Maybe this would help? http://maven.apache.org/plugins/maven-patch-plugin/
________________________________________ From: Sana Riaz <sana.r...@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.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 <timothy.mil...@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.fi...@childrens.harvard.edu<mailto:%22Finan,% > 20sean%22%20%3csean.fi...@childrens.harvard.edu%3e>> > Reply-to: <dev@ctakes.apache.org> > To: dev@ctakes.apache.org <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 +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.r...@xflowresearch.com<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 > >
