/** * Finds a name for the variable. * @param ele element to check * @return a name */ public String getAName(BioPAXElement ele) { String name = null; if (ele instanceof Named) { Named n = (Named) ele; if (n.getDisplayName() != null && n.getDisplayName().length() > 0) name = n.getDisplayName(); else if (n.getStandardName() != null && n.getStandardName().length() > 0) name = n.getStandardName(); else if (!n.getName().isEmpty() && n.getName().iterator().next().length() > 0) name = n.getName().iterator().next(); } if (name == null ) name = ele.getUri(); return name + " (" + ele.getModelInterface().getName().substring( ele.getModelInterface().getName().lastIndexOf(".") + 1) + ")"; } }
if (named.getDisplayName() == null) { if(validation.isFix()) { if (named.getStandardName() != null) { named.setDisplayName(named.getStandardName()); fixed = true; else if (!named.getName().isEmpty()) { String dsp = named.getName().iterator().next(); for (String name : named.getName()) { if (name.length() < dsp.length()) dsp = name; named.setDisplayName(dsp); fixed = true; String name = named.getDisplayName(); if (name != null) { // if existed or was added above Integer max = (named instanceof Provenance) ? 50 : MAX_DISPLAYNAME_LEN;
/** * Gets all names, if any. * * @param bpe BioPAX element * @return Collection of names. */ public static Collection<String> getSynonyms(BioPAXElement bpe) { Collection<String> names = new HashSet<String>(); if(bpe instanceof Named) { names = ((Named)bpe).getName(); } return names; }
/** * Gets the Short Name (or Display Name). * * @param bpe BioPAX element * @return short name field, or null if not available. */ private static String getShortName(BioPAXElement bpe) { String shortName = null; if(bpe instanceof Named) { shortName = ((Named)bpe).getDisplayName(); } return shortName; }
/** * Gets the Name Field. * * @param bpe BioPAX element * @return name field, or null if not available. */ private static String getStandardName(BioPAXElement bpe) { if(bpe instanceof Named) { return ((Named)bpe).getStandardName(); } else return null; }
if (named.getDisplayName() == null) { if(fix) { if (named.getStandardName() != null) { named.setDisplayName(named.getStandardName()); fixed = true; else if (!named.getName().isEmpty()) { String dsp = named.getName().iterator().next(); for (String name : named.getName()) { if (name.length() < dsp.length()) dsp = name; named.setDisplayName(dsp); fixed = true; String name = named.getDisplayName(); if (name != null) { // if existed or was added above Class<? extends BioPAXElement> cl = ((BioPAXElement)named).getModelInterface();
/** * Gets all names, if any present. * * @param bpe BioPAX element * @return Collection of names. */ private static Collection<String> getSynonyms(BioPAXElement bpe) { Collection<String> names = new HashSet<String>(); if(bpe instanceof Named) { names = ((Named)bpe).getName(); } return names; }
/** * Gets the display name of the node * or URI. * * @param bpe BioPAX Element * @return */ public static String getName(BioPAXElement bpe) { String nodeName = null; if(bpe instanceof Named) nodeName = ((Named)bpe).getDisplayName(); return (nodeName == null || nodeName.isEmpty()) ? bpe.getRDFId() : StringEscapeUtils.unescapeHtml(nodeName); }
/** * Gets the Name Field. * * @param bpe BioPAX element * @return name field, or null if not available. */ public static String getStandardName(BioPAXElement bpe) { String stdName = null; if(bpe instanceof Named) { stdName = ((Named)bpe).getStandardName(); } else if(bpe instanceof sequenceFeature) { stdName = ((sequenceFeature)bpe).getNAME(); } else if(bpe instanceof physicalEntityParticipant){ stdName = getStandardName(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof entity) { stdName = ((entity)bpe).getNAME(); } else if(bpe instanceof bioSource) { stdName = ((bioSource)bpe).getNAME(); } else if(bpe instanceof dataSource) { stdName = ((dataSource)bpe).getNAME().toString(); } return stdName; }
if (e.getDisplayName() == null) { if (e.getStandardName() != null) { e.setDisplayName(e.getStandardName()); } else if (!e.getName().isEmpty()) { String dsp = e.getName().iterator().next(); for (String name : e.getName()) { if (name.length() < dsp.length()) dsp = name; e.setDisplayName(dsp);
if (e.getDisplayName() != null && !e.getDisplayName().contains("...")) set.add(e.getDisplayName()); else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { Set<String> names = new TreeSet<String>(); for(String name : e.getName()) { if(!name.contains("...")) names.add(name);
/** * Gets the Short Name (or Display Name). * * @param bpe BioPAX element * @return short name field, or null if not available. */ public static String getShortName(BioPAXElement bpe) { String shortName = null; if(bpe instanceof Named) { shortName = ((Named)bpe).getDisplayName(); } else if(bpe instanceof sequenceFeature) { shortName = ((sequenceFeature)bpe).getSHORT_NAME(); } else if(bpe instanceof physicalEntityParticipant){ // fix PEPs shortName = getShortName(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof entity) { shortName = ((entity)bpe).getSHORT_NAME(); } return shortName; }
if (e.getDisplayName() == null) { if (e.getStandardName() != null) { e.setDisplayName(e.getStandardName()); if (log.isInfoEnabled()) log.info(e + " displayName auto-fix: " + e.getDisplayName() + ". " + extraInfo()); if(validation != null) validation.setFixed(BiopaxValidatorUtils.getId(e), "displayNameRule", "no.display.name", null); } else if (!e.getName().isEmpty()) { String dsp = e.getName().iterator().next(); for (String name : e.getName()) { if (name.length() < dsp.length()) dsp = name; e.setDisplayName(dsp); if (log.isInfoEnabled()) log.info(e + " displayName auto-fix: " + dsp
if (e.getDisplayName() != null && !e.getDisplayName().contains("...")) set.add(e.getDisplayName()); else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { Set<String> names = new TreeSet<String>(); for(String name : e.getName()) { if(!name.contains("...")) names.add(name);
/** * Duplicate names syntax rule: * if a value is set either for the standardName * or displayName, adding it to the name is not necessary * (best practices) * * @param jp * @param name */ @Before("target(org.biopax.paxtools.model.level3.Named) " + "&& ( execution(public void addName(*)) || execution(public void set*(*)) ) " + "&& args(name)") public void adviseAddName(JoinPoint jp, String name) { Named bpe = (Named) jp.getTarget(); if (log.isDebugEnabled()) { log.debug("duplicateNamesControl rule checks: " + bpe + " gets name " + name); } if (bpe.getName().contains(name)) { report(bpe, BiopaxValidatorUtils.getId(bpe), "duplicate.names", "duplicateNamesAdvice", Behavior.WARNING, true, name); } }
/** * Gets synonym names. * * @param bpe BioPAX element * @return Collection of Synonym String Objects. */ public static Collection<String> getSynonymList(BioPAXElement bpe) { Collection<String> names = new HashSet<String>(); if(bpe instanceof Named) { names = ((Named)bpe).getName(); } else if(bpe instanceof sequenceFeature) { names = ((sequenceFeature)bpe).getSYNONYMS(); } else if(bpe instanceof physicalEntityParticipant){ names = getSynonymList(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof entity) { names = ((entity)bpe).getSYNONYMS(); } return names; }