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Revision 37bb08e2

Added by Andreas Müller over 5 years ago

cleanup

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelFactsImport.java
110 110 
	    getVocabularyService().save(newVoc);
111 111 

  		




  112
  112
  
    
	    return newVoc;


  		




  113
  
  
    

  		




  114
  
  
    
//	    try {


  		




  115
  
  
    
//			//TODO work around until service method works


  		




  116
  
  
    
//			TermVocabulary<Feature> featureVocabulary =  BerlinModelTransformer.factCategory2Feature(1).getVocabulary();


  		




  117
  
  
    
//			//TermVocabulary<Feature> vocabulary = getTermService().getVocabulary(vocabularyUuid);


  		




  118
  
  
    
//			return featureVocabulary;


  		




  119
  
  
    
//		} catch (UnknownCdmTypeException e) {


  		




  120
  
  
    
//			logger.error("Feature vocabulary not available. New vocabulary created");


  		




  121
  
  
    
//			return TermVocabulary.NewInstance(TermType.Feature, "User Defined Feature Vocabulary", "User Defined Feature Vocabulary", null, null);


  		




  122
  
  
    
//		}


  		




  123
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	}


  		




  124
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  125
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	private Map<Integer, Feature>  invokeFactCategories(BerlinModelImportState state){


  		




  ......




  320
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	}


  		




  321
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  322
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	@Override


  		




  323
  
  
    
	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {


  		




  
  313
  
    
	public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {


  		




  324
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		boolean success = true ;


  		




  325
  
  
    
		BerlinModelImportConfigurator config = state.getConfig();


  		




  326
  
  
    
		Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();


  		




  
  315
  
    
		Set<TaxonBase> taxaToSave = new HashSet<>();


  		




  327
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		Map<String, TaxonBase> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);


  		




  328
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		Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);


  		




  329
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  ......




  392
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						}


  		




  393
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						if(newTextData == true)	{


  		




  394
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							textData = TextData.NewInstance();


  		




  
  384
  
    
						}else if (textData == null){


  		




  
  385
  
    
						    throw new RuntimeException("Textdata must not be null");  //does not happen, only to avoid potential NPE warnings


  		




  395
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						}


  		




  396
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      app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelOccurrenceImport.java
    
  





  60
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    private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceImport.class);


  		




  61
  61
  
    

  		




  62
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	public static final String NAMESPACE = "Occurrence";


  		




  63
  
  
    
	private static final String EM_AREA_NAMESPACE = "emArea";


  		




  64
  63
  
    

  		




  65
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	private static int modCount = 5000;


  		




  66
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	private static final String pluralString = "occurrences";


  		




  ......




  81
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  82
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	@Override


  		




  83
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	protected String getRecordQuery(BerlinModelImportConfigurator config) {


  		




  84
  
  
    
			String emCode = config.isIncludesAreaEmCode()? ", emArea.EMCode" : "";


  		




  
  83
  
    
			String emCode = config.isIncludesAreaEmCode()? ", ar.EMCode" : "";


  		




  85
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			String strQuery =   //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution


  		




  86
  
  
    
            " SELECT DISTINCT PTaxon.RIdentifier AS taxonId, emOccurrence.OccurrenceId, emOccurrence.Native, emOccurrence.Introduced, " +


  		




  87
  
  
    
            		" emOccurrence.Cultivated, emOccurrence.Notes occNotes, " +


  		




  88
  
  
    
            		" emOccurSumCat.emOccurSumCatId, emOccurSumCat.Short, emOccurSumCat.Description, " +


  		




  89
  
  
    
                	" emOccurSumCat.OutputCode, emArea.AreaId, emArea.TDWGCode " + emCode +


  		




  90
  
  
    
                " FROM emOccurrence INNER JOIN " +


  		




  91
  
  
    
                	" emArea ON emOccurrence.AreaFk = emArea.AreaId INNER JOIN " +


  		




  92
  
  
    
                	" PTaxon ON emOccurrence.PTNameFk = PTaxon.PTNameFk AND emOccurrence.PTRefFk = PTaxon.PTRefFk LEFT OUTER JOIN " +


  		




  93
  
  
    
                	" emOccurSumCat ON emOccurrence.SummaryStatus = emOccurSumCat.emOccurSumCatId LEFT OUTER JOIN " +


  		




  94
  
  
    
                	" emOccurrenceSource ON emOccurrence.OccurrenceId = emOccurrenceSource.OccurrenceFk " +


  		




  95
  
  
    
            " WHERE (emOccurrence.OccurrenceId IN (" + ID_LIST_TOKEN + ")  )" +


  		




  
  85
  
    
                " SELECT DISTINCT pt.RIdentifier AS taxonId, occ.OccurrenceId, occ.Native, occ.Introduced, " +


  		




  
  86
  
    
            		" occ.Cultivated, occ.Notes occNotes, " +


  		




  
  87
  
    
            		" sumcat.emOccurSumCatId, sumcat.Short, sumcat.Description, " +


  		




  
  88
  
    
                	" sumcat.OutputCode, ar.AreaId, ar.TDWGCode " + emCode +


  		




  
  89
  
    
                " FROM emOccurrence occ " +


  		




  
  90
  
    
                	" INNER JOIN emArea ar ON occ.AreaFk = ar.AreaId " +


  		




  
  91
  
    
                	" INNER JOIN PTaxon pt ON occ.PTNameFk = pt.PTNameFk AND occ.PTRefFk = pt.PTRefFk " +


  		




  
  92
  
    
                	" LEFT OUTER JOIN emOccurSumCat sumcat ON occ.SummaryStatus = sumcat.emOccurSumCatId " +


  		




  
  93
  
    
                	" LEFT OUTER JOIN emOccurrenceSource ocs ON occ.OccurrenceId = ocs.OccurrenceFk " +


  		




  
  94
  
    
                " WHERE (occ.OccurrenceId IN (" + ID_LIST_TOKEN + ")  )" +


  		




  96
  95
  
    
                " ORDER BY PTaxon.RIdentifier";


  		




  97
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		return strQuery;


  		




  98
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	}


  		




  99
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  100
  
  
    
//	private Map<Integer, NamedArea> euroMedAreas = new HashMap<>();


  		




  101
  
  
    

  		




  102
  99
  
    

  		




  103
  100
  
    
	@Override


  		




  104
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	public void doInvoke(BerlinModelImportState state) {


  		




  105
  
  
    
//		if (state.getConfig().isUseEmAreaVocabulary()){


  		




  106
  
  
    
//			try {


  		




  107
  
  
    
//				createEuroMedAreas(state);


  		




  108
  
  
    
//			} catch (Exception e) {


  		




  109
  
  
    
//				logger.error("Exception occurred when trying to create euroMed Areas");


  		




  110
  
  
    
//				e.printStackTrace();


  		




  111
  
  
    
//				state.setSuccess(false);


  		




  112
  
  
    
//			}


  		




  113
  
  
    
//		}


  		




  114
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		super.doInvoke(state);


  		




  115
  
  
    
		//reset


  		




  116
  
  
    
//		euroMedAreas = new HashMap<>();


  		




  117
  103
  
    
	}


  		




  118
  104
  
    

  		




  119
  
  
    
    /**


  		




  120
  
  
    
     * @param emCode


  		




  121
  
  
    
     * @return


  		




  122
  
  
    
     */


  		




  123
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    private NamedArea getAreaByAreaId(int areaId) {


  		




  124
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        NamedArea result = null;


  		




  125
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        String areaIdStr = String.valueOf(areaId);


  		




  ......




  156
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	}


  		




  157
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  158
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	@Override


  		




  159
  
  
    
	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {


  		




  
  141
  
    
	public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {


  		




  160
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		boolean success = true;


  		




  161
  
  
    
		Set<TaxonBase> taxaToSave = new HashSet<>();


  		




  
  143
  
    
		@SuppressWarnings("rawtypes")


  		




  
  144
  
    
        Set<TaxonBase> taxaToSave = new HashSet<>();


  		




  162
  145
  
    

  		




  163
  
  
    
		Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);


  		




  
  146
  
    
		@SuppressWarnings("unchecked")


  		




  
  147
  
    
        Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);


  		




  164
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  165
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		ResultSet rs = partitioner.getResultSet();


  		




  166
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  ......




  267
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	 * @throws SQLException


  		




  268
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	 */


  		




  269
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	//Create area list


  		




  270
  
  
    
	private List<NamedArea> makeAreaList(BerlinModelImportState state, ResultSetPartitioner partitioner, ResultSet rs, int occurrenceId) throws SQLException {


  		




  
  254
  
    
	private List<NamedArea> makeAreaList(BerlinModelImportState state,


  		




  
  255
  
    
	        @SuppressWarnings("rawtypes") ResultSetPartitioner partitioner,


  		




  
  256
  
    
	        ResultSet rs, int occurrenceId) throws SQLException {


  		




  271
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  272
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	    List<NamedArea> areas = new ArrayList<>();


  		




  273
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  ......




  329
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			String nameSpace = BerlinModelTaxonImport.NAMESPACE;


  		




  330
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			Class<?> cdmClass = TaxonBase.class;


  		




  331
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			Set<String> idSet = taxonIdSet;


  		




  332
  
  
    
			Map<String, ? extends CdmBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);


  		




  
  318
  
    
			@SuppressWarnings("unchecked")


  		




  
  319
  
    
            Map<String, ? extends CdmBase> objectMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);


  		




  333
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			result.put(nameSpace, objectMap);


  		




  334
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  335
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			return result;


  		












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