initial code upload

buschlab · Sep 20, 2021 · cf1e75c · cf1e75c
1 parent c736e86
commit cf1e75c
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diff --git a/.gitattributes b/.gitattributes
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+# When shell scripts end in CRLF, bash gives a cryptic error message
+*.sh text eol=lf
diff --git a/.gitignore b/.gitignore
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+#
+# Standard Maven .gitignore
+#
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+.mvn/timing.properties
+
+#
+# IntelliJ
+#
+*.iml
+.idea/*
+!.idea/runConfigurations/
+
+#
+# Visual Studio Code
+#
+.settings/
+.classpath
+.factorypath
+.project
+.vscode/
+.editorconfig
+
+**/.DS_Store
+settings.yaml
diff --git a/Dockerfile b/Dockerfile
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+FROM maven:3.8.1-openjdk-11-slim as build
+
+COPY $PWD /mtbimporter
+WORKDIR /mtbimporter
+
+RUN mvn install
+
+FROM r-base:4.1.0
+
+RUN apt-get update && apt-get install -y default-jre
+
+RUN wget https://download.docker.com/linux/debian/dists/bullseye/pool/stable/amd64/docker-ce-cli_20.10.7~3-0~debian-bullseye_amd64.deb && dpkg -i docker-ce-cli_20.10.7~3-0~debian-bullseye_amd64.deb && rm docker-ce-cli_20.10.7~3-0~debian-bullseye_amd64.deb
+
+COPY --from=build /mtbimporter/target/mtbimporter-*-jar-with-dependencies.jar /app/mtbimporter.jar
+CMD ["java", "-jar", "/app/mtbimporter.jar"]
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -0,0 +1,15 @@
+version: "3"
+services:
+  mtbimporter:
+    restart: unless-stopped
+    build: ./
+    image: ghcr.io/buschlab/mtbimporter:latest
+    volumes:
+      - "/var/run/docker.sock:/var/run/docker.sock"
+      - "./settings.yaml:/app/settings.yaml"
+
+    networks:
+     - mtbimporter_net
+
+networks:
+  mtbimporter_net:
diff --git a/pom.xml b/pom.xml
@@ -0,0 +1,182 @@
+<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/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>de.uzl.lied</groupId>
+  <artifactId>mtbimporter</artifactId>
+  <version>1.0-SNAPSHOT</version>
+  <properties>
+    <maven.compiler.source>11</maven.compiler.source>
+    <maven.compiler.target>11</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <exec.mainClass>de.uzl.lied.mtbimporter.mtbimporter</exec.mainClass>
+    <maven-source-plugin.version>3.2.1</maven-source-plugin.version>
+    <maven-surefire-plugin.version>3.0.0-M5</maven-surefire-plugin.version>
+    <maven-javadoc-plugin.version>3.2.0</maven-javadoc-plugin.version>
+    <maven-enforcer-plugin.version>3.0.0-M3</maven-enforcer-plugin.version>
+  </properties>
+  <dependencies>
+    <dependency>
+      <groupId>ca.uhn.hapi.fhir</groupId>
+      <artifactId>hapi-fhir-base</artifactId>
+      <version>5.4.1</version>
+    </dependency>
+    <dependency>
+      <groupId>ca.uhn.hapi.fhir</groupId>
+      <artifactId>hapi-fhir-client</artifactId>
+      <version>5.4.1</version>
+    </dependency>
+    <dependency>
+      <groupId>ca.uhn.hapi.fhir</groupId>
+      <artifactId>hapi-fhir-structures-r4</artifactId>
+      <version>5.4.1</version>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-core</artifactId>
+      <version>2.11.3</version>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+      <version>2.11.3</version>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.dataformat</groupId>
+      <artifactId>jackson-dataformat-csv</artifactId>
+      <version>2.11.3</version>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.dataformat</groupId>
+      <artifactId>jackson-dataformat-properties</artifactId>
+      <version>2.11.3</version>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.dataformat</groupId>
+      <artifactId>jackson-dataformat-yaml</artifactId>
+      <version>2.11.3</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-text</artifactId>
+      <version>1.9</version>
+    </dependency>
+    <dependency>
+      <groupId>commons-io</groupId>
+      <artifactId>commons-io</artifactId>
+      <version>2.8.0</version>
+    </dependency>
+    <dependency>
+      <groupId>com.google.guava</groupId>
+      <artifactId>guava</artifactId>
+      <version>30.0-jre</version>
+    </dependency>
+    <dependency>
+      <groupId>org.springframework</groupId>
+      <artifactId>spring-web</artifactId>
+      <version>5.3.8</version>
+    </dependency>
+    <dependency>
+      <groupId>de.samply</groupId>
+      <artifactId>mdrclient</artifactId>
+      <version>3.0.0</version>
+    </dependency>
+    <dependency>
+      <groupId>com.github.albfernandez</groupId>
+      <artifactId>juniversalchardet</artifactId>
+      <version>2.4.0</version>
+    </dependency>
+    <dependency>
+      <groupId>org.codehaus.groovy</groupId>
+      <artifactId>groovy-all</artifactId>
+      <version>3.0.8</version>
+      <type>pom</type>
+    </dependency>
+    <dependency>
+      <groupId>org.codehaus.groovy</groupId>
+      <artifactId>groovy-dateutil</artifactId>
+      <version>2.5.0</version>
+      <classifier>indy</classifier>
+  </dependency>
+  </dependencies>
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-enforcer-plugin</artifactId>
+        <version>${maven-enforcer-plugin.version}</version>
+        <executions>
+          <execution>
+            <goals>
+              <goal>enforce</goal>
+            </goals>
+            <configuration>
+              <rules>
+                <requireMavenVersion>
+                  <version>3.6.3</version>
+                </requireMavenVersion>
+              </rules>
+              <fail>true</fail>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>${maven-surefire-plugin.version}</version>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-javadoc-plugin</artifactId>
+        <version>${maven-javadoc-plugin.version}</version>
+        <executions>
+          <execution>
+            <id>attach-javadocs</id>
+            <goals>
+              <goal>jar</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-source-plugin</artifactId>
+        <version>${maven-source-plugin.version}</version>
+        <executions>
+          <execution>
+            <id>attach-sources</id>
+            <goals>
+              <goal>jar</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+        </executions>
+        <configuration>
+          <descriptorRefs>
+            <descriptorRef>jar-with-dependencies</descriptorRef>
+          </descriptorRefs>
+          <archive>
+            <manifest>
+              <mainClass>de.uzl.lied.mtbimporter.MtbImporter</mainClass>
+            </manifest>
+          </archive>
+        </configuration>
+      </plugin>
+    </plugins>
+    <resources>
+      <resource>
+        <directory>src/main/resources</directory>
+        <filtering>true</filtering>
+      </resource>
+    </resources>
+  </build>
+</project>
diff --git a/src/main/java/de/uzl/lied/mtbimporter/MtbImporter.java b/src/main/java/de/uzl/lied/mtbimporter/MtbImporter.java
@@ -0,0 +1,66 @@
+package de.uzl.lied.mtbimporter;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Timer;
+
+import de.uzl.lied.mtbimporter.jobs.CheckDropzone;
+import de.uzl.lied.mtbimporter.jobs.FhirResolver;
+import de.uzl.lied.mtbimporter.jobs.mdr.centraxx.CxxMdrLogin;
+import de.uzl.lied.mtbimporter.model.CbioPortalStudy;
+import de.uzl.lied.mtbimporter.settings.ConfigurationLoader;
+import de.uzl.lied.mtbimporter.settings.Mdr;
+import de.uzl.lied.mtbimporter.settings.Settings;
+import de.uzl.lied.mtbimporter.tasks.AddClinicalData;
+import de.uzl.lied.mtbimporter.tasks.AddGeneticData;
+import de.uzl.lied.mtbimporter.tasks.AddResourceData;
+import de.uzl.lied.mtbimporter.tasks.AddSignatureData;
+import de.uzl.lied.mtbimporter.tasks.AddTimelineData;
+
+public final class MtbImporter {
+    /**
+     * 
+     * @param args The arguments of the program.
+     * @throws InterruptedException
+     * @throws IOException
+     */
+    public static void main(String[] args) throws InterruptedException, IOException {
+        InputStream settingsYaml = ClassLoader.getSystemClassLoader().getResourceAsStream("settings.yaml");
+        if (args.length == 1) {
+            settingsYaml = new FileInputStream(args[0]);
+        }
+
+        ConfigurationLoader configLoader = new ConfigurationLoader();
+        configLoader.loadConfiguration(settingsYaml, Settings.class);
+
+        FhirResolver.initalize();
+        for (Mdr m : Settings.getMdr()) {
+            if(m.getCxx() != null) {
+                CxxMdrLogin.login(m.getCxx());
+            }
+        }
+
+        CbioPortalStudy study = new CbioPortalStudy();
+        AddGeneticData.processMafFile(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_mutation_extended.maf"));
+        AddGeneticData.processSegFile(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_cna.seg"));
+        AddGeneticData.processGenePanelFile(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_gene_panel_matrix.txt"));
+        AddClinicalData.processClinicalPatient(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_clinical_patient.txt"));
+        AddClinicalData.processClinicalSample(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_clinical_sample.txt"));
+        study.setSampleResources(AddResourceData.readResourceFile(new File(Settings.getStudyFolder() + Settings.getState() + "/data_resource_sample.txt")));
+        AddSignatureData.processContribution(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_mutational_signature_contribution.txt"));
+        AddSignatureData.processLimit(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_mutational_signature_limit.txt"));
+        AddGeneticData.processCnaFile(study, new File(Settings.getStudyFolder() + Settings.getState() + "/data_cna.txt"));
+        File[] timelines = new File(Settings.getStudyFolder() + Settings.getState()).listFiles((File f) -> f.getName().startsWith("data_timeline"));
+        for(File t : timelines) {
+            AddTimelineData.processTimelineFile(study, t);
+        }
+
+        Timer t = new Timer();
+        CheckDropzone checkDropzone = new CheckDropzone(study);
+        t.scheduleAtFixedRate(checkDropzone, 0, Settings.getCronIntervall());
+
+        System.out.println("MtbImporter started!");
+    }
+}
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		# When shell scripts end in CRLF, bash gives a cryptic error message
		*.sh text eol=lf