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Upgraded JChem to look at Repository for JAR #349

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Upgraded JChem to look at Repository for JAR #349

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21 changes: 11 additions & 10 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,23 +1,24 @@
ARG CHEMISTRY_PACKAGE=jchem
FROM maven:3-openjdk-8 as builder
FROM maven:3-openjdk-11 as builder

FROM builder as dependencies
ARG CHEMISTRY_PACKAGE
ENV CHEMISTRY_PACKAGE=${CHEMISTRY_PACKAGE}

FROM dependencies as jchem
ADD lib/jchem-16.4.25.0.jar /lib/jchem-16.4.25.0.jar
RUN mvn install:install-file -Dfile=/lib/jchem-16.4.25.0.jar -DartifactId=jchem -DgroupId=com.chemaxon -Dversion=16.4.25.0 -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
# ADD lib/jchem-16.4.25.0.jar /lib/jchem-16.4.25.0.jar
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Previously we'd been assuming this jar file would be supplied despite it not being in the repo. Perhaps you could do something similar for the API keys?

# RUN mvn install:install-file -Dfile=/lib/jchem-16.4.25.0.jar -DartifactId=jchem -DgroupId=com.chemaxon -Dversion=16.4.25.0 -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true

FROM ${CHEMISTRY_PACKAGE} as compile
ADD settings.xml /root/.m2/settings.xml
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What's this file? I don't see it in the repo. Is this the API key?

ADD pom.xml /src/pom.xml
WORKDIR /src
RUN mvn dependency:resolve -P ${CHEMISTRY_PACKAGE}
RUN mvn dependency:resolve -P ${CHEMISTRY_PACKAGE} -X
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I don't think we need the maven debug flag on permanently. Can this be removed once you've finished debugging?

ADD . /src
RUN mvn clean && \
mvn compile war:war -P ${CHEMISTRY_PACKAGE}

FROM tomcat:9.0.62-jre8-openjdk-slim-buster
mvn compile war:war -P ${CHEMISTRY_PACKAGE} -X
# RUN mvn compile war:war -P ${CHEMISTRY_PACKAGE}
FROM tomcat:9.0.62-jre11-openjdk-slim-buster

RUN apt-get update && \
apt-get install -y openssl libfontconfig libfreetype6 curl
Expand All @@ -36,10 +37,10 @@ ENV NODE_PATH /usr/lib/node_modules
RUN useradd -u 1000 -ms /bin/bash runner

# Allow certificates to be added by runner
RUN chgrp runner /usr/local/openjdk-8/lib/security/cacerts && \
chmod g+w /usr/local/openjdk-8/lib/security/cacerts && \
RUN chgrp runner /usr/local/openjdk-11/lib/security/cacerts && \
chmod g+w /usr/local/openjdk-11/lib/security/cacerts && \
mkdir -p /usr/lib/jvm/java/jre/lib/security && \
ln -s /usr/local/openjdk-8/lib/security/cacerts /usr/lib/jvm/java/jre/lib/security/cacerts
ln -s /usr/local/openjdk-11/lib/security/cacerts /usr/lib/jvm/java/jre/lib/security/cacerts

# Get acas-roo-server compiled code
COPY --chown=runner:runner --from=compile /src/target/acas*.war /usr/local/tomcat/webapps/acas.war
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22 changes: 7 additions & 15 deletions pom.xml
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Expand Up @@ -33,7 +33,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.]]>
<description>ACAS Java persistence layer</description>
<properties>
<aspectj.version>1.9.7</aspectj.version>
<java.version>1.8</java.version>
<java.version>11</java.version>
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This is a big change. Was this required for the new JChem version?

<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.build.timestamp.format>yyyyMMdd_HHmm</maven.build.timestamp.format>
<date>${maven.build.timestamp}</date>
Expand All @@ -58,6 +58,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.]]>
<url>https://github.com/mcneilco/acas-roo-server.git</url>
</scm>
<repositories>
<repository>
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Could this <repository> be moved into the jchem build profile so it isn't contacted during non-jchem builds?

<id>Chemaxon Public Repository</id>
<url>https://hub.chemaxon.com/artifactory/libs-release</url>
</repository>
<repository>
<id>spring-release</id>
<name>Spring Release</name>
Expand Down Expand Up @@ -104,20 +108,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.]]>
<dependencies>
<dependency>
<groupId>com.chemaxon</groupId>
<artifactId>jchem</artifactId>
<version>${jchem.version}</version>
</dependency>
<!-- JCHEM 16 requires dom4j 1.3. This depdendency can be removed when we upgrade jchem to jchem > 17 -->
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
<version>1.3</version>
</dependency>
<!-- JHEM 16 requires trove4j https://mvnrepository.com/artifact/net.sf.trove4j/trove4j -->
<dependency>
<groupId>net.sf.trove4j</groupId>
<artifactId>trove4j</artifactId>
<version>3.0.3</version>
<artifactId>jchem-main</artifactId>
<version>22.12.0</version>
</dependency>
</dependencies>
<properties>
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