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-system/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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&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/apache/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_bcdc25420eede623a0889b1db26e1307a2b193bf&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=c2oayQ5_G3YgHT5iX9AJw9kuhIr94bFRZ7nxj3ebpuw&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_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=aRH4KLtGndnC-b7UTdMqjej6vTDKxavocQwUokE6EHw&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_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=-PwjGWv5MEFT_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. 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. > > 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. > 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. >
