I'll have a poke around in an alpine container this evening, does seem odd.
A third option is nested-vm version, we used this in JChemPaint when it was an Applet - (see inchi-nestedvm in https://github.com/JChemPaint/jchempaint ). On Tue, 11 Sep 2018 at 16:03, Maria Sorokina <maria.ssorok...@gmail.com> wrote: > 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) 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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