Hi Sean, Glad I'm on the right path with assumeTrue, I will come back shortly with a patch for it.
Checking for a buildID, would make cTAKES dependent on the Apache build service (Jenkins), making it less portable. I think it would impact adoption for community. What do you think? Alex On Wed, Nov 15, 2017 at 1:36 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Alex, > > I like your assumeTrue idea. I think that you wrote about it earlier? > The only problem that I can think of right now is the different ways that > the umls credentials can be supplied. It may be difficult to check them > all. However, maybe just one being available is all that is needed. > > What about using assumeTrue to check for a Jenkins environment instead of > checking for umls credentials? We could check for a $BUILD_TAG that starts > with "jenkins-" and/or $JENKINS_URL. > > https://wiki.jenkins.io/display/JENKINS/Building+a+software+project > > > Don't follow my lead ... we'll both get lost. > > Sean > > > -----Original Message----- > From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] > Sent: Wednesday, November 15, 2017 12:41 PM > To: Apache cTAKES Dev > Subject: Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL] > > Hi Sean, > > Your links are very informative. I think using Categories is a great idea. > Categories can also be used to differentiate between tests that require: > DB (MySQL, Oracle, HSQLDB etc) vs non-DB, slow vs fast, UMLS vs non-UMLS. > > In the solution you propose, if I understand right, the discriminator > between running or not running UMLSs tests would be if the category has > been added to the default profile. I wonder if it might not create the > behavior, for the community, to not run some categories of tests. > > What I was thinking is to use Assume.assumeTrue [1] (as a side note, it > can be used together with Categories ) and ignore the execution of the test > if UMLSs account is not setup and enforce to use UMLS if the realease > profile is being used. The reason I say this is because when the release is > going to be built, the owner will be forced to certify that all tests run. > Just my $0.02. What we can also do, is to create a PR, and upload the > patch, and based on a consensus to apply the patch. > > I will follow your lead on this. What do you think? > Alex > > [1] - > https://urldefense.proofpoint.com/v2/url?u=http-3A__junit. > sourceforge.net_javadoc_org_junit_Assume.html-23assumeTrue-28boolean-29&d= > DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=K0KP_ > M1BTpGUsPOHy6q6q78mS9FKvIj6-B7UEjVOUmc&s=K1pRo0hnemAlUChvke7CvCFXgl7z9u > zTgm-oVgSUV6k&e= > > On Wed, Nov 15, 2017 at 10:05 AM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Alex, > > > > That might work, but I don't know that playing with the release > > profile is the best course of action. I have found a few other > > possibilities. I am leaning toward #3 (@Category) > > > > This approach separates tests into two different directories and > > profiles. It requires a good number of pom changes.: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.testwithsprin > > g.com_lesson_running-2D&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio > > CoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=K0KP_M1BTpGUs > > POHy6q6q78mS9FKvIj6-B7UEjVOUmc&s=IER3aq60g2KOYhWTLp_kCyZBvd4bYMJG0hoin > > OcDAKM&e= > > integration-tests-with-maven/ > > which is an update of this: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.petrikainulai > > nen.net_programming_maven_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=K0KP_M1BTp > > GUsPOHy6q6q78mS9FKvIj6-B7UEjVOUmc&s=99_M-9YUyTCzKBrV5A62i_csb1_NgNlSIn > > r4UHz1UTQ&e= > > integration-testing-with-maven/ > > > > Another approach looks simpler and more straightforward, using > > filenames for tests and a profile: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__semaphoreci.com_c > > ommunity_tutorials_how-2Dto-2Dsplit-2Djunit-2Dtests-2Din-2Da-2D&d=DwIB > > aQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCY > > NYmQCP6r0bcpKGd4f7d4gTao&m=K0KP_M1BTpGUsPOHy6q6q78mS9FKvIj6-B7UEjVOUmc > > &s=RYlK-TTW_2rK8ckOLjw6rhog5KuCPIr6Obe_h523eXg&e= > > continuous-integration-environment > > Since this could be done with the -regression module alone we wouldn't > > need to rename all unit test files in other modules. > > > > That being said, it looks like junit 4.8 (or earlier?) has @Category > > annotations that can be used: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_junit- > > 2Dteam_junit4_wiki_categories&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=K0KP_M1 > > BTpGUsPOHy6q6q78mS9FKvIj6-B7UEjVOUmc&s=1WDCmSYL50NCHMSCi6nEYXfYnOoUDcX > > VfWXY89luqaY&e= > > slightly reworded ...: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__dzone.com_article > > s_closer-2Dlook-2Djunit-2Dcategories&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xh > > KwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > K0KP_M1BTpGUsPOHy6q6q78mS9FKvIj6-B7UEjVOUmc&s=nSAIYioeUSIi17JHmiluKlq9 > > aqOZ7g1mKNF-bhpr_UQ&e= > > > > Any thoughts on these approaches? > > > > I think that the regression test should be rewritten. It is pretty > > old and doesn't actually test the default clinical pipeline as > > executed by bin/ scripts anymore. > > > > Sean > > > > -----Original Message----- > > From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] > > Sent: Tuesday, November 14, 2017 7:47 PM > > To: Apache cTAKES Dev > > Subject: Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL] > > > > Hi, > > > > It seems that the patch for the org.apache.ctakes.ytex.ConceptDaoTest > > was already provided on CTAKES-334. > > > > Applying the fix passes the test. > > > > The only test that needs to be fixed seems to be: > > RegressionPipelineTest:testCPE. For this, the fix is to export the > > UMLS credentials. > > > > I am currently working on enabling the the test based on the umls > > credentials being available and enforcing the execution on a release > > profile, which now seems to be disabled: > > useReleaseProfile>false</useReleaseProfile > > > > Any feedback? > > Alex > > > > [1] - > > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. > > apache.org_view_C_view_Apache-2520cTAKES_job_ctakes-2Dtrunk- > > 2Dcompiletest_1124_org.apache.ctakes-24ctakes-2Dregression- > > 2Dtest_testReport_org.apache.ctakes.regression.test_ > > RegressionPipelineTest_testCPE_&d=DwIBaQ&c=qS4goWBT7poplM69zy_ > > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao > > &m= > > zeyWc75KvsxXPw3cJmG6oF2TBpxrlbOGRwQyh3CZ-eY&s=kgBJTLtXcwxSXuviL2BBBT- > > j5xGFN4uLHQbEkzPeww0&e= > > > > > > On Tue, Nov 14, 2017 at 9:47 AM, Gandhi Rajan Natarajan < > > gandhi.natara...@arisglobal.com> wrote: > > > > > Hi Alex, > > > > > > The error we got in ConceptDaoTest is different from yours. We got > > > the > > > following: > > > > > > testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): > > > Unable to initialize group definition. Group resource name > > > [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], > > > factory key [kernelApplicationContext]; nested exception is > > > org.springframework.beans.factory.BeanCreationException: Error > > > creating bean with name 'kernelApplicationContext' defined in URL > > > [file:/D:/Gandhi/ArisG/cTAKES/ctakes_src_new%20-%20Copy/ctak > > > es-ytex-res/src/main/resources/org/apache/ctakes/ > > ytex/kernelBeanRefContext.xml]: > > > Instantiation of bean failed; nested exception is > > > org.springframework.beans.BeanInstantiationException: Could not > > > instantiate bean class [org.springframework.context.s > > > upport.ClassPathXmlApplicationContext]: Constructor threw exception; > > > nested exception is org.springframework.beans. > > factory.BeanCreationException: > > > Error creating bean with name 'gramMatrixExporter' defined in class > > > path resource [org/apache/ctakes/ytex/beans-kernel.xml]: > > > Initialization of bean failed; nested exception is > > org.springframework.beans.FatalBeanException: > > > Failed to obtain BeanInfo for class > > > [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; > > > nested exception is java.beans.IntrospectionException: type mismatch > > > between read and write methods > > > > > > Can you do a full build once and try? > > > > > > Regards, > > > Gandhi > > > > > > > > > -----Original Message----- > > > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > > > Sent: Tuesday, November 14, 2017 7:36 PM > > > To: dev@ctakes.apache.org > > > Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL] > > > > > > Hi Alex, > > > > > > Major kudos for trying to track this down. > > > > > > I am not sure why you are seeing that particular problem. Metadata > > > class should be auto-generated from the type system, and it does > > > have the > > > getPatientIdentifier() method. > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_ > > > re > > > pos_asf_ctakes_trunk_ctakes-2Dtype-2Dsy&d=DwIBaQ&c=qS4goWBT7poplM69z > > > y_ > > > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gT > > > ao > > > &m=zeyWc75KvsxXPw3cJmG6oF2TBpxrlbOGRwQyh3CZ-eY&s=kWkYEuKO59NQE3OMhtI > > > Yc > > > dGfi0U_56Szw8fxzngfm_0&e= > > > stem/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem. > > > xml > > > > > > Do you think that it is possible that the jcasgen is not being run > > > before the test? I think that it is run for ctakes-util, which is a > > > dependency for all modules. > > > > > > Regardless, I cannot see where getPatientIdentifier() is used in > > > ConceptDaoTest. I can't see where the class Metadata is used in > > > ConceptDaoTest. From a quick code search, Metadata is only used by > > > the class SourceMetadataUtil in core. SourceMetadataUtil is only > > > used by two classes, both in core. I think that the change in test > > > status is actually unrelated to the Metadata checkin. That being > > > said, I don't have any good idea about what is causing it. > > > > > > Thanks, > > > Sean > > > > > > -----Original Message----- > > > From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] > > > Sent: Monday, November 13, 2017 6:24 PM > > > To: Apache cTAKES Dev > > > Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL] > > > > > > Hi, > > > > > > The official Jenkins job (referenced in the pom.xml) is: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. > > > apache.org_job_ctakes-2Dtrunk_&d=DwIBaQ&c=qS4goWBT7poplM69zy > > > _3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpK > > > Gd4f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s= > > > ul6gCHWXUReDCZccgemrhL9EEFs0Id7WilYITMNr5yw&e=. As one may notice, > > > the status is Unstable. I was working on the cTAKES-trunk-Java-1.8 > > > Jenkins job [1] to try to fix the issues there. As such the tests > > > failed can be found here [2]. > > > > > > So trying to fix one by one, I discovered that for > > > ctakes-ytex:ConceptDaoTest.java:testCreateConceptGraph: > > > > > > There is the construction: > > > metadata.getPatientIdentifier() > > > (where metadata:org.apache.ctakes.typesystem.type.structured. > Metadata). > > > > > > Researching where this comes (because it seems it is a new issue), I > > > realized that is related to: > > > ctakes-type-system/target/generated-sources/jcasgen/org/apac > > > he/ctakes/typesystem/type/structured/Metadata.java > > > :75: public String getPatientIdentifier() { > > > > > > more: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > > com_apache_ctakes_commit_bcdc25420eede623a0889b1db26e1307a2b > > > 193bf&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU > > > &r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l0_Tnqk6P-i > > > MIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=c2oayQ5_G3YgHT5iX9AJw9kuh > > > Ir94bFRZ7nxj3ebpuw&e= > > > (10 Oct 2017) > > > > > > I thought that it will be a quick fix just replacing: > > > > > > metadata.getPatientIdentifier() > > > > > > with > > > > > > String.format("%d", metadata.getPatientID()); > > > > > > > > > Any feedback? > > > Alex > > > > > > [1] - > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. > > > apache.org_view_C_view_Apache-2520cTAKES_job_cTAKES-2Dtrunk- > > > 2DJava-2D1.8_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio > > > CoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l0_ > > > Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=aRH4KLtGndnC-b7UT > > > dMqjej6vTDKxavocQwUokE6EHw&e= > > > [2] - > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. > > > apache.org_view_C_view_Apache-2520cTAKES_job_cTAKES-2Dtrunk- > > > 2DJava-2D1.8_25_testReport_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3x > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4 > > > f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=-Pw > > > jGWv5MEFT_1Jui9b27fdgkKfFRa29hts-FMalo8I&e= > > > > > > > > > On Nov 13, 2017 10:41, "Finan, Sean" > > > <sean.fi...@childrens.harvard.edu> > > > wrote: > > > > > > > Thanks Gandhi! > > > > > > > > -----Original Message----- > > > > From: Gandhi Rajan Natarajan > > > > [mailto:gandhi.natara...@arisglobal.com] > > > > Sent: Monday, November 13, 2017 10:40 AM > > > > To: dev@ctakes.apache.org > > > > Subject: RE: Disable yTEX and Regression tests on Jenkins > > > > [EXTERNAL] > > > > > > > > Hi All, > > > > > > > > We had a look at ctakes-Ytex module's failing test cases and looks > > > > like it will not have an impact once we upgrade Spring 4x in cTAKES. > > > > > > > > We will have a run through at other modules and check the failing > > > > test cases if any. > > > > > > > > Regards, > > > > Gandhi > > > > > > > > > > > > -----Original Message----- > > > > From: Sandeep Byatha Gururaja rao > > > > [mailto:sandeep...@arisglobal.com] > > > > Sent: Monday, November 13, 2017 6:50 PM > > > > To: dev@ctakes.apache.org > > > > Subject: RE: Disable yTEX and Regression tests on Jenkins > > > > [EXTERNAL] > > > > > > > > Hi Sean, > > > > > > > > Myself and Gandhi will work on this and try to fix the issues. > > > > > > > > Regards, > > > > Sandeep > > > > > > > > ------------------------------------ > > > > > > > > Hi Gandhi, > > > > > > > > Many thanks for volunteering. I am slammed with work right now, > > > > but if anybody else can also help out ... > > > > > > > > Sean > > > > > > > > -----Original Message----- > > > > From: Gandhi Rajan Natarajan > > > > [mailto:gandhi.natara...@arisglobal.com] > > > > Sent: Thursday, November 09, 2017 12:43 AM > > > > To: dev@ctakes.apache.org > > > > Subject: RE: Disable yTEX and Regression tests on Jenkins > > > > [EXTERNAL] > > > > > > > > Hi Sean, > > > > > > > > I can take it up if someone is willing to guide me on this. > > > > > > > > Regards, > > > > Gandhi > > > > > > > > > > > > -----Original Message----- > > > > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > > > > Sent: Wednesday, November 08, 2017 9:45 PM > > > > To: dev@ctakes.apache.org > > > > Subject: Disable yTEX and Regression tests on Jenkins > > > > > > > > Hi all, > > > > > > > > The Jenkins builds have been failing for about a month now because > > > > of internal Jenkins changes and 'unit' tests in the > > > > ctakes-Regression and ctakes-yTEX modules. This is holding up the > > > > build for all of our primary clinical-pipeline modules. > > > > > > > > If anybody can take a look at the problems and fix them please > > > > respond to this email. Otherwise I would like to create a jira > > > > issue and disable them until somebody does have the time to take > > > > care > > of them. > > > > If you have a good reason for these tests not being disabled (e.g. > > > > we might forget to fix > > > > them) please state a case. I do not intend to act unilaterally on > > > > this issue. > > > > > > > > Please respond by midnight Friday, November 10. > > > > > > > > Thank you, > > > > > > > > Sean > > > > This email and any files transmitted with it are confidential and > > > > intended solely for the use of the individual or entity to whom > > > > they are > > > addressed. > > > > If you are not the named addressee you should not disseminate, > > > > distribute or copy this e-mail. 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