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From Sana Riaz <sana.r...@xflowresearch.com>
Subject Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Date Mon, 14 Jan 2019 09:59:07 GMT
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 <Timothy.Miller@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: <dev@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<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
>
>

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