August 2009 - IPT - lists.gbif.org

IPT Maven build error
by Aaron Steele 02 Sep '09

02 Sep '09

I'm having problems building gbif-providertool/pom.xml via Maven in r1442 of trunk. Here is the Maven output for the test task in pom.xml: http://txtb.in/4ba This doesn't appear to be a known issue. Has anyone run into this before?

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Re: [IPT] IPT Production installations, Extensions
by Dag Terje Filip Endresen 01 Sep '09

01 Sep '09

Hi Jörg, I believe the NordGen dataset is in the progress to be indexed from the IPT provider. And yes, I have added an extension for genebanks to the IPT. Resource 77 from the NordGen IPT is mapped to this new draft germplasm extension. http://ipt.nordgen.org/ipt/occResource.html?resource_id=77 I believe that this germplasm extension is already available from the GBRDS registry: http://gbrds.gbif.org/registry/ipt/extensions.json I have collected some more information on the URL used as the namespace: http://rs.nordgen.org/dwc/ I have yet to start indexing data shared on this germplasm extension, but browsing this dataset (77) on the NordGen IPT installation works fine. One of my main objective with this extension is to start the sharing of datasets with measurements of trait properties on germplasm specimens. The trait evaluation datasets are the next big thing for the European genebanks this year. Cheers Dag Terje _____ From: Holetschek, Jörg [mailto:j.holetschek@bgbm.org] To: ipt(a)lists.gbif.org [mailto:ipt@lists.gbif.org] Sent: Mon, 31 Aug 2009 11:36:54 +0200 Subject: [IPT] IPT Production installations, Extensions Dear all, does anyone have already an IPT installation published on GBIF? That means, the data is visible on the GBIF data portal? And I wonder if anyone is already using the extension mechanism of the IPT? Does anyone have any experiences? Best wishes from Berlin, Jörg ------------------------------------------------------------ Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Biodiversity Informatics and Laboratories Königin-Luise-Str. 6-8 D-14195 Berlin phone: +49 (0)30/838-50150 eMail: j.holetschek(a)bgbm.org ------------------------------------------------------------ _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

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IPT Production installations, Extensions
by Holetschek, Jörg 01 Sep '09

01 Sep '09

Dear all, does anyone have already an IPT installation published on GBIF? That means, the data is visible on the GBIF data portal? And I wonder if anyone is already using the extension mechanism of the IPT? Does anyone have any experiences? Best wishes from Berlin, Jörg ------------------------------------------------------------ Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Biodiversity Informatics and Laboratories Königin-Luise-Str. 6-8 D-14195 Berlin phone: +49 (0)30/838-50150 eMail: j.holetschek(a)bgbm.org ------------------------------------------------------------

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Re: [IPT] IPT Maven build error
by "Markus Döring (GBIF)" 31 Aug '09

31 Aug '09

just quick guys: we only use maven from the commandline, but run main classes and JUnit tests from within eclipse. I used eclipse 3.3 and 3.4 so far on OSX to setup an eclipse IPT project I do: a) svn checkout ... # into folder workspace/ipt b) mvn eclipse:eclipse # generates eclipse artifacts but uses the M2_REPO variable to locate your local maven repository c) set the M2_REPO variable via project properties-> java build path - > add variable to point to your local maven repository (on OSX this is ~/.m2/repository) d) mvn -P prod # runs IPT locally with jetty on port 8080, skips tests, uses gbifs production registry and a local data dir in the webapps folder if you use no profile at all and just run $mvn jetty IPT should use jetty on port 8080. But because currently not all tests succeed the build fails. I have to admit that I switched to Java6 during this year, so there might be issues with java5. Although we run IPT using the WAR on gbif servers with java5 currently and there is no real reason why java5 should not be supported. If so, this is not intended and could surely be solved rather simply (e.g. SQLException I will look into). sorry for being brief, but hope this still helps a bit. Markus On Aug 27, 2009, at 18:27, Paul J. Morris wrote: > Aaron, > > I haven't seen any documentation on it. I did your step 1, then, by > hand in eclipse, set the source directories as sources, and added the > jar files in gbif-providertool/target/gbif-ipt-1.0-SNAPSHOT/ > WEB-INF/lib to the build path. I've had no luck with eclipse-maven > integration (with eclipse 3.4.0 on debian etch), but I can build a > working war file for the provider from the command line with > > cd ~/workspace/ipt/gbif-providertool > export JAVA_HOME=/[...]/jdk1.6.[...]] > mvn -fn > or with > mvn -Dmaven.test.skip=true > > In the current (1463) revision, I'm seeing 11 test failures and 2 > errors, at least one of which looks like a reference to a GBIF network > resource. > Running org.gbif.provider.service.impl.RegistryManagerImplTest > WARN main-HttpBaseManager.succeeded(214) | Http request to > http://gbrds.gbif.org/registrydev/organisation/null?op=login failed: > HTTP/1.1 404 Not Found Tests run: 1, Failures: 1, Errors: 0, Skipped: > 0, Time elapsed: 0.343 sec <<< FAILURE! > This looks like it is testing a value found in gbif-provider/pom.xml > <ipt.registry.url>http://gbrds.gbif.org/registrydev</ipt.registry.url> > > Since I do a lot of development not attached to the network, a build > dependency on a network resource is a problem (likewise another test > that expects geoserver to be running on localhost:8080), and so I > haven't gone hunting after the possible causes of the other test > failures, and am just switching off the tests to build (which works > allright as I'm working on some experimental filtered push annotation > integration, and the resulting war file just needs to run). > > Merry Snailing, > -Paul > > On Wed, 26 Aug 2009 15:45:47 -0700 > Aaron Steele <eightysteele(a)gmail.com> wrote: > >> Also, do we have documentation for setting up Eclipse for IPT >> development? Here's how I've set things up in Eclipse so far: >> >> 1) SVN checkout of trunk/gbif-providertool > > -- > Paul J. Morris > Biodiversity Informatics Manager > Harvard University Herbaria/Museum of Comparative Zoölogy > mole(a)morris.net AA3SD PGP public key available >

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Re: [IPT] IPT Maven build error
by "Markus Döring (GBIF)" 28 Aug '09

28 Aug '09

Paul, how come you dont have the pom, was it deleted by maven itself? Without the pom maven of course cannot do anything. Ah, I see. You have checked out the entire trunk! We use a subproject layout with parallel projects under trunk. Because Maven and Eclipse are not good buddies we also do not use hierarchical maven projects, but use the <parent> directive to refer to a pom parent. So in order to build the IPT you need to checkout trunk/gbif- providertool like this: cd ~/workspace svn co http://gbif-providertoolkit.googlecode.com/svn/trunk/gbif-providertool ipt this will create an ipt folder in your workspace that contains a pom.xml ! in that ipt dir you should be able to do: mvn eclipse:eclipse Any better? Markus On Aug 28, 2009, at 1:34, Paul J. Morris wrote: > On Thu, 27 Aug 2009 15:05:53 -0700 > Aaron Steele <eightysteele(a)gmail.com> wrote: > >>> That's not working for me, nor is mvn eclipse:eclipse, maven >>> complains that there's no eclipse profile in the one case and no >>> pom.xml file in the other. >> >> If you run 'mvn -Peclipse -X' and post the output that might give us >> some clues. > > It can't find either an eclipse profile or the pom file in the > directory that should end up as the root of the project. > > Effectively this comes from: > mkdir ~/workspace/ipt > cd ~/workspace/ > svn checkout http://gbif-providertoolkit.googlecode.com/svn/trunk/ > ipt/ > cd ipt/ > > though it's gone through a number of updates since then, and has some > local changes to the code (but the same thing happens with a fresh > checkout). > > then: > > mole@chicoreus:~/workspace/ipt$ mvn -Peclipse -X > + Error stacktraces are turned on. > Apache Maven 2.1.0 (r755702; 2009-03-18 15:10:27-0400) > Java version: 1.6.0_06 > Java home: /usr/local/java/jdk1.6.0_06/jre > Default locale: en_US, platform encoding: UTF-8 > OS name: "linux" version: "2.6.18-6-686" arch: "i386" Family: "unix" > [DEBUG] Building Maven user-level plugin registry from: > '/home/mole/.m2/plugin-registry.xml' [DEBUG] Building Maven > global-level plugin registry from: > '/usr/local/java/apache-maven-2.1.0/conf/plugin-registry.xml' [INFO] > Scanning for projects... [WARNING] Profile with id: 'eclipse' has not > been activated. > > [INFO] > ------------------------------------------------------------------------ > [ERROR] BUILD FAILURE [INFO] > ------------------------------------------------------------------------ > [INFO] > > You must specify at least one goal or lifecycle phase to perform build > steps. The following list illustrates some commonly used build > commands: > > mvn clean > Deletes any build output (e.g. class files or JARs). > mvn test > Runs the unit tests for the project. > mvn install > Copies the project artifacts into your local repository. > mvn deploy > Copies the project artifacts into the remote repository. > mvn site > Creates project documentation (e.g. reports or Javadoc). > > Please see > http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.h… > for a complete description of available lifecycle phases. > > Use "mvn --help" to show general usage information about Maven's > command line. > > > [INFO] > ------------------------------------------------------------------------ > [DEBUG] Trace org.apache.maven.BuildFailureException: > > You must specify at least one goal or lifecycle phase to perform build > steps. The following list illustrates some commonly used build > commands: > > mvn clean > Deletes any build output (e.g. class files or JARs). > mvn test > Runs the unit tests for the project. > mvn install > Copies the project artifacts into your local repository. > mvn deploy > Copies the project artifacts into the remote repository. > mvn site > Creates project documentation (e.g. reports or Javadoc). > > Please see > http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.h… > for a complete description of available lifecycle phases. > > Use "mvn --help" to show general usage information about Maven's > command line. > > > at > org > .apache > .maven > .lifecycle > .DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:173) > at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:356) at > org.apache.maven.DefaultMaven.execute(DefaultMaven.java:137) at > org.apache.maven.cli.MavenCli.main(MavenCli.java:356) at > sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at > sun > .reflect > .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun > .reflect > .DelegatingMethodAccessorImpl > .invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) at > org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) at > org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at > org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) > at org.codehaus.classworlds.Launcher.main(Launcher.java:375) [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: < 1 second [INFO] Finished at: Thu Aug 27 19:21:48 > EDT 2009 [INFO] Final Memory: 1M/40M [INFO] > ------------------------------------------------------------------------ > > > Merry Snailing, > -Paul > -- > Paul J. Morris > Biodiversity Informatics Manager > Harvard University Herbaria/Museum of Comparative Zoölogy > mole(a)morris.net AA3SD PGP public key available >

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Re: [IPT] IPT Maven build error
by "Markus Döring (GBIF)" 28 Aug '09

28 Aug '09

Aaron, Paul, the maven eclipse plugin is configurred already in the pom, although in the parent "motherpom" from which the ipt pom inherits: <parent> <groupId>org.gbif</groupId> <artifactId>motherpom</artifactId> <version>1.0-SNAPSHOT</version> </parent> From the motherpom: http://code.google.com/p/gbif-providertoolkit/source/browse/trunk/motherpom… <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-eclipse-plugin</artifactId> <configuration> <downloadSources>true</downloadSources> <downloadJavadocs>true</downloadJavadocs> </configuration> </plugin> It seems we desperately need some developer documentation on the wiki for how to setup your dev environment... On Aug 28, 2009, at 6:46, Aaron Steele wrote: >> It can't find either an eclipse profile or the pom file in the >> directory that should end up as the root of the project. > > Try checking out and installing the Maven Eclipse Plugin: > > svn checkout http://svn.apache.org/repos/asf/maven/plugins/tags/maven-eclipse-plugin-2.7 > maven-eclipse-plugin > > Then, in the maven-eclipse-plugin directory, run 'mvn install' and > then retry the IPT mvn command. Success? >

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IPT on linux.
by Tim Noble 17 Aug '09

17 Aug '09

"Haven't been able to get it to work" By which I meant to say that we are unable to import sources. Tim.

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IPT with linux
by Tim Noble 17 Aug '09

17 Aug '09

Just wondering if anybody is running IPT on linux? If so what version? Were there any firewall or other issues? I haven't been able to get it to work on Ubuntu. Tim.

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