Hi all, I don't think that I have any of the original communications, but just picking up here:
* From your dump, it looks as if the main concept dictionary is missing. If you just need the standard dictionary, you can use the information on this ctakes wiki page: https://github.com/apache/ctakes/wiki/cTAKES+UMLS+Package+Fetcher The beginning of that page briefly outlines the UMLS key requirement. If you don't want to build a binary distributable to run the script in bin/ you can execute the class org.apache.ctakes.gui.dictionary.DictionaryDownloader * The dictionary in question is rather dated and intended to be a sample. I found it here: That dictionary is pretty old, and though it contains a lot of standard terms it is not "complete" for every purpose. The dictionary on that github page is a copy of the ctakes dictionary. We had to get specific permission to distribute any part of the umls, so by copying our dictionary in a public repo for redistribution this github group is doing a -bad thing-. Please use the * There are also models you may need, but not have. Models for ctakes are in separate repositories. When you build ctakes from the source obtained on github the models will automatically be downloaded from maven central. Just for an example reference https://central.sonatype.com/artifact/org.apache.ctakes/ctakes-assertion-models * *But first I recommend you get your license key and follow the instructions about how to configure it into the WAR file.* I think that I missed this part of the original communication. I concur with what Peter said: "you will continue to get a rather cryptic resource initialization error until you've passed the API key correctly." For a quick "my first ctakes run", use the piper file submitter gui. https://github.com/apache/ctakes/wiki/Piper+File+Submitter As you can see from the images on the wiki page, the default clinical pipeline does demand a key for the umls. It can be entered on line 4 of the parameter table. You'll notice that the value in the "Option" column, line 4, is "--key". When you run ctakes through a command line, you can add the parameter --key followed by your umls key. This older wiki page has a little information on the key https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0.0.1 Sean ________________________________ From: Peter Abramowitsch <pabramowit...@gmail.com> Sent: Thursday, May 9, 2024 5:07 PM To: dev@ctakes.apache.org <dev@ctakes.apache.org>; joel-paul.jeripoth...@achalahealth.com <joel-paul.jeripoth...@achalahealth.com> Subject: Resending without attachments., [EXTERNAL] * External Email - Caution * Shifting this thread back to the main ctakes thread where it belongs... Hi Joel, >From your dump, it looks as if the main concept dictionary is missing. *"No Resource at resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.script"* It's currently configured to run with a standard but older dictionary. But first we need to establish whether you have a UMLS api-key that gives you access to use that vocabulary resource. If not, here's where to begin https://urldefense.com/v3/__https://documentation.uts.nlm.nih.gov/rest/authentication.html__;!!NZvER7FxgEiBAiR_!urKhCyJIGdr9FsV1dFNY3SP-VPO7Yh5yl-4bxLGt8UhOTSuGRzDH3r7uKnMcHT2PLgLFXXjJiV-nntNYRZIDb3yckvI7_OO62A$ The dictionary in question is rather dated and intended to be a sample. I found it here: https://urldefense.com/v3/__https://github.com/CDCgov/NLPWorkbench/blob/master/ctakes-patch/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.script__;!!NZvER7FxgEiBAiR_!urKhCyJIGdr9FsV1dFNY3SP-VPO7Yh5yl-4bxLGt8UhOTSuGRzDH3r7uKnMcHT2PLgLFXXjJiV-nntNYRZIDb3yckvJQR3Zu_A$ . Once you have your UMLS license you can also download the entire UMLS vocabulary resource onto your machine, then run the cTakes Dictionary Creator application to build the vocabulary you need. It selectively fetches the parts you want from the UMLS files and builds a database for use in cTakes. I think most cTakes users build their own dictionaries after they've become familiar with the application. There are also models you may need, but not have. These large binary objects got shifted when the source was transferred onto GitHub and I'm not sure where they are stored now. Others on this thread will know. *But first I recommend you get your license key and follow the instructions about how to configure it into the WAR file.* I haven't used that module before and it's probably been a decade since I last used apache tomcat. In any case, you will continue to get a rather cryptic resource initialization error until you've passed the API key correctly. I'm about to head off to Europe, so you may need to lean on another resource to get started. That's why I've cc'd the ctakes thread and you can take it from there. Peter
