Hi Tim, Not sure which fix you are talking about? modify pipeline or ignore test? Are this is test meaningful? Since I don't know if this test is valuable, I assume that it is and spend time trying to figure out what's wrong with tests and found two Jira issues - CTAKES-361 and CTAKES-307 which directly related to this particular issue. For me still does not clear why if XML specified resource as file: and how it is lately translated to jar:file: protocol which cause the issue. I could modify LvgCmdApiResourceImpl to unpack data to temporary location, but I have to be confident that jar:file: appearance is expected for UIMA pipeline. If somebody know where this happens, could he point me in right direction.
Best regards, Andrey 2016-12-14 20:57 GMT+06:00 Miller, Timothy < timothy.mil...@childrens.harvard.edu>: > 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 > > > > > > > > > > > > > > > > >
