Merge branch 'toolboxJsonDesc' into 'develop'

[toolbox] Galaxy wrappers and json description See merge request !11

Merge branch 'toolboxJsonDesc' into 'develop'
[toolbox] Galaxy wrappers and json description See merge request !11
2abf493a · Ludovic Cottret · b3df96bd · 5a829478 · 2abf493a · 2abf493a
Commit 2abf493a authored May 23, 2022 by Ludovic Cottret
--- a/.gitignore
+++ b/.gitignore
@@ -19,4 +19,4 @@ met4j-core/src/main/java/fr/inra/toulouse/metexplore/met4j_core/Test\.java


 dependency-reduced-pom.xml
-/met4j.sif
+*.sif
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,6 +3,7 @@
 stages:
  - build
  - test
+  - package
  - deploy
  - build-containers

@@ -11,10 +12,34 @@ stages:
  image: docker:latest
  services:
    - docker:dind
+  script:
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then docker build -t "$DOCKER_IMAGE:latest" .; fi
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then docker push "$DOCKER_IMAGE:latest"; fi
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" ]; then docker build -t "$DOCKER_IMAGE:$VERSION" .; fi
+    # version in lower case
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION" ]; then docker build -t "$DOCKER_IMAGE:$LOWER_CASE_VERSION" .; fi
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION" ]; then docker push "$DOCKER_IMAGE:$LOWER_CASE_VERSION"; fi
+    - docker build -t "$DOCKER_IMAGE:$CI_COMMIT_BRANCH" .
+    - docker push "$DOCKER_IMAGE:$CI_COMMIT_BRANCH"
+    # branch in lower case
+    - docker build -t "$DOCKER_IMAGE:$LOWER_CASE_COMMIT_BRANCH" .
+    - docker push "$DOCKER_IMAGE:$LOWER_CASE_COMMIT_BRANCH"
+  rules:
+    - if: $CI_COMMIT_BRANCH == "master"
+      when: always
+    - if: $CI_COMMIT_BRANCH == "develop"
+      when: always
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      when: never
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: manual
+  needs:
+    - build
+    - package

 variables:
  MAVEN_CLI_OPTS: "-s .m2/settings.xml --batch-mode"
-  MAVEN_OPTS: "-Dmaven.repo.local=.m2/repository"
+  MAVEN_OPTS: "-Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository"

 cache:
  paths:
@@ -24,15 +49,45 @@ build:
  image: maven:3.6-adoptopenjdk-14
  stage: build
  script:
-    - mvn compile
+    - mvn $MAVEN_OPTS compile
+    - TRUEVERSION=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)
+    - VERSION=$TRUEVERSION
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then VERSION=${VERSION%"-SNAPSHOT"}; fi
+    - LOWER_CASE_VERSION=${VERSION,,}
+    - LOWER_CASE_COMMIT_BRANCH=${CI_COMMIT_BRANCH,,}
+    - echo "VERSION=$VERSION" >> build.env
+    - echo "TRUEVERSION=$TRUEVERSION" >> build.env
+    - echo "LOWER_CASE_VERSION=$LOWER_CASE_VERSION" >> build.env
+    - echo "LOWER_CASE_COMMIT_BRANCH=$LOWER_CASE_COMMIT_BRANCH" >> build.env
+  artifacts:
+    expire_in: 60 min
+    paths:
+      - target/
+      - "*/target"
+    reports:
+      dotenv: build.env

 test:
  image: maven:3.6-adoptopenjdk-14
  stage: test
  script:
-    - mvn clean test
+    - find . -name "*.class" -exec touch {} \+
+    - mvn $MAVEN_OPTS clean test
    - cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'

+package:
+  image: maven:3.6-adoptopenjdk-14
+  stage: package
+  script:
+    - mvn $MAVEN_OPTS clean install -DskipTests=true
+    - cd met4j-toolbox
+    - mvn $MAVEN_OPTS package -DskipTests=true
+    - cd ..
+  artifacts:
+    expire_in: 60 min
+    paths:
+      - "met4j-toolbox/target/met4j-toolbox-$TRUEVERSION.jar"
+
 deploySnapshot:
  image: maven:3.6-adoptopenjdk-14
  stage: deploy
@@ -71,39 +126,35 @@ buildSingularity:
    entrypoint: [ "" ]
  script:
    - singularity build met4j-toolbox.sif met4j.singularity
-    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_TAG"
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"latest"; fi
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" ]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$VERSION"; fi
+    # version in lower case
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION"]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$LOWER_CASE_VERSION"; fi
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_BRANCH"
+    # branch in lower case
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$LOWER_CASE_COMMIT_BRANCH"
  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      when: manual
+    - if: $CI_COMMIT_BRANCH == "master"
+      when: always
+    - if: $CI_COMMIT_BRANCH == "develop"
+      when: always
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      when: never
    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
      when: manual
+  needs:
+    - build
+    - package

 buildDockerProdGitlab:
  extends: .template_docker
  before_script:
    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-  script:
-    - docker build -t "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest" .
-    - docker push "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest"
-  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      when: manual
-    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
-      when: manual
+    - DOCKER_IMAGE="$CI_REGISTRY/metexplore/met4j/met4j-docker"
+

 buildDockerProdDockerhub:
  extends: .template_docker
  before_script:
    - docker login -u "$DOCKERHUB_USER" -p "$DOCKERHUB_PASSWORD" $DOCKERHUB_REGISTRY
-  script:
-    - docker build --pull -t "$DOCKERHUB_IMAGE:latest" .
-    - docker push "$DOCKERHUB_IMAGE:latest"
-  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      when: manual
-    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
-      when: manual
-
-
-
-
+    - DOCKER_IMAGE=$DOCKERHUB_IMAGE
\ No newline at end of file
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,25 +4,16 @@ RUN export DEBIAN_FRONTEND=noninteractive

 RUN apt-get update \
 && apt-get upgrade -y \
-&& apt-get install -y openjdk-11-jre git maven \
+&& apt-get install -y openjdk-11-jre maven \
 && apt-get clean \
 && apt-get purge

-RUN mkdir -p /opt && cd /opt \
-&& git clone https://forgemia.inra.fr/metexplore/met4j.git \
-&& cd met4j \
-&& mvn install \
-&& cd met4j-toolbox \
-&& mvn package
-
-RUN mkdir -p /opt/bin \
-&& cd /opt/met4j/met4j-toolbox \
-&& cp target/met4j*.jar /opt/bin/met4j.jar \
-&& cd /opt \
-&& rm -rf met4j ~/.m2  \
-&& apt-get remove -y git && apt-get autoremove -y
+RUN mkdir -p /opt/bin

 COPY ./docker_files/met4j.sh /opt/bin
+COPY ./met4j-toolbox/target/met4j*.jar /opt/bin/met4j.jar
+
+RUN chmod a+x /opt/bin/met4j.sh

-ENTRYPOINT ["/opt/bin/met4j.sh"]
+RUN cd /usr/bin && ln -s /opt/bin/met4j.sh

--- a/README.md
+++ b/README.md
@@ -10,17 +10,14 @@
 **Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.**


-Met4j is composed by several modules:
+Met4j is composed by three main modules:
 - [met4j-core](met4j-core/README.md): it's the key module which contains all the core 
 classes for handling metabolic networks
 - [met4j-io](met4j-io/README.md): for importing/exporting metabolic networks in several 
 formats (SBML, MetExploreXml, KEGG)
 - [met4j-graph](met4j-graph/README.md): for performing graph-based topological analysis of metabolic networks.  

-The other modules contains utilities to serve the main modules listed here.  
-
-The full list of implemented metabolic network analysis can be found in the [met4j-toolbox](met4j-toolbox/README.md) 
-
+The package [met4j-toolbox](met4j-toolbox/README.md) contains high-level apps that can be run in command line by using either jar file or Singularity or Docker containers.


 ## Installation
@@ -52,41 +49,22 @@ git clone https://forgemia.inra.fr/metexplore/met4j.git;
 cd met4j;
 mvn clean install 
 ```
-to build the executable toolbox jar:
-```
-cd met4j-toolbox
-mvn clean compile assembly:single
-mv ./target/*-jar-with-dependencies.jar ../../../
-```

 ## Usage

 Documentation for the library modules can be found in each module's own README.  
-Detailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).  
-
-The toolbox can be launched using
-```
-java -jar met4j-toolbox-0.8.0-jar-with-dependencies.jar
-```
-which will list all the contained applications that can be called using
-
-```
-java -cp met4j-toolbox-0.8.0-jar-with-dependencies.jar <App full name> -h
-```
-
-### With singularity
-
-You need at least [singularity](https://sylabs.io/guides/3.5/user-guide/quick_start.html) v3.5.
-
-```console
-singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:latest
-```
+Detailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).

 ## Contributing
+
 Pull requests are welcome **on the gitlab repo** ([https://forgemia.inra.fr/metexplore/met4j](https://forgemia.inra.fr/metexplore/met4j)). For major changes, please open an issue first to discuss what you would like to change.  

 Please make sure to update tests as appropriate.  

+## Issues
+
+Issues or suggestions can be posted [here](https://forgemia.inra.fr/metexplore/met4j/-/issues).
+
 ## License
 Met4J is distributed under the open license [CeCILL-2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html) (compatible GNU-GPL).  


--- a/docker_files/met4j.sh
+++ b/docker_files/met4j.sh
@@ -44,6 +44,6 @@ if [ $# -lt 1 ]
        echo "display Help"
        exec java -jar $path_jar
    else
-        echo "Lauch met4j-toolbox"
+        echo "Launch met4j-toolbox"
 	      exec java -Dlog4j.configuration= -cp $path_jar fr.inrae.toulouse.metexplore.met4j_toolbox."$@"
 fi
\ No newline at end of file
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
@@ -81,7 +81,7 @@ public abstract class BioEntity {
     */
    public BioEntity(String id, String name) {
        if (StringUtils.isVoid(id)) {
-            String newId = UUID.randomUUID().toString().replaceAll("-", "_");
+            String newId = "_"+UUID.randomUUID().toString().replaceAll("-", "_");
            this.id = newId;
        } else {
            this.id = id;

--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java
@@ -64,234 +64,225 @@ import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.*;
 * because they do not extend the {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity} class
 *
 * @author Benjamin
- * @since 3.0
 * @version $Id: $Id
+ * @since 3.0
 */
 public class AnnotationParser implements PackageParser, AdditionalDataTag, ReaderSBML1Compatible, ReaderSBML2Compatible,
-		ReaderSBML3Compatible {
-
-	/** Constant <code>ORIGIN="SBML"</code> */
-	public static final String ORIGIN = "SBML";
-
-	/**
-	 * The Jsbml Model
-	 */
-	public Model model;
-	/**
-	 * The BioNetwork
-	 */
-	public BioNetwork bionetwork;
-
-	/**
-	 * The user defined annotation pattern used in the regular expression of
-	 * this class
-	 */
-	public String annotationPattern;
-
-	/**
-	 * The default annotation pattern:
-	 * <ul>
-	 * <li>http://identifiers.org/([^/]+)/(.*)
-	 * </ul>
-	 * The first parenthesis group is
-	 */
-	public static final String defaultAnnotationPattern = "https?://identifiers.org/([^/]+)/(.*)";
-
-	/**
-	 * Constructor
-	 *
-	 * @param useDefault
-	 *            true to use the {@link #defaultAnnotationPattern}
-	 */
-	public AnnotationParser(boolean useDefault) {
-		if (useDefault)
-			this.setAnnotationPattern(defaultAnnotationPattern);
-	}
-
-	/**
-	 * Constructor
-	 *
-	 * @param pattern
-	 *            the user defined pattern
-	 */
-	public AnnotationParser(String pattern) {
-		this.annotationPattern = pattern;
-	}
-
-	/**
-	 * <p>getAssociatedPackageName.</p>
-	 *
-	 * @return a {@link java.lang.String} object.
-	 */
-	public String getAssociatedPackageName() {
-		return "annot";
-	}
-
-	/** {@inheritDoc} */
-	public boolean isPackageUseableOnModel(Model model) {
-		return true;
-	}
-
-	/**
-	 * {@inheritDoc}
-	 *
-	 * Parse all model entities to retrieve their annotations and extract the
-	 * desired information
-	 */
-	public void parseModel(Model model, BioNetwork bionetwork) {
-		System.err.println("Starting " + this.getAssociatedPackageName() + " plugin...");
-
-		this.setBionetwork(bionetwork);
-		this.setModel(model);
-
-		this.parseAnnotation(bionetwork,model.getAnnotation());
-		
-		this.parseSbmlAnnotations(bionetwork.getReactionsView());
-		this.parseSbmlAnnotations(bionetwork.getMetabolitesView());
-		this.parseSbmlAnnotations(bionetwork.getGenesView());
-		this.parseSbmlAnnotations(bionetwork.getCompartmentsView());
-	}
-
-	/**
-	 * 
-	 *            One of the different lists present in the {@link BioNetwork}
-	 *            class
-	 */
-	private void parseSbmlAnnotations(BioCollection<?> collection) {
-
-		for (BioEntity entry : collection) {
-
-			String id = entry.getId();
-
-			if(entry.getAttribute("oldId") != null)
-			{
-				id = (String) entry.getAttribute("oldId");
-			}
-
-			UniqueNamedSBase sbase = this.getModel().findUniqueNamedSBase(id);
-
-			if (sbase != null && !sbase.getAnnotation().isEmpty() && sbase.hasValidAnnotation()) {
-
-				this.parseAnnotation(entry, sbase.getAnnotation());
-
-			}
-		}
-	}
-
-	/**
-	 * Parse entity's annotation to extract external identifiers
-	 * 
-	 * @param annot
-	 *            the SBML annotation element
-	 */
-	private void parseAnnotation(BioEntity ent, Annotation annot) {
-
-		Matcher m;
-		for (CVTerm cv : annot.getListOfCVTerms()) {
-			
-			String qual;
-			
-			if(cv.isBiologicalQualifier()) {
-			
-				qual = cv.getBiologicalQualifierType().getElementNameEquivalent();
-			}
-			else {
-				qual = cv.getModelQualifierType().getElementNameEquivalent();
-			}
-			
-			for (String ress : cv.getResources()) {
-				if (this.getAnnotationPattern() != null
-						&& (m = Pattern.compile(this.getAnnotationPattern()).matcher(ress)).matches()) {
-
-					if (m.group(1).equalsIgnoreCase("ec-code") && ent instanceof BioReaction) {
-						String oldEc = ((BioReaction) ent).getEcNumber();
-						if(isVoid(oldEc))
-						{
-							((BioReaction) ent).setEcNumber(m.group(2));
-						}
-						else {
-							((BioReaction) ent).setEcNumber(oldEc+";"+m.group(2));
-						}
-					}
-					ent.addRef(m.group(1), m.group(2), 1, qual, ORIGIN);
-				}
-			}
-		}
-
-		String nonrdfAnnot = annot.getNonRDFannotationAsString();
-		if (ent instanceof BioMetabolite && nonrdfAnnot != null && !nonrdfAnnot.isEmpty()) {
-
-			String specialInchiPattern = "<in:inchi xmlns:in=\"([^\"]+)\">InChI=([^<]+)</in:inchi>";
-
-			m = Pattern.compile(specialInchiPattern, Pattern.DOTALL).matcher(nonrdfAnnot);
-
-			while (m.find()) {
-
-				if (m.group(1).equalsIgnoreCase("http://biomodels.net/inchi")) {
-					String inchi = m.group(2);
-					if (!ent.hasRef("inchi", inchi)) {
-						ent.addRef("inchi", inchi, 1, "is", ORIGIN);
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * <p>Getter for the field <code>model</code>.</p>
-	 *
-	 * @return the model
-	 */
-	public Model getModel() {
-		return model;
-	}
-
-	/**
-	 * <p>Setter for the field <code>model</code>.</p>
-	 *
-	 * @param model
-	 *            the model to set
-	 */
-	public void setModel(Model model) {
-		this.model = model;
-	}
-
-	/**
-	 * <p>Getter for the field <code>bionetwork</code>.</p>
-	 *
-	 * @return the bionetwork
-	 */
-	public BioNetwork getBionetwork() {
-		return bionetwork;
-	}
-
-	/**
-	 * <p>Setter for the field <code>bionetwork</code>.</p>
-	 *
-	 * @param bionetwork
-	 *            the bionetwork to set
-	 */
-	public void setBionetwork(BioNetwork bionetwork) {
-		this.bionetwork = bionetwork;
-	}
-
-	/**
-	 * <p>Getter for the field <code>annotationPattern</code>.</p>
-	 *
-	 * @return the annotationPattern
-	 */
-	public String getAnnotationPattern() {
-		return annotationPattern;
-	}
-
-	/**
-	 * <p>Setter for the field <code>annotationPattern</code>.</p>
-	 *
-	 * @param annotationPattern
-	 *            the annotationPattern to set
-	 */
-	public void setAnnotationPattern(String annotationPattern) {
-		this.annotationPattern = annotationPattern;
-	}
+        ReaderSBML3Compatible {
+
+    /**
+     * Constant <code>ORIGIN="SBML"</code>
+     */
+    public static final String ORIGIN = "SBML";
+
+    /**
+     * The Jsbml Model
+     */
+    public Model model;
+    /**
+     * The BioNetwork
+     */
+    public BioNetwork bionetwork;
+
+    /**
+     * The user defined annotation pattern used in the regular expression of
+     * this class
+     */
+    public String annotationPattern;
+
+    /**
+     * The default annotation pattern:
+     * <ul>
+     * <li>http://identifiers.org/([^/]+)/(.*)
+     * </ul>
+     * The first parenthesis group is
+     */
+    public static final String defaultAnnotationPattern = "https?://identifiers.org/([^/]+)/(.*)";
+
+    /**
+     * Constructor
+     *
+     * @param useDefault true to use the {@link #defaultAnnotationPattern}
+     */
+    public AnnotationParser(boolean useDefault) {
+        if (useDefault)
+            this.setAnnotationPattern(defaultAnnotationPattern);
+    }
+
+    /**
+     * Constructor
+     *
+     * @param pattern the user defined pattern
+     */
+    public AnnotationParser(String pattern) {
+        this.annotationPattern = pattern;
+    }
+
+    /**
+     * <p>getAssociatedPackageName.</p>
+     *
+     * @return a {@link java.lang.String} object.
+     */
+    public String getAssociatedPackageName() {
+        return "annot";
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    public boolean isPackageUseableOnModel(Model model) {
+        return true;
+    }
+
+    /**
+     * {@inheritDoc}
+     * <p>
+     * Parse all model entities to retrieve their annotations and extract the
+     * desired information
+     */
+    public void parseModel(Model model, BioNetwork bionetwork) {
+        System.err.println("Starting " + this.getAssociatedPackageName() + " plugin...");
+
+        this.setBionetwork(bionetwork);
+        this.setModel(model);
+
+        this.parseAnnotation(bionetwork, model.getAnnotation());
+
+        this.parseSbmlAnnotations(bionetwork.getReactionsView());
+        this.parseSbmlAnnotations(bionetwork.getMetabolitesView());
+        this.parseSbmlAnnotations(bionetwork.getGenesView());
+        this.parseSbmlAnnotations(bionetwork.getCompartmentsView());
+    }
+
+    /**
+     * One of the different lists present in the {@link BioNetwork}
+     * class