Docker build failed

Question

Docker build failed

latchukarthick98 opened this issue 3 years ago · 5 comments

I tried building the docker image. I got this error when doing docker-compose up -d.

executor failed running [/bin/sh -c ln -s ../apache-ctakes/resources resources && ln -s ../apache-ctakes/desc desc && mvn package]: exit code: 137 ERROR: Service 'ctakes' failed to build : Build failed

Here is a detailed log
Building ctakes
[+] Building 161.0s (19/19) FINISHED
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 37B 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/library/maven:3.5.4-jdk-8-alpine 0.3s
=> [internal] load build context 0.0s
=> => transferring context: 355B 0.0s
=> [ 1/12] FROM docker.io/library/maven:3.5.4-jdk-8-alpine@sha256:72922abc95d38e02f 0.0s
=> https://phoenixnap.dl.sourceforge.net/project/ctakesresources/sno_rx_16ab.zip 0.3s
=> https://iweb.dl.sourceforge.net/project/ctakesresources/ctakes-resources-4.0-bin 0.2s
=> https://dlcdn.apache.org//ctakes/ctakes-4.0.0.1/apache-ctakes-4.0.0.1-bin.tar.g 23.1s
=> CACHED [ 2/12] RUN apk update && apk add unzip 0.0s
=> CACHED [ 3/12] ADD https://dlcdn.apache.org//ctakes/ctakes-4.0.0.1/apache-ctakes 0.0s
=> CACHED [ 4/12] ADD https://iweb.dl.sourceforge.net/project/ctakesresources/ctake 0.0s
=> CACHED [ 5/12] RUN tar -xvzf apache-ctakes-4.0.0.1-bin.tar.gz && ln -s /apac 0.0s
=> CACHED [ 6/12] ADD https://phoenixnap.dl.sourceforge.net/project/ctakesresources 0.0s
=> CACHED [ 7/12] RUN unzip sno_rx_16ab/sno_rx_16ab.zip && mv sno_rx_16ab /apac 0.0s
=> CACHED [ 8/12] WORKDIR /app 0.0s
=> CACHED [ 9/12] RUN mkdir src 0.0s
=> CACHED [10/12] ADD src /app/src 0.0s
=> CACHED [11/12] ADD pom.xml /app 0.0s
=> ERROR [12/12] RUN ln -s ../apache-ctakes/resources resources && ln -s ../a 137.5s

[12/12] RUN ln -s ../apache-ctakes/resources resources && ln -s ../apache-ctakes/desc desc && mvn package:
#19 0.937 [INFO] Scanning for projects...
#19 0.975 [INFO]
#19 0.975 [INFO] ----------------------< de.dfki.lt:ctakes-server >----------------------
#19 0.977 [INFO] Building ctakes-server 0.1
#19 0.977 [INFO] --------------------------------[ jar ]---------------------------------
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executor failed running [/bin/sh -c ln -s ../apache-ctakes/resources resources && ln -s ../apache-ctakes/desc desc && mvn package]: exit code: 137
ERROR: Service 'ctakes' failed to build : Build failed

Answer 1 · 2022-01-31T20:11:32.000Z

Let me know how the alternative goes, replace build: . with image: ghcr.io/choyiny/ctakes-server/ctakes-server:55c663d4362c and run docker-compose up -d.

Answer 2 · 2022-01-31T20:43:13.000Z

Thanks for the alternative. I was up successfully. But unfortunately the GET request didn't return anything.
This is the request I made http://localhost:9999/ctakes?text=Pain in the left leg.

This is what I got as response:
Error: Server returned nothing (no headers, no data)

Answer 3 · 2022-02-01T19:35:19.000Z

Did you start the server with the proper UMLS credentials?

-Dctakes.umls_apikey=${UMLSAPIKEY}

the environment variable UMLSAPIKEY needs to be set properly

Answer 4 · 2022-02-02T00:14:26.000Z

Yes, I did. I passed the UMLS API Key in the .env file.

…

On Tue, Feb 1, 2022, 1:35 PM Cho Yin Yong ***@***.***> wrote: Did you start the server with the proper UMLS credentials? — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF5RRESQ4PDD327HQRY5TPDUZAYYFANCNFSM5NHADERQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

Answer 5 · 2022-02-02T19:22:36.000Z

Unfortunately I wasn't able to get it to work either. I've been looking at alternatives anyways as it is not scalable to do NLP on documents by making HTTP calls anyway.

Cool alternative with Python: https://github.com/medspacy/medspacy