Thanks for testing! And thank you for bringing it to our attention! Sean
-----Original Message----- From: Andrey Kurdumov [mailto:kant2...@googlemail.com] Sent: Friday, December 16, 2016 3:29 AM To: dev@ctakes.apache.org Subject: Re: Infrastructures questions. `mvn clean package` also working for me. Could someone close CTAKES-361, since this is issue reported couple years ago? Thanks for helping out and impatiently waiting for release :) 2016-12-16 5:30 GMT+06:00 Pei Chen <pei.c...@wiredinformatics.com>: > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__bit.ly_1pHmTcL&d= > DgIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyI > isCYNYmQCP6r0bcpKGd4f7d4gTao&m=RpnZ_dTeCOXN_4E5NiNcjAZzgz9IavLK1O3hDfR > 0AZQ&s=ux_Y5kG24tLreI5dM6PyRXXAKVf_zTfl3lKyXXiluAk&e= > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m= > > v58bHfswf4lrCGRXVvbZcOuRlfxX4A2JFW3Y0a7wEy0&s=XzjL16KbCkVYgzwzcBN71X > > tHS- > > 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 > > > > > > > > > > > > > > > > > > > > > > > >
