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://builds.apache.org/view/C/view/Apache%20cTAKES/job/ctakes-trunk-compiletest/1124/org.apache.ctakes$ctakes-regression-test/testReport/org.apache.ctakes.regression.test/RegressionPipelineTest/testCPE/ On Tue, Nov 14, 2017 at 9:47 AM, Gandhi Rajan Natarajan < [email protected]> 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:[email protected]] > Sent: Tuesday, November 14, 2017 7:36 PM > To: [email protected] > 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://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-sy > 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:[email protected]] > 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" <[email protected]> > wrote: > > > Thanks Gandhi! > > > > -----Original Message----- > > From: Gandhi Rajan Natarajan [mailto:[email protected]] > > Sent: Monday, November 13, 2017 10:40 AM > > To: [email protected] > > 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:[email protected]] > > Sent: Monday, November 13, 2017 6:50 PM > > To: [email protected] > > 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:[email protected]] > > Sent: Thursday, November 09, 2017 12:43 AM > > To: [email protected] > > 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:[email protected]] > > Sent: Wednesday, November 08, 2017 9:45 PM > > To: [email protected] > > 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. Please notify the sender or system > > manager by email immediately if you have received this e-mail by > > mistake and delete this e-mail from your system. 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If you are not the > > intended recipient you are notified that disclosing, copying, > > distributing or taking any action in reliance on the contents of this > > information is strictly prohibited and against the law. > > > 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. Please notify the sender or system manager by email > immediately if you have received this e-mail by mistake and delete this > e-mail from your system. If you are not the intended recipient you are > notified that disclosing, copying, distributing or taking any action in > reliance on the contents of this information is strictly prohibited and > against the law. >
