test_class.declarator: parser
test_class.modifier: static private
test_class.original_string: static private OrphanetXML2HpoDiseaseModelParser parser;
test_class.type: OrphanetXML2HpoDiseaseModelParser
test_class.var_name: parser
test_class.declarator: diseaseModels
test_class.modifier: static private
test_class.original_string: static private Map<TermId, HpoAnnotationModel> diseaseModels;
test_class.type: Map<TermId, HpoAnnotationModel>
test_class.var_name: diseaseModels
test_class.declarator: veryFrequent = TermId.of("HP:0040281")
test_class.modifier: static private final
test_class.original_string: static private final TermId veryFrequent = TermId.of("HP:0040281");
test_class.type: TermId
test_class.var_name: veryFrequent
test_class.declarator: frequent = TermId.of("HP:0040282")
test_class.modifier: static private final
test_class.original_string: static private final TermId frequent = TermId.of("HP:0040282");
test_class.type: TermId
test_class.var_name: frequent
test_class.file: phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/hpo/OrphanetXML2HpoDiseaseModelParserTest.java
test_class.identifier: OrphanetXML2HpoDiseaseModelParserTest
test_case.body: @Test
    void ifThreeDiseaseModelsRetrieved_thenOk() {
      Map<TermId, HpoAnnotationModel> diseaseModels = parser.getOrphanetDiseaseMap();
      assertEquals(3, diseaseModels.size());
    }
test_case.class_method_signature: OrphanetXML2HpoDiseaseModelParserTest.ifThreeDiseaseModelsRetrieved_thenOk()
test_case.full_signature: @Test void ifThreeDiseaseModelsRetrieved_thenOk()
test_case.identifier: ifThreeDiseaseModelsRetrieved_thenOk
test_case.invocations: getOrphanetDiseaseMap assertEquals size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void ifThreeDiseaseModelsRetrieved_thenOk()
focal_class.declarator: logger = LoggerFactory.getLogger(OrphanetXML2HpoDiseaseModelParser.class)
focal_class.modifier: private final static
focal_class.original_string: private final static Logger logger = LoggerFactory.getLogger(OrphanetXML2HpoDiseaseModelParser.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: orphanetXmlPath
focal_class.modifier: private final
focal_class.original_string: private final String orphanetXmlPath;
focal_class.type: String
focal_class.var_name: orphanetXmlPath
focal_class.declarator: ontology
focal_class.modifier: private final
focal_class.original_string: private final Ontology ontology;
focal_class.type: Ontology
focal_class.var_name: ontology
focal_class.declarator: orphanetBiocurationString
focal_class.modifier: private final
focal_class.original_string: private final String orphanetBiocurationString;
focal_class.type: String
focal_class.var_name: orphanetBiocurationString
focal_class.declarator: orphanetDiseaseMap = new HashMap<>()
focal_class.modifier: private final
focal_class.original_string: private final Map<TermId, HpoAnnotationModel> orphanetDiseaseMap = new HashMap<>();
focal_class.type: Map<TermId, HpoAnnotationModel>
focal_class.var_name: orphanetDiseaseMap
focal_class.declarator: replaceObsoleteTermId
focal_class.modifier: private final
focal_class.original_string: private final boolean replaceObsoleteTermId;
focal_class.type: boolean
focal_class.var_name: replaceObsoleteTermId
focal_class.declarator: DISORDER = "Disorder"
focal_class.modifier: private static final
focal_class.original_string: private static final String DISORDER = "Disorder";
focal_class.type: String
focal_class.var_name: DISORDER
focal_class.declarator: ORPHA_NUMBER = "OrphaNumber"
focal_class.modifier: private static final
focal_class.original_string: private static final String ORPHA_NUMBER = "OrphaNumber";
focal_class.type: String
focal_class.var_name: ORPHA_NUMBER
focal_class.declarator: ORPHA_CODE = "OrphaCode"
focal_class.modifier: private static final
focal_class.original_string: private static final String ORPHA_CODE = "OrphaCode";
focal_class.type: String
focal_class.var_name: ORPHA_CODE
focal_class.declarator: NAME = "Name"
focal_class.modifier: private static final
focal_class.original_string: private static final String NAME = "Name";
focal_class.type: String
focal_class.var_name: NAME
focal_class.declarator: HPO_DISORDER_ASSOCIATION = "HPODisorderAssociation"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_DISORDER_ASSOCIATION = "HPODisorderAssociation";
focal_class.type: String
focal_class.var_name: HPO_DISORDER_ASSOCIATION
focal_class.declarator: DIAGNOSTIC_CRITERIA = "DiagnosticCriteria"
focal_class.modifier: private static final
focal_class.original_string: private static final String DIAGNOSTIC_CRITERIA = "DiagnosticCriteria";
focal_class.type: String
focal_class.var_name: DIAGNOSTIC_CRITERIA
focal_class.declarator: DISORDER_TYPE = "DisorderType"
focal_class.modifier: private static final
focal_class.original_string: private static final String DISORDER_TYPE = "DisorderType";
focal_class.type: String
focal_class.var_name: DISORDER_TYPE
focal_class.declarator: DISORDER_GROUP = "DisorderGroup"
focal_class.modifier: private static final
focal_class.original_string: private static final String DISORDER_GROUP = "DisorderGroup";
focal_class.type: String
focal_class.var_name: DISORDER_GROUP
focal_class.declarator: EXPERT_LINK = "ExpertLink"
focal_class.modifier: private static final
focal_class.original_string: private static final String EXPERT_LINK = "ExpertLink";
focal_class.type: String
focal_class.var_name: EXPERT_LINK
focal_class.declarator: HPO_DISORDER_ASSOCIATION_LIST = "HPODisorderAssociationList"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_DISORDER_ASSOCIATION_LIST = "HPODisorderAssociationList";
focal_class.type: String
focal_class.var_name: HPO_DISORDER_ASSOCIATION_LIST
focal_class.declarator: HPO_DISORDER_SET_STATUS = "HPODisorderSetStatus"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_DISORDER_SET_STATUS = "HPODisorderSetStatus";
focal_class.type: String
focal_class.var_name: HPO_DISORDER_SET_STATUS
focal_class.declarator: HPO_DISORDER_SET_STATUS_LIST = "HPODisorderSetStatusList"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_DISORDER_SET_STATUS_LIST = "HPODisorderSetStatusList";
focal_class.type: String
focal_class.var_name: HPO_DISORDER_SET_STATUS_LIST
focal_class.declarator: HPO_FREQUENCY = "HPOFrequency"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_FREQUENCY = "HPOFrequency";
focal_class.type: String
focal_class.var_name: HPO_FREQUENCY
focal_class.declarator: HPO = "HPO"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO = "HPO";
focal_class.type: String
focal_class.var_name: HPO
focal_class.declarator: HPO_ID = "HPOId"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_ID = "HPOId";
focal_class.type: String
focal_class.var_name: HPO_ID
focal_class.declarator: HPO_TERM = "HPOTerm"
focal_class.modifier: private static final
focal_class.original_string: private static final String HPO_TERM = "HPOTerm";
focal_class.type: String
focal_class.var_name: HPO_TERM
focal_class.declarator: JDBOR = "JDBOR"
focal_class.modifier: private static final
focal_class.original_string: private static final String JDBOR = "JDBOR";
focal_class.type: String
focal_class.var_name: JDBOR
focal_class.declarator: AVAILABILITY = "Availability"
focal_class.modifier: private static final
focal_class.original_string: private static final String AVAILABILITY = "Availability";
focal_class.type: String
focal_class.var_name: AVAILABILITY
focal_class.declarator: FULL_NAME = "FullName"
focal_class.modifier: private static final
focal_class.original_string: private static final String FULL_NAME = "FullName";
focal_class.type: String
focal_class.var_name: FULL_NAME
focal_class.declarator: SHORT_IDENTIFIER = "ShortIdentifier"
focal_class.modifier: private static final
focal_class.original_string: private static final String SHORT_IDENTIFIER = "ShortIdentifier";
focal_class.type: String
focal_class.var_name: SHORT_IDENTIFIER
focal_class.declarator: LEGAL_CODE = "LegalCode"
focal_class.modifier: private static final
focal_class.original_string: private static final String LEGAL_CODE = "LegalCode";
focal_class.type: String
focal_class.var_name: LEGAL_CODE
focal_class.declarator: LICENSE = "Licence"
focal_class.modifier: private static final
focal_class.original_string: private static final String LICENSE = "Licence";
focal_class.type: String
focal_class.var_name: LICENSE
focal_class.declarator: SOURCE = "Source"
focal_class.modifier: private static final
focal_class.original_string: private static final String SOURCE = "Source";
focal_class.type: String
focal_class.var_name: SOURCE
focal_class.declarator: VALIDATION_DATE = "ValidationDate"
focal_class.modifier: private static final
focal_class.original_string: private static final String VALIDATION_DATE = "ValidationDate";
focal_class.type: String
focal_class.var_name: VALIDATION_DATE
focal_class.declarator: VALIDATION_STATUS = "ValidationStatus"
focal_class.modifier: private static final
focal_class.original_string: private static final String VALIDATION_STATUS = "ValidationStatus";
focal_class.type: String
focal_class.var_name: VALIDATION_STATUS
focal_class.declarator: ONLINE = "Online"
focal_class.modifier: private static final
focal_class.original_string: private static final String ONLINE = "Online";
focal_class.type: String
focal_class.var_name: ONLINE
focal_class.declarator: allowableXmlNodeNames = Stream.of(AVAILABILITY,
      DIAGNOSTIC_CRITERIA,
      DISORDER,
      DISORDER_GROUP,
      DISORDER_TYPE,
      EXPERT_LINK,
      FULL_NAME,
      HPO_DISORDER_ASSOCIATION,
      HPO_DISORDER_ASSOCIATION_LIST,
      HPO_DISORDER_SET_STATUS,
      HPO_DISORDER_SET_STATUS_LIST,
      HPO_FREQUENCY,
      HPO_ID,
      HPO,
      HPO_TERM,
      JDBOR,
      LEGAL_CODE,
      LICENSE,
      NAME,
      ONLINE,
      ORPHA_CODE,
      ORPHA_NUMBER,
      SOURCE,
      SHORT_IDENTIFIER,
      VALIDATION_DATE,
      VALIDATION_STATUS)
      .collect(Collectors.toCollection(HashSet::new))
focal_class.modifier: private final
focal_class.original_string: private final Set<String> allowableXmlNodeNames = Stream.of(AVAILABILITY,
      DIAGNOSTIC_CRITERIA,
      DISORDER,
      DISORDER_GROUP,
      DISORDER_TYPE,
      EXPERT_LINK,
      FULL_NAME,
      HPO_DISORDER_ASSOCIATION,
      HPO_DISORDER_ASSOCIATION_LIST,
      HPO_DISORDER_SET_STATUS,
      HPO_DISORDER_SET_STATUS_LIST,
      HPO_FREQUENCY,
      HPO_ID,
      HPO,
      HPO_TERM,
      JDBOR,
      LEGAL_CODE,
      LICENSE,
      NAME,
      ONLINE,
      ORPHA_CODE,
      ORPHA_NUMBER,
      SOURCE,
      SHORT_IDENTIFIER,
      VALIDATION_DATE,
      VALIDATION_STATUS)
      .collect(Collectors.toCollection(HashSet::new));
focal_class.type: Set<String>
focal_class.var_name: allowableXmlNodeNames
focal_class.file: phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/hpo/OrphanetXML2HpoDiseaseModelParser.java
focal_class.identifier: OrphanetXML2HpoDiseaseModelParser
focal_class.class_method_signature: OrphanetXML2HpoDiseaseModelParser.OrphanetXML2HpoDiseaseModelParser(String xmlpath, Ontology onto, boolean tolerant)
focal_class.full_signature: public  OrphanetXML2HpoDiseaseModelParser(String xmlpath, Ontology onto, boolean tolerant)
focal_class.identifier: OrphanetXML2HpoDiseaseModelParser
focal_class.modifiers: public
focal_class.parameters: (String xmlpath, Ontology onto, boolean tolerant)
focal_class.signature:  OrphanetXML2HpoDiseaseModelParser(String xmlpath, Ontology onto, boolean tolerant)
focal_class.class_method_signature: OrphanetXML2HpoDiseaseModelParser.getOrphanetDiseaseMap()
focal_class.full_signature: public Map<TermId, HpoAnnotationModel> getOrphanetDiseaseMap()
focal_class.identifier: getOrphanetDiseaseMap
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Map<TermId, HpoAnnotationModel>
focal_class.signature: Map<TermId, HpoAnnotationModel> getOrphanetDiseaseMap()
focal_class.class_method_signature: OrphanetXML2HpoDiseaseModelParser.string2frequency(String fstring)
focal_class.full_signature: private TermId string2frequency(String fstring)
focal_class.identifier: string2frequency
focal_class.modifiers: private
focal_class.parameters: (String fstring)
focal_class.return: TermId
focal_class.signature: TermId string2frequency(String fstring)
focal_class.class_method_signature: OrphanetXML2HpoDiseaseModelParser.parse()
focal_class.full_signature: @SuppressWarnings("ConstantConditions") private void parse()
focal_class.identifier: parse
focal_class.modifiers: @SuppressWarnings("ConstantConditions") private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parse()
focal_class.class_method_signature: OrphanetXML2HpoDiseaseModelParser.getTodaysDate()
focal_class.full_signature: private String getTodaysDate()
focal_class.identifier: getTodaysDate
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getTodaysDate()
focal_method.body: public Map<TermId, HpoAnnotationModel> getOrphanetDiseaseMap() {
      return this.orphanetDiseaseMap;
    }
focal_method.class_method_signature: OrphanetXML2HpoDiseaseModelParser.getOrphanetDiseaseMap()
focal_method.full_signature: public Map<TermId, HpoAnnotationModel> getOrphanetDiseaseMap()
focal_method.identifier: getOrphanetDiseaseMap
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: Map<TermId, HpoAnnotationModel>
focal_method.signature: Map<TermId, HpoAnnotationModel> getOrphanetDiseaseMap()