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Closes #147 - modification of the alwaysShowInvestigation property to…
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… true will ensure that the investigation is always shown in the user interface.
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@eamonnmag
eamonnmag committed May 16, 2012
1 parent 8c56e2b commit e83c165
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5 changes: 4 additions & 1 deletion src/main/java/org/isatools/isacreator/gui/DataEntryEnvironment.java
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Expand Up @@ -48,6 +48,7 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
import org.isatools.isacreator.model.Study;
import org.isatools.isacreator.ontologymanager.OntologyManager;
import org.isatools.isacreator.ontologymanager.OntologySourceRefObject;
import org.isatools.isacreator.settings.ISAcreatorProperties;
import org.isatools.isacreator.spreadsheet.Spreadsheet;
import org.isatools.isacreator.spreadsheet.model.TableReferenceObject;
import org.isatools.isacreator.utils.datastructures.CollectionUtils;
Expand Down Expand Up @@ -294,7 +295,9 @@ public void run() {
* @return - DefaultMutableTreeNode. The root node with all nodes contained within it.
*/
private DefaultMutableTreeNode buildTreeFromInvestigation(Investigation inv) {
if (inv.getStudies().size() > 1) {
boolean alwaysShowInvestigation = Boolean.valueOf(ISAcreatorProperties.getProperty("alwaysShowInvestigation"));
System.out.println("Should I always show the investigation? " + alwaysShowInvestigation);
if (inv.getStudies().size() > 1 || alwaysShowInvestigation) {
inv.getUserInterface().update();
overviewTreeRoot = new DefaultMutableTreeNode(inv);

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3 changes: 2 additions & 1 deletion src/main/resources/defaultConfigs/defaultsettings.properties
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@@ -1 +1,2 @@
strictValidation.isOn=false
strictValidation.isOn=false
alwaysShowInvestigation=false

16 comments on commit e83c165

@vedina
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@vedina vedina commented on e83c165 Jun 28, 2013

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ISACreator 1.7.0 doesn't seem to use this option (no investigation is displayed if set to true), and is overwriting the entry in the settings.properties with
alwaysShowInvestigation=${isacreator.alwaysShowInvestigation}

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Yes, because you have a profile in your pom which you need to supply for it to be set.

<profile>
     <id>toxbank</id>
     <properties>
         <isacreator.alwaysShowInvestigation>true</isacreator.alwaysShowInvestigation>
     </properties>
</profile>

Although, if you modified the settings file directly, it would work.

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I'm assuming this is happening when you build from source?

@vedina
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@vedina vedina commented on e83c165 Jun 28, 2013

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No, I am using ISACreator 1.7.0 downloaded from isa-tools site, and edited the Settings/settings.properties file.

It will probably work if building form source, but I tried to avoid it ;)

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@eamonnmag eamonnmag commented on e83c165 Jun 28, 2013 via email

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I found the issue. When we initially added this functionality we made a properties file called defaultsettings.properties override anything in the user settings. In the current ISAcreator build, the property for alwaysShowInvestigation is ${isacreator.alwaysShowInvestigation}, therefore even if settings.properties contains alwaysShowInvestigation=true, this is overridden with alwaysShowInvestigation=${isacreator.alwaysShowInvestigation}. If however, you had built a fresh installation with the toxbank profile, alwaysShowInvestigation would have been populated with true in the defaultsettings.properties file - I've now removed this overriding functionality, and settings.properties overrides the system defaults.

@vedina
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@vedina vedina commented on e83c165 Jul 1, 2013

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Thanks a lot! Would you recommend using ISACreator 1.7.0 or 1.7.1 source ?

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We'll be doing a push today of some new code. If you build from source, you'll remove a few small issues.

@vedina
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@vedina vedina commented on e83c165 Jul 1, 2013

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Compiling 1.7.2 development branch gives the following errors

mvn clean test

Tests in error:
importFileTest(org.isatools.isacreator.io.importisa.ISAtabFilesImporterFromGUITest)
saveISAFilesTest(org.isatools.isacreator.io.exportisa.OutputISAFilesTest)
createISATabProgrammatically(org.isatools.isacreator.io.ProgrammaticISATabCreationTest)
importFileTest(org.isatools.isacreator.io.importisa.ISAtabFilesImporterTest)

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@eamonnmag eamonnmag commented on e83c165 Jul 1, 2013 via email

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@eamonnmag eamonnmag commented on e83c165 Jul 2, 2013 via email

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@vedina
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@vedina vedina commented on e83c165 Jul 2, 2013

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Yes, I'm using the development branch

~/dev/ISAcreator$ git branch

  • development

Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.45 sec
Running org.isatools.isacreator.io.importisa.ISAtabFilesImporterTest
java.io.IOException: The specified directory /home/nina/dev/ISAcreator/Configurations/isaconfig-default_v2013-02-13/ is wrong!
at org.isatools.isacreator.configuration.io.ConfigXMLParser.getTableDefinitions(ConfigXMLParser.java:175)
at org.isatools.isacreator.configuration.io.ConfigXMLParser.loadConfiguration(ConfigXMLParser.java:91)
...
Growth control of the eukaryote cell: a systems biology study in yeast
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.505 sec <<< FAILURE!
Running org.isatools.isacreator.model.ProtocolTest
Post Extraction
Derivatization
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
Running org.isatools.isacreator.model.PublicationTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec
Running org.isatools.isacreator.io.importisa.InvestigationImportTest
__TESTING loadInvestigationFile() on i_investigation.txt
Growth control of the eukaryote cell: a systems biology study in yeast
Investigation title: Growth control of the eukaryote cell: a systems biology study in yeast
Number of studies: 2
Getting investigation publications:
Publication identifier: 17439666
Publication title: Growth control of the eukaryote cell: a systems biology study in yeast.
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.351 sec

Results :

Tests in error:
importFileTest(org.isatools.isacreator.io.importisa.ISAtabFilesImporterFromGUITest)
saveISAFilesTest(org.isatools.isacreator.io.exportisa.OutputISAFilesTest)
createISATabProgrammatically(org.isatools.isacreator.io.ProgrammaticISATabCreationTest)
importFileTest(org.isatools.isacreator.io.importisa.ISAtabFilesImporterTest)

Tests run: 40, Failures: 0, Errors: 4, Skipped: 0

It seems the Configuration directory is not in the git repository.

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@eamonnmag eamonnmag commented on e83c165 Jul 2, 2013 via email

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@agbeltran
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You can run ./package.sh to get it.

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@vedina vedina commented on e83c165 Jul 2, 2013

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@agbeltran thanks!
OK, it pulls the Configuration directory, but throws an error at the end (there is a hard coded path for maven). The error doesn't seem to be critical.

./package.sh: line 49: /Users/eamonnmaguire/dev/maven/bin/mvn: No such file or directory

zip error: Invalid command arguments (no such option: -)
mv: cannot stat ISAcreator-1.7.2-jar-with-dependencies.jar': No such file or directory zip warning: name not matched: ISAcreator.jar zip warning: ISAcreator-1.7.2-all.zip not found or empty Packaging up jars to run within a native MacOS container cp: cannot statISAcreator.jar': No such file or directory
Packaging completed successfully!

zip error: Invalid command arguments (no such option: -)

Running now mvn clean tests gives only two failures.
Tests in error:
importFileTest(org.isatools.isacreator.io.importisa.ISAtabFilesImporterFromGUITest) Time elapsed: 1.091 sec <<< ERROR!
java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159)

createISATabProgrammatically(org.isatools.isacreator.io.ProgrammaticISATabCreationTest) Time elapsed: 0.002 sec <<< ERROR!
java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159)

(yes, this is a headless machine, I guess I'll just skip tests on this build)

Finally, a minor issue - the use of "apt" in the pom.xml (and ./package.sh) prevents from running ISAcreator build on Windows, which is normally supported by maven builds.

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Sorry about that - it seems that that version of the script got pushed by mistake. It should be fixed now.

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