I am building my jar with Maven, but I don’t think that it is the problem, as I tried tu run the jar on a Centos7 VM having just Java and it worked without any problem. I also desperately tried the dirty solution of downloading the manifest and the jniinchi-1.03_1-LINUX-AMD64.so files the ini-inchi seems to search for and put them where it seems to search them within the container, but, of course it failed.
I’ll try to search for a solution, but for now I’ll just do my thing without containerizing this part of my app. If I find a solution, I’ll post it here. Meanwhile, I’m still very open to any suggestion! 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 14:51, John Mayfield <john.wilkinson...@gmail.com> a écrit > : > > 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 > <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 > <mailto: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 > <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 > <mailto: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 <http://cheminf.uni-jena.de/> > >> Le 11 sept. 2018 à 00:13, John Mayfield <john.wilkinson...@gmail.com >> <mailto: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 >> <mailto: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 >> <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/> >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net <mailto:Cdk-user@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> <https://lists.sourceforge.net/lists/listinfo/cdk-user> >
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