Right, alpine was probably a red herring. Looking again I presume you build app.jar yourself? It looks like you've removed the MANIFEST.xml that is needed by JNI InChI to locate the native dependency. How are you building the JAR?
Unfortunately v1.03 of InChI is all we have for JNI ATM. My former colleague has been looking at JNA InChI version ( https://github.com/dan2097/jna-inchi) but this is very different to the JNI bindings and not a drop in replacement. John On Tue, 11 Sep 2018 at 09:48, Maria Sorokina <maria.ssorok...@gmail.com> wrote: > 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="maria.ssorok...@gmail.com" > > > 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 <john.wilkinson...@gmail.com> a > écrit : > > Unlikely to work in alpine, have you tried ubuntu/debian slim? > > John > > On Mon, 10 Sep 2018 at 18:16, Maria Sorokina <maria.ssorok...@gmail.com> > 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 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 >> >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > >
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