Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Thanks Tim. There is a patch in the jira item, but I don't know if it was ever applied (checked in). Does anybody know? From: Miller, Timothy Sent: Friday, January 11, 2019 11:32 AM To: dev@ctakes.apache.org Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Looks like someone fixed that as part of a different issue: https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D500&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1stOSUyvduxWyRf5ExkM407a94mlzdOtd52cdYQb3WQ&s=eSMr6VoSvH5sGvOa4s3OzFHOWPSUigB1hED4x2wu27A&e= Tim -Original Message- From: "Finan, Sean" mailto:%22Finan,%20sean%22%20%3csean.fi...@childrens.harvard.edu%3e>> Reply-to: To: dev@ctakes.apache.org mailto:%22...@ctakes.apache.org%22%20%3c...@ctakes.apache.org%3e>> Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] Date: Fri, 11 Jan 2019 16:05:21 + Hi Sana, This might be related to https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D450-3Ffilter-3D-2D5-26jql-3Dproject-2520-253D-2520CTAKES-2520AND-2520resolution-2520-253D-2520Unresolved-2520AND-2520-2522Attachment-2520count-2522-2520-253C-253D-2520-25222-2522-2520AND-2520-2522Attachment-2520count-2522-2520-253E-253D-2520-25221-2522-2520order-2520by-2520priority-2520DESC-252Cupdated-2520DESC&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Ojz-Ww86QvcLG1VBfECfCcNudtXNQIe7c-jJ_UMXtiE&s=sd2GH6n5nOzk4vtOA4qKh0kULci4rCiBDMWyM0IKU0Y&e= If anybody has time to test and approve the patch attached to that tar please let me know so that it can be checked in. Thanks, Sean From: Sana Riaz mailto:sana.r...@xflowresearch.com>> Sent: Friday, January 11, 2019 5:33 AM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] Hi, I am trying to process CDA documents with AggregateCdaUMLSProcessor.xml descriptor (clinical-pipeline). The cda document includes sections like problems, medications, allergies, tests etc. In the plain_view, all these section are visible in CVD but all the annotations extracted by AggregateCdaUMLSProcessor are only on last section. i.e. there's no annotation on the medications or problems. I've looked into CdaCasInitializer output , and it only passes one segment (the last one) so all the other annotators only process on that. In addition to that, every section's id (including last) is assigned null as [start section id="null"] [end section id="null"] Do i have to assign section id's myself? Any suggestion would be very helpful. Warm Regards, Sana Riaz
Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Sean, Thanks for your reply. Can you please help me how can I apply these patches to my current project. I have added ctakes libraries as jar files through maven dependencies. how would i update those jar files with these changes. Currently, I have tried using maven-plugin as following but it didnt change anything. > org.apache.maven.plugins > maven-patch-plugin > 1.2 > > > > https://issues.apache.org/jira/secure/attachment/12916325/CTAKES-500.patch > > > > > > patch > process-sources > > apply > > > > Warm Regards, Sana Riaz On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Thanks Tim. > There is a patch in the jira item, but I don't know if it was ever applied > (checked in). > Does anybody know? > > > From: Miller, Timothy > Sent: Friday, January 11, 2019 11:32 AM > To: dev@ctakes.apache.org > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Looks like someone fixed that as part of a different issue: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D500&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1stOSUyvduxWyRf5ExkM407a94mlzdOtd52cdYQb3WQ&s=eSMr6VoSvH5sGvOa4s3OzFHOWPSUigB1hED4x2wu27A&e= > Tim > > > -Original Message- > From: "Finan, Sean" mailto:%22Finan,% > 20sean%22%20%3csean.fi...@childrens.harvard.edu%3e>> > Reply-to: > To: dev@ctakes.apache.org 22...@ctakes.apache.org%22%20%3c...@ctakes.apache.org%3e>> > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] [SUSPICIOUS] > Date: Fri, 11 Jan 2019 16:05:21 + > > > Hi Sana, > > This might be related to > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D450-3Ffilter-3D-2D5-26jql-3Dproject-2520-253D-2520CTAKES-2520AND-2520resolution-2520-253D-2520Unresolved-2520AND-2520-2522Attachment-2520count-2522-2520-253C-253D-2520-25222-2522-2520AND-2520-2522Attachment-2520count-2522-2520-253E-253D-2520-25221-2522-2520order-2520by-2520priority-2520DESC-252Cupdated-2520DESC&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Ojz-Ww86QvcLG1VBfECfCcNudtXNQIe7c-jJ_UMXtiE&s=sd2GH6n5nOzk4vtOA4qKh0kULci4rCiBDMWyM0IKU0Y&e= > > If anybody has time to test and approve the patch attached to that tar > please let me know so that it can be checked in. > > Thanks, > Sean > > From: Sana Riaz sana.r...@xflowresearch.com>> > Sent: Friday, January 11, 2019 5:33 AM > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> > Subject: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] > > Hi, > I am trying to process CDA documents with AggregateCdaUMLSProcessor.xml > descriptor (clinical-pipeline). The cda document includes sections like > problems, medications, allergies, tests etc. In the plain_view, all these > section are visible in CVD but all the annotations extracted by > AggregateCdaUMLSProcessor are only on last section. i.e. there's no > annotation on the medications or problems. > > I've looked into CdaCasInitializer output , and it only passes one segment > (the last one) so all the other annotators only process on that. In > addition to that, every section's id (including last) is assigned null as > [start section id="null"] > > [end section id="null"] > > Do i have to assign section id's myself? Any suggestion would be very > helpful. > > Warm Regards, > > Sana Riaz > >
Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Maybe this would help? http://maven.apache.org/plugins/maven-patch-plugin/ From: Sana Riaz Sent: Monday, January 14, 2019 4:59 AM To: dev@ctakes.apache.org Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Hi Sean, Thanks for your reply. Can you please help me how can I apply these patches to my current project. I have added ctakes libraries as jar files through maven dependencies. how would i update those jar files with these changes. Currently, I have tried using maven-plugin as following but it didnt change anything. > org.apache.maven.plugins > maven-patch-plugin > 1.2 > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_secure_attachment_12916325_CTAKES-2D500.patch&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=gPZ5JJ-v0kMpDC-vOJTwHP3Ygmn5Ayabo1Rt2xwetpM&s=Ec0ElrVtO9JsYMvjj46U0V07C6KOBvt3Hstk82MR-Og&e= > > > > > > patch > process-sources > > apply > > > > Warm Regards, Sana Riaz On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Thanks Tim. > There is a patch in the jira item, but I don't know if it was ever applied > (checked in). > Does anybody know? > > ____ > From: Miller, Timothy > Sent: Friday, January 11, 2019 11:32 AM > To: dev@ctakes.apache.org > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Looks like someone fixed that as part of a different issue: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D500&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1stOSUyvduxWyRf5ExkM407a94mlzdOtd52cdYQb3WQ&s=eSMr6VoSvH5sGvOa4s3OzFHOWPSUigB1hED4x2wu27A&e= > Tim > > > -Original Message- > From: "Finan, Sean" mailto:%22Finan,% > 20sean%22%20%3csean.fi...@childrens.harvard.edu%3e>> > Reply-to: > To: dev@ctakes.apache.org 22...@ctakes.apache.org%22%20%3c...@ctakes.apache.org%3e>> > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] [SUSPICIOUS] > Date: Fri, 11 Jan 2019 16:05:21 + > > > Hi Sana, > > This might be related to > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D450-3Ffilter-3D-2D5-26jql-3Dproject-2520-253D-2520CTAKES-2520AND-2520resolution-2520-253D-2520Unresolved-2520AND-2520-2522Attachment-2520count-2522-2520-253C-253D-2520-25222-2522-2520AND-2520-2522Attachment-2520count-2522-2520-253E-253D-2520-25221-2522-2520order-2520by-2520priority-2520DESC-252Cupdated-2520DESC&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Ojz-Ww86QvcLG1VBfECfCcNudtXNQIe7c-jJ_UMXtiE&s=sd2GH6n5nOzk4vtOA4qKh0kULci4rCiBDMWyM0IKU0Y&e= > > If anybody has time to test and approve the patch attached to that tar > please let me know so that it can be checked in. > > Thanks, > Sean > > From: Sana Riaz sana.r...@xflowresearch.com>> > Sent: Friday, January 11, 2019 5:33 AM > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> > Subject: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] > > Hi, > I am trying to process CDA documents with AggregateCdaUMLSProcessor.xml > descriptor (clinical-pipeline). The cda document includes sections like > problems, medications, allergies, tests etc. In the plain_view, all these > section are visible in CVD but all the annotations extracted by > AggregateCdaUMLSProcessor are only on last section. i.e. there's no > annotation on the medications or problems. > > I've looked into CdaCasInitializer output , and it only passes one segment > (the last one) so all the other annotators only process on that. In > addition to that, every section's id (including last) is assigned null as > [start section id="null"] > > [end section id="null"] > > Do i have to assign section id's myself? Any suggestion would be very > helpful. > > Warm Regards, > > Sana Riaz > >
Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Sean. Sorry for bothering you again. I tried applying the above patches. I am getting following error after changing the typesystem as mentioned in https://issues.apache.org/jira/browse/CTAKES-500 org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.canehealth.spring.ctakes.service.CtakesService]: Constructor threw e xception; nested exception is org.apache.uima.cas.CASRuntimeException: CAS type system doesn''t match JCas Type definition for type "{0}". at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:182) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1228) ... 30 more Caused by: org.apache.uima.cas.CASRuntimeException: CAS type system doesn''t match JCas Type definition for type "{0}". at org.apache.uima.jcas.impl.JCasImpl.logAndThrow(JCasImpl.java:493) at org.apache.uima.jcas.impl.JCasImpl.makeInstanceOf_Type(JCasImpl.java:1036) at org.apache.uima.jcas.impl.JCasImpl.instantiateJCas_Types(JCasImpl.java:714) at org.apache.uima.jcas.impl.JCasImpl.(JCasImpl.java:545) at org.apache.uima.jcas.impl.JCasImpl.getJCas(JCasImpl.java:785) at org.apache.uima.cas.impl.CASImpl.getJCas(CASImpl.java:3105) at org.apache.uima.jcas.impl.JCasImpl.(JCasImpl.java:528) at org.apache.uima.jcas.impl.JCasImpl.getJCas(JCasImpl.java:785) at org.apache.uima.cas.impl.CASImpl.getJCas(CASImpl.java:3105) at com.canehealth.spring.ctakes.service.CtakesService.(CtakesService.java:85) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:170) ... 32 more Caused by: java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at org.apache.uima.jcas.impl.JCasImpl.makeInstanceOf_Type(JCasImpl.java:1017) ... 45 more Caused by: java.lang.Error: Unresolved compilation problem: The method addGeneratorForType(TypeImpl, FSGenerator) is undefined for the type FSClassRegistry at org.apache.ctakes.typesystem.type.textspan.SectionHeading_Type.(SectionHeading_Type.java:83) ... 50 more *CAS type system doesn''t match JCas Type definition for type "{0}".*i understand that this error occured due to new typedescription "SectionHeading" but I couldnt find what this error means or how to solve it. It would be very kind if you'd help me through this. Warm Regards, Sana Riaz On Mon, Jan 14, 2019 at 8:05 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Maybe this would help? > http://maven.apache.org/plugins/maven-patch-plugin/ > > > From: Sana Riaz > Sent: Monday, January 14, 2019 4:59 AM > To: dev@ctakes.apache.org > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA > document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Hi Sean, > Thanks for your reply. Can you please help me how can I apply these patches > to my current project. I have added ctakes libraries as jar files through > maven dependencies. how would i update those jar files with these changes. > Currently, I have tried using maven-plugin as following but it didnt change > anything. > > > > org.apache.maven.plugins > > maven-patch-plugin > > 1.2 > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_secure_attachment_12916325_CTAKES-2D500.patch&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=gPZ5JJ-v0kMpDC-vOJTwHP3Ygmn5Ayabo1Rt2xwetpM&s=Ec0ElrVtO9JsYMvjj46U0V07C6KOBvt3Hstk82MR-Og&e= > > > > > > > > > > > > patch > > process-sources > > > > apply > > > > > > > > > > > > > Warm Regards, > > Sana Riaz > > > On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Thanks Tim. > > Th