Haags opened a new issue, #8:
URL: https://github.com/apache/ctakes/issues/8
I was wondering if anybody had any advice for me on the following error, I
am trying to clean install from the head of the main branch in git.
Below are my commands; this error start with commit
d998331c1cfe
seanfinan commented on issue #8:
URL: https://github.com/apache/ctakes/issues/8#issuecomment-1416323145
Hi Scott,
Thanks for the report - especially the setup, failure message and commit
details. Would you mind copying it into the GitHub issues area?
https://urldefense.com/v3/__htt
seanfinan commented on issue #8:
URL: https://github.com/apache/ctakes/issues/8#issuecomment-1416323915
I just checked in the revert on ctakes-ytex/scripts/data/build.xml
Packaging works on my machine, but it had also worked for all previous tests
so reopen if this is still an issue.
S
seanfinan closed issue #8: Issue clean install using maven for ctakes-ytex
URL: https://github.com/apache/ctakes/issues/8
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Haags commented on issue #8:
URL: https://github.com/apache/ctakes/issues/8#issuecomment-1420973532
I tested and it works now for me, thank you!
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dcronkite opened a new issue, #17:
URL: https://github.com/apache/ctakes/issues/17
I've been using the `DefaultFastPipeline.piper` configuration on version
4.0.0.1 and wanted to include the published [Smoking
Status](https://cwiki.apache.org/confluence/display/CTAKES/cTAKES%204.0%20-%20Smok
andytubeee opened a new issue, #19:
URL: https://github.com/apache/ctakes/issues/19
I have a CSV file of dictionary vocabulary and concept code. Are there any
documentations on how we can set up a custom dictionary for when using
**bin/runClinicalPipeline.sh**?
Thanks
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seanfinan commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2142787585
There is/was documentation somewhere, but it is spread out and would take me
some time to find the latest and most accurate. However, you have have a look
at the example here
https://
seanfinan commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2142793964
https://github.com/apache/ctakes/wiki/ctakes-dictionary-lookup-fast
If you expand DictionarySubPipe
https://github.com/apache/ctakes/wiki/ctakes-dictionary-lookup-fast#dictionary-sub-
andytubeee commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2143935250
Thanks for sharing, I converted csv to bsv, then created a xml based on your
tinyDictSpec.xml, and then used the -l flag with ./bin/runClinicalPipeline.
I didn't run into any iss
seanfinan commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2145296789
Hi Andrew,
Thank you for the update!
Sean
From: Andrew Yang ***@***.***>
Sent: Sunday, June 2, 2024 12:40 PM
To: apache/ctakes *
seanfinan closed issue #19: cTAKES custom dictionary setup documentation
URL: https://github.com/apache/ctakes/issues/19
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seanfinan closed issue #20: Crossgrade to SLF4J
URL: https://github.com/apache/ctakes/issues/20
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silwalr opened a new issue, #23:
URL: https://github.com/apache/ctakes/issues/23
Hi all,
I am running into `type Annotation was not declared in the XML descriptor`
error with ctakes-6.0-SNAPSHOT when using
`org.apache.ctakes.ytex.uima.annotators.DBConsumer` in a pipeline.
ERR
reckart commented on issue #23:
URL: https://github.com/apache/ctakes/issues/23#issuecomment-2302798213
Try adding the workaround to the `PiperFileRunner`.
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silwalr closed issue #23: Exception: org.apache.uima.jcas.tcas.Annotation was
not declared in the XML type descriptor (ctakes-ytex-uima)
URL: https://github.com/apache/ctakes/issues/23
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silwalr commented on issue #23:
URL: https://github.com/apache/ctakes/issues/23#issuecomment-2304521128
@reckart Amazing. That resolved it! Thank you so much!
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seanfinan commented on issue #23:
URL: https://github.com/apache/ctakes/issues/23#issuecomment-2305205631
@silwalr Can you tell me where you inserted the line in PiperFileRunner?
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silwalr commented on issue #23:
URL: https://github.com/apache/ctakes/issues/23#issuecomment-2305489541
@seanfinan Here's a screen grab of inline diff of my fix:
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seanfinan commented on issue #23:
URL: https://github.com/apache/ctakes/issues/23#issuecomment-2305511966
Cheers!
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silwalr opened a new issue, #24:
URL: https://github.com/apache/ctakes/issues/24
Hi all,
I am running into the following issue when I attempt to load tables into
**MSSQL Server** using Java Data Loader (jdl) utility in
**cTAKES-6.0.0-SNAPSHOT**. The jdl utility worked fine in cTAKES
seanfinan commented on issue #24:
URL: https://github.com/apache/ctakes/issues/24#issuecomment-2346419283
Hi silwalr,
I will try to look into this if I can, but this is fairly far outside my
range of experience. Out of curiosity, what are you using this for? There are
plans to remove l
silwalr commented on issue #24:
URL: https://github.com/apache/ctakes/issues/24#issuecomment-2346522468
Hi @seanfinan,
We are working on upgrading our system that runs cTAKES-4.0 to the most
recent version of cTAKES at UVA health System. We use the jdl utilities to
create/drop UMLS, SNOM
seanfinan commented on issue #24:
URL: https://github.com/apache/ctakes/issues/24#issuecomment-2346724319
It looks like the problem might just be a drop of feature in one of the
updated 3rd party libraries.
It may be a bit of a cheap escape, but I am tempted to release as-is with a
"know
silwalr commented on issue #24:
URL: https://github.com/apache/ctakes/issues/24#issuecomment-2346840327
Releasing it as-is with a "known-issue" sounds like a reasonable thing to
do, considering that there are other tools out there that can easily do this
job.
Good to know that semantic
seanfinan closed issue #24: Java Data Loader (jdl) fails in
cTAKES-6.0.0-SNAPSHOT
URL: https://github.com/apache/ctakes/issues/24
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seanfinan commented on issue #24:
URL: https://github.com/apache/ctakes/issues/24#issuecomment-2346877426
Excellent, Thanks!
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niallkp opened a new pull request, #1:
URL: https://github.com/apache/ctakes-site/pull/1
See https://issues.apache.org/jira/browse/CTAKES-566
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seanfinan merged PR #1:
URL: https://github.com/apache/ctakes-site/pull/1
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Johnsd11 commented on issue #27:
URL: https://github.com/apache/ctakes/issues/27#issuecomment-2730600971
Turns out that this problem was indeed due to the fact that package names
had changed from v4.x.x to v5.x.x from ...drugner... to ..drug.ner..
But across the sources and typesystem f
Johnsd11 commented on issue #29:
URL: https://github.com/apache/ctakes/issues/29#issuecomment-2730715037
I think that your oob exception is, as you guess, coming from missing or bad
parameters. You can try using the following in your piper file:
package org.apache.ctakes.drugner.ae
Johnsd11 opened a new issue, #26:
URL: https://github.com/apache/ctakes/issues/26
### What problem does this solve?
Apache cTAKES website is using Google Analytics which is not permitted by
the ASF Privacy Policy[1]. PMCs were notified of this by the VP Data Privacy in
April 2022
Johnsd11 commented on issue #26:
URL: https://github.com/apache/ctakes/issues/26#issuecomment-2730382457
Pull request of deleted js lines merged.
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Johnsd11 closed issue #26: [Feature]: CTAKES-566 Remove Google Analytics cTAKES
Website [ctakes-site]
URL: https://github.com/apache/ctakes/issues/26
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Johnsd11 opened a new issue, #25:
URL: https://github.com/apache/ctakes/issues/25
User Install Guide states that a windowing system is now needed to
use cTakes, which isn't possible on a headless server machine.
Is it still possible to install and utilize cTakes on a server?
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Johnsd11 opened a new issue, #27:
URL: https://github.com/apache/ctakes/issues/27
### What’s your question?
Has anyone has tried using the Drugner in 5.1.0 have they run into this
error when its process() method is run.
message: JCas type
"org.apache.ctakes.drugner.type.Fr
Johnsd11 opened a new issue, #29:
URL: https://github.com/apache/ctakes/issues/29
### What’s your question?
Processing creates nothing at all due to an out of bounds exception that may
be due to some parameters
that need passing to the annotator. It generates DrugMentions, then it
Johnsd11 commented on issue #29:
URL: https://github.com/apache/ctakes/issues/29#issuecomment-2730715607
Yes, those parameters did enable the code to run without erroring. But
like you said all it did was highlight the fact that it's not a good
solution and creates vast numbers of bloat
Johnsd11 commented on issue #27:
URL: https://github.com/apache/ctakes/issues/27#issuecomment-2730600626
This looks like the same problem encountered here:
https://github.com/apache/ctakes/issues/23
It was fixed for -standard- ctakes workflows in 6.0.0, but if you don't use
the Pip
Johnsd11 closed issue #27: [Question]: About DrugNerAnnotator
URL: https://github.com/apache/ctakes/issues/27
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Johnsd11 closed issue #27: [Question]: About DrugNerAnnotator
URL: https://github.com/apache/ctakes/issues/27
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