List of usage examples for org.apache.commons.lang StringUtils containsIgnoreCase
public static boolean containsIgnoreCase(String str, String searchStr)
Checks if String contains a search String irrespective of case, handling null.
From source file:ubic.gemma.search.SearchServiceImpl.java
/** * @param settings//ww w.j av a 2s.c om * @return results, if the settings.termUri is populated. This includes gene uris. */ private Map<Class<?>, List<SearchResult>> ontologyUriSearch(SearchSettings settings) { Map<Class<?>, List<SearchResult>> results = new HashMap<Class<?>, List<SearchResult>>(); // 1st check to see if the query is a URI (from an ontology). // Do this by seeing if we can find it in the loaded ontologies. // Escape with general utilities because might not be doing a lucene backed search. (just a hibernate one). String termUri = settings.getTermUri(); if (StringUtils.isBlank(termUri)) { termUri = settings.getQuery(); } if (!termUri.startsWith("http://")) { return results; } OntologyTerm matchingTerm = null; String uriString = null; uriString = StringEscapeUtils.escapeJava(StringUtils.strip(termUri)); if (StringUtils.containsIgnoreCase(uriString, NCBI_GENE)) { // Perhaps is a valid gene URL. Want to search for the gene in gemma. // 1st get objects tagged with the given gene identifier Collection<Class<?>> classesToFilterOn = new HashSet<Class<?>>(); classesToFilterOn.add(ExpressionExperiment.class); Collection<Characteristic> foundCharacteristics = characteristicService.findByUri(classesToFilterOn, uriString); Map<Characteristic, Object> parentMap = characteristicService.getParents(classesToFilterOn, foundCharacteristics); Collection<SearchResult> characteristicOwnerResults = filterCharacteristicOwnersByClass( classesToFilterOn, parentMap); if (!characteristicOwnerResults.isEmpty()) { results.put(ExpressionExperiment.class, new ArrayList<SearchResult>()); results.get(ExpressionExperiment.class).addAll(characteristicOwnerResults); } if (settings.getSearchGenes()) { // Get the gene String ncbiAccessionFromUri = StringUtils.substringAfterLast(uriString, "/"); Gene g = null; try { g = geneService.findByNCBIId(Integer.parseInt(ncbiAccessionFromUri)); } catch (NumberFormatException e) { // ok } if (g != null) { results.put(Gene.class, new ArrayList<SearchResult>()); results.get(Gene.class).add(new SearchResult(g)); } } return results; } /* * Not searching for a gene. */ Collection<SearchResult> matchingResults; Collection<Class<?>> classesToSearch = new HashSet<Class<?>>(); if (settings.getSearchExperiments()) { classesToSearch.add(ExpressionExperiment.class); // not sure ... classesToSearch.add(BioMaterial.class); classesToSearch.add(FactorValue.class); } // this doesn't seem to be implemented yet, LiteratureEvidence and GenericEvidence aren't handled in the // fillValueObjects method downstream /* * if ( settings.getSearchPhenotypes() ) { classesToSearch.add( PhenotypeAssociationImpl.class ); } */ matchingTerm = this.ontologyService.getTerm(uriString); if (matchingTerm == null || matchingTerm.getUri() == null) { /* * Maybe the ontology isn't loaded. Look anyway. */ Map<Characteristic, Object> parentMap = characteristicService.getParents(classesToSearch, characteristicService.findByUri(classesToSearch, uriString)); matchingResults = filterCharacteristicOwnersByClass(classesToSearch, parentMap); } else { log.info("Found ontology term: " + matchingTerm); // Was a URI from a loaded ontology soo get the children. Collection<OntologyTerm> terms2Search4 = matchingTerm.getChildren(true); terms2Search4.add(matchingTerm); matchingResults = this.databaseCharacteristicExactUriSearchForOwners(classesToSearch, terms2Search4); } for (SearchResult searchR : matchingResults) { if (results.containsKey(searchR.getResultClass())) { results.get(searchR.getResultClass()).add(searchR); } else { List<SearchResult> rs = new ArrayList<SearchResult>(); rs.add(searchR); results.put(searchR.getResultClass(), rs); } } return results; }
From source file:uk.ac.ebi.bioinvindex.model.HasReferences.java
/** * It's like {@link #getXrefs(String)}, but uses a containment criterion * /*from ww w . j a va2 s. c o m*/ */ @SuppressWarnings("unchecked") public List<Xref> getXrefsContaining(final String sourceAcc) { return (List<Xref>) CollectionUtils.select(refs, new Predicate() { public boolean evaluate(Object xref) { ReferenceSource source = ((Xref) xref).getSource(); if (source == null) return false; if (sourceAcc == null) return source.getAcc() == null; return StringUtils.containsIgnoreCase(source.getAcc(), sourceAcc); } }); }
From source file:uk.ac.ebi.bioinvindex.utils.processing.ProcessingUtils.java
/** * Finds the biomaterials that contains a given string in the type. When some material is found, does not further the * search downstream if shallowSearch is true. Does not work if you haven't assigned the type to * the materials. When shallowSearch is true takes only the steps from which the end node * directly derives. Results are returned in breadth-first fashion. * /* ww w. j ava 2 s . com*/ */ public static Collection<MaterialNode> findBackwardMaterialNodes(final Node<?, ?> endNode, final String typeStr, final boolean shallowSearch) { Collection<MaterialNode> result = new HashSet<MaterialNode>(); Collection<Processing<?, ?>> downStreamProcessings = (Collection<Processing<?, ?>>) endNode .getDownstreamProcessings(); for (Processing<?, ?> downProc : downStreamProcessings) { for (Node<?, ?> inNode : downProc.getInputNodes()) { if (!(inNode instanceof MaterialNode)) continue; MaterialNode mnode = (MaterialNode) inNode; // Add if the current node is of the requested type Material inMaterial = mnode.getMaterial(); MaterialRole inType = inMaterial.getType(); if (inType != null && StringUtils.containsIgnoreCase(inType.getAcc(), typeStr)) result.add(mnode); } } if (shallowSearch) return result; // It's better to return results in Breath-first fashion for (Processing<?, ?> downProc : downStreamProcessings) for (Node<?, ?> inNode : downProc.getInputNodes()) result.addAll(findBackwardMaterialNodes(inNode, typeStr, shallowSearch)); return result; }
From source file:uk.ac.ebi.bioinvindex.utils.processing.ProcessingUtils.java
/** * Finds all the processing steps applying a given protocol * /*from ww w .ja va 2 s. c om*/ * @param pname protocol name must contain this (AND search, ignored if null) * @param ptype protocol type name must contain this * @param shallowSearch when true takes only the steps from which the end node * directly derives. * @return */ public static Collection<Processing<?, ?>> findBackwardProcessings(final Node<?, ?> endNode, final String ptype, final String pname, final boolean shallowSearch) { Collection<Processing<?, ?>> result = new HashSet<Processing<?, ?>>(); Collection<Processing<?, ?>> downStreamProcessings = (Collection<Processing<?, ?>>) endNode .getDownstreamProcessings(); for (Processing<?, ?> downProc : downStreamProcessings) { for (ProtocolApplication papp : downProc.getProtocolApplications()) { Protocol proto = papp.getProtocol(); String piname = null, pitypeStr = null; if (proto != null) { piname = proto.getName(); ProtocolType pitype = proto.getType(); if (pitype != null) pitypeStr = pitype.getName(); } if ((pname == null || StringUtils.containsIgnoreCase(piname, pname)) && (ptype == null || StringUtils.containsIgnoreCase(pitypeStr, ptype))) { result.add(downProc); break; } } } if (shallowSearch) return result; // We better return results in Breath-first fashion for (Processing<?, ?> downProc : downStreamProcessings) for (Node<?, ?> inNode : downProc.getInputNodes()) result.addAll(findBackwardProcessings(inNode, ptype, pname, shallowSearch)); return result; }
From source file:uk.ac.ebi.bioinvindex.utils.processing.ProcessingUtils.java
/** * Finds all protocol applications needed to produce a certain end node. Filters by protocol type or protocol name * (partial matching supported). When shallowSearch is true takes only the steps from which the end node * directly derives. // w w w . ja va 2 s . c o m * */ public static Collection<ProtocolApplication> findBackwardProtocolApplications(final Node<?, ?> endNode, final String ptype, final String pname, final boolean shallowSearch) { Collection<ProtocolApplication> result = new LinkedList<ProtocolApplication>(); for (Processing<?, ?> proc : findBackwardProcessings(endNode, ptype, pname, shallowSearch)) for (ProtocolApplication papp : proc.getProtocolApplications()) { Protocol proto = papp.getProtocol(); String piname = null, pitypeStr = null; if (proto != null) { piname = proto.getName(); ProtocolType pitype = proto.getType(); if (pitype != null) pitypeStr = pitype.getName(); } if ((pname == null || StringUtils.containsIgnoreCase(piname, pname)) && (ptype == null || StringUtils.containsIgnoreCase(pitypeStr, ptype))) result.add(papp); } return result; }
From source file:uk.ac.ebi.metabolights.utils.sampletab.SampleTabExporter.java
/** * Get additional data from the file, the sample file in ISAcreator is not enough for the sampleDb output * @param sampleData/*ww w. j av a2s . c o m*/ * @param study * @return TRUE if we managed to get and set the sample data from the s_*.txt file(s) */ private boolean setSampleObjectData(SampleData sampleData, Study study) { if (sampleData == null || study == null) return false; //Must have a valid sampleData object and assay information from the study to add to it. //Get additional data from the file, the sample file in ISAcreator is not good enough for the sampleDb List<Map<String, String>> additionalFileData = isaTabReader.getAdditionalData(study, isaTabReader.getStudyFactors(study)); for (Map<String, String> columns : additionalFileData) { SampleNode samplenode = new SampleNode(); //Per sample row in ISA-tab if (columns.containsKey(isaTabReader.SAMPLE_NAME)) { String sampleName = columns.get(isaTabReader.SAMPLE_NAME); samplenode.setNodeName(sampleName); //The proper name of the sample } String organism = null; if (columns.containsKey(isaTabReader.ORGANISM)) { organism = columns.get(isaTabReader.ORGANISM); if (organism == null || organism == "") continue; //Skip this row String termSource = columns.get(isaTabReader.ORGANISM_TERM_SOURCE_REF); String termNumber = tools .cleanTermAttributes(columns.get(isaTabReader.ORGANISM_TERM_ACCESSION_NUMBER)); if (!tools.isInteger(termNumber)) { //Check if the term is a number logger.error("Term number from the sample file is not a number or is empty!"); return false; } Integer termId = new Integer(termNumber); //samplenode.addAttribute(new CharacteristicAttribute(isaTabReader.ORGANISM_HEADER,organism)); OrganismAttribute organismAttribute = new OrganismAttribute(organism, termSource, termId); samplenode.addAttribute(organismAttribute); } if (columns.containsKey(isaTabReader.ORGANISM_PART)) { //TODO, should also reflect the ontology String organismPart = columns.get(isaTabReader.ORGANISM_PART); if (organismPart != "") { //The Organism part column is normally present but with an empty string value if no data recorded, ignore this boolean addStrain = false; for (String subs : subClassification) { if (StringUtils.containsIgnoreCase(organismPart, subs)) { organismPart = cleanStrainName(organismPart, subs); //Remove the 'offending' words addStrain = true; break; //Don't loop through the rest } } if (!organismPart.equals(organism)) { //QuickFix. Make sure that the Organism Part is different from Organism String orgPartHeader = isaTabReader.ORGANISM_PART_HEADER; if (addStrain) orgPartHeader = "strain or line"; samplenode.addAttribute(new CharacteristicAttribute(orgPartHeader, organismPart)); } //Add two new named attributes to capture the ontologies for organism part String termSource = columns.get(isaTabReader.ORGPART_TERM_SOURCE_REF); NamedAttribute orgPartTermSource = new NamedAttribute(isaTabReader.TERM_SOURCE_REF, termSource); samplenode.addAttribute(orgPartTermSource); String termNumber = tools .cleanTermAttributes(columns.get(isaTabReader.ORGPART_TERM_ACCESSION_NUMBER)); NamedAttribute orgPartTermNumber = new NamedAttribute(isaTabReader.TERM_SOURCE_ID, termNumber); samplenode.addAttribute(orgPartTermNumber); } } //TODO, add the study design factors as well //Check what has been used for study desing in the investigation, then add dynamically as "Comment[other]" on the sample List<String> allAttributes = isaTabReader.getStudyFactors(study); for (String attribute : allAttributes) { if (columns.containsKey(attribute)) { CommentAttribute commentAttribute = new CommentAttribute("other", columns.get(attribute)); //commentAttribute.setAttributeValue(columns.get(attribute)); String termSourceHeader = "TSI " + attribute; if (columns.containsKey(termSourceHeader)) { String termSourceId = columns.get(termSourceHeader); commentAttribute.setTermSourceID(termSourceId); if (tools.isInteger(termSourceId)) commentAttribute.setTermSourceIDInteger(new Integer(termSourceId)); } String termSourceRefHeader = "TSR " + attribute; if (columns.containsKey(termSourceRefHeader)) commentAttribute.setTermSourceREF(columns.get(termSourceRefHeader)); if (commentAttribute.getAttributeValue() != "") samplenode.addAttribute(commentAttribute); } } try { sampleData.scd.addNode(samplenode); } catch (Exception e) { logger.error(e.getMessage()); return false; } } return true; }
From source file:uk.ac.edukapp.renderer.LtiRenderer.java
private void setOwner(WidgetInstance widgetInstance, Map<String, String[]> parameters) { boolean isModerator = false; if (parameters.get("roles") != null && parameters.get("roles").length > 0) { for (String role : BASICLTI_ADMIN_ROLES) { if (StringUtils.containsIgnoreCase(parameters.get("roles")[0], role)) isModerator = true;/*from w w w. j a va2s. c o m*/ } } if (isModerator) setPreference(widgetInstance, "moderator", "true"); }