Revision a81acd75
Added by Katja Luther over 5 years ago
cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/monitor/RemotingProgressMonitorThread.java | ||
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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 | ||
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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. " + |
|
136 |
"Test failure may also be due to GBIF!" + |
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134 |
Assert.assertEquals("Usually this query retrieves at least two units. " + |
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135 |
"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 | ||
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66 | 66 |
} |
67 | 67 |
|
68 | 68 |
@Test |
69 |
@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 | ||
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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 | ||
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1 |
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2 |
|
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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 | ||
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78 | 78 |
</dependencies> |
79 | 79 |
</plugin> |
80 | 80 |
</plugins> |
81 |
<pluginManagement> |
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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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88 |
<configuration> |
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<lifecycleMappingMetadata> |
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90 |
<pluginExecutions> |
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91 |
<pluginExecution> |
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92 |
<pluginExecutionFilter> |
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<groupId>org.apache.maven.plugins</groupId> |
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<artifactId>maven-antrun-plugin</artifactId> |
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95 |
<versionRange>[1.3,)</versionRange> |
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96 |
<goals> |
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<goal>run</goal> |
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98 |
</goals> |
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99 |
</pluginExecutionFilter> |
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100 |
<action> |
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101 |
<ignore></ignore> |
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</action> |
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</pluginExecution> |
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104 |
</pluginExecutions> |
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</lifecycleMappingMetadata> |
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106 |
</configuration> |
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</plugin> |
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108 |
</plugins> |
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109 |
</pluginManagement> |
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110 | 81 |
</build> |
111 | 82 |
<dependencies> |
112 | 83 |
<dependency> |
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java | ||
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161 | 161 |
@XmlElementWrapper(name = "Sources", nillable = true) |
162 | 162 |
@XmlElement(name = "IdentifiableSource") |
163 | 163 |
@OneToMany(fetch = FetchType.LAZY) |
164 |
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE}) |
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164 |
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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|
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 | ||
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442 | 442 |
return this.determinations; |
443 | 443 |
} |
444 | 444 |
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445 |
// public DeterminationEvent getPreferredDetermination() { |
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446 |
// if(determinations == null) { |
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447 |
// return null; |
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448 |
// } |
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449 |
// for (DeterminationEvent determination: determinations){ |
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450 |
// if (determination.getPreferredFlag()){ |
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451 |
// return determination; |
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452 |
// } |
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453 |
// } |
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454 |
// return null; |
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455 |
// } |
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456 |
|
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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 | ||
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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 | ||
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324 | 324 |
*/ |
325 | 325 |
protected void setParent(TaxonNode parent) { |
326 | 326 |
this.parent = parent; |
327 |
// this.treeIndex = parent.treeIndex() + "#"+this.getId()+"#";
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327 |
// this.treeIndex = parent.treeIndex() + |
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328 | 328 |
} |
329 | 329 |
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330 | 330 |
// *************** Excluded Note *************** |
... | ... | |
526 | 526 |
*/ |
527 | 527 |
@Transient |
528 | 528 |
private void setClassificationRecursively(Classification newClassification) { |
529 |
try{ |
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530 |
if (newClassification == null){ |
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531 |
throw new IllegalArgumentException("New Classification must not be 'null' when setting new classification."); |
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532 |
} |
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if(! newClassification.equals(this.getClassification())){ |
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534 |
this.setClassification(newClassification); |
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535 |
for(TaxonNode childNode : this.getChildNodes()){ |
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536 |
childNode.setClassificationRecursively(newClassification); |
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} |
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529 |
if (newClassification == null){ |
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throw new IllegalArgumentException("New Classification must not be 'null' when setting new classification."); |
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531 |
} |
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532 |
if(! newClassification.equals(this.getClassification())){ |
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this.setClassification(newClassification); |
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534 |
for(TaxonNode childNode : this.getChildNodes()){ |
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535 |
childNode.setClassificationRecursively(newClassification); |
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538 | 536 |
} |
539 |
}catch (NullPointerException e){ |
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540 |
System.err.println("NPE???"); |
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541 | 537 |
} |
542 | 538 |
} |
543 | 539 |
|
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/common/IoResultBase.java | ||
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12 | 12 |
import java.util.ArrayList; |
13 | 13 |
import java.util.List; |
14 | 14 |
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15 |
import org.apache.commons.lang.StringUtils; |
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15 |
import org.apache.commons.lang3.StringUtils;
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16 | 16 |
|
17 | 17 |
/** |
18 | 18 |
* @author a.mueller |
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SortIndexUpdater.java | ||
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105 | 105 |
public String createIndexMapQuery(){ |
106 | 106 |
String resultsetQuery = "SELECT @id as id, @parentColumn " + |
107 | 107 |
" FROM @tableName " + |
108 |
// " WHERE @parentColumn IS NOT NULL " +
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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 | ||
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131 | 131 |
|
132 | 132 |
//add blockedBy_id |
133 | 133 |
stepName= "Add blockedBy_id to Registration"; |
134 |
firstTableName = "Registration";
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135 |
secondTableName = "Registration";
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136 |
attributeName = "blockedBy";
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isList = ! IS_LIST;
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134 |
firstTableName = "Registration"; |
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secondTableName = "Registration"; |
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attributeName = "blockedBy"; |
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isList = ! IS_LIST; |
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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";
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163 |
referencedTable = "FeatureNode"; |
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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 | ||
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90 | 90 |
for (Object bean :beanList){ |
91 | 91 |
Collections.sort(propertyPaths); |
92 | 92 |
for(String propPath : propertyPaths){ |
93 |
initializePropertyPath(bean, propPath); |
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93 |
// initializePropertyPath(bean, propPath);
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|
94 | 94 |
} |
95 | 95 |
} |
96 | 96 |
|
cdmlib-remote-webapp/.gitignore | ||
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1 | 1 |
.externalToolBuilders/ |
2 | 2 |
maven-eclipse.xml |
3 |
/bin/ |
cdmlib-remote-webapp/ide/eclipse/Jetty Launcher/cdmlib-remote-webapp - run (swagger).launch | ||
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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="${jetty-runtime-9}"/> |
26 | 26 |
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.version" value="JETTY_9_3"/> |
... | ... | |
56 | 56 |
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="net.sourceforge.eclipsejetty.launcher.JettyLaunchClassPathProvider"/> |
57 | 57 |
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="net.sourceforge.eclipsejetty.starter.jetty9.Jetty9LauncherMain"/> |
58 | 58 |
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="cdmlib-remote-webapp"/> |
59 |
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx500M -XX:PermSize=150m -Dlog4j.configDebug=true -Dlog4j.configuration=file:///${system_property:user.home}/.cdmLibrary/log4j.properties -Dcdm.forceSchemaUpdate=true -Dspring.profiles.active=remoting,swagger"/>
|
|
59 |
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx500M -XX:PermSize=150m -Dlog4j.configDebug=true -Dlog4j.configuration=file:///${system_property:user.home}/.cdmLibrary/log4j.properties -Dcdm.forceSchemaUpdate=true -Dspring.profiles.active=remoting,swagger"/>
|
|
60 | 60 |
</launchConfiguration> |
cdmlib-remote-webapp/ide/eclipse/Jetty Launcher/cdmlib-remote-webapp-unit-test.launch | ||
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21 | 21 |
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.config.type.0" value="DEFAULT"/> |
22 | 22 |
<booleanAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.embedded" value="false"/> |
23 | 23 |
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.microVersion" value="1"/> |
24 |
<<<<<<< HEAD |
|
24 | 25 |
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.minorVersion" value="2"/> |
25 | 26 |
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.path" value="C:\Program Files\jetty-distribution-9.2.14.v20151106"/> |
26 | 27 |
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.version" value="JETTY_9"/> |
28 |
======= |
|
29 |
<intAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.minorVersion" value="4"/> |
|
30 |
<stringAttribute key="net.sourceforge.eclipsejetty.launcher.jetty.path" value="${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 | ||
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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 | ||
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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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