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mozzy11mozzy11
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Merge pull request #31 from mozzy11/develop
add test loinc csv file mapper
2 parents 6144b82 + 5048467 commit de8e612

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‎.github/workflows/build-plugins.yml‎

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name: Build OpenELIS-Global-2 Plugins
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on:
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release:
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types: [published]
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jobs:
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build-and-upload-plugins:
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runs-on: ubuntu-latest
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steps:
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- name: Set up JDK 11
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uses: actions/setup-java@v1
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with:
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java-version: 11
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- name: Cache local Maven repository
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uses: actions/cache@v4
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with:
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path: ~/.m2/repository
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key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
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restore-keys: |
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${{ runner.os }}-maven-
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- name: Checkout openelisglobal-plugins
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uses: actions/checkout@v2
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with:
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repository: ${{github.repository}}
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- name: Build openelisglobal-plugins
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run: mvn clean install
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- name: check plugins
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run: ls plugins
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- name: Compress Folder
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run: |
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tar -czf plugins.tar.gz -C plugins .
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echo "FILE_PATH=plugins.tar.gz" >> $GITHUB_ENV
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echo "FILE_NAME=plugins.tar.gz" >> $GITHUB_ENV
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- name: Upload Release Asset
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ github.event.release.upload_url }}
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asset_path: ${{ env.FILE_PATH }}
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asset_name: ${{ env.FILE_NAME }}
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asset_content_type: application/gzip
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‎.gitignore‎

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*.classpath
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analyzers/**/.gitignore
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*/*/target
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*.vscode/*
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target/*
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.DS_Store

‎README.md‎

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```mvn clean install```
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1. Find the built plugin jars under the `plugins` directory
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ASTM PLugins
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GeneXpert (PNG) , SysmeXXN-L ,SysmexXP ,pocH-100i (HAITI)
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‎analyzers/CobasC111/pom.xml‎

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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.openelisglobal.plugins</groupId>
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<artifactId>CobasC111</artifactId>
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<parent>
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<groupId>org.openelisglobal</groupId>
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<artifactId>openelisglobal-plugins</artifactId>
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<version>1.0</version>
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<relativePath>../../pom.xml</relativePath>
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</parent>
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<?xml version="1.0" encoding="UTF-8"?>
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<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">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.openelisglobal</groupId>
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<artifactId>openelisglobal-plugins</artifactId>
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<version>1.0</version>
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<relativePath>../../pom.xml</relativePath>
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</parent>
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<groupId>org.openelisglobal.plugins</groupId>
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<artifactId>CobasC111</artifactId>
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<version>1.0</version>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<version>1.0</version>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<build>
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<sourceDirectory>src</sourceDirectory>
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<resources>
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<resource>
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<directory>src</directory>
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<excludes>
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<exclude>**/*.java</exclude>
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</excludes>
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</resource>
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</resources>
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<plugins>
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<plugin>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>3.8.0</version>
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<configuration>
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<source>1.8</source>
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<target>1.8</target>
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</configuration>
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</plugin>
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<plugin>
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<artifactId>maven-resources-plugin</artifactId>
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<version>2.4.3</version>
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<executions>
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<execution>
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<id>copy-resources</id>
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<!-- here the phase you need -->
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<phase>install</phase>
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<goals>
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<goal>copy-resources</goal>
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</goals>
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<configuration>
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<outputDirectory>${project.basedir}/../../plugins</outputDirectory>
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<resources>
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<resource>
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<!-- Get main artifact -->
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<directory>target/</directory>
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<includes>
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<include>${project.build.finalName}.jar</include>
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</includes>
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<!-- Don't filter binary files -->
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<filtering>false</filtering>
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</resource>
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</resources>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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</project>
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<build>
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<resources>
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<resource>
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<directory>src</directory>
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<excludes>
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<exclude>**/*.java</exclude>
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</excludes>
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</resource>
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</resources>
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<plugins>
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<plugin>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>3.8.0</version>
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<configuration>
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<source>1.8</source>
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<target>1.8</target>
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</configuration>
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</plugin>
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<plugin>
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<artifactId>maven-resources-plugin</artifactId>
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<version>2.4.3</version>
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<executions>
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<execution>
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<id>copy-resources</id>
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<goals>
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<goal>copy-resources</goal>
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</goals>
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<!-- here the phase you need -->
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<phase>install</phase>
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<configuration>
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<outputDirectory>${project.basedir}/../../plugins</outputDirectory>
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<resources>
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<resource>
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<!-- Get main artifact -->
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<directory>target/</directory>
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<includes>
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<include>${project.build.finalName}.jar</include>
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</includes>
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<!-- Don't filter binary files -->
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<filtering>false</filtering>
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</resource>
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</resources>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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<sourceDirectory>src</sourceDirectory>
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</build>
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</project>

‎analyzers/CobasC111/src/oe/plugin/analyzer/CobasC111Analyzer.java‎

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2020

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import java.util.ArrayList;
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import java.util.List;
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import org.openelisglobal.analyzerimport.analyzerreaders.AnalyzerLineInserter;
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import org.openelisglobal.common.services.PluginAnalyzerService;
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import org.openelisglobal.plugin.AnalyzerImporterPlugin;
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public class CobasC111Analyzer implements AnalyzerImporterPlugin {
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public boolean connect(){
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List<PluginAnalyzerService.TestMapping> nameMappinng = new ArrayList<PluginAnalyzerService.TestMapping>();
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nameMappinng.add(new PluginAnalyzerService.TestMapping("GLU2", "Glucose"));
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nameMappinng.add(new PluginAnalyzerService.TestMapping("CREJ2", "Créatinine"));
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nameMappinng.add(new PluginAnalyzerService.TestMapping("ALTL", "Transaminases GPT (37°C)"));
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getInstance().addAnalyzerDatabaseParts("CobasC111Analyzer", "Plugin for Cobas C111 analyzer",nameMappinng);
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getInstance().registerAnalyzer(this);
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return true;
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}
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@Override
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public boolean isTargetAnalyzer(List<String> lines) {
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if(getColumnsLine(lines)<0) return false;
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return true;
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}
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@Override
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public AnalyzerLineInserter getAnalyzerLineInserter() {
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return new CobasC111AnalyzerImplementation();
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public boolean connect() {
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List<PluginAnalyzerService.TestMapping> nameMappinng =
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new ArrayList<PluginAnalyzerService.TestMapping>();
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nameMappinng.add(new PluginAnalyzerService.TestMapping("GLU2", "Glucose"));
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nameMappinng.add(new PluginAnalyzerService.TestMapping("CREJ2", "Créatinine"));
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nameMappinng.add(new PluginAnalyzerService.TestMapping("ALTL", "Transaminases GPT (37°C)"));
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getInstance()
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.addAnalyzerDatabaseParts(
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"CobasC111Analyzer", "Plugin for Cobas C111 analyzer", nameMappinng);
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getInstance().registerAnalyzer(this);
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return true;
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}
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@Override
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public boolean isTargetAnalyzer(List<String> lines) {
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if (getColumnsLine(lines) < 0) return false;
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return true;
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}
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@Override
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public AnalyzerLineInserter getAnalyzerLineInserter() {
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return new CobasC111AnalyzerImplementation();
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}
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public int getColumnsLine(List<String> lines) {
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for (int k = 0; k < lines.size(); k++) {
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if (lines.get(k).contains("Instr")) return k;
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}
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public int getColumnsLine(List<String> lines) {
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for(int k=0;k<lines.size();k++){
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if(lines.get(k).contains("Instr"))
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return k;
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}
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return -1;
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}
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return -1;
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}
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}

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