You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by Sana Riaz <sa...@xflowresearch.com> on 2019/01/11 10:33:24 UTC
AggregateCdaUmlsprocessor only annotates last section of CDA document
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]
Posted by Sana Riaz <sa...@xflowresearch.com>.
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.<init>(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.<init>(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.<init>(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<capture#1-of ?>) is
undefined for the type FSClassRegistry
at
org.apache.ctakes.typesystem.type.textspan.SectionHeading_Type.<init>(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.Finan@childrens.harvard.edu> wrote:
> Maybe this would help?
> http://maven.apache.org/plugins/maven-patch-plugin/
>
> ________________________________________
> From: Sana Riaz <sa...@xflowresearch.com>
> 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.
>
> <plugin>
> > <groupId>org.apache.maven.plugins</groupId>
> > <artifactId>maven-patch-plugin</artifactId>
> > <version>1.2</version>
> > <configuration>
> > <patches>
> > <patch>
> >
> 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>
> > </patches>
> > </configuration>
> > <executions>
> > <execution>
> > <id>patch</id>
> > <phase>process-sources</phase>
> > <goals>
> > <goal>apply</goal>
> > </goals>
> > </execution>
> > </executions>
> > </plugin>
>
>
>
>
> Warm Regards,
>
> Sana Riaz
>
>
> On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean <
> Sean.Finan@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 <Ti...@childrens.harvard.edu>
> > 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" <Sean.Finan@childrens.harvard.edu<mailto:%22Finan,%
> > 20Sean%22%20%3cSean.Finan@childrens.harvard.edu%3e>>
> > Reply-to: <de...@ctakes.apache.org>
> > To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%
> > 22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
> > Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA
> > document [EXTERNAL] [SUSPICIOUS]
> > Date: Fri, 11 Jan 2019 16:05:21 +0000
> >
> >
> > 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.riaz@xflowresearch.com<mailto:
> > sana.riaz@xflowresearch.com>>
> > Sent: Friday, January 11, 2019 5:33 AM
> > To: dev@ctakes.apache.org<ma...@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]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Maybe this would help?
http://maven.apache.org/plugins/maven-patch-plugin/
________________________________________
From: Sana Riaz <sa...@xflowresearch.com>
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.
<plugin>
> <groupId>org.apache.maven.plugins</groupId>
> <artifactId>maven-patch-plugin</artifactId>
> <version>1.2</version>
> <configuration>
> <patches>
> <patch>
> 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>
> </patches>
> </configuration>
> <executions>
> <execution>
> <id>patch</id>
> <phase>process-sources</phase>
> <goals>
> <goal>apply</goal>
> </goals>
> </execution>
> </executions>
> </plugin>
Warm Regards,
Sana Riaz
On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean <
Sean.Finan@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 <Ti...@childrens.harvard.edu>
> 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" <Sean.Finan@childrens.harvard.edu<mailto:%22Finan,%
> 20Sean%22%20%3cSean.Finan@childrens.harvard.edu%3e>>
> Reply-to: <de...@ctakes.apache.org>
> To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%
> 22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
> Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA
> document [EXTERNAL] [SUSPICIOUS]
> Date: Fri, 11 Jan 2019 16:05:21 +0000
>
>
> 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.riaz@xflowresearch.com<mailto:
> sana.riaz@xflowresearch.com>>
> Sent: Friday, January 11, 2019 5:33 AM
> To: dev@ctakes.apache.org<ma...@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]
Posted by Sana Riaz <sa...@xflowresearch.com>.
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.
<plugin>
> <groupId>org.apache.maven.plugins</groupId>
> <artifactId>maven-patch-plugin</artifactId>
> <version>1.2</version>
> <configuration>
> <patches>
> <patch>
> https://issues.apache.org/jira/secure/attachment/12916325/CTAKES-500.patch
> </patch>
> </patches>
> </configuration>
> <executions>
> <execution>
> <id>patch</id>
> <phase>process-sources</phase>
> <goals>
> <goal>apply</goal>
> </goals>
> </execution>
> </executions>
> </plugin>
Warm Regards,
Sana Riaz
On Fri, Jan 11, 2019 at 9:36 PM Finan, Sean <
Sean.Finan@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 <Ti...@childrens.harvard.edu>
> 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" <Sean.Finan@childrens.harvard.edu<mailto:%22Finan,%
> 20Sean%22%20%3cSean.Finan@childrens.harvard.edu%3e>>
> Reply-to: <de...@ctakes.apache.org>
> To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%
> 22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
> Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA
> document [EXTERNAL] [SUSPICIOUS]
> Date: Fri, 11 Jan 2019 16:05:21 +0000
>
>
> 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.riaz@xflowresearch.com<mailto:
> sana.riaz@xflowresearch.com>>
> Sent: Friday, January 11, 2019 5:33 AM
> To: dev@ctakes.apache.org<ma...@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]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <Ti...@childrens.harvard.edu>
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" <Sean.Finan@childrens.harvard.edu<mailto:%22Finan,%20Sean%22%20%3cSean.Finan@childrens.harvard.edu%3e>>
Reply-to: <de...@ctakes.apache.org>
To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS]
Date: Fri, 11 Jan 2019 16:05:21 +0000
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 <sa...@xflowresearch.com>>
Sent: Friday, January 11, 2019 5:33 AM
To: dev@ctakes.apache.org<ma...@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]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Looks like someone fixed that as part of a different issue:
https://issues.apache.org/jira/browse/CTAKES-500
Tim
-----Original Message-----
From: "Finan, Sean" <Sean.Finan@childrens.harvard.edu<mailto:%22Finan,%20Sean%22%20%3cSean.Finan@childrens.harvard.edu%3e>>
Reply-to: <de...@ctakes.apache.org>
To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS]
Date: Fri, 11 Jan 2019 16:05:21 +0000
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 <sa...@xflowresearch.com>>
Sent: Friday, January 11, 2019 5:33 AM
To: dev@ctakes.apache.org<ma...@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]
Posted by gandhi rajan <ga...@gmail.com>.
Sean, Thanks for the response. I m interested in testing this but
unfortunately the infrastructure issues I have currently is stopping me
from doing this. That's why the apology for my helplessness currently. Will
have a check once my setup is ready but at this point the timelines are not
clear to me.
On Friday, January 11, 2019, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Gandhi,
>
> It would be great if you could test this! Why are you sorry?
>
> - I shouldn't have said "let me know", but rather "let the group know" or
> something like that.
>
>
> Cheers,
> Sean
>
> ________________________________________
> From: gandhi rajan <ga...@gmail.com>
> Sent: Friday, January 11, 2019 12:35 PM
> To: dev@ctakes.apache.org
> Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA
> document [EXTERNAL]
>
> Sorry Sean. I would love to do this but my old setup is all gone with my
> previous organization. Gotta do a fresh setup in my personal machine all
> over again. Sorry about that.
>
> On Friday, January 11, 2019, Finan, Sean <Sean.Finan@childrens.harvard.edu
> >
> wrote:
>
> > 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&d=DwIBaQ&c=
> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GSH42JyRAyTSQdrgKBYhzxD-
> 6j2sEhEwivjJTCh6YOQ&s=9rfxDksaU1nnkKao1IAuhngpM8fW0eVT8YWMcY-gne0&e=
> > -5&jql=project%20%3D%20CTAKES%20AND%20resolution%20%3D%
> > 20Unresolved%20AND%20%22Attachment%20count%22%20%3C%
> 3D%20%222%22%20AND%20%
> > 22Attachment%20count%22%20%3E%3D%20%221%22%20order%20by%
> > 20priority%20DESC%2Cupdated%20DESC
> >
> > 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 <sa...@xflowresearch.com>
> > Sent: Friday, January 11, 2019 5:33 AM
> > To: 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
> >
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: AggregateCdaUmlsprocessor only annotates last section of CDA
document [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Gandhi,
It would be great if you could test this! Why are you sorry?
- I shouldn't have said "let me know", but rather "let the group know" or something like that.
Cheers,
Sean
________________________________________
From: gandhi rajan <ga...@gmail.com>
Sent: Friday, January 11, 2019 12:35 PM
To: dev@ctakes.apache.org
Subject: Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL]
Sorry Sean. I would love to do this but my old setup is all gone with my
previous organization. Gotta do a fresh setup in my personal machine all
over again. Sorry about that.
On Friday, January 11, 2019, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> 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&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GSH42JyRAyTSQdrgKBYhzxD-6j2sEhEwivjJTCh6YOQ&s=9rfxDksaU1nnkKao1IAuhngpM8fW0eVT8YWMcY-gne0&e=
> -5&jql=project%20%3D%20CTAKES%20AND%20resolution%20%3D%
> 20Unresolved%20AND%20%22Attachment%20count%22%20%3C%3D%20%222%22%20AND%20%
> 22Attachment%20count%22%20%3E%3D%20%221%22%20order%20by%
> 20priority%20DESC%2Cupdated%20DESC
>
> 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 <sa...@xflowresearch.com>
> Sent: Friday, January 11, 2019 5:33 AM
> To: 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
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: AggregateCdaUmlsprocessor only annotates last section of CDA
document [EXTERNAL]
Posted by gandhi rajan <ga...@gmail.com>.
Sorry Sean. I would love to do this but my old setup is all gone with my
previous organization. Gotta do a fresh setup in my personal machine all
over again. Sorry about that.
On Friday, January 11, 2019, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Sana,
>
> This might be related to
>
> https://issues.apache.org/jira/browse/CTAKES-450?filter=
> -5&jql=project%20%3D%20CTAKES%20AND%20resolution%20%3D%
> 20Unresolved%20AND%20%22Attachment%20count%22%20%3C%3D%20%222%22%20AND%20%
> 22Attachment%20count%22%20%3E%3D%20%221%22%20order%20by%
> 20priority%20DESC%2Cupdated%20DESC
>
> 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 <sa...@xflowresearch.com>
> Sent: Friday, January 11, 2019 5:33 AM
> To: 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
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: AggregateCdaUmlsprocessor only annotates last section of CDA
document [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sana,
This might be related to
https://issues.apache.org/jira/browse/CTAKES-450?filter=-5&jql=project%20%3D%20CTAKES%20AND%20resolution%20%3D%20Unresolved%20AND%20%22Attachment%20count%22%20%3C%3D%20%222%22%20AND%20%22Attachment%20count%22%20%3E%3D%20%221%22%20order%20by%20priority%20DESC%2Cupdated%20DESC
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 <sa...@xflowresearch.com>
Sent: Friday, January 11, 2019 5:33 AM
To: 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