I can recreate what Tim suggested.
1) Comment out LVG from the dependency parser test/pipeline
2) The same thing would need to be done in the Regression Test (comment out
LVG in the test)
3) Update the regression test suite newly generated output -> expected
I'll commit the changes. Basically with the above, junit tests won't run
into the URI hierarchal issue when the "mvn package" command is issued.
A bit of background- I remember digging deeper into this some time ago:
Even if we fixed our impl/LVG wrapper, there are hard coded references
inside LVG itself that uses file:// instead of ResourceAsStream forcing
resources to be unpacked. This doesn't jive well during the package phase
of the maven build cycle where it references your .m2 repo. mvn test works
fine because it will reference the explicit local unpacked lvg resources.
Pei Chen
Wired Informatics <http://bit.ly/1pHmTcL>
265 Franklin St Ste 1702
Boston, MA 02110
tel: (617) 433-7544
pei.c...@wiredinformatics.com
On Wed, Dec 14, 2016 at 9:57 AM, Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Dependency tests pass with my change; new test error in regression test
> module that I'm not familiar with and error type I've never seen before
> -- reaching out for help debugging:
>
>
> > Exception in thread "BaseCPMImpl-Thread"
> > junit.framework.AssertionFailedError:
> Verifying Test Output: testpatient_plaintext_2.txt.
> xmlorg.custommonkey.xmlunit.Diff
> > [different] Expected number of element attributes '7' but was '6' -
> comparing <org.apache.ctakes.typesystem.type.syntax.NewlineToken...> at
> /CAS[1]/org.apache.ctakes.typesystem.type.syntax.NewlineToken[1] to
> <org.apache.ctakes.typesystem.type.syntax.NewlineToken...> at
> /CAS[1]/org.apache.ctakes.typesystem.type.syntax.NewlineToken[1]
> >
> > at junit.framework.Assert.fail(Assert.java:50)
> > at junit.framework.Assert.assertTrue(Assert.java:20)
> > at org.apache.ctakes.regression.test.RegressionPipelineTest.
> compareXMLOutput(RegressionPipelineTest.java:147)
> > at org.apache.ctakes.regression.test.RegressionPipelineTest$
> StatusCallbackListenerImpl.collectionProcessComplete(
> RegressionPipelineTest.java:200)
> > at org.apache.uima.collection.impl.cpm.BaseCPMImpl.run(
> BaseCPMImpl.java:538)
> > at java.lang.Thread.run(Thread.java:745)
>
>
> Thanks
> Tim
>
> On Tue, 2016-12-13 at 16:15 +0000, Miller, Timothy wrote:
> > Quick followup - the test passes in eclipse, both with and without LVG
> > enabled. Can someone try to replicate at the command line and see if mvn
> > package works with LVG commented out? This is line 130 in
> > WriteClearNLPDescriptors.java. Otherwise I can try this afternoon.
> > Tim
> >
> > On Tue, 2016-12-13 at 15:57 +0000, Miller, Timothy wrote:
> > > Pretty sure this particular issue is caused by LVG being part of the
> > > test pipeline and the "URI is not hierarchical" bug from not having its
> > > files unpacked from the jar. A simple fix is to disable that test in
> > > code; a slightly more complex fix is to run the test with a modified
> > > pipeline that doesn't include LVG.
> > > Tim
> > >
> > >
> > > On Tue, 2016-12-13 at 10:51 -0500, Pei Chen wrote:
> > > > That's right. mvn compile and test should work fine. The benign test
> > > > failed error from junit tests is coming from install/package; it's
> > > > been there since the beginning of time [1]. It would be a nice to
> > > > have and remove the benign warning messages. If a proposed critical
> > > > patch release passes the regression tests, doesn't break any existing
> > > > behavior, enhances the project, and we have volunteers for RM, I do
> > > > not see these superious reasons as valid to block releases and keep
> > > > things moving along.
> > > > Sean: it would great if you can open a Jira and apply the patch; we
> > > > can always cut another release next time- I'll be happy to be RM for
> > > > that one whenever you feel it's' ready.
> > > >
> > > > [1] https://urldefense.proofpoint.com/v2/url?u=http-3A__
> markmail.org_search_-3Fq-3Dctakes-2520mvn-2520package-
> 2520-2DDskipTests-23query-3Actakes-2520mvn-2520package-
> 2520-2DDskipTests-2Bpage-3A1-2Bmid-3Aoxgrkslhhjimpv4k-
> 2Bstate-3Aresults&d=DgIFaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=xkJKj22zARpX6Nb06fIYl84-
> gdaEmosSya1Wa40jup4&s=HIc4d0eWT6Wv0UY2Ytxm_oq5c-sUzay1SSq7XE4rDtE&e=
> > > >
> > > > On Tue, Dec 13, 2016 at 9:19 AM, Andrey Kurdumov
> > > > <kant2...@googlemail.com> wrote:
> > > > > NP for broken build. Finally I manage to run it, so I just report
> issue so
> > > > > other don't have have to go through hoops like me.
> > > > >
> > > > > I just want to made small correction - mvn compile works. mvn test
> works
> > > > > too, but mvn package require -DskipTests.
> > > > > The problem with build is somehow related to how Maven package
> stuff, I
> > > > > suspect.
> > > > >
> > > > > Packaging failed for me at "Apache cTAKES Dependency Parser
> > > > > .................... FAILURE", I also attach report from Surefire
> with
> > > > > error.
> > > > >
> > > > > I will try to figure out why is that error happens, but it could
> take a
> > > > > while until I understand how Maven works.
> > > > > Thanks for prompt response!
> > > > >
> > > > > Also I start looking how cTakes working, and investigate
> dependencies
> > > > > between packages, and found following comment: "Temporary
> workaround: Adding
> > > > > in the system scoped libraries. Remove these once they are in
> Maven Central"
> > > > > in the ctakes-distribution\src\main\assembly\bin.xml . These
> comment related
> > > > > to dependencies which checked in in the source code, but for me
> seems to be
> > > > > that they are now on MAven Central See
> > > > > (https://urldefense.proofpoint.com/v2/url?u=https-
> 3A__mvnrepository.com_artifact_net.sf.mastif_mastif-2Dzoner&d=DgIFaQ&c=
> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=xkJKj22zARpX6Nb06fIYl84-
> gdaEmosSya1Wa40jup4&s=xZ3YWIU31z3w7M1FOLaGQLoCVngpvleCf9mPKdZXyeg&e= ).
> > > > > I saw issue
> > > > >
> > > > > CTAKES-185
> > > > >
> > > > > which could be appropriate for that, and I could create patch for
> that
> > > > > change. During the course of my next project, very likely I would
> be
> > > > > involved in the activities similar to cTakes, so I potentially
> could
> > > > > contribute something back, so I try to familiarize myself with the
> project.
> > > > >
> > > > >
> > > > >
> > > > > 2016-12-13 19:30 GMT+06:00 Finan, Sean <
> sean.fi...@childrens.harvard.edu>:
> > > > >>
> > > > >> Hi Andrey,
> > > > >>
> > > > >> The requirement of skipping tests for a successful build is
> something that
> > > > >> all ctakes developers have stumbled across, but after initial
> setup we all
> > > > >> forget about it and it has never been handled. Apologies.
> > > > >>
> > > > >> The github mirror is something that would be great to have, but
> getting it
> > > > >> up has been a nightmare. The problem is that historically we
> have had
> > > > >> binary files that are larger than the 100MB limit enforced by
> github.
> > > > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__help.
> github.com_articles_working-2Dwith-2Dlarge-2Dfiles_&d=
> DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=
> xkJKj22zARpX6Nb06fIYl84-gdaEmosSya1Wa40jup4&s=i2JxC1bWoyzIpDK_jkYp7Y-
> lZHnbKjsvPP1EcWiO3d0&e=
> > > > >> This causes github to reject the creation of the repository.
> > > > >>
> > > > >> I do think that, should somebody feel like putting in the effort,
> we could
> > > > >> work with apache infra and get a working solution ... possibly
> starting with
> > > > >> 3.2.4-SNAPSHOT and ignoring the rest of the history?
> Unfortunately I do not
> > > > >> have the time to tackle the problem.
> > > > >>
> > > > >> Sean
> > > > >>
> > > > >>
> > > > >> -----Original Message-----
> > > > >> From: Andrey Kurdumov [mailto:kant2...@googlemail.com]
> > > > >> Sent: Monday, December 12, 2016 10:01 PM
> > > > >> To: dev@ctakes.apache.org
> > > > >> Subject: Infrastructures questions.
> > > > >>
> > > > >> Hi, I very new to cTakes and interested to take a look at it, and
> maybe
> > > > >> create custom pipeline on top of it. Right now I checkout source
> code and
> > > > >> successfully build it, but have following question.
> > > > >>
> > > > >> Why mvn package does not run successfully for me until I exclude
> tests
> > > > >> from build? I'm not very good at Java, so maybe I miss something
> obivious.
> > > > >>
> > > > >> Also, you seems to be have not only SVN repository, but Git also (
> > > > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_apache_ctakes_&d=DgIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> v58bHfswf4lrCGRXVvbZcOuRlfxX4A2JFW3Y0a7wEy0&s=XzjL16KbCkVYgzwzcBN71XtHS-
> Bf5CtQ27hsmHKwizg&e=
> > > > >> ) but it is very outdated. I even initially think that project is
> dead,
> > > > >> since Git show activity only from
> > > > >> 2013 year! If you could restore Git, that would be awesome.
> > > > >>
> > > > >> Best regards,
> > > > >> Andrey Kurdyumov
> > > > >
> > > > >
> > >
> >
>
>
