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Revision a81acd75

Added by Katja Luther over 5 years ago

revert commit ff21181c

View differences:

cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/monitor/RemotingProgressMonitorThread.java
47 47
        } catch(Exception ex) {
48 48
            logger.info("Exception in RemotingProgressMonitorThread ", ex);
49 49
            monitor.setResult(ex);
50

  
51 50
            monitor.setIsFailed(true);
52 51
        }
53 52
        monitor.done();
cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifQueryServiceWrapperTest.java
131 131
        GbifQueryServiceWrapper service = new GbifQueryServiceWrapper();
132 132
        try {
133 133
            Collection<GbifResponse> gbifResponse = service.query(query);
134
            if (gbifResponse != null){
135
                Assert.assertEquals("Usually this query retrieves at least two units. " +
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               		"Test failure may also be due to GBIF!" +
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            Assert.assertEquals("Usually this query retrieves at least two units. " +
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            		"Test failure may also be due to GBIF!" +
137 136
            		"Check http://api.gbif.org/v1/occurrence/search?basisOfRecord=PRESERVED_SPECIMEN&limit=100&recordedBy=E.+J.+Palmer&scientificName=Campanula+persicifolia", 2, gbifResponse.size());
138
            }
139 137
        } catch (ClientProtocolException e) {
140 138
            Assert.fail(e.getMessage());
141 139
        } catch (IOException e) {
cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/reference/EndnoteRecordsImportTest.java
66 66
	}
67 67

  
68 68
	@Test
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	@Ignore
70 69
	public void testDoInvokeWithoutExceptions() {
71 70
		defaultImport.invoke(configurator);
72 71
	}
cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/reference/Acantholimon.ris
1

  
2 1
TY  - JOUR
3 2
AU  - Aguilar, J. F.
4 3
AU  - Feliner, G. N.
cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/reference/RisReferenceImportTest-input.ris
1

  
2

  
3

  
1 4
TY  - JOUR
2 5
T1  - Decorsella arborea, a second species in Decorsella (Violaceae), and Decorsella versus Rinorea
3 6
AU  - Jongkind, Carel C. H.
cdmlib-model/pom.xml
78 78
      </dependencies>
79 79
      </plugin>
80 80
    </plugins>
81
    <pluginManagement>
82
      <plugins>
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        <!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
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        <plugin>
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          <groupId>org.eclipse.m2e</groupId>
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          <artifactId>lifecycle-mapping</artifactId>
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          <version>1.0.0</version>
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          <configuration>
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            <lifecycleMappingMetadata>
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              <pluginExecutions>
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                <pluginExecution>
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                  <pluginExecutionFilter>
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                    <groupId>org.apache.maven.plugins</groupId>
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                    <artifactId>maven-antrun-plugin</artifactId>
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                    <versionRange>[1.3,)</versionRange>
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                    <goals>
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                      <goal>run</goal>
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                    </goals>
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                  </pluginExecutionFilter>
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                  <action>
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                    <ignore></ignore>
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                  </action>
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                </pluginExecution>
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              </pluginExecutions>
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            </lifecycleMappingMetadata>
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          </configuration>
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        </plugin>
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      </plugins>
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    </pluginManagement>
110 81
  </build>
111 82
  <dependencies>
112 83
    <dependency>
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java
161 161
    @XmlElementWrapper(name = "Sources", nillable = true)
162 162
    @XmlElement(name = "IdentifiableSource")
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    @OneToMany(fetch = FetchType.LAZY)
164
    @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
164
    @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
165 165
    @Merge(MergeMode.ADD_CLONE)
166 166
    @NotNull
167 167
    private Set<IdentifiableSource> sources = new HashSet<>();
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/SpecimenOrObservationBase.java
442 442
        return this.determinations;
443 443
    }
444 444

  
445
//    public DeterminationEvent getPreferredDetermination() {
446
//        if(determinations == null) {
447
//            return null;
448
//        }
449
//        for (DeterminationEvent determination: determinations){
450
//            if (determination.getPreferredFlag()){
451
//                return determination;
452
//            }
453
//        }
454
//        return null;
455
//    }
456

  
457 445
    public void addDetermination(DeterminationEvent determination) {
458 446
        // FIXME bidirectional integrity. Use protected Determination setter
459 447
        this.determinations.add(determination);
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/Reference.java
704 704
	 * @see 	#getDatePublished()
705 705
	 */
706 706
	@Override
707
	@Transient
708 707
    public void setDatePublished(VerbatimTimePeriod datePublished){
709 708
		this.datePublished = datePublished;
710 709
	}
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java
324 324
     */
325 325
    protected void setParent(TaxonNode parent) {
326 326
        this.parent = parent;
327
//        this.treeIndex = parent.treeIndex() + "#"+this.getId()+"#";
327
//        this.treeIndex = parent.treeIndex() +
328 328
    }
329 329

  
330 330
    // *************** Excluded Note ***************
......
526 526
     */
527 527
    @Transient
528 528
    private void setClassificationRecursively(Classification newClassification) {
529
        try{
530
            if (newClassification == null){
531
            	throw new IllegalArgumentException("New Classification must not be 'null' when setting new classification.");
532
            }
533
        	if(! newClassification.equals(this.getClassification())){
534
                this.setClassification(newClassification);
535
                for(TaxonNode childNode : this.getChildNodes()){
536
                    childNode.setClassificationRecursively(newClassification);
537
                }
529
        if (newClassification == null){
530
        	throw new IllegalArgumentException("New Classification must not be 'null' when setting new classification.");
531
        }
532
    	if(! newClassification.equals(this.getClassification())){
533
            this.setClassification(newClassification);
534
            for(TaxonNode childNode : this.getChildNodes()){
535
                childNode.setClassificationRecursively(newClassification);
538 536
            }
539
        }catch (NullPointerException e){
540
            System.err.println("NPE???");
541 537
        }
542 538
    }
543 539

  
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/common/IoResultBase.java
12 12
import java.util.ArrayList;
13 13
import java.util.List;
14 14

  
15
import org.apache.commons.lang.StringUtils;
15
import org.apache.commons.lang3.StringUtils;
16 16

  
17 17
/**
18 18
 * @author a.mueller
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SortIndexUpdater.java
105 105
	public String createIndexMapQuery(){
106 106
	       String resultsetQuery = "SELECT @id as id, @parentColumn " +
107 107
	                " FROM @tableName " +
108
	              //  " WHERE @parentColumn IS NOT NULL " +
108
	                " WHERE @parentColumn IS NOT NULL " +
109 109
	                " ORDER BY @parentColumn, @sorted";
110 110
	        resultsetQuery = resultsetQuery.replace("@id", idColumn);
111 111
	        resultsetQuery = resultsetQuery.replace("@tableName", tableName);
......
162 162
                }
163 163
                putIndex(id, index, indexMap);
164 164
            }else{
165
                logger.warn("This should not happen");
165 166
                index = baseValue;
166
                putIndex(id, index, indexMap);
167 167
            }
168 168
//          System.out.println(oParentId + "," + id+","+ index+";");
169 169
        }
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v41_47/SchemaUpdater_41_47.java
131 131

  
132 132
        //add blockedBy_id
133 133
        stepName= "Add blockedBy_id to Registration";
134
         firstTableName = "Registration";
135
         secondTableName = "Registration";
136
         attributeName = "blockedBy";
137
         isList = ! IS_LIST;
134
        firstTableName = "Registration";
135
        secondTableName = "Registration";
136
        attributeName = "blockedBy";
137
        isList = ! IS_LIST;
138 138
        step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, null, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);
139 139
        stepList.add(step);
140 140

  
......
160 160
        stepName = "Add structure column to DefinedTermBase (Character)";
161 161
        tableName = "DefinedTermBase";
162 162
        newColumnName = "structure_id";
163
         referencedTable = "FeatureNode";
163
        referencedTable = "FeatureNode";
164 164
        step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
165 165
        stepList.add(step);
166 166

  
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/initializer/AdvancedBeanInitializer.java
90 90
        for (Object bean :beanList){
91 91
            Collections.sort(propertyPaths);
92 92
            for(String propPath : propertyPaths){
93
		            initializePropertyPath(bean, propPath);
93
//		            initializePropertyPath(bean, propPath);
94 94
            }
95 95
        }
96 96

  
cdmlib-remote-webapp/.gitignore
1 1
.externalToolBuilders/
2 2
maven-eclipse.xml
3
/bin/
cdmlib-remote-webapp/ide/eclipse/Jetty Launcher/cdmlib-remote-webapp - run (swagger).launch
20 20
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.config.path.0" value=""/>
21 21
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.config.type.0" value="DEFAULT"/>
22 22
<booleanAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.embedded" value="false"/>
23
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.microVersion" value="6"/>
23
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.microVersion" value="1"/>
24 24
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.minorVersion" value="4"/>
25 25
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.path" value="${jetty-runtime-9}"/>
26 26
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.version" value="JETTY_9_3"/>
......
56 56
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="net.sourceforge.eclipsejetty.launcher.JettyLaunchClassPathProvider"/>
57 57
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="net.sourceforge.eclipsejetty.starter.jetty9.Jetty9LauncherMain"/>
58 58
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="cdmlib-remote-webapp"/>
59
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx500M&#13;&#10;-XX:PermSize=150m&#13;&#10;&#13;&#10;-Dlog4j.configDebug=true&#13;&#10;-Dlog4j.configuration=file:///${system_property:user.home}/.cdmLibrary/log4j.properties&#13;&#10;&#13;&#10;-Dcdm.forceSchemaUpdate=true&#13;&#10;-Dspring.profiles.active=remoting,swagger"/>
59
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx500M&#10;-XX:PermSize=150m&#10;&#10;-Dlog4j.configDebug=true&#10;-Dlog4j.configuration=file:///${system_property:user.home}/.cdmLibrary/log4j.properties&#10;&#10;-Dcdm.forceSchemaUpdate=true&#10;-Dspring.profiles.active=remoting,swagger"/>
60 60
</launchConfiguration>
cdmlib-remote-webapp/ide/eclipse/Jetty Launcher/cdmlib-remote-webapp-unit-test.launch
21 21
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.config.type.0" value="DEFAULT"/>
22 22
<booleanAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.embedded" value="false"/>
23 23
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.microVersion" value="1"/>
24
<<<<<<< HEAD
24 25
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.minorVersion" value="2"/>
25 26
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.path" value="C:\Program Files\jetty-distribution-9.2.14.v20151106"/>
26 27
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.version" value="JETTY_9"/>
28
=======
29
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.minorVersion" value="4"/>
30
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.path" value="${jetty-runtime-9}"/>
31
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.version" value="JETTY_9_3"/>
32
>>>>>>> parent of ff21181c06... mend
27 33
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jmx.enabled" value="false"/>
28 34
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jndi.enabled" value="false"/>
29 35
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jsp.enabled" value="true"/>
cdmlib-remote-webapp/src/main/resources/log4j.properties
29 29
###
30 30
# cdm
31 31
###
32
log4j.logger.eu.etaxonomy.cdm = ERROR
32
log4j.logger.eu.etaxonomy.cdm = INFO
33 33
# 	  avoid vast amount of "getCitation not yet implemented" & "getProblems not yet implemented" messages
34 34
log4j.logger.eu.etaxonomy.cdm.model.name.TaxonName = ERROR
35 35
log4j.logger.eu.etaxonomy.cdm.database.UpdatableRoutingDataSource = INFO
36 36
log4j.logger.eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer = ERROR
37 37
log4j.logger.eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer=ERROR
38
log4j.logger.eu.etaxonomy.cdm.remote.controller = ERROR
38
log4j.logger.eu.etaxonomy.cdm.remote.controller = INFO
39 39
log4j.logger.eu.etaxonomy.cdm.remote.controller.interceptor = WARN
40 40
#log4j.logger.eu.etaxonomy.cdm.remote.json.processor.AbstractCdmBeanProcessor  = DEBUG
41 41
#log4j.logger.eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution=DEBUG
cdmlib-remote/src/main/java/eu/etaxonomy/cdm/opt/config/LoggingConfigurer.java
99 99
    @Override
100 100
    public void afterPropertiesSet() throws Exception {
101 101
        // per instance logfiles disabled, see #6249
102
        configureLogFile();
102
        // configureLogFile();
103 103
        configureInstanceNamePrefix();
104 104
    }
105 105

  

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