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.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
