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Create library runtime jar #1510

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merged 1 commit into from
Jun 29, 2023
Merged

Create library runtime jar #1510

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2 changes: 1 addition & 1 deletion lib/python/MANIFEST.in
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@@ -1,2 +1,2 @@
global-exclude *.py[cod] __pycache__ .DS_Store
recursive-include target/dependency *-all.jar
recursive-include target/dependency library-runtime-*.jar
2 changes: 1 addition & 1 deletion lib/python/pathling/etc.py
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Expand Up @@ -41,7 +41,7 @@ def find_jar(verbose: bool = False) -> str:
)
verbose and print("Project dir is: %s" % project_dir)
jars_dir = os.path.join(project_dir, "target", "dependency")
jar_file = glob.glob(os.path.join(jars_dir, "library-api-*-all.jar"))
jar_file = glob.glob(os.path.join(jars_dir, "library-runtime-*.jar"))
verbose and print("Found jar file(s): %s" % jar_file)
if not jar_file:
raise RuntimeError("Pathling jar not present at: %s" % jars_dir)
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4 changes: 1 addition & 3 deletions lib/python/pom.xml
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Expand Up @@ -43,8 +43,7 @@
<dependencies>
<dependency>
<groupId>au.csiro.pathling</groupId>
<artifactId>library-api</artifactId>
<classifier>all</classifier>
<artifactId>library-runtime</artifactId>
</dependency>
</dependencies>

Expand Down Expand Up @@ -90,7 +89,6 @@
<goal>copy-dependencies</goal>
</goals>
<configuration>
<classifier>all</classifier>
<excludeTransitive>true</excludeTransitive>
</configuration>
</execution>
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4 changes: 2 additions & 2 deletions lib/python/setup.py
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Expand Up @@ -41,7 +41,7 @@
# Check for existence of uber-jar for packaging
#
JARS_DIR = os.path.join(HERE, "target", "dependency")
UBER_JAR_GLOB = os.path.join(JARS_DIR, "library-api-*-all.jar")
UBER_JAR_GLOB = os.path.join(JARS_DIR, "library-runtime-*.jar")
jar_files = glob.glob(UBER_JAR_GLOB)
if not jar_files:
print(
Expand Down Expand Up @@ -91,7 +91,7 @@
"pathling.jars": "target/dependency",
},
package_data={
"pathling.jars": ["*-all.jar"],
"pathling.jars": ["library-runtime-*.jar"],
},
data_files=[
("share/pathling/examples", glob.glob("examples/*.py")),
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29 changes: 0 additions & 29 deletions library-api/pom.xml
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Expand Up @@ -222,35 +222,6 @@
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>all</shadedClassifierName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/MANIFEST.MF</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
</transformers>
</configuration>
</plugin>
</plugins>
</build>

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1 change: 1 addition & 0 deletions library-runtime/.gitignore
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@@ -0,0 +1 @@
/dependency-reduced-pom.xml
137 changes: 137 additions & 0 deletions library-runtime/pom.xml
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@@ -0,0 +1,137 @@
<?xml version="1.0" encoding="UTF-8"?>

<!--
~ Copyright 2023 Commonwealth Scientific and Industrial Research
~ Organisation (CSIRO) ABN 41 687 119 230.
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->

<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<parent>
<artifactId>pathling</artifactId>
<groupId>au.csiro.pathling</groupId>
<version>6.2.2</version>
</parent>
<artifactId>library-runtime</artifactId>
<packaging>jar</packaging>

<name>Pathling Library Runtime</name>
<description>The uber-jar for Pathling Libray API.</description>

<properties>
<shaded.dependency.prefix>au.csiro.pathling.shaded</shaded.dependency.prefix>
<!-- We contain no source -->
<maven.javadoc.skip>true</maven.javadoc.skip>
</properties>

<dependencies>

<dependency>
<groupId>au.csiro.pathling</groupId>
<artifactId>library-api</artifactId>
<scope>compile</scope>
<exclusions>
<exclusion>
<groupId>org.apache.spark</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<configuration>
<filesets>
<fileset>
<directory>${project.basedir}</directory>
<includes>
<include>dependency-reduced-pom.xml</include>
</includes>
</fileset>
</filesets>
</configuration>
</plugin>
<!-- We contain no source -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<configuration>
<skipSource>true</skipSource>
</configuration>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<createDependencyReducedPom>true</createDependencyReducedPom>
<shadedArtifactAttached>false</shadedArtifactAttached>
<useDependencyReducedPomInJar>true</useDependencyReducedPomInJar>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/MANIFEST.MF</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
</transformers>
<relocations>
<relocation>
<pattern>com/</pattern>
<shadedPattern>${shaded.dependency.prefix}.com.</shadedPattern>
<includes>
<include>com/github/benmanes/caffeine/**</include>
</includes>
</relocation>
</relocations>
</configuration>
</plugin>
</plugins>
</build>
</project>
10 changes: 5 additions & 5 deletions pom.xml
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Expand Up @@ -100,6 +100,7 @@
<modules>
<module>encoders</module>
<module>library-api</module>
<module>library-runtime</module>
<module>terminology</module>
<module>fhirpath</module>
<module>fhir-server</module>
Expand Down Expand Up @@ -193,9 +194,8 @@
</dependency>
<dependency>
<groupId>au.csiro.pathling</groupId>
<artifactId>library-api</artifactId>
<artifactId>library-runtime</artifactId>
<version>${project.version}</version>
<classifier>all</classifier>
</dependency>
<dependency>
<groupId>au.csiro.pathling</groupId>
Expand Down Expand Up @@ -581,7 +581,7 @@
<artifactId>logback-core</artifactId>
<version>${pathling.logbackVersion}</version>
</dependency>

<!-- CVE-2022-42889-->
<dependency>
<groupId>org.apache.commons</groupId>
Expand All @@ -595,14 +595,14 @@
<artifactId>snakeyaml</artifactId>
<version>1.33</version>
</dependency>

<!-- CVE-2022-37865 -->
<dependency>
<groupId>org.apache.ivy</groupId>
<artifactId>ivy</artifactId>
<version>2.5.1</version>
</dependency>

</dependencies>
</dependencyManagement>

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4 changes: 0 additions & 4 deletions utilities/pom.xml
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Expand Up @@ -58,10 +58,6 @@
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.curator</groupId>
<artifactId>curator-client</artifactId>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
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3 changes: 1 addition & 2 deletions utilities/src/main/java/au/csiro/pathling/utilities/ObjectHolder.java
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Expand Up @@ -26,7 +26,6 @@
import java.util.function.Function;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.apache.curator.utils.CloseableUtils;
import org.apache.hadoop.util.ShutdownHookManager;

/**
Expand Down Expand Up @@ -91,7 +90,7 @@ public synchronized V getOrCreate(@Nonnull final C config) {
@Override
public synchronized void reset() {
if (instance instanceof Closeable) {
CloseableUtils.closeQuietly((Closeable) instance);
closeQuietly((Closeable) instance);
instance = null;
configuration = null;
}
Expand Down