Thanks Remy, that makes sense, but I'm wondering why I get the correct offsets in one way of accessing ctakes (the CVD) but the wrong offsets through another way (the REST interface)?
I guess for the fake notes I'm fully in favor of saving as plain text/ascii files to simplify things. But there are more unicode characters than we can write smart rules for and I'd like to make sure unicode strings at least don't screw up offsets, even if we don't process them meaningfully. I'm sure we all look forward to generation Z doctor's notes that use the thumbs up/down emojis for patient prognosis :). Tim -----Original Message----- From: Remy Sanouillet <re...@foreseemed.com<mailto:remy%20sanouillet%20%3cre...@foreseemed.com%3e>> Reply-to: <dev@ctakes.apache.org> To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: unicode issues [EXTERNAL] Date: Thu, 18 Jul 2019 13:37:33 -0700 Hi Tim, What is happening is that your o'clock contains a smart quote (Unicode U+2019) which is encoded as three bytes: 0x6f9980, so you have to take those two extra bytes into account when counting offsets. For that particular character, it is much easier to just preprocess the text and replace all occurrences with the simple apostrophe (ASCII 0x6f). The one on your keyboard. It won't change any interpretation and it makes life simpler for everyone downstream. You probably will want to deal with all extended Unicode characters like emojis otherwise, you will encounter the same offset issues. Rémy Sanouillet NLP Engineer re...@foreseemed.com<mailto:xx...@foreseemed.com> [cid:347EAEF1-26E8-42CB-BAE3-6CB228301B15] ForeSee Medical, Inc. 12555 High Bluff Drive, Suite 100 San Diego, CA 92130 NOTICE: This e-mail message and all attachments transmitted with it are intended solely for the use of the addressee and may contain legally privileged and confidential information. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any dissemination, distribution, copying, or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately by replying to this message and please delete it from your computer. On Thu, Jul 18, 2019 at 1:20 PM Miller, Timothy <timothy.mil...@childrens.harvard.edu<mailto:timothy.mil...@childrens.harvard.edu>> wrote: I'm having a weird issue with unicode characters in one of the sample notes distributed with ctakes. The sentence is: The right breast and axilla were sterilely prepped and draped in the usual standard fashion. First the right 1 o’clock position 5 cm from the nipple was targeted. Local anesthesia was obtained with 2% xylocaine. A small skin incision was made. Under ultrasound guidance from a medial approach, 2 passes with a 14 gauge biopsy device were performed and sent to pathology. A clip was placed. The unicode characters are the right single quotes in "o'clock". If I just put it in the CVD everything works fine, e.g. I find the drug "xylocaine" at location 203-212 and it's highlighted correctly. However, if I use the REST interface and send it using the python requests API, I get back the span 205:214. If we then grab that span we get the wrong string (offset by 2, so something like "locaine. " Any thoughts on where things might be going wrong for the REST interface? Does anyone more knowledgeable than me know how UIMA and cTAKES (and java for that matter) normally handle unicode? Tim
