Permalink
Browse files

Merge branch 'master' of github.com:ISA-tools/ISAcreator into develop…

…ment
  • Loading branch information...
2 parents 07ceac8 + 9b96cf6 commit 3f7a16ccae9e57474efdd24769d4c3aeeb32aed7 @eamonnmag eamonnmag committed Mar 8, 2012
View
@@ -0,0 +1,135 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="FacetManager">
+ <facet type="Osmorc" name="OSGi">
+ <configuration osmorcControlsManifest="true" manifestLocation="" jarfileLocation="ISAcreator.jar" outputPathType="CompilerOutputPath" useBndFile="false" bndFileLocation="" useBundlorFile="false" bundlorFileLocation="" bundleActivator="org.isatools.isacreator.gui.modeselection.ModeSelector" bundleSymbolicName="org.isatools.ISAcreator" bundleVersion="" ignoreFilePattern="" useProjectDefaultManifestFileLocation="true" alwaysRebuildBundleJAR="false">
+ <additionalProperties>
+ <property key="Bundle-Vendor" value="ISA team, http://isa-tools.org" />
+ <property key="Bundle-Name" value="ISAcreator" />
+ </additionalProperties>
+ <additionalJARContents />
+ </configuration>
+ </facet>
+ </component>
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_5" inherit-compiler-output="false">
+ <output url="file://$MODULE_DIR$/target/classes" />
+ <output-test url="file://$MODULE_DIR$/target/test-classes" />
+ <content url="file://$MODULE_DIR$">
+ <sourceFolder url="file://$MODULE_DIR$/target/generated-sources/xmlbeans" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/src/main/resources" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
+ <excludeFolder url="file://$MODULE_DIR$/target/Configurations" />
+ <excludeFolder url="file://$MODULE_DIR$/target/Plugins" />
+ <excludeFolder url="file://$MODULE_DIR$/target/Settings" />
+ <excludeFolder url="file://$MODULE_DIR$/target/archive-tmp" />
+ <excludeFolder url="file://$MODULE_DIR$/target/classes" />
+ <excludeFolder url="file://$MODULE_DIR$/target/generated" />
+ <excludeFolder url="file://$MODULE_DIR$/target/generated-classes" />
+ <excludeFolder url="file://$MODULE_DIR$/target/isatab files" />
+ <excludeFolder url="file://$MODULE_DIR$/target/jaxws" />
+ <excludeFolder url="file://$MODULE_DIR$/target/surefire-reports" />
+ <excludeFolder url="file://$MODULE_DIR$/target/test-classes" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="Maven: net.java.dev.fuse:fuse-swing:0.4" level="project" />
+ <orderEntry type="library" name="Maven: net.java.dev.fuse:fuse-core:0.4" level="project" />
+ <orderEntry type="library" name="Maven: commons-net:commons-net:2.0" level="project" />
+ <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:2.0.2" level="project" />
+ <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.0.3" level="project" />
+ <orderEntry type="library" name="Maven: net.sourceforge.collections:collections-generic:4.01" level="project" />
+ <orderEntry type="library" name="Maven: net.sf.opencsv:opencsv:2.1" level="project" />
+ <orderEntry type="library" name="Maven: org.prefuse:prefuse:20071021" level="project" />
+ <orderEntry type="library" name="Maven: org.profusians:profusians:beta-20080629" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi:ols:1.18" level="project" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.14" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.2" level="project" />
+ <orderEntry type="library" name="Maven: mysql:mysql-connector-java:5.1.6" level="project" />
+ <orderEntry type="library" name="Maven: ojb:db-ojb:1.0.3" level="project" />
+ <orderEntry type="library" name="Maven: commons-dbcp:commons-dbcp:1.2.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-beanutils:commons-beanutils:1.7.0" level="project" />
+ <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-pool:commons-pool:1.2" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.3.02" level="project" />
+ <orderEntry type="library" name="Maven: xerces:xercesImpl:2.8.1" level="project" />
+ <orderEntry type="library" name="Maven: xalan:xalan:2.4.0" level="project" />
+ <orderEntry type="library" name="Maven: p6spy:p6spy:1.1" level="project" />
+ <orderEntry type="library" name="Maven: hsqldb:hsqldb:1.8.0.7" level="project" />
+ <orderEntry type="library" name="Maven: proteomics:proteomics-common:1.5" level="project" />
+ <orderEntry type="library" name="Maven: jakarta-regexp:jakarta-regexp:1.4" level="project" />
+ <orderEntry type="library" name="Maven: lucene:lucene:1.4.3" level="project" />
+ <orderEntry type="library" name="Maven: obo:obo:2.0" level="project" />
+ <orderEntry type="library" name="Maven: obo:bbop:2.0" level="project" />
+ <orderEntry type="library" name="Maven: org.geneontology:oboedit:1.101" level="project" />
+ <orderEntry type="library" name="Maven: org.geneontology:org.geneontology:1.101" level="project" />
+ <orderEntry type="library" name="Maven: jcvsii:jcvsii:5.4.2" level="project" />
+ <orderEntry type="library" name="Maven: sshtools:j2ssh-core:0.2.2" level="project" />
+ <orderEntry type="library" name="Maven: sshtools:j2ssh-common:0.2.2" level="project" />
+ <orderEntry type="library" name="Maven: com.svnkit:svnkit:1.1.0" level="project" />
+ <orderEntry type="library" name="Maven: ch.ethz.ganymed:ganymed-ssh2:build210" level="project" />
+ <orderEntry type="library" name="Maven: com.ice:tar:1.0" level="project" />
+ <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.4" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.bind:jaxb-api:2.1" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.stream:stax-api:1.0-2" level="project" />
+ <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml.ws:jaxws-api:2.1-1" level="project" />
+ <orderEntry type="library" name="Maven: javax.xml:jaxrpc-api:1.1" level="project" />
+ <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+ <orderEntry type="library" name="Maven: net.sourceforge.jexcelapi:jxl:2.6.3" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.3.0" level="project" />
+ <orderEntry type="library" name="Maven: org.isatools:ISAtabErrorReporter:0.3" level="project" />
+ <orderEntry type="library" name="Maven: com.explodingpixels:scroller:0.1" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi:jutils:1.2" level="project" />
+ <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
+ <orderEntry type="library" name="Maven: org.isatools:HelpWebUtility:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.felix:org.apache.felix.main:1.8.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.felix:org.apache.felix.framework:1.8.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.felix:org.apache.felix.shell:1.2.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.felix:org.apache.felix.shell.tui:1.2.0" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.felix:org.apache.felix.bundlerepository:1.4.0" level="project" />
+ <orderEntry type="library" name="Maven: org.isatools:import_layer:1.3.2" level="project" />
+ <orderEntry type="library" name="Maven: com.google.collections:google-collections:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.isatools:graph2tab:3.0" level="project" />
+ <orderEntry type="library" name="Maven: commons-io:commons-io:2.0.1" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi.bioinvindex:model:1.4.1" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.lucene:lucene-core:2.9.2" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.lucene:lucene-queries:2.9.2" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.lucene:lucene-misc:2.9.2" level="project" />
+ <orderEntry type="library" name="Maven: uk.ac.ebi.pride:pride-core:2.7.1" level="project" />
+ <orderEntry type="library" name="Maven: xpp3:xpp3:1.1.3.4.O" level="project" />
+ <orderEntry type="library" name="Maven: psidev.psi.tools:xxindex:0.3-SNAPSHOT" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.commons:commons-io:1.3.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.mail:mail:1.4" level="project" />
+ <orderEntry type="library" name="Maven: ols:ols-client:1.14" level="project" />
+ <orderEntry type="library" name="Maven: soap:soap:2.3.1" level="project" />
+ <orderEntry type="library" name="Maven: axis:axis:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis-jaxrpc:1.4" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis-saaj:1.4" level="project" />
+ <orderEntry type="library" name="Maven: axis:axis-wsdl4j:1.5.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-discovery:commons-discovery:20040218.194635" level="project" />
+ <orderEntry type="library" name="Maven: msv:msv:20050913" level="project" />
+ <orderEntry type="library" name="Maven: msv:isorelax:20050913" level="project" />
+ <orderEntry type="library" name="Maven: msv:relaxngDatatype:20050913" level="project" />
+ <orderEntry type="library" name="Maven: msv:xsdlib:20050913" level="project" />
+ <orderEntry type="library" name="Maven: cpdetector:cpdetector:1.04" level="project" />
+ <orderEntry type="library" name="Maven: com.h2database:h2:1.3.150" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans-xpath:2.3.0" level="project" />
+ <orderEntry type="library" name="Maven: net.sf.saxon:saxon:8.7" level="project" />
+ <orderEntry type="library" name="Maven: net.sf.saxon:saxon-dom:8.7" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.axis:axis:1.4" level="project" />
+ <orderEntry type="library" name="Maven: commons-cli:commons-cli:1.2" level="project" />
+ <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.5.6" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:3.3.1.GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate:hibernate-annotations:3.4.0.GA" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate:hibernate-commons-annotations:3.3.0.ga" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate:hibernate-validator:3.1.0.GA" level="project" />
+ <orderEntry type="library" name="Maven: javax.persistence:persistence-api:1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate:hibernate-search:3.1.1.GA" level="project" />
+ <orderEntry type="library" name="Maven: javax.transaction:jta:1.1" level="project" />
+ <orderEntry type="library" name="Maven: org.hibernate:hibernate-entitymanager:3.4.0.GA" level="project" />
+ <orderEntry type="library" name="Maven: javassist:javassist:3.4.GA" level="project" />
+ </component>
+</module>
+
@@ -5,15 +5,15 @@ ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ);
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
- Software distributed under the License is distributed on an ÒAS ISÓ basis,
+ Software distributed under the License is distributed on an �AS IS� basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
@@ -114,6 +114,8 @@ public Component getTreeCellRendererComponent(JTree tree, Object val, boolean se
icon.setIcon(selected ? isMapped ? mappedSelected : unmappedSelected :
isMapped ? mappedUnselected : unmappedUnselected);
+
+ text.setForeground(mappedElement.isRequired() ? UIHelper.RED_COLOR : UIHelper.GREY_COLOR);
} else {
icon.setIcon(expanded ? openedNode : closedNode);
}
@@ -5,15 +5,15 @@ ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ);
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
- Software distributed under the License is distributed on an ÒAS ISÓ basis,
+ Software distributed under the License is distributed on an �AS IS� basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
@@ -80,6 +80,8 @@ void createGUI() {
JPanel useFieldPanel = new JPanel(new GridLayout(1, 1));
+
+
useField = new JCheckBox("use " + fieldName.toLowerCase() + "?", mappings != null);
UIHelper.renderComponent(useField, UIHelper.VER_11_PLAIN, UIHelper.GREY_COLOR, false);
@@ -5,15 +5,15 @@ ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ);
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
- Software distributed under the License is distributed on an ÒAS ISÓ basis,
+ Software distributed under the License is distributed on an �AS IS� basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
@@ -47,10 +47,16 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
private String fieldName;
private MappingInformation display;
+ private boolean required;
public MappedElement(String fieldName, MappingInformation display) {
+ this(fieldName, display, false);
+ }
+
+ public MappedElement(String fieldName, MappingInformation display, boolean required) {
this.fieldName = fieldName;
this.display = display;
+ this.required = required;
}
public MappingInformation getDisplay() {
@@ -65,4 +71,12 @@ public String getFieldName() {
public String toString() {
return fieldName;
}
+
+ public boolean isRequired() {
+ return required;
+ }
+
+ public void setDisplay(MappingInformation toUse) {
+ this.display = toUse;
+ }
}
@@ -5,15 +5,15 @@ ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
- ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ);
+ �The contents of this file are subject to the CPAL version 1.0 (the �License�);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
- Software distributed under the License is distributed on an ÒAS ISÓ basis,
+ Software distributed under the License is distributed on an �AS IS� basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
@@ -218,14 +218,11 @@ public JComponent createTree() {
private void addHeadersToTree() {
TableReferenceObjectWrapper wrapperForMapper = new TableReferenceObjectWrapper(tableReferenceObject);
- for (String column : wrapperForMapper.getStdHeaders()) {
- if (!column.equals(GeneralFieldTypes.UNIT.name) && !column.equals(TableReferenceObject.ROW_NO_TEXT)) {
- MappingInformation toUse = chooseDisplay(column);
- MappedElement mn = new MappedElement(column, toUse);
- mappingRef.add(mn);
-
- rootNode.add(new DefaultMutableTreeNode(mn));
- }
+ for (MappedElement mappingField : wrapperForMapper.getStdHeaders()) {
+ MappingInformation toUse = chooseDisplay(mappingField.getFieldName());
+ mappingField.setDisplay(toUse);
+ mappingRef.add(mappingField);
+ rootNode.add(new DefaultMutableTreeNode(mappingField));
}
}
@@ -264,6 +261,8 @@ public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
mappingRef.add(count + 1, new MappedElement(newFieldName, toUse));
addedFields.add(newFieldName);
+
+
reformTree();
statusPanel.setVisible(false);
}
@@ -287,6 +286,7 @@ public MappedElement getMappingNodeForField(String fieldName) {
if (mn.getFieldName().equals(fieldName)) {
return mn;
}
+
}
return null;
}
@@ -544,6 +544,7 @@ private void createGUI() {
ISAFieldMapping mapping = mn.getDisplay().createISAFieldMapping();
if (mapping != null) {
fields.put(mn.getFieldName(), mapping);
+
}
}
Oops, something went wrong.

0 comments on commit 3f7a16c

Please sign in to comment.