I tried the ubuntu 16.04 based image with Java 8 added, I get exactly the same
error, only at the InChi generation. I have the feeling that something is
missing in this minimal linux images for the InChi generator to run correctly,
but I cannot find what.
I also noticed that for an old version of ini-inchi (1.03, and the latest and
only available is 1.6):
npls-db-filler_1 | 2181 [main] INFO
net.sf.jnati.deploy.repository.RemoteRepository - Searching remote repository
for: jniinchi-1.03_1-LINUX-AMD64 (http://jnati.sourceforge.net/jnati-repo)
What am I missing in my configuration ? Knowing that everything works fine
outside of Docker?
The Dockerfile using Ubuntu:
FROM ubuntu:16.04
LABEL maintainer="[email protected]"
RUN apt-get update && \
apt-get upgrade -y && \
apt-get install -y software-properties-common && \
add-apt-repository ppa:webupd8team/java -y && \
apt-get update && \
echo oracle-java7-installer shared/accepted-oracle-license-v1-1 select true
| /usr/bin/debconf-set-selections && \
apt-get install -y oracle-java8-installer && \
apt-get clean
EXPOSE 8080
VOLUME /tmp
ARG JAR_FILE
COPY ${JAR_FILE} app.jar
ENTRYPOINT ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"]
Thank you for your help!
Kind regards,
Maria Sorokina, PhD
Steinbeck Research Group
Analytical Chemistry - Cheminformatics and Chemometrics
Friedrich-Schiller-University Jena, Germany
http://cheminf.uni-jena.de
> Le 11 sept. 2018 à 00:13, John Mayfield <[email protected]> a écrit
> :
>
> Unlikely to work in alpine, have you tried ubuntu/debian slim?
>
> John
>
> On Mon, 10 Sep 2018 at 18:16, Maria Sorokina <[email protected]
> <mailto:[email protected]>> wrote:
> Hi,
>
> I developed an app using CDK, and in particular it’s InChi Generator. It runs
> perfectly with IntelliJ, and as a jar on MacOS and on CentOS. I wanted to
> make it run within a Docker container (openjdk:8-jdk-alpine with additional
> installation of gcc), the image is created without any problem, but when I
> run the container, I get the following error just once:
>
>
> npls-db-filler_1 | 0 [main] INFO
> net.sf.jnati.deploy.artefact.ConfigManager - Loading global configuration
> npls-db-filler_1 | 4 [main] DEBUG
> net.sf.jnati.deploy.artefact.ConfigManager - Loading defaults:
> jar:file:/app.jar!/BOOT-INF/lib/jnati-deploy-0.3.jar!/META-INF/jnati/jnati.default-properties
> npls-db-filler_1 | 5 [main] INFO
> net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact configuration:
> jniinchi-1.03_1
> npls-db-filler_1 | 6 [main] DEBUG
> net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults:
> jar:file:/app.jar!/BOOT-INF/lib/jnati-deploy-0.3.jar!/META-INF/jnati/jnati.instance.default-properties
> npls-db-filler_1 | 9 [main] INFO
> net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath
> for: jniinchi-1.03_1-LINUX-AMD64
> npls-db-filler_1 | 14 [main] INFO
> net.sf.jnati.deploy.repository.LocalRepository - Searching local repository
> for: jniinchi-1.03_1-LINUX-AMD64
> npls-db-filler_1 | 16 [main] DEBUG
> net.sf.jnati.deploy.repository.LocalRepository - Artefact path:
> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64
> npls-db-filler_1 | 16 [main] INFO
> net.sf.jnati.deploy.repository.LocalRepository - Creating artefact:
> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64
> npls-db-filler_1 | 18 [main] DEBUG net.sf.jnati.deploy.source.JarSource -
> Opening jar: /app.jar
> npls-db-filler_1 | 19 [main] WARN
> net.sf.jnati.deploy.NativeArtefactLocator - Error resolving artefact to
> local repository
> npls-db-filler_1 | java.io.FileNotFoundException: File not found:
> MANIFEST.xml
> npls-db-filler_1 | at
> net.sf.jnati.deploy.source.JarSource.openFile(JarSource.java:67)
> npls-db-filler_1 | at
> net.sf.jnati.deploy.source.ArtefactSource.loadManifest(ArtefactSource.java:41)
>
> And this every time the InChiGenerator is called in my code:
>
>
> Error loading JNI InChI native code.
> npls-db-filler_1 | You may need to compile the native code for your platform.
> npls-db-filler_1 | See http://jni-inchi.sourceforge.net
> <http://jni-inchi.sourceforge.net/> for instructions.
> npls-db-filler_1 |
> npls-db-filler_1 | 1033 [main] INFO
> net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact configuration:
> jniinchi-1.03_1
> npls-db-filler_1 | 1037 [main] DEBUG
> net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults:
> jar:file:/app.jar!/BOOT-INF/lib/jnati-deploy-0.3.jar!/META-INF/jnati/jnati.instance.default-properties
> npls-db-filler_1 | 1039 [main] INFO
> net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath
> for: jniinchi-1.03_1-LINUX-AMD64
> npls-db-filler_1 | 1039 [main] INFO
> net.sf.jnati.deploy.repository.LocalRepository - Searching local repository
> for: jniinchi-1.03_1-LINUX-AMD64
> npls-db-filler_1 | 1039 [main] DEBUG
> net.sf.jnati.deploy.repository.LocalRepository - Artefact path:
> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64
> npls-db-filler_1 | 1040 [main] INFO
> net.sf.jnati.deploy.repository.LocalRepository - Creating artefact:
> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64
> npls-db-filler_1 | 1040 [main] DEBUG net.sf.jnati.deploy.source.JarSource -
> Opening jar: /app.jar
> npls-db-filler_1 | 1041 [main] WARN
> net.sf.jnati.deploy.NativeArtefactLocator - Error resolving artefact to
> local repository
> npls-db-filler_1 | java.io.FileNotFoundException: File not found:
> MANIFEST.xml
> npls-db-filler_1 | at
> net.sf.jnati.deploy.source.JarSource.openFile(JarSource.java:67)
>
>
> Have anybody tried and succeed using InChiGenerator within a Docker
> container? Which package/library/software I should add to either my Docker
> image, either to my Maven repo to make it work within this container?
>
> Thank you for your help!
>
> Kind regards,
>
> Maria Sorokina, PhD
> Steinbeck Research Group
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> http://cheminf.uni-jena.de <http://cheminf.uni-jena.de/>
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> Cdk-user mailing list
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