Set version 4.0.0 and fixed javadoc, updated JAXB plugin, generated x…

…ml schema, etc.
BioPAX · Sep 14, 2018 · 74ec67f · 74ec67f
1 parent c5a7251
commit 74ec67f
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Showing 30 changed files with 735 additions and 823 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,5 @@ target
 .springBeans
 geo_data
 .extract
+*.versionsBackup
+
diff --git a/biopax-validator-client/pom.xml b/biopax-validator-client/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>org.biopax.validator</groupId>
 		<artifactId>parent</artifactId>
-		<version>4.0.0-SNAPSHOT</version>
+		<version>4.0.0</version>
 	</parent>
 
     <artifactId>biopax-validator-client</artifactId>
@@ -45,8 +45,9 @@
 					<clearOutputDir>false</clearOutputDir>
 					<packageName>org.biopax.validator.jaxb</packageName>
 					<failOnNoSchemas>true</failOnNoSchemas>
-					<schemaDirectory>${basedir}/src/main/resources</schemaDirectory>
-<!-- 					<arguments>-enableIntrospection</arguments> -->
+					<sources>
+						<source>src/main/resources/validator-response-2.0.xsd</source>
+					</sources>
 				</configuration>
 			</plugin>
 			<plugin>

diff --git a/biopax-validator-client/src/main/resources/validator-response-2.0.xsd b/biopax-validator-client/src/main/resources/validator-response-2.0.xsd
@@ -1,27 +1,19 @@
-<xs:schema version="1.0" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" version="1.0">
 
   <xs:element name="validatorResponse" type="ValidatorResponse"/>
 
-  <xs:complexType name="Validation">
+  <xs:complexType name="ErrorCaseType">
     <xs:sequence>
-      <xs:element name="modelData" type="xs:string" minOccurs="0"/>
-      <xs:element name="error" type="ErrorType" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:element name="comment" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element minOccurs="0" name="message" type="xs:string"/>
     </xs:sequence>
-    <xs:attribute name="description" type="xs:string"/>
-    <xs:attribute name="notFixedProblems" type="xs:int" use="required"/>
-    <xs:attribute name="notFixedErrors" type="xs:int" use="required"/>
-    <xs:attribute name="totalProblemsFound" type="xs:int" use="required"/>
-    <xs:attribute name="fix" type="xs:boolean" use="required"/>
-    <xs:attribute name="threshold" type="Behavior"/>
-    <xs:attribute name="maxErrors" type="xs:int" use="required"/>
-    <xs:attribute name="profile" type="xs:string"/>
-    <xs:attribute name="summary" type="xs:string"/>
+    <xs:attribute name="object" type="xs:string"/>
+    <xs:attribute name="reportedBy" type="xs:string"/>
+    <xs:attribute name="fixed" type="xs:boolean" use="required"/>
   </xs:complexType>
 
   <xs:complexType name="ErrorType">
     <xs:sequence>
-      <xs:element name="errorCase" type="ErrorCaseType" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element maxOccurs="unbounded" minOccurs="0" name="errorCase" type="ErrorCaseType"/>
     </xs:sequence>
     <xs:attribute name="code" type="xs:string"/>
     <xs:attribute name="message" type="xs:string"/>
@@ -31,22 +23,36 @@
     <xs:attribute name="totalCases" type="xs:int" use="required"/>
   </xs:complexType>
 
-  <xs:complexType name="ErrorCaseType">
+  <xs:complexType name="Validation">
     <xs:sequence>
-      <xs:element name="message" type="xs:string" minOccurs="0"/>
+      <xs:element minOccurs="0" name="modelData" type="xs:string"/>
+      <xs:element maxOccurs="unbounded" minOccurs="0" name="error" type="ErrorType"/>
+      <xs:element maxOccurs="unbounded" minOccurs="0" name="comment" type="xs:string"/>
     </xs:sequence>
-    <xs:attribute name="object" type="xs:string"/>
-    <xs:attribute name="reportedBy" type="xs:string"/>
-    <xs:attribute name="fixed" type="xs:boolean" use="required"/>
+    <xs:attribute name="description" type="xs:string"/>
+    <xs:attribute name="notFixedProblems" type="xs:int" use="required"/>
+    <xs:attribute name="notFixedErrors" type="xs:int" use="required"/>
+    <xs:attribute name="totalProblemsFound" type="xs:int" use="required"/>
+    <xs:attribute name="fix" type="xs:boolean" use="required"/>
+    <xs:attribute name="threshold" type="Behavior"/>
+    <xs:attribute name="maxErrors" type="xs:int" use="required"/>
+    <xs:attribute name="profile" type="xs:string"/>
+    <xs:attribute name="summary" type="xs:string"/>
   </xs:complexType>
 
   <xs:complexType name="ValidatorResponse">
     <xs:sequence>
-      <xs:element name="validation" type="Validation" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element maxOccurs="unbounded" minOccurs="0" name="validation" type="Validation"/>
     </xs:sequence>
   </xs:complexType>
 
   <xs:simpleType name="Behavior">
+    <xs:annotation>
+      <xs:documentation><![CDATA[Validation rule behavior:
+      IGNORE -- skip: do not validate, nor report any messages;
+      ERROR -- report as error, fail if error limit is exceeded;
+      WARNING -- report as warning.]]></xs:documentation>
+    </xs:annotation>
     <xs:restriction base="xs:string">
       <xs:enumeration value="IGNORE"/>
       <xs:enumeration value="WARNING"/>
@@ -55,6 +61,9 @@
   </xs:simpleType>
 
   <xs:simpleType name="Category">
+    <xs:annotation>
+      <xs:documentation><![CDATA[Validation error category.]]></xs:documentation>
+    </xs:annotation>
     <xs:restriction base="xs:string">
       <xs:enumeration value="SYNTAX"/>
       <xs:enumeration value="SPECIFICATION"/>
@@ -63,4 +72,3 @@
     </xs:restriction>
   </xs:simpleType>
 </xs:schema>
-
diff --git a/biopax-validator-web/pom.xml b/biopax-validator-web/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>parent</artifactId>
 		<groupId>org.biopax.validator</groupId>
-		<version>4.0.0-SNAPSHOT</version>
+		<version>4.0.0</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/biopax-validator/pom.xml b/biopax-validator/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>parent</artifactId>
 		<groupId>org.biopax.validator</groupId>
-		<version>4.0.0-SNAPSHOT</version>
+		<version>4.0.0</version>
 	</parent>
 
 	<modelVersion>4.0.0</modelVersion>

diff --git a/biopax-validator/src/main/java/org/biopax/validator/impl/AbstractCvRule.java b/biopax-validator/src/main/java/org/biopax/validator/impl/AbstractCvRule.java
@@ -1,9 +1,5 @@
 package org.biopax.validator.impl;
 
-import java.util.*;
-
-import javax.annotation.PostConstruct;
-
 import org.biopax.paxtools.controller.PropertyEditor;
 import org.biopax.paxtools.model.BioPAXElement;
 import org.biopax.validator.api.AbstractRule;
@@ -12,124 +8,129 @@
 import org.biopax.validator.api.CvValidator;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.PostConstruct;
+import java.util.HashSet;
+import java.util.Set;
+
 /**
  * An abstract class for CV terms checks.
- * 
- * @author rodche
  *
  * @param <D> property domain
+ * @author rodche
  */
 public abstract class AbstractCvRule<D extends BioPAXElement> extends AbstractRule<D> implements CvRule<D> {
-
-    @Autowired
-	protected CvValidator ontologyManager;
-
-    protected final Class<D> domain;
-    protected final String property; // helps validate generic ControlledVocabulary instances
-    protected final Set<CvRestriction> restrictions;
-	private Set<String> validTerms;
-	protected PropertyEditor<? super D, ?> editor;
-
-    /**
-     * Constructor.
-     * 
-     * @param domain a BioPAX class for which the CV terms restrictions apply
-     * @param property the name of the BioPAX property to get controlled vocabularies or null
-     * @param restrictions a list of beans, each defining names (a subtree of an ontology) that 
-     * is either to include or exclude (when 'not' flag is set) from the valid names set.
-     */
-    public AbstractCvRule(Class<D> domain, String property, CvRestriction... restrictions)
-    {
-    	this.domain = domain;
-    	this.property = property;
-        this.restrictions = new HashSet<CvRestriction>(restrictions.length);
-    	for(CvRestriction c: restrictions) {
-        	this.restrictions.add(c);
-        }    	
+
+  @Autowired
+  protected CvValidator ontologyManager;
+
+  protected final Class<D> domain;
+  protected final String property; // helps validate generic ControlledVocabulary instances
+  protected final Set<CvRestriction> restrictions;
+  private Set<String> validTerms;
+  protected PropertyEditor<? super D, ?> editor;
+
+  /**
+   * Constructor.
+   *
+   * @param domain       a BioPAX class for which the CV terms restrictions apply
+   * @param property     the name of the BioPAX property to get controlled vocabularies or null
+   * @param restrictions a list of beans, each defining names (a subtree of an ontology) that
+   *                     is either to include or exclude (when 'not' flag is set) from the valid names set.
+   */
+  public AbstractCvRule(Class<D> domain, String property, CvRestriction... restrictions) {
+    this.domain = domain;
+    this.property = property;
+    this.restrictions = new HashSet<CvRestriction>(restrictions.length);
+    for (CvRestriction c : restrictions) {
+      this.restrictions.add(c);
+    }
+  }
+
+  @PostConstruct
+  public void init() {
+    if (ontologyManager != null) {
+      setValidTerms(ontologyManager.getValidTermNames(this));
+    } else {
+      throw new IllegalStateException("ontologyManager is NULL!");
     }
-
-    @PostConstruct
-    public void init() {
-    	if(ontologyManager != null) {
-    		setValidTerms(ontologyManager.getValidTermNames(this));
-    	} else {
-    		throw new IllegalStateException("ontologyManager is NULL!");
-    	}
-    };
-
-
-	public boolean canCheck(Object thing) {
-		return domain.isInstance(thing);
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biopax.validator.impl.CvRule#getValidTerms()
-	 */
-	public Set<String> getValidTerms() {
-		return validTerms;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biopax.validator.impl.CvRule#setValidTerms(java.util.Set)
-	 */
-	public void setValidTerms(Set<String> validTerms) {
-		this.validTerms = validTerms;
-	}
-
-	// for unit testing
-
-	/* (non-Javadoc)
-	 * @see org.biopax.validator.impl.CvRule#getRestrictions()
-	 */
-	public Set<CvRestriction> getRestrictions() {
-		return restrictions;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biopax.validator.impl.CvRule#getDomain()
-	 */
-	public Class<D> getDomain() {
-		return domain;
-	}
-
-	/* (non-Javadoc)
-	 * @see org.biopax.validator.impl.CvRule#getProperty()
-	 */
-	public String getProperty() {
-		return property;
-	}
-
-	/**
-	 * Gets the internal BiopaxOntologyManager instance
-	 * @return
-	 */
-	public CvValidator getBiopaxOntologyManager() {
-		return ontologyManager;
-	}
-
-	/**
-	 * Gets the corresponding CV property editor.
-	 * Returns null if either the 'domain' itself is of CV type
-	 * or the 'property' is null.
-	 * 
-	 * @return
-	 */
-	public PropertyEditor<? super D, ?> getEditor() {
-		return editor;
-	}
-
-	/**
-	 * OntologyAccess IDs used to check this CV rule.
-	 * These can be extracted from the CV rescrictions 
-	 * used to define the rule.
-	 * (other ontologies are not used).
-	 * 
-	 * @return
-	 */
-	protected Set<String> getOntologyIDs() {
-		Set<String> ids = new HashSet<String>();
-		for(CvRestriction restriction : restrictions)
-			ids.add(restriction.getOntologyId());
-		return ids;
-	}
+  }
+
+  ;
+
+
+  public boolean canCheck(Object thing) {
+    return domain.isInstance(thing);
+  }
+
+  /* (non-Javadoc)
+   * @see org.biopax.validator.impl.CvRule#getValidTerms()
+   */
+  public Set<String> getValidTerms() {
+    return validTerms;
+  }
+
+  /* (non-Javadoc)
+   * @see org.biopax.validator.impl.CvRule#setValidTerms(java.util.Set)
+   */
+  public void setValidTerms(Set<String> validTerms) {
+    this.validTerms = validTerms;
+  }
+
+  // for unit testing
+
+  /* (non-Javadoc)
+   * @see org.biopax.validator.impl.CvRule#getRestrictions()
+   */
+  public Set<CvRestriction> getRestrictions() {
+    return restrictions;
+  }
+
+  /* (non-Javadoc)
+   * @see org.biopax.validator.impl.CvRule#getDomain()
+   */
+  public Class<D> getDomain() {
+    return domain;
+  }
+
+  /* (non-Javadoc)
+   * @see org.biopax.validator.impl.CvRule#getProperty()
+   */
+  public String getProperty() {
+    return property;
+  }
+
+  /**
+   * Gets the internal BiopaxOntologyManager instance
+   *
+   * @return ontology manager
+   */
+  public CvValidator getBiopaxOntologyManager() {
+    return ontologyManager;
+  }
+
+  /**
+   * Gets the corresponding CV property editor.
+   * Returns null if either the 'domain' itself is of CV type
+   * or the 'property' is null.
+   *
+   * @return biopax property editor
+   */
+  public PropertyEditor<? super D, ?> getEditor() {
+    return editor;
+  }
+
+  /**
+   * OntologyAccess IDs used to check this CV rule.
+   * These can be extracted from the CV restrictions
+   * used to define the rule.
+   * (other ontologies are not used).
+   *
+   * @return ontology IDs, such as e.g. 'MI', 'GO'
+   */
+  protected Set<String> getOntologyIDs() {
+    Set<String> ids = new HashSet<String>();
+    for (CvRestriction restriction : restrictions)
+      ids.add(restriction.getOntologyId());
+    return ids;
+  }
 }