RE: Infrastructures questions.
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= > DgIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyI > isCYNYmQCP6r0bcpKGd4f7d4gTao=RpnZ_dTeCOXN_4E5NiNcjAZzgz9IavLK1O3hDfR > 0AZQ=ux_Y5kG24tLreI5dM6PyRXXAKVf_zTfl3lKyXXiluAk= > > 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 > > at /CAS[1]/org.apache.ctakes.typesystem.type.syntax.NewlineToken[1] > > to 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 +, 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 +, 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 b
Re: Infrastructures questions.
or 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=DgIFaQ= > qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=xkJKj22zARpX6Nb06fIYl84- > gdaEmosSya1Wa40jup4=xZ3YWIU31z3w7M1FOLaGQLoCVngpvleCf9mPKdZXyeg= ). > > > > > 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_= > DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU= > Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h= > xkJKj22zARpX6Nb06fIYl84-gdaEmosSya1Wa40jup4=i2JxC1bWoyzIpDK_jkYp7Y- > lZHnbKjsvPP1EcWiO3d0= > > > > >> 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_=DgIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > v58bHfswf4lrCGRXVvbZcOuRlfxX4A2JFW3Y0a7wEy0=XzjL16KbCkVYgzwzcBN71XtHS- > Bf5CtQ27hsmHKwizg= > > > > >> ) 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 > > > > > > > > > > > > > > > > >
Re: Infrastructures questions.
gt; > > > 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=DgIFaQ= > qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=xkJKj22zARpX6Nb06fIYl84- > gdaEmosSya1Wa40jup4=xZ3YWIU31z3w7M1FOLaGQLoCVngpvleCf9mPKdZXyeg= ). > > > > > 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_= > DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU= > Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h= > xkJKj22zARpX6Nb06fIYl84-gdaEmosSya1Wa40jup4=i2JxC1bWoyzIpDK_jkYp7Y- > lZHnbKjsvPP1EcWiO3d0= > > > > >> 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_=DgIBaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao= > v58bHfswf4lrCGRXVvbZcOuRlfxX4A2JFW3Y0a7wEy0=XzjL16KbCkVYgzwzcBN71XtHS- > Bf5CtQ27hsmHKwizg= > > > > >> ) 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 > > > > > > > > > > > > > > > > >
RE: Infrastructures questions.
Have you initiated a vote to release a 3.2.3 binary? Or do you want to wait until the branch has gone through testing? Just curious. Btw, thanks for writing the report. I don't know if anybody ever thanks you for that. Sean -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, December 13, 2016 11:15 AM To: dev@ctakes.apache.org Subject: Re: Infrastructures questions. What release are you referring to? On Tue, Dec 13, 2016 at 11:08 AM, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > By the way, did we ever vote on the release? > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.apache.org_dev > _release.html-23approving-2Da-2Drelease=DgIFaQ=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao > =1uvuZ-lCXmVb-q727eqDdfs75xcHBlHb5YbvO5MDZKQ=fDQuQs0XzMQHSXAda8Qiz > o04I7Mr91Je1VweuWqNsh8= > > > -Original Message- > From: Pei Chen [mailto:chen...@apache.org] > Sent: Tuesday, December 13, 2016 10:51 AM > To: dev@ctakes.apache.org > Subject: Re: Infrastructures questions. > > 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_searc > h_-3Fq-3Dctakes-2520mvn-2520package-2520-2DDskipTests-23query-3Actakes > -2520mvn-2520package-2520-2DDskipTests-2Bpage-3A1-2Bmid-3Aoxgrkslhhjim > pv4k-2Bstate-3Aresults=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC > oppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LL_nmgQ_ea-8hW > 5p-lXaiDLX2zp58A5ZuDimQJunDQ0=XZK-oW6nrKdzKmgZCnIW_zO-b-vqwKSaVWKzYM > FIP6g= > > 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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=DwFSPNSn27AvMjRSNXGHueqTsyc_T5Aetds4ipSzuYo= >> ). >> 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 probl
Re: Infrastructures questions.
What release are you referring to? On Tue, Dec 13, 2016 at 11:08 AM, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > By the way, did we ever vote on the release? > http://www.apache.org/dev/release.html#approving-a-release > > > -Original Message- > From: Pei Chen [mailto:chen...@apache.org] > Sent: Tuesday, December 13, 2016 10:51 AM > To: dev@ctakes.apache.org > Subject: Re: Infrastructures questions. > > 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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=XZK-oW6nrKdzKmgZCnIW_zO-b-vqwKSaVWKzYMFIP6g= > > 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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=DwFSPNSn27AvMjRSNXGHueqTsyc_T5Aetds4ipSzuYo= >> ). >> 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_=DgIFaQ=qS4goWBT7poplM69z >>> y_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g >>> Tao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=rdkXOpLdPvaAw15Zv >>> gsqVztehD5Bc7SSClGDl5KTcMs= 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
RE: Infrastructures questions.
By the way, did we ever vote on the release? http://www.apache.org/dev/release.html#approving-a-release -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, December 13, 2016 10:51 AM To: dev@ctakes.apache.org Subject: Re: Infrastructures questions. 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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=XZK-oW6nrKdzKmgZCnIW_zO-b-vqwKSaVWKzYMFIP6g= 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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=DwFSPNSn27AvMjRSNXGHueqTsyc_T5Aetds4ipSzuYo= > ). > 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_=DgIFaQ=qS4goWBT7poplM69z >> y_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g >> Tao=LL_nmgQ_ea-8hW5p-lXaiDLX2zp58A5ZuDimQJunDQ0=rdkXOpLdPvaAw15Zv >> gsqVztehD5Bc7SSClGDl5KTcMs= 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 cTake
Re: Infrastructures questions.
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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=xkJKj22zARpX6Nb06fIYl84-gdaEmosSya1Wa40jup4=HIc4d0eWT6Wv0UY2Ytxm_oq5c-sUzay1SSq7XE4rDtE= > > > 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=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=xkJKj22zARpX6Nb06fIYl84-gdaEmosSya1Wa40jup4=xZ3YWIU31z3w7M1FOLaGQLoCVngpvleCf9mPKdZXyeg= > > ). > > 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_=DgIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=xkJKj22zARpX6Nb06fIYl84-gdaEmosSya1Wa40jup4=i2JxC1bWoyzIpDK_jkYp7Y-lZHnbKjsvPP1EcWiO3d0= > >> > >> 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
FW: Infrastructures questions.
This is a great question. mvn compile requires -DskipTests otherwise the build breaks. This is very poor form and everybody that installs runs into this. It would be great if we could fix this before the release. Any volunteers? 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_=DgIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=v58bHfswf4lrCGRXVvbZcOuRlfxX4A2JFW3Y0a7wEy0=XzjL16KbCkVYgzwzcBN71XtHS-Bf5CtQ27hsmHKwizg= ) 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
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://github.com/apache/ctakes/) 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
