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Merge pull request #354 from MassBank/release-2.2
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Release 2.2
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@meier-rene
meier-rene authored Jun 20, 2022
2 parents 1a09049 + 6aa5973 commit 5d7f3c4
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14 changes: 8 additions & 6 deletions Documentation/MassBankRecordFormat.md
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# MassBank Record Format 2.5.2
MassBank Consortium (September 22, 2021)
# MassBank Record Format 2.6.0
MassBank Consortium (May 13, 2022)

#### Updated
- **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.
- **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.
- **March 2020**: Add new tag for the inlet type.
- **October 2019**: Add UVPD dissociation method and some undocumented or new tags.
Expand Down Expand Up @@ -356,17 +357,18 @@ Identifier of the MassBank Record. Mandatory

Example:
```
ACCESSION: ZMS00006
ACCESSION: MSBNK-AAFC-AC000101
```
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.

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.
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.

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.

Example:
```
ACCESSION: XY000010
DEPRECATED: 2019-05-03 considered noisy
ACCESSION: MSBNK-ISAS_Dortmund-IA000311
DEPRECATED: 2019-11-25 Wrong MS measurement assigned
```


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13 changes: 13 additions & 0 deletions MassBank-Project/.mvn/local-settings.xml
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<settings xmlns="http://maven.apache.org/SETTINGS/1.2.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.2.0 http://maven.apache.org/xsd/settings-1.2.0.xsd">
<mirrors>
<mirror>
<id>releases-http-unblocker</id>
<name>Fiehnlab Public Maven Repository</name>
<mirrorOf>releases</mirrorOf>
<url>http://gose.fiehnlab.ucdavis.edu:55000/content/groups/public</url>
<blocked>false</blocked>
</mirror>
</mirrors>
</settings>
16 changes: 16 additions & 0 deletions MassBank-Project/Dockerfile-openapi
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FROM maven:3.8-jdk-11 as build
COPY ./MassBank-lib/ /build/MassBank-lib/
COPY ./MassBank-OpenAPI/pom.xml /build/MassBank-OpenAPI/pom.xml
COPY ./MassBank-web /build/MassBank-web/
COPY ./pom.xml /build/
COPY ./.mvn/* /build/.mvn/
WORKDIR /build/
RUN mvn verify -pl MassBank-OpenAPI --fail-never --settings ./.mvn/local-settings.xml
ADD ./MassBank-OpenAPI/ /build/MassBank-OpenAPI/
RUN mvn package -pl MassBank-OpenAPI -am --settings ./.mvn/local-settings.xml

FROM openjdk:11-jdk-slim
ARG JAR_FILE=/build/MassBank-OpenAPI/target/*.jar
COPY --from=build ${JAR_FILE} /
EXPOSE 8080/tcp
ENTRYPOINT java -jar *.jar
3 changes: 3 additions & 0 deletions MassBank-Project/MassBank-OpenAPI/generate.sh
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#!/bin/bash
#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
java -jar openapi-generator-cli.jar generate -g spring -i src/main/resources/openapi.yaml -c openapi-generator-config.json -o ../spring-boot-codegenerator
15 changes: 15 additions & 0 deletions MassBank-Project/MassBank-OpenAPI/openapi-generator-config.json
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{
"basePackage": "massbank.openapi",
"configPackage": "massbank.openapi.config",
"apiPackage": "massbank.openapi.api",
"modelPackage": "massbank.openapi.model",
"parentArtifactId": "MassBank-Project",
"parentGroupId": "de.ipb-halle.msbi",
"parentVersion": "2.1.11-SNAPSHOT",
"artifactId": "MassBank-OpenAPI",
"groupId": "de.ipb-halle.msbi",
"artifactVersion": "2.1.11-SNAPSHOT",
"delegatePattern": true

}

140 changes: 54 additions & 86 deletions MassBank-Project/MassBank-OpenAPI/pom.xml
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<?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 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<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>MassBank-Project</artifactId>
<groupId>de.ipb-halle.msbi</groupId>
<version>2.1.10</version>
<artifactId>MassBank-Project</artifactId>
<version>2.2</version>
</parent>

<artifactId>MassBank-OpenAPI</artifactId>
<packaging>war</packaging>
<packaging>jar</packaging>

<name>MassBank OpenAPI REST interface</name>

<properties>
<swagger-codegen-version>3.0.30</swagger-codegen-version>
<swagger-core-version>2.1.11</swagger-core-version>
<jersey2-version>2.35</jersey2-version>
<jackson-version>2.13.0</jackson-version>
<jetty-version>9.4.24.v20191120</jetty-version>
<logback-version>1.2.3</logback-version>
<yaml.file>${project.basedir}/src/main/resources/openapi.yaml</yaml.file>
<generated-sources-path>${project.build.directory}/generated-sources</generated-sources-path>
<generated-sources-java-path>main/java</generated-sources-java-path>
<springdoc.version>1.6.4</springdoc.version>
</properties>

<build>
<!-- <finalName>${project.artifactId}</finalName> -->
<!-- <sourceDirectory>src/main/java</sourceDirectory> -->
<plugins>
<plugin>
<groupId>io.swagger.codegen.v3</groupId>
<artifactId>swagger-codegen-maven-plugin</artifactId>
<version>${swagger-codegen-version}</version>
<groupId>org.openapitools</groupId>
<artifactId>openapi-generator-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>generate</goal>
</goals>
<configuration>
<inputSpec>${yaml.file}</inputSpec>
<language>jaxrs-jersey</language>
<!-- <generateSupportingFiles>false</generateSupportingFiles> -->
<generatorName>spring</generatorName>
<configOptions>
<sourceFolder>${generated-sources-java-path}</sourceFolder>
<hideGenerationTimestamp>true</hideGenerationTimestamp>
<basePackage>massbank.openapi</basePackage>
<configPackage>massbank.openapi.config</configPackage>
<apiPackage>massbank.openapi.api</apiPackage>
<modelPackage>massbank.openapi.model</modelPackage>
<delegatePattern>true</delegatePattern>
</configOptions>
<output>${generated-sources-path}</output>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
<goal>repackage</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-generated-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>${generated-sources-path}/${generated-sources-java-path}</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

Expand All @@ -97,58 +59,64 @@
<dependency>
<groupId>de.ipb-halle.msbi</groupId>
<artifactId>MassBank-lib</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>io.swagger.codegen.v3</groupId>
<artifactId>swagger-codegen-maven-plugin</artifactId>
<version>${swagger-codegen-version}</version>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-jaxrs2</artifactId>
<scope>compile</scope>
<version>${swagger-core-version}</version>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
</dependency>
<!--SpringDoc dependencies -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>${servlet-api-version}</version>
<groupId>org.springdoc</groupId>
<artifactId>springdoc-openapi-ui</artifactId>
<version>${springdoc.version}</version>
</dependency>
<!-- @Nullable annotation -->
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
<version>${jersey2-version}</version>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-multipart</artifactId>
<version>${jersey2-version}</version>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
<version>${jersey2-version}</version>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-joda</artifactId>
<version>${jackson-version}</version>
<groupId>org.openapitools</groupId>
<artifactId>jackson-databind-nullable</artifactId>
<version>0.2.2</version>
</dependency>
<!-- Bean Validation API support -->
<dependency>
<groupId>com.fasterxml.jackson.jaxrs</groupId>
<artifactId>jackson-jaxrs-json-provider</artifactId>
<version>${jackson-version}</version>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-validation</artifactId>
</dependency>
<dependency>
<groupId>com.github.petitparser</groupId>
<artifactId>petitparser-core</artifactId>
<version>${petitparser-version}</version>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.32</version>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-devtools</artifactId>
</dependency>
</dependencies>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-dependencies</artifactId>
<version>2.7.0</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
</project>
12 changes: 0 additions & 12 deletions ...ject/MassBank-OpenAPI/src/main/java/io/swagger/api/factories/RecordApiServiceFactory.java
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91 changes: 0 additions & 91 deletions ...Bank-Project/MassBank-OpenAPI/src/main/java/io/swagger/api/impl/RecordApiServiceImpl.java
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