Project

General

Profile

« Previous | Next » 

Revision c98ea2df

Added by Patrick Plitzner almost 7 years ago

#5448 Add taxa to their respective families

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java
68 68 

  		




  69
  69
  
    
    @Override


  		




  70
  70
  
    
    protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {


  		




  71
  
  
    
        String result = " SELECT * "


  		




  72
  
  
    
                + " FROM V_TAXATLAS_D20_EXPORT t "


  		




  73
  
  
    
                + " WHERE t.NAMNR IN (@IDSET)";


  		




  
  71
  
    
        String result = "select e.*, f.FAMILIE "


  		




  
  72
  
    
                + "from V_TAXATLAS_D20_EXPORT e, V_TAXATLAS_D20_FAMILIEN f "


  		




  
  73
  
    
                + "where e.NAMNR = f.NAMNR and e.NAMNR IN (@IDSET)";


  		




  74
  74
  
    
        result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);


  		




  75
  75
  
    
        return result;


  		




  76
  76
  
    
    }


  		




  77
  77
  
    

  		




  78
  78
  
    
    @Override


  		




  79
  79
  
    
    protected void doInvoke(RedListGefaesspflanzenImportState state) {


  		




  80
  
  
    
        makeClassification("Gesamtliste", state.getConfig().getClassificationUuid(), "Gesamtliste", null, RedListUtil.gesamtListeReferenceUuid, state);


  		




  81
  
  
    
        makeClassification("Checkliste", RedListUtil.checkListClassificationUuid, "Checkliste", null, RedListUtil.checkListReferenceUuid, state);


  		




  
  80
  
    
        Classification gesamtListe = makeClassification("Gesamtliste", state.getConfig().getClassificationUuid(), "Gesamtliste", null, RedListUtil.gesamtListeReferenceUuid, state);


  		




  
  81
  
    
        Classification checkliste = makeClassification("Checkliste", RedListUtil.checkListClassificationUuid, "Checkliste", null, RedListUtil.checkListReferenceUuid, state);


  		




  82
  82
  
    
        makeClassification("E", RedListUtil.uuidClassificationE, "Ehrendorfer", null, RedListUtil.uuidClassificationReferenceE, state);


  		




  83
  83
  
    
        makeClassification("W", RedListUtil.uuidClassificationW, "Wisskirchen (Standardliste)", 1998, RedListUtil.uuidClassificationReferenceW, state);


  		




  84
  84
  
    
        makeClassification("K", RedListUtil.uuidClassificationK, "Korneck (Rote Liste)", 1996, RedListUtil.uuidClassificationReferenceK, state);


  		




  ......




  87
  87
  
    
        makeClassification("R", RedListUtil.uuidClassificationR, "Rothmaler", 2011, RedListUtil.uuidClassificationReferenceR, state);


  		




  88
  88
  
    
        makeClassification("O", RedListUtil.uuidClassificationO, "Oberdorfer", 2001, RedListUtil.uuidClassificationReferenceO, state);


  		




  89
  89
  
    
        makeClassification("S", RedListUtil.uuidClassificationS, "Schmeil-Fitschen", 2011, RedListUtil.uuidClassificationReferenceS, state);


  		




  
  90
  
    
        importFamilies(gesamtListe, checkliste, state);


  		




  90
  91
  
    
        super.doInvoke(state);


  		




  91
  92
  
    
    }


  		




  92
  93
  
    

  		




  93
  94
  
    

  		




  
  95
  
    
    private void importFamilies(Classification gesamtListe, Classification checkliste,


  		




  
  96
  
    
            RedListGefaesspflanzenImportState state) {


  		




  
  97
  
    
        for(UUID uuid:state.getFamilyMap().values()){


  		




  
  98
  
    
            Taxon familyGL = HibernateProxyHelper.deproxy(getTaxonService().load(uuid), Taxon.class);


  		




  
  99
  
    
            Taxon familyCL = (Taxon) familyGL.clone();


  		




  
  100
  
    

  		




  
  101
  
    
            gesamtListe.addChildTaxon(familyGL, null, null);


  		




  
  102
  
    
            familyGL.setSec(gesamtListe.getReference());


  		




  
  103
  
    

  		




  
  104
  
    
            checkliste.addChildTaxon(familyCL, null, null);


  		




  
  105
  
    
            familyCL.setSec(checkliste.getReference());


  		




  
  106
  
    
        }


  		




  
  107
  
    
    }


  		




  
  108
  
    

  		




  94
  109
  
    
    @Override


  		




  95
  110
  
    
    public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {


  		




  96
  111
  
    
        ResultSet rs = partitioner.getResultSet();


  		




  ......




  131
  146
  
    
        String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));


  		




  132
  147
  
    
        String gueltString = rs.getString(RedListUtil.GUELT);


  		




  133
  148
  
    
        String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);


  		




  
  149
  
    
        String familieString = rs.getString(RedListUtil.FAMILIE);


  		




  134
  150
  
    

  		




  135
  151
  
    
        String relationE = rs.getString(RedListUtil.E);


  		




  136
  152
  
    
        String relationW = rs.getString(RedListUtil.W);


  		




  ......




  148
  164
  
    
            RedListUtil.logMessage(id, parentBaseGL+" is no taxon but is a parent of "+taxonBaseGL+" (Gesamtliste)", logger);


  		




  149
  165
  
    
        }


  		




  150
  166
  
    
        Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);


  		




  151
  
  
    
        createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);


  		




  
  167
  
    
        //add to family if no parent found


  		




  
  168
  
    
        if(parentGL==null){


  		




  
  169
  
    
            if(taxonBaseGL.isInstanceOf(Taxon.class)){


  		




  
  170
  
    
                Taxon family = HibernateProxyHelper.deproxy(getTaxonService().load(state.getFamilyMap().get(familieString)), Taxon.class);


  		




  
  171
  
    
                gesamtListeClassification.addParentChild(family, HibernateProxyHelper.deproxy(taxonBaseGL, Taxon.class), null, null);


  		




  
  172
  
    
            }


  		




  
  173
  
    
            else{


  		




  
  174
  
    
                RedListUtil.logMessage(id, taxonBaseGL+" has no parent but is not a taxon.", logger);


  		




  
  175
  
    
            }


  		




  
  176
  
    
        }


  		




  
  177
  
    
        else{


  		




  
  178
  
    
            createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);


  		




  
  179
  
    
        }


  		




  152
  180
  
    

  		




  153
  181
  
    
        //Checkliste


  		




  154
  182
  
    
        TaxonBase<?> taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);


  		




  ......




  157
  185
  
    
            RedListUtil.logMessage(id, parentBaseCL+" is no taxon but is a parent of "+taxonBaseCL+" (Checkliste)", logger);


  		




  158
  186
  
    
        }


  		




  159
  187
  
    
        Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);


  		




  160
  
  
    
        if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist


  		




  161
  
  
    
            createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);


  		




  
  188
  
    
        //add to family if no parent found


  		




  
  189
  
    
        if(parentCL==null){


  		




  
  190
  
    

  		




  
  191
  
    
        }


  		




  
  192
  
    
        else{


  		




  
  193
  
    
            if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist


  		




  
  194
  
    
                createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);


  		




  
  195
  
    
            }


  		




  162
  196
  
    
        }


  		




  163
  197
  
    

  		




  
  198
  
    
        //check uuids


  		




  164
  199
  
    
        if(taxonBaseGL!= null && taxonBaseCL!=null


  		




  165
  200
  
    
                && taxonBaseGL.getUuid().equals(taxonBaseCL.getUuid())){


  		




  166
  201
  
    
            RedListUtil.logMessage(id, "Same UUID for "+taxonBaseGL+ " (Gesamtliste) and "+taxonBaseCL+" (Checkliste)", logger);


  		




  ......




  320
  355
  
    
        return result;


  		




  321
  356
  
    
    }


  		




  322
  357
  
    

  		




  323
  
  
    
    private void makeClassification(String classificationName, UUID classificationUuid, String referenceName, Integer yearPublished, UUID referenceUuid, RedListGefaesspflanzenImportState state) {


  		




  
  358
  
    
    private Classification makeClassification(String classificationName, UUID classificationUuid, String referenceName, Integer yearPublished, UUID referenceUuid, RedListGefaesspflanzenImportState state) {


  		




  324
  359
  
    
        Classification classification = Classification.NewInstance(classificationName, Language.DEFAULT());


  		




  325
  360
  
    
        classification.setUuid(classificationUuid);


  		




  326
  361
  
    
        Reference reference = ReferenceFactory.newGeneric();


  		




  ......




  331
  366
  
    
            reference.setDatePublished(TimePeriod.NewInstance(yearPublished));


  		




  332
  367
  
    
        }


  		




  333
  368
  
    
        getClassificationService().save(classification);


  		




  
  369
  
    
        return classification;


  		




  334
  370
  
    
    }


  		




  335
  371
  
    

  		




  336
  372
  
    
    @Override


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListUtil.java
    
  





  106
  106
  
    
    public static final String EHRD = "EHRD";


  		




  107
  107
  
    
    public static final String WISSK = "WISSK";


  		




  108
  108
  
    

  		




  
  109
  
    
    public static final String FAMILIE = "FAMILIE";


  		




  
  110
  
    

  		




  109
  111
  
    
    public static final String E = "E";


  		




  110
  112
  
    
    public static final String W = "W";


  		




  111
  113
  
    
    public static final String K = "K";


  		












Also available in:  Unified diff