Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Relative file paths are relative to tree file directory #91

Merged
merged 1 commit into from
Aug 20, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
305 changes: 153 additions & 152 deletions pom.xml
Original file line number Diff line number Diff line change
@@ -1,170 +1,171 @@
<?xml version="1.0" encoding="UTF-8"?>
<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.2.2</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.2.2</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>

<groupId>org.molgenis</groupId>
<artifactId>vip-decision-tree</artifactId>
<version>4.1.1</version>
<groupId>org.molgenis</groupId>
<artifactId>vip-decision-tree</artifactId>
<version>4.1.2</version>

<name>vip-decision-tree</name>
<description>Decision tree module for filtering and labelling VCF files</description>
<name>vip-decision-tree</name>
<description>Decision tree module for filtering and labelling VCF files</description>

<licenses>
<license>
<name>The GNU Lesser General Public License, Version 3.0</name>
<url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<licenses>
<license>
<name>The GNU Lesser General Public License, Version 3.0</name>
<url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>

<scm>
<connection>scm:git:git://github.com/molgenis/vip-decision-tree.git</connection>
<developerConnection>scm:git:ssh://git@github.com/molgenis/vip-decision-tree.git
</developerConnection>
<url>https://github.com/molgenis/vip-decision-tree</url>
</scm>
<scm>
<connection>scm:git:git://github.com/molgenis/vip-decision-tree.git</connection>
<developerConnection>scm:git:ssh://git@github.com/molgenis/vip-decision-tree.git
</developerConnection>
<url>https://github.com/molgenis/vip-decision-tree</url>
</scm>

<issueManagement>
<system>GitHub</system>
<url>https://github.com/molgenis/vip-decision-tree/issues</url>
</issueManagement>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/molgenis/vip-decision-tree/issues</url>
</issueManagement>

<properties>
<java.version>17</java.version>
<commons.cli.version>1.6.0</commons.cli.version>
<samtools.htsjdk.version>4.1.0</samtools.htsjdk.version>
<jacoco-maven-plugin.version>0.8.11</jacoco-maven-plugin.version>
<vip.utils.version>2.0.0</vip.utils.version>
</properties>
<properties>
<java.version>17</java.version>
<commons.cli.version>1.6.0</commons.cli.version>
<samtools.htsjdk.version>4.1.0</samtools.htsjdk.version>
<jacoco-maven-plugin.version>0.8.11</jacoco-maven-plugin.version>
<vip.utils.version>2.0.0</vip.utils.version>
</properties>

<profiles>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco-maven-plugin.version}</version>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<profiles>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco-maven-plugin.version}</version>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.molgenis</groupId>
<artifactId>vip-utils</artifactId>
<version>${vip.utils.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons.cli.version}</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${samtools.htsjdk.version}</version>
</dependency>
</dependencies>
</dependencyManagement>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.molgenis</groupId>
<artifactId>vip-utils</artifactId>
<version>${vip.utils.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons.cli.version}</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${samtools.htsjdk.version}</version>
</dependency>
<dependency>
<groupId>org.molgenis</groupId>
<artifactId>vip-utils</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</dependencyManagement>

<dependencies>
<dependency>
<groupId>org.molgenis</groupId>
<artifactId>vip-utils</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<finalName>vcf-decision-tree</finalName>

<build>
<finalName>vcf-decision-tree</finalName>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<compilerArgs>
<arg>-Xlint</arg>
<arg>-Xlint:-processing
</arg><!-- disable: perfectly normal for annotations to not have a processor -->
</compilerArgs>
</configuration>
</plugin>
</plugins>
</pluginManagement>

<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<compilerArgs>
<arg>-Xlint</arg>
<arg>-Xlint:-processing</arg><!-- disable: perfectly normal for annotations to not have a processor -->
</compilerArgs>
</configuration>
</plugin>
</plugins>
</pluginManagement>

<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<excludes>
<!-- By default provided dependencies are included -->
<exclude>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
</plugin>
</plugins>
</build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<excludes>
<!-- By default provided dependencies are included -->
<exclude>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
</plugin>
</plugins>
</build>

</project>
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ public ConfigDecisionTree load(Path decisionTreeConfigPath) {
ObjectMapper mapper = new ObjectMapper();
SimpleModule module = new SimpleModule();
module.addDeserializer(ConfigNode.class, new ConfigNodeDeserializer());
module.addDeserializer(Path.class, new PathDeserializer());
module.addDeserializer(Path.class, new PathDeserializer(decisionTreeConfigPath));
mapper.registerModule(module);

ConfigDecisionTree configDecisionTree;
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,24 @@
import java.io.IOException;
import java.nio.file.Path;

import static java.util.Objects.requireNonNull;

public class PathDeserializer extends JsonDeserializer<Path> {
private final Path rootPath;

public PathDeserializer(Path decisionTreeConfigPath) {
this.rootPath = requireNonNull(decisionTreeConfigPath);
}

@Override
public Path deserialize(JsonParser jp, DeserializationContext context) throws IOException {
ObjectCodec objectCodec = jp.getCodec();
ObjectNode root = objectCodec.readTree(jp);
String pathString = root.get("path").asText();
return Path.of(pathString);
Path path = Path.of(pathString);
if (!path.isAbsolute()) {
path = Path.of(rootPath.getParent().toString(), pathString).normalize();
}
return path;
}
}
2 changes: 1 addition & 1 deletion src/test/resources/example.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"files": {
"clinvar" : {
"path" : "src/test/resources/clinvar.txt"
"path" : "clinvar.txt"
}
},
"rootNode": "filter",
Expand Down