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Merge pull request #354 from MassBank/release-2.2
Release 2.2
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‎Documentation/MassBankRecordFormat.md‎

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# MassBank Record Format 2.5.2
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MassBank Consortium (September 22, 2021)
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# MassBank Record Format 2.6.0
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MassBank Consortium (May 13, 2022)
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#### Updated
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- **May 2022**: With version 2.6.0 MassBank introduces a new ACCESSION scheme.ch offers more freedom for contributors in the naming of their records. The new scheme consists of three fields separated by 'minus' signs and follows the format ID-[A-Z0–9_]{1,32}-[A-Z0–9_]{1,64}. The field ID will always be MSBNK for official MassBank releases. The second field is the contributor ID and is usually assigned by MassBank staff. Now it can be up to 32 characters long and is comprised of letters, digits and the '_' sign. The third field is the ID assigned by the contributor and can be up to 64 characters long and is also comprised of letters, digits and the '_' sign.
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- **July 2021**: Move to a semantic versioning scheme X.Y.Z with Z increases for changes in the description or fixing of typos, Y increases for changes that also change the Validator software and X increases with changes that break compatibility with older versions of the software.
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- **March 2020**: Add new tag for the inlet type.
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- **October 2019**: Add UVPD dissociation method and some undocumented or new tags.
@@ -356,17 +357,18 @@ Identifier of the MassBank Record. Mandatory
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Example:
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```
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ACCESSION: ZMS00006
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ACCESSION: MSBNK-AAFC-AC000101
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```
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The MassBank accession consists of three fields separated by `-` signs and follows the format ID-[A-Z0–9_]{1,32}-[A-Z0–9_]{1,64}. The field ID will always be MSBNK for official MassBank releases. The second field is the contributor ID and is usually assigned by MassBank staff. It can be up to 32 characters long and is comprised of letters, digits and the `_` sign. The third field is the ID assigned by the contributor and an be up to 64 characters long and is also comprised of letters, digits and the `_` sign.
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8-character fix-length string. Prefix two or three alphabetical capital characters specify the site, database or contributor, where the record was submitted or who has contributed. Prefixes currently used are listed in the “Prefix of ID” column of the MassBank "List of contributors, prefixes and projects" (https://github.com/MassBank/MassBank-data/blob/master/List_of_Contributors_Prefixes_and_Projects.md). Rest of the field are decimal letters which are the identifier of the record at each site.
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The list of List of contributors and projects is maintained at https://github.com/MassBank/MassBank-data/blob/master/List_of_Contributors_Prefixes_and_Projects.md.
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A deprecated record is marked with the tag `DEPRECATED: ` followed by date and reason on the second line. The content of a deprecated record may not be valid.
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Example:
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```
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ACCESSION: XY000010
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DEPRECATED: 2019-05-03 considered noisy
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ACCESSION: MSBNK-ISAS_Dortmund-IA000311
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DEPRECATED: 2019-11-25 Wrong MS measurement assigned
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```
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‎MassBank-Project/.mvn/local-settings.xml‎

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<settings xmlns="http://maven.apache.org/SETTINGS/1.2.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.2.0 http://maven.apache.org/xsd/settings-1.2.0.xsd">
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<mirrors>
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<mirror>
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<id>releases-http-unblocker</id>
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<name>Fiehnlab Public Maven Repository</name>
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<mirrorOf>releases</mirrorOf>
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<url>http://gose.fiehnlab.ucdavis.edu:55000/content/groups/public</url>
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<blocked>false</blocked>
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</mirror>
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</mirrors>
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</settings>

‎MassBank-Project/Dockerfile-openapi‎

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FROM maven:3.8-jdk-11 as build
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COPY ./MassBank-lib/ /build/MassBank-lib/
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COPY ./MassBank-OpenAPI/pom.xml /build/MassBank-OpenAPI/pom.xml
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COPY ./MassBank-web /build/MassBank-web/
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COPY ./pom.xml /build/
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COPY ./.mvn/* /build/.mvn/
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WORKDIR /build/
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RUN mvn verify -pl MassBank-OpenAPI --fail-never --settings ./.mvn/local-settings.xml
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ADD ./MassBank-OpenAPI/ /build/MassBank-OpenAPI/
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RUN mvn package -pl MassBank-OpenAPI -am --settings ./.mvn/local-settings.xml
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FROM openjdk:11-jdk-slim
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ARG JAR_FILE=/build/MassBank-OpenAPI/target/*.jar
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COPY --from=build ${JAR_FILE} /
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EXPOSE 8080/tcp
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ENTRYPOINT java -jar *.jar

‎MassBank-Project/MassBank-OpenAPI/generate.sh‎

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#!/bin/bash
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#wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.4.0/openapi-generator-cli-5.4.0.jar -O openapi-generator-cli.jar
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java -jar openapi-generator-cli.jar generate -g spring -i src/main/resources/openapi.yaml -c openapi-generator-config.json -o ../spring-boot-codegenerator

‎MassBank-Project/MassBank-OpenAPI/openapi-generator-config.json‎

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{
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"basePackage": "massbank.openapi",
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"configPackage": "massbank.openapi.config",
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"apiPackage": "massbank.openapi.api",
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"modelPackage": "massbank.openapi.model",
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"parentArtifactId": "MassBank-Project",
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"parentGroupId": "de.ipb-halle.msbi",
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"parentVersion": "2.1.11-SNAPSHOT",
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"artifactId": "MassBank-OpenAPI",
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"groupId": "de.ipb-halle.msbi",
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"artifactVersion": "2.1.11-SNAPSHOT",
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"delegatePattern": true
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}
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‎MassBank-Project/MassBank-OpenAPI/pom.xml‎

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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"
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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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<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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<artifactId>MassBank-Project</artifactId>
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<groupId>de.ipb-halle.msbi</groupId>
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<version>2.1.10</version>
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<artifactId>MassBank-Project</artifactId>
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<version>2.2</version>
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</parent>
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<artifactId>MassBank-OpenAPI</artifactId>
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<packaging>war</packaging>
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<packaging>jar</packaging>
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<name>MassBank OpenAPI REST interface</name>
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<properties>
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<swagger-codegen-version>3.0.30</swagger-codegen-version>
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<swagger-core-version>2.1.11</swagger-core-version>
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<jersey2-version>2.35</jersey2-version>
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<jackson-version>2.13.0</jackson-version>
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<jetty-version>9.4.24.v20191120</jetty-version>
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<logback-version>1.2.3</logback-version>
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<yaml.file>${project.basedir}/src/main/resources/openapi.yaml</yaml.file>
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<generated-sources-path>${project.build.directory}/generated-sources</generated-sources-path>
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<generated-sources-java-path>main/java</generated-sources-java-path>
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<springdoc.version>1.6.4</springdoc.version>
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</properties>
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<build>
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<!-- <finalName>${project.artifactId}</finalName> -->
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<!-- <sourceDirectory>src/main/java</sourceDirectory> -->
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<plugins>
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<plugin>
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<groupId>io.swagger.codegen.v3</groupId>
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<artifactId>swagger-codegen-maven-plugin</artifactId>
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<version>${swagger-codegen-version}</version>
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<groupId>org.openapitools</groupId>
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<artifactId>openapi-generator-maven-plugin</artifactId>
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<executions>
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<execution>
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<goals>
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<goal>generate</goal>
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</goals>
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<configuration>
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<inputSpec>${yaml.file}</inputSpec>
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<language>jaxrs-jersey</language>
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<!-- <generateSupportingFiles>false</generateSupportingFiles> -->
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<generatorName>spring</generatorName>
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<configOptions>
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<sourceFolder>${generated-sources-java-path}</sourceFolder>
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<hideGenerationTimestamp>true</hideGenerationTimestamp>
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<basePackage>massbank.openapi</basePackage>
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<configPackage>massbank.openapi.config</configPackage>
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<apiPackage>massbank.openapi.api</apiPackage>
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<modelPackage>massbank.openapi.model</modelPackage>
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<delegatePattern>true</delegatePattern>
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</configOptions>
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<output>${generated-sources-path}</output>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-war-plugin</artifactId>
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<configuration>
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<failOnMissingWebXml>false</failOnMissingWebXml>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-failsafe-plugin</artifactId>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-maven-plugin</artifactId>
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<executions>
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<execution>
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<goals>
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<goal>integration-test</goal>
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<goal>verify</goal>
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<goal>repackage</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>build-helper-maven-plugin</artifactId>
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<executions>
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<execution>
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<id>add-generated-source</id>
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<phase>generate-sources</phase>
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<goals>
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<goal>add-source</goal>
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</goals>
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<configuration>
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<sources>
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<source>${generated-sources-path}/${generated-sources-java-path}</source>
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</sources>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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<dependency>
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<groupId>de.ipb-halle.msbi</groupId>
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<artifactId>MassBank-lib</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>io.swagger.codegen.v3</groupId>
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<artifactId>swagger-codegen-maven-plugin</artifactId>
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<version>${swagger-codegen-version}</version>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-web</artifactId>
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</dependency>
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<dependency>
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<groupId>io.swagger.core.v3</groupId>
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<artifactId>swagger-jaxrs2</artifactId>
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<scope>compile</scope>
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<version>${swagger-core-version}</version>
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<groupId>org.springframework.data</groupId>
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<artifactId>spring-data-commons</artifactId>
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</dependency>
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<!--SpringDoc dependencies -->
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<dependency>
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<groupId>javax.servlet</groupId>
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<artifactId>javax.servlet-api</artifactId>
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<version>${servlet-api-version}</version>
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<groupId>org.springdoc</groupId>
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<artifactId>springdoc-openapi-ui</artifactId>
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<version>${springdoc.version}</version>
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</dependency>
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<!-- @Nullable annotation -->
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<dependency>
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<groupId>org.glassfish.jersey.containers</groupId>
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<artifactId>jersey-container-servlet</artifactId>
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<version>${jersey2-version}</version>
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<groupId>com.google.code.findbugs</groupId>
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<artifactId>jsr305</artifactId>
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<version>3.0.2</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.media</groupId>
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<artifactId>jersey-media-multipart</artifactId>
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<version>${jersey2-version}</version>
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<groupId>com.fasterxml.jackson.dataformat</groupId>
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<artifactId>jackson-dataformat-yaml</artifactId>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.inject</groupId>
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<artifactId>jersey-hk2</artifactId>
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<version>${jersey2-version}</version>
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<groupId>com.fasterxml.jackson.datatype</groupId>
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<artifactId>jackson-datatype-jsr310</artifactId>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.datatype</groupId>
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<artifactId>jackson-datatype-joda</artifactId>
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<version>${jackson-version}</version>
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<groupId>org.openapitools</groupId>
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<artifactId>jackson-databind-nullable</artifactId>
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<version>0.2.2</version>
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</dependency>
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<!-- Bean Validation API support -->
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<dependency>
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<groupId>com.fasterxml.jackson.jaxrs</groupId>
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<artifactId>jackson-jaxrs-json-provider</artifactId>
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<version>${jackson-version}</version>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-starter-validation</artifactId>
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</dependency>
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<dependency>
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<groupId>com.github.petitparser</groupId>
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<artifactId>petitparser-core</artifactId>
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<version>${petitparser-version}</version>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId>
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</dependency>
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-log4j12</artifactId>
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<version>1.7.32</version>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-devtools</artifactId>
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</dependency>
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</dependencies>
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<dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>org.springframework.boot</groupId>
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<artifactId>spring-boot-dependencies</artifactId>
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<version>2.7.0</version>
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<type>pom</type>
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<scope>import</scope>
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</dependency>
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</dependencies>
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</dependencyManagement>
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</project>

‎MassBank-Project/MassBank-OpenAPI/src/main/java/io/swagger/api/factories/RecordApiServiceFactory.java‎

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‎MassBank-Project/MassBank-OpenAPI/src/main/java/io/swagger/api/impl/RecordApiServiceImpl.java‎

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