Knew it was the JAR packaging, I did try to send the JAR file I has working in debain-slim but Gmail blocks JAR attachments.
Interestingly I stopped using SpringBoot (for another reason I can't remember) a few years ago and use the TomCat (exec-war) plugin instead. Jetty also has a plugin which is another option. I think the best option here is to use the TomCat DockerHub images and deploy it as a WAR file. https://github.com/cdk/depict/blob/master/pom.xml#L88-L109 <plugin> > <groupId>org.apache.tomcat.maven</groupId> > <artifactId>tomcat7-maven-plugin</artifactId> > <version>2.1</version> > <executions> > <execution> > <id>tomcat-run</id> > <goals> > <goal>exec-war-only</goal> > </goals> > <phase>package</phase> > <configuration> > <finalName>${project.name > }-${project.version}.jar</finalName> > <path>/</path> > <attachArtifactClassifier>boot > </attachArtifactClassifier> > <attachArtifactClassifierType>jar > </attachArtifactClassifierType> > </configuration> > </execution> > </executions> > </plugin> On Fri, 14 Sep 2018 at 07:12, Egon Willighagen <egon.willigha...@gmail.com> wrote: > > Oh, very happy to hear that! Are you going to put it up on DockerHub? > > Egon > > On Thu, Sep 13, 2018 at 10:42 PM Maria Sorokina <maria.ssorok...@gmail.com> > wrote: > >> I managed to make my app function. >> >> The problem comes from the way a Spring Boot application packages the jar >> - internally, the jar is different from plain old Java, so the deployment >> of artefacts is also different. The Jnati library that allows the wrapping >> of the InChi factory is not adapted to that special deployment and is >> simply lost and doesn’t find the artifacts in correct places *if it never >> ran on the system before* (case of a brand new minimal image). >> The trick I found to make a Spring Boot application using InChis run in >> Docker is not very elegant, but functional. In the container, during the >> compilation, or at the execution of the container, before running the main >> Spring Boot jar, run the simples possible mini POJO jar containing the >> InChiGeneratorFactory, that will create the correct environment. >> Now everything works! >> >> This is my Dockerfile: >> >> FROM openjdk:8u171-slim >> EXPOSE 8080 >> VOLUME /tmp >> ARG JAR_FILE >> COPY ${JAR_FILE} app.jar >> COPY inchiPet.jar / >> >> RUN java -jar inchiPet.jar >> >> ENTRYPOINT >> ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"] >> >> Where « inchiPet.jar » is the tiny regular jar with only a call to an >> inchiGeneratorFactory, and « app.jar » is my main app. >> >> However, I used a bunch of libraries from CDK and until now, only the >> InChi generator caused this problem within the Spring Boot - Docker >> ecosystem. >> >> Hope this solution could help anybody encountering this kind of problem >> in the future! >> >> Maria Sorokina, PhD >> Steinbeck Research Group >> Analytical Chemistry - Cheminformatics and Chemometrics >> Friedrich-Schiller-University Jena, Germany >> http://cheminf.uni-jena.de >> > > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> > ImpactStory: https://impactstory.org/u/egonwillighagen >
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