubmissionNode.TITLE_PROPERTY, titleSt); long submissionId; IndexHits<Long> submissionTitleIndexHits = submissionTitleIndex .get(SubmissionNode.SUBMISSION_TITLE_INDEX, titleSt); if (submissionTitleIndexHits.hasNext()) { submissionId = submissionTitleIndexHits.getSingle(); submissionTitleIndexHits.close(); } else { //---submission node creation and indexing submissionId = inserter.createNode(submissionProperties); //--indexing node by type--- nodeTypeIndex.add(submissionId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, SubmissionNode.NODE_TYPE)); if (!titleSt.isEmpty()) { //--indexing node by title--- submissionTitleIndex.add(submissionId, MapUtil.map(SubmissionNode.SUBMISSION_TITLE_INDEX, titleSt)); submissionTitleIndex.flush(); } } //---authors association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(submissionId, personId, submissionAuthorRel, null); } //---authors consortium association----- for (long consortiumId : authorsConsortiumNodesIds) { inserter.createRelationship(submissionId, consortiumId, submissionAuthorRel, null); } if (dbSt != null) { long dbId = -1; IndexHits<Long> dbNameIndexHits = dbNameIndex.get(DBNode.DB_NAME_INDEX, dbSt); if (dbNameIndexHits.hasNext()) { dbId = dbNameIndexHits.getSingle(); } dbNameIndexHits.close(); if (dbId < 0) { dbProperties.put(DBNode.NODE_TYPE_PROPERTY, DBNode.NODE_TYPE); dbProperties.put(DBNode.NAME_PROPERTY, dbSt); dbId = createDbNode(dbProperties, inserter, dbNameIndex, nodeTypeIndex); dbNameIndex.flush(); } //-----submission db relationship----- inserter.createRelationship(submissionId, dbId, submissionDbRel, null); } //--protein citation relationship inserter.createRelationship(submissionId, currentProteinId, submissionProteinCitationRel, null); } //---------------------------------------------------------------------------- //-----------------------------BOOK----------------------------------------- break; case BookNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getBooks()) { String nameSt = citation.getAttributeValue("name"); String dateSt = citation.getAttributeValue("date"); String titleSt = citation.getChildText("title"); String publisherSt = citation.getAttributeValue("publisher"); String firstSt = citation.getAttributeValue("first"); String lastSt = citation.getAttributeValue("last"); String citySt = citation.getAttributeValue("city"); String volumeSt = citation.getAttributeValue("volume"); if (nameSt == null) { nameSt = ""; } if (dateSt == null) { dateSt = ""; } if (titleSt == null) { titleSt = ""; } if (publisherSt == null) { publisherSt = ""; } if (firstSt == null) { firstSt = ""; } if (lastSt == null) { lastSt = ""; } if (citySt == null) { citySt = ""; } if (volumeSt == null) { volumeSt = ""; } long bookId = -1; IndexHits<Long> bookNameIndexHits = bookNameIndex.get(BookNode.BOOK_NAME_FULL_TEXT_INDEX, nameSt); if (bookNameIndexHits.hasNext()) { bookId = bookNameIndexHits.getSingle(); } bookNameIndexHits.close(); if (bookId < 0) { bookProperties.put(BookNode.NAME_PROPERTY, nameSt); bookProperties.put(BookNode.DATE_PROPERTY, dateSt); //---book node creation and indexing bookId = inserter.createNode(bookProperties); bookNameIndex.add(bookId, MapUtil.map(BookNode.BOOK_NAME_FULL_TEXT_INDEX, nameSt)); //--indexing node by type--- nodeTypeIndex.add(bookId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, BookNode.NODE_TYPE)); //--flushing book name index--- bookNameIndex.flush(); //---authors association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(bookId, personId, bookAuthorRel, null); } //---editor association----- Element editorListElem = citation.getChild("editorList"); if (editorListElem != null) { List<Element> editorsElems = editorListElem.getChildren("person"); for (Element person : editorsElems) { //long editorId = indexService.getSingleNode(PersonNode.PERSON_NAME_INDEX, person.getAttributeValue("name")); long editorId = -1; IndexHits<Long> personNameIndexHits = personNameIndex.get( PersonNode.PERSON_NAME_FULL_TEXT_INDEX, person.getAttributeValue("name")); if (personNameIndexHits.hasNext()) { editorId = personNameIndexHits.getSingle(); } personNameIndexHits.close(); if (editorId < 0) { personProperties.put(PersonNode.NAME_PROPERTY, person.getAttributeValue("name")); editorId = createPersonNode(personProperties, inserter, personNameIndex, nodeTypeIndex); } //---flushing person name index--- personNameIndex.flush(); //editor association inserter.createRelationship(bookId, editorId, bookEditorRel, null); } } //----publisher-- if (!publisherSt.equals("")) { //long publisherId = indexService.getSingleNode(PublisherNode.PUBLISHER_NAME_INDEX, publisherSt); long publisherId = -1; IndexHits<Long> publisherNameIndexHits = publisherNameIndex .get(PublisherNode.PUBLISHER_NAME_INDEX, publisherSt); if (publisherNameIndexHits.hasNext()) { publisherId = publisherNameIndexHits.getSingle(); } publisherNameIndexHits.close(); if (publisherId < 0) { publisherProperties.put(PublisherNode.NAME_PROPERTY, publisherSt); publisherId = inserter.createNode(publisherProperties); //--indexing node by type--- nodeTypeIndex.add(publisherId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, PublisherNode.NODE_TYPE)); publisherNameIndex.add(publisherId, MapUtil.map(PublisherNode.PUBLISHER_NAME_INDEX, publisherSt)); //--flushing publisher name index-- publisherNameIndex.flush(); } inserter.createRelationship(bookId, publisherId, bookPublisherRel, null); } //-----city----- if (!citySt.equals("")) { //long cityId = indexService.getSingleNode(CityNode.CITY_NAME_INDEX, citySt); long cityId = -1; IndexHits<Long> cityNameIndexHits = cityNameIndex.get(CityNode.CITY_NAME_INDEX, citySt); if (cityNameIndexHits.hasNext()) { cityId = cityNameIndexHits.getSingle(); } cityNameIndexHits.close(); if (cityId < 0) { cityProperties.put(CityNode.NAME_PROPERTY, citySt); cityId = createCityNode(cityProperties, inserter, cityNameIndex, nodeTypeIndex); //-----flushing city name index--- cityNameIndex.flush(); } inserter.createRelationship(bookId, cityId, bookCityRel, null); } } bookProteinCitationProperties.put(BookProteinCitationRel.FIRST_PROPERTY, firstSt); bookProteinCitationProperties.put(BookProteinCitationRel.LAST_PROPERTY, lastSt); bookProteinCitationProperties.put(BookProteinCitationRel.VOLUME_PROPERTY, volumeSt); bookProteinCitationProperties.put(BookProteinCitationRel.TITLE_PROPERTY, titleSt); //--protein citation relationship inserter.createRelationship(bookId, currentProteinId, bookProteinCitationRel, bookProteinCitationProperties); } //---------------------------------------------------------------------------- //-----------------------------ONLINE ARTICLE----------------------------------------- break; case OnlineArticleNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getOnlineArticles()) { String locatorSt = citation.getChildText("locator"); String nameSt = citation.getAttributeValue("name"); String titleSt = citation.getChildText("title"); if (titleSt == null) { titleSt = ""; } if (nameSt == null) { nameSt = ""; } if (locatorSt == null) { locatorSt = ""; } long onlineArticleId = -1; IndexHits<Long> onlineArticleTitleIndexHits = onlineArticleTitleIndex .get(OnlineArticleNode.ONLINE_ARTICLE_TITLE_FULL_TEXT_INDEX, titleSt); if (onlineArticleTitleIndexHits.hasNext()) { onlineArticleId = onlineArticleTitleIndexHits.getSingle(); } onlineArticleTitleIndexHits.close(); if (onlineArticleId < 0) { onlineArticleProperties.put(OnlineArticleNode.TITLE_PROPERTY, titleSt); onlineArticleId = inserter.createNode(onlineArticleProperties); //--indexing node by type--- nodeTypeIndex.add(onlineArticleId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, OnlineArticleNode.NODE_TYPE)); if (!titleSt.equals("")) { onlineArticleTitleIndex.add(onlineArticleId, MapUtil .map(OnlineArticleNode.ONLINE_ARTICLE_TITLE_FULL_TEXT_INDEX, titleSt)); //-----flushing online article title index--- onlineArticleTitleIndex.flush(); } //---authors person association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(onlineArticleId, personId, onlineArticleAuthorRel, null); } //---authors consortium association----- for (long consortiumId : authorsConsortiumNodesIds) { inserter.createRelationship(onlineArticleId, consortiumId, onlineArticleAuthorRel, null); } //------online journal----------- if (!nameSt.equals("")) { long onlineJournalId = -1; IndexHits<Long> onlineJournalNameIndexHits = onlineJournalNameIndex .get(OnlineJournalNode.ONLINE_JOURNAL_NAME_INDEX, nameSt); if (onlineJournalNameIndexHits.hasNext()) { onlineJournalId = onlineJournalNameIndexHits.getSingle(); } onlineJournalNameIndexHits.close(); if (onlineJournalId < 0) { onlineJournalProperties.put(OnlineJournalNode.NAME_PROPERTY, nameSt); onlineJournalId = inserter.createNode(onlineJournalProperties); //--indexing node by type--- nodeTypeIndex.add(onlineJournalId, MapUtil .map(Bio4jManager.NODE_TYPE_INDEX_NAME, OnlineJournalNode.NODE_TYPE)); onlineJournalNameIndex.add(onlineJournalId, MapUtil.map(OnlineJournalNode.ONLINE_JOURNAL_NAME_INDEX, nameSt)); //---flushing online journal name index--- onlineJournalNameIndex.flush(); } onlineArticleJournalProperties.put(OnlineArticleJournalRel.LOCATOR_PROPERTY, locatorSt); inserter.createRelationship(onlineArticleId, onlineJournalId, onlineArticleJournalRel, onlineArticleJournalProperties); } //---------------------------- } //protein citation inserter.createRelationship(onlineArticleId, currentProteinId, onlineArticleProteinCitationRel, null); } //---------------------------------------------------------------------------- //-----------------------------ARTICLE----------------------------------------- break; case ArticleNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getArticles()) { String journalNameSt = citation.getAttributeValue("name"); String dateSt = citation.getAttributeValue("date"); String titleSt = citation.getChildText("title"); String firstSt = citation.getAttributeValue("first"); String lastSt = citation.getAttributeValue("last"); String volumeSt = citation.getAttributeValue("volume"); String doiSt = ""; String medlineSt = ""; String pubmedSt = ""; if (journalNameSt == null) { journalNameSt = ""; } if (dateSt == null) { dateSt = ""; } if (firstSt == null) { firstSt = ""; } if (lastSt == null) { lastSt = ""; } if (volumeSt == null) { volumeSt = ""; } if (titleSt == null) { titleSt = ""; } List<Element> dbReferences = citation.getChildren("dbReference"); for (Element tempDbRef : dbReferences) { switch (tempDbRef.getAttributeValue("type")) { case "DOI": doiSt = tempDbRef.getAttributeValue("id"); break; case "MEDLINE": medlineSt = tempDbRef.getAttributeValue("id"); break; case "PubMed": pubmedSt = tempDbRef.getAttributeValue("id"); break; } } //long articleId = indexService.getSingleNode(ArticleNode.ARTICLE_TITLE_FULL_TEXT_INDEX, titleSt); long articleId = -1; IndexHits<Long> articleTitleIndexHits = articleTitleIndex .get(ArticleNode.ARTICLE_TITLE_FULL_TEXT_INDEX, titleSt); if (articleTitleIndexHits.hasNext()) { articleId = articleTitleIndexHits.getSingle(); } articleTitleIndexHits.close(); if (articleId < 0) { articleProperties.put(ArticleNode.TITLE_PROPERTY, titleSt); articleProperties.put(ArticleNode.DOI_ID_PROPERTY, doiSt); articleProperties.put(ArticleNode.MEDLINE_ID_PROPERTY, medlineSt); articleProperties.put(ArticleNode.PUBMED_ID_PROPERTY, pubmedSt); articleId = inserter.createNode(articleProperties); //--indexing node by type--- nodeTypeIndex.add(articleId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, ArticleNode.NODE_TYPE)); if (!titleSt.equals("")) { articleTitleIndex.add(articleId, MapUtil.map(ArticleNode.ARTICLE_TITLE_FULL_TEXT_INDEX, titleSt)); //--flushing article title index--- articleTitleIndex.flush(); } //---indexing by medline, doi and pubmed-- if (!doiSt.isEmpty()) { articleDoiIdIndex.add(articleId, MapUtil.map(ArticleNode.ARTICLE_DOI_ID_INDEX, doiSt)); } if (!medlineSt.isEmpty()) { articleMedlineIdIndex.add(articleId, MapUtil.map(ArticleNode.ARTICLE_MEDLINE_ID_INDEX, medlineSt)); } if (!pubmedSt.isEmpty()) { articlePubmedIdIndex.add(articleId, MapUtil.map(ArticleNode.ARTICLE_PUBMED_ID_INDEX, pubmedSt)); } //---authors person association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(articleId, personId, articleAuthorRel, null); } //---authors consortium association----- for (long consortiumId : authorsConsortiumNodesIds) { inserter.createRelationship(articleId, consortiumId, articleAuthorRel, null); } //------journal----------- if (!journalNameSt.equals("")) { //long journalId = indexService.getSingleNode(JournalNode.JOURNAL_NAME_INDEX, journalNameSt); long journalId = -1; IndexHits<Long> journalNameIndexHits = journalNameIndex .get(JournalNode.JOURNAL_NAME_INDEX, journalNameSt); if (journalNameIndexHits.hasNext()) { journalId = journalNameIndexHits.getSingle(); } journalNameIndexHits.close(); if (journalId < 0) { journalProperties.put(JournalNode.NAME_PROPERTY, journalNameSt); journalId = inserter.createNode(journalProperties); //--indexing node by type--- nodeTypeIndex.add(journalId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, JournalNode.NODE_TYPE)); journalNameIndex.add(journalId, MapUtil.map(JournalNode.JOURNAL_NAME_INDEX, journalNameSt)); //----flushing journal name index---- journalNameIndex.flush(); } articleJournalProperties.put(ArticleJournalRel.DATE_PROPERTY, dateSt); articleJournalProperties.put(ArticleJournalRel.FIRST_PROPERTY, firstSt); articleJournalProperties.put(ArticleJournalRel.LAST_PROPERTY, lastSt); articleJournalProperties.put(ArticleJournalRel.VOLUME_PROPERTY, volumeSt); inserter.createRelationship(articleId, journalId, articleJournalRel, articleJournalProperties); } //---------------------------- } //protein citation inserter.createRelationship(articleId, currentProteinId, articleProteinCitationRel, null); } //---------------------------------------------------------------------------- //----------------------UNPUBLISHED OBSERVATIONS----------------------------------------- break; case UnpublishedObservationNode.UNIPROT_ATTRIBUTE_TYPE_VALUE: if (uniprotDataXML.getUnpublishedObservations()) { String dateSt = citation.getAttributeValue("date"); if (dateSt == null) { dateSt = ""; } unpublishedObservationProperties.put(UnpublishedObservationNode.DATE_PROPERTY, dateSt); long unpublishedObservationId = inserter.createNode(unpublishedObservationProperties); //--indexing node by type--- nodeTypeIndex.add(unpublishedObservationId, MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, UnpublishedObservationNode.NODE_TYPE)); //---authors person association----- for (long personId : authorsPersonNodesIds) { inserter.createRelationship(unpublishedObservationId, personId, unpublishedObservationAuthorRel, null); } inserter.createRelationship(unpublishedObservationId, currentProteinId, unpublishedObservationProteinCitationRel, null); } break; } } } }
From source file:com.cats.version.VersionCfgParseAndSave.java
License:Apache License
public List<VersionInfo> getVersionInfo(String fullPath) { SAXBuilder builder = new SAXBuilder(); List<VersionInfo> infos = new ArrayList<VersionInfo>(); try {//from w ww . jav a2 s . c o m Document doc = builder.build(new File(fullPath)); Element root = doc.getRootElement(); List<Element> softEles = root.getChildren("software"); for (Element softEle : softEles) { String appName = softEle.getAttribute("name").getValue(); String versionCode = softEle.getChildText("latest-version-code"); String versionName = softEle.getChildText("latest-version"); String versionPath = softEle.getChildText("latest-version-abspath"); String startupName = softEle.getChildText("latest-version-startup"); Element detailEles = softEle.getChild("latest-version-detail"); List<Element> detailItemEles = detailEles.getChildren("item"); List<VersionInfoDetail> details = new ArrayList<VersionInfoDetail>(); for (Element detailItem : detailItemEles) { String title = detailItem.getAttributeValue("name"); List<Element> detailEleList = detailItem.getChildren("detail"); List<String> detailList = new ArrayList<String>(); for (Element detailEle : detailEleList) { String strDetail = detailEle.getText(); detailList.add(strDetail); } details.add(new VersionInfoDetail(title, detailList)); } Element ignoreEles = softEle.getChild("ignore-files"); List<String> ignoreFiles = new ArrayList<String>(); if (ignoreEles != null) { List<Element> ignoreItems = ignoreEles.getChildren("item"); for (Element ignoreItem : ignoreItems) { ignoreFiles.add(ignoreItem.getText()); } } VersionInfo versionInfo = new VersionInfo(); versionInfo.setAppName(appName); versionInfo.setVersion(versionName); versionInfo.setStartupName(startupName); versionInfo.setVersionCode(Integer.parseInt(versionCode)); versionInfo.setPath(versionPath); versionInfo.setDetails(details); versionInfo.setIgnoreFiles(ignoreFiles); infos.add(versionInfo); } } catch (Exception e) { e.printStackTrace(); return null; } return infos; }
From source file:com.cedarsoft.serialization.test.performance.XmlParserPerformance.java
License:Open Source License
public void benchJdom() { runBenchmark(new Runnable() { @Override//from ww w .j a v a 2s.c om public void run() { try { for (int i = 0; i < SMALL; i++) { Document doc = new SAXBuilder().build(new StringReader(CONTENT_SAMPLE)); Element fileTypeElement = doc.getRootElement(); Element extensionElement = fileTypeElement.getChild("extension"); Extension extension = new Extension(extensionElement.getAttributeValue("delimiter"), extensionElement.getText(), extensionElement.getAttribute("default").getBooleanValue()); FileType fileType = new FileType(fileTypeElement.getChildText("id"), extension, fileTypeElement.getAttribute("dependent").getBooleanValue()); assertNotNull(fileType); } } catch (Exception e) { throw new RuntimeException(e); } } }, 4); }
From source file:com.forum.action.eder.TemaACT.java
private Hilo tema(int id, String url) { String megacadena = ""; Hilo h = new Hilo(); Document document = getDocument(url); Element root = document.getRootElement(); Element temas = root.getChild("temas"); List<Element> child = temas.getChildren(); for (Element e : child) { try {/* ww w.j a v a2 s. co m*/ if (e.getAttribute("id").getIntValue() == id) { h.setTitulo(e.getChildText("titulo")); h.setDetalles(e.getChildText("detalles")); List<Element> e2 = e.getChildren("tags"); for (int i = 0; i < e2.size(); i++) { megacadena += e2.get(i).getValue() + ","; } h.setEtiquetas(megacadena); break; } } catch (DataConversionException ex) { } } return h; }
From source file:com.googlecode.mipnp.extension.rhythmbox.RhythmboxExtension.java
License:Open Source License
private List<MusicTrack> getMusicTracks() { List<MusicTrack> tracks = new ArrayList<MusicTrack>(); Map<String, MusicAlbum> albums = new HashMap<String, MusicAlbum>(); try {//from w ww.j a v a 2s . c om Document document = builder.build(db); Element rootNode = document.getRootElement(); List<Element> list = rootNode.getChildren("entry"); for (Element entry : list) { if (entry.getAttribute("type").getValue().equals("song")) { try { MusicTrack track = new MusicTrack(); track.setTitle(entry.getChildText("title")); track.setArtist(entry.getChildText("artist")); track.setGenre(entry.getChildText("genre")); track.setDuration(Integer.parseInt(entry.getChildText("duration")) * 1000); track.setTrackNumber(Integer.parseInt(entry.getChildText("track-number"))); track.setBitRate(Integer.parseInt(entry.getChildText("bitrate"))); track.setFile(new File(new URI(entry.getChildText("location")))); String strAlbum = entry.getChildText("album"); MusicAlbum album = albums.get(strAlbum); if (album == null) { album = new MusicAlbum(strAlbum, entry.getChildText("album-artist")); albums.put(strAlbum, album); } track.setAlbum(album); tracks.add(track); } catch (NumberFormatException ex) { System.err.println("ERROR: " + ex.getMessage()); } catch (URISyntaxException ex) { System.err.println("ERROR: " + ex.getMessage()); } } } } catch (JDOMException ex) { System.err.println("ERROR: " + ex.getMessage()); } catch (IOException ex) { System.err.println("ERROR: " + ex.getMessage()); } return tracks; }
From source file:com.khodev.oradiff.io.XmlSchemaReader.java
License:Open Source License
private Trigger getTrigger(Element child) { return new Trigger(child.getAttributeValue("name"), child.getAttributeValue("type"), child.getAttributeValue("event"), child.getAttributeValue("table"), child.getChildText("when"), child.getAttributeValue("status"), child.getAttributeValue("description"), child.getChildText("body")); }