org.sbml.jsbml.ext.comp.ExternalModelDefinition Maven / Gradle / Ivy
/*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
* Copyright (C) 2009-2022 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
* 5. The Babraham Institute, Cambridge, UK
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as .
* ----------------------------------------------------------------------------
*/
package org.sbml.jsbml.ext.comp;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.Creator;
import org.sbml.jsbml.LevelVersionError;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.SubModel;
/**
* The {@link ExternalModelDefinition} objects are model definitions - in and of
* themselves, they are definitions of the models but not uses of those models.
* The class provides a way to declare and identify them so that {@link Model}
* objects in the present {@link SBMLDocument} can use them in {@link SubModel}
* objects.
*
* @author Nicolas Rodriguez
* @since 1.0
*/
public class ExternalModelDefinition extends AbstractNamedSBase
implements UniqueNamedSBase {
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger =
Logger.getLogger(Creator.class);
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 2005205309846284624L;
/**
* The source of this model (anyURI): Specifies a file as relative or absolute
* path, URL or URN
*/
private String source;
/**
*
*/
private String modelRef;
/**
*
*/
private String md5;
/**
* Creates an ExternalModelDefinition instance
*/
public ExternalModelDefinition() {
super();
initDefaults();
}
/**
* Creates a ExternalModelDefinition instance with an id.
*
* @param id
* the id
*/
public ExternalModelDefinition(String id) {
super(id);
initDefaults();
}
/**
* Creates a ExternalModelDefinition instance with an id, level, and version.
*
* @param id
* the id
* @param level
* the SBML level
* @param version
* the SBML version
*/
public ExternalModelDefinition(String id, int level, int version) {
this(id, null, level, version);
}
/**
* Creates a ExternalModelDefinition instance with an id, name, level, and
* version.
*
* @param id
* the id
* @param name
* the name
* @param level
* the SBML level
* @param version
* the SBML version
*/
public ExternalModelDefinition(String id, String name, int level,
int version) {
super(id, name, level, version);
if (getLevelAndVersion().compareTo(
Integer.valueOf(CompConstants.MIN_SBML_LEVEL),
Integer.valueOf(CompConstants.MIN_SBML_VERSION)) < 0) {
throw new LevelVersionError(getElementName(), level, version);
}
initDefaults();
}
/**
* Clone constructor
*
* @param obj
* the instance to clone
*/
public ExternalModelDefinition(ExternalModelDefinition obj) {
super(obj);
if (obj.isSetSource()) {
setSource(obj.getSource());
}
if (obj.isSetModelRef()) {
setModelRef(obj.getModelRef());
}
if (obj.isSetMd5()) {
setMd5(obj.getMd5());
}
}
/**
* clones this class
*/
@Override
public ExternalModelDefinition clone() {
return new ExternalModelDefinition(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
/*
* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 3209;
int result = super.hashCode();
result = prime * result + ((md5 == null) ? 0 : md5.hashCode());
result = prime * result + ((modelRef == null) ? 0 : modelRef.hashCode());
result = prime * result + ((source == null) ? 0 : source.hashCode());
return result;
}
/*
* (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (!super.equals(obj)) {
return false;
}
if (getClass() != obj.getClass()) {
return false;
}
ExternalModelDefinition other = (ExternalModelDefinition) obj;
if (md5 == null) {
if (other.md5 != null) {
return false;
}
} else if (!md5.equals(other.md5)) {
return false;
}
if (modelRef == null) {
if (other.modelRef != null) {
return false;
}
} else if (!modelRef.equals(other.modelRef)) {
return false;
}
if (source == null) {
if (other.source != null) {
return false;
}
} else if (!source.equals(other.source)) {
return false;
}
return true;
}
/**
* Returns the value of source or an empty {@link String} if it is not set.
*
* @return the value of source or an empty {@link String} if it is not set.
*/
public String getSource() {
if (isSetSource()) {
return source;
}
return "";
}
/**
* Returns whether source is set
*
* @return whether source is set
*/
public boolean isSetSource() {
return source != null;
}
/**
* Sets the value of the required source attribute.
*
* The source attribute is used to locate the SBML document containing an
* {@link ExternalModelDefinition}. The value of the attribute must be a URI,
* which includes URLs, URNs, or relative/absolute file locations. The source
* attribute must refer specifically to an SBML Level 3 Version 1 document.
* The
* entire file at the given location is referenced. The source attribute must
* have a value for every {@link ExternalModelDefinition}.
*
*
* @param source
* the value of the source
*/
public void setSource(String source) {
String oldSource = this.source;
this.source = source;
firePropertyChange(CompConstants.source, oldSource, this.source);
}
/**
* Unsets the variable source
*
* @return {@code true }, if source was set before, otherwise {@code false}
*/
public boolean unsetSource() {
if (isSetSource()) {
String oldSource = source;
source = null;
firePropertyChange(CompConstants.source, oldSource, source);
return true;
}
return false;
}
/**
* Returns the value of modelRef or an empty {@link String} if it is not set.
*
* @return the value of modelRef or an empty {@link String} if it is not set.
*/
public String getModelRef() {
if (isSetModelRef()) {
return modelRef;
}
return "";
}
/**
* Returns whether modelRef is set
*
* @return whether modelRef is set
*/
public boolean isSetModelRef() {
return modelRef != null;
}
/**
* Sets the value of the optional modelRef attribute.
*
* modelRef is used to identify a {@link Model} or
* {@link ExternalModelDefinition} object within the SBML document located at
* source. The object referenced may be the main model in the document, or it
* may be a model definition contained in the SBML document's
* listOfModelDefinitions or listOfExternalModelDefinitions. Loops are not
* allowed: it must be possible to follow a chain of
* {@link ExternalModelDefinition} objects to its end in a {@link Model}
* object.
*
*
* In core SBML, the id on {@link Model} is an optional attribute, and
* therefore, it is possible that the {@link Model} object in a given SBML
* document does not have an identifier. In that case, there is no value to
* give
* to the modelRef attribute in {@link ExternalModelDefinition}. If modelRef
* does not have a value, then the main model (i.e., the model element within
* the sbml element) in the referenced file is interpreted as being the model
* referenced by this {@link ExternalModelDefinition} instance.
*
*
* @param modelRef
* the value of modelRef
*/
public void setModelRef(String modelRef) {
String oldModelRef = this.modelRef;
if (modelRef != null && modelRef.trim().length() == 0) {
modelRef = null;
}
this.modelRef = modelRef;
firePropertyChange(CompConstants.modelRef, oldModelRef, this.modelRef);
}
/**
* Unsets the variable modelRef
*
* @return {@code true}, if modelRef was set before, otherwise {@code false}
*/
public boolean unsetModelRef() {
if (isSetModelRef()) {
String oldModelRef = modelRef;
modelRef = null;
firePropertyChange(CompConstants.modelRef, oldModelRef, modelRef);
return true;
}
return false;
}
/**
* Returns the value of md5 or an empty {@link String} if it is not set.
*
* @return the value of md5 or an empty {@link String} if it is not set.
*/
public String getMd5() {
if (isSetMd5()) {
return md5;
}
return "";
}
/**
* Returns whether md5 is set
*
* @return whether md5 is set
*/
public boolean isSetMd5() {
return md5 != null;
}
/**
* Sets the value of the optional md5 attribute.
*
* The md5 attribute takes a string value. If set, it must be an MD5 checksum
* value computed over the document referenced by source. This checksum can
* serve as a data integrity check over the contents of the source.
* Applications
* may use this to verify that the contents have not changed since the time
* that
* the {@link ExternalModelDefinition} reference was constructed.
*
*
* @param md5
* the value of md5
*/
public void setMd5(String md5) {
String oldMd5 = this.md5;
if (md5 != null && md5.trim().length() == 0) {
md5 = null;
}
this.md5 = md5;
firePropertyChange(CompConstants.md5, oldMd5, this.md5);
}
/**
* Unsets the variable md5
*
* @return {@code true}, if md5 was set before, otherwise {@code false}
*/
public boolean unsetMd5() {
if (isSetMd5()) {
String oldMd5 = md5;
md5 = null;
firePropertyChange(CompConstants.md5, oldMd5, md5);
return true;
}
return false;
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetId()) {
attributes.remove("id");
attributes.put(CompConstants.shortLabel + ":id", getId());
}
if (isSetName()) {
attributes.remove("name");
attributes.put(CompConstants.shortLabel + ":name", getName());
}
if (isSetSource()) {
attributes.put(CompConstants.shortLabel + ":" + CompConstants.source,
getSource());
}
if (isSetModelRef()) {
attributes.put(CompConstants.shortLabel + ":" + CompConstants.modelRef,
getModelRef());
}
if (isSetMd5()) {
attributes.put(CompConstants.shortLabel + ":" + CompConstants.md5,
getMd5());
}
return attributes;
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#readAttribute(java.lang.String,
* java.lang.String, java.lang.String)
*/
@Override
public boolean readAttribute(String attributeName, String prefix,
String value) {
boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(CompConstants.source)) {
setSource(value);
} else if (attributeName.equals(CompConstants.modelRef)) {
setModelRef(value);
} else if (attributeName.equals(CompConstants.md5)) {
setMd5(value);
} else {
isAttributeRead = false;
}
}
return isAttributeRead;
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@Override
public boolean isIdMandatory() {
return true;
}
/**
* Resolves the external {@link Model} referenced by this and
* returns that model, for a given path to the directory containing the
* SBML-file wherein this
* {@link ExternalModelDefinition} was made/the root directory for references
* by relative paths.
*
* The referenced {@link Model} is not modified and may thus contain
* {@link Submodel}s referencing further (external) {@link ModelDefinition}s.
*
* @param absoluteContainingURI
* absolute URI to the directory containing the
* file that defines this (needed to resolve local
* references): Undefined behaviour for opaque URIs (URNs or other),
* resolve URNs before calling this method
* @return The referenced {@link Model}
* @throws IOException
* if the source cannot be found/resolved
* @throws XMLStreamException
* if the file at source is not a valid SBMLDocument.
* @throws URISyntaxException
*/
public Model getReferencedModel(URI absoluteContainingURI)
throws XMLStreamException, IOException, URISyntaxException {
String sourceURIString;
URI sourceURI;
SBMLDocument externalFile;
sourceURI = getAbsoluteSourceURI(absoluteContainingURI);
URL sourceUrl = new URL(sourceURI.toString());
// Work under the assumption that sourceURI is a URL (file or https, ...),
// not some kind of opaque URI (like a URN)
if (sourceUrl.getProtocol().equals("file")) {
externalFile = org.sbml.jsbml.SBMLReader.read(new File(sourceURI));
} else {
logger.info("externalModelDefinition " + getId()
+ " points to an online-resource. Trying to open connection to: "
+ source);
InputStream stream = sourceUrl.openStream();
externalFile = org.sbml.jsbml.SBMLReader.read(stream);
externalFile.getSBMLDocument().setLocationURI(sourceUrl.toURI().toString());
logger.info("Successfully read online source of externalModelDefinition "
+ getId());
}
sourceURIString = sourceURI.toString();
// The referenced model can be the main model of the referenced File
// (comp-documentation page 14)
if (externalFile.getModel().getId().equals(modelRef)) {
return externalFile.getModel();
} else if (externalFile.isPackageEnabled(CompConstants.shortLabel)) {
CompSBMLDocumentPlugin externalFileCompPlugin =
(CompSBMLDocumentPlugin) externalFile.getExtension(
CompConstants.shortLabel);
ModelDefinition localModelDefinition =
externalFileCompPlugin.getModelDefinition(modelRef);
ExternalModelDefinition nextLayer =
externalFileCompPlugin.getExternalModelDefinition(modelRef);
if (localModelDefinition != null) {
return localModelDefinition;
} else if (nextLayer != null) {
// Allowed by the specification: This ExternalModelDefinition may
// reference an ExternalModelDefinition in the source; which may again
// reference an External definition. As by the specification, no loops
// are allowed (so they are not checked for here)
// The source may be at an entirely different location OR at a location
// relative to the current one
if (!sourceURIString.startsWith(absoluteContainingURI.toString())
|| sourceURIString.substring(
absoluteContainingURI.toString().length()).indexOf("/") != -1) {
return nextLayer.getReferencedModel(new URI(
sourceURIString.substring(0, sourceURIString.lastIndexOf("/"))));
// Or just the current one
} else {
return nextLayer.getReferencedModel(absoluteContainingURI);
}
}
}
return null;
}
/**
* Resolves the external {@link Model} referenced by this and returns that
* model, under the assumption that the containing {@link SBMLDocument} a)
* exists and b) has a valid locationURI set (cf
* {@link SBMLDocument#isSetLocationURI()}). This location of the containing
* file is needed to resolve references to external models by relative paths.
* URNs/opaque URIs cannot be resolved by this method, resolve them before
* calling it.
*
* The referenced {@link Model} is not modified and may thus contain
* {@link Submodel}s referencing further (external) {@link ModelDefinition}s.
*
* @return the {@link Model} referenced by this
* @throws XMLStreamException
* if the file referenced by this is not a valid xml/sbml
* @throws IOException
* if the file referenced by this cannot be found
* @throws URISyntaxException
* if parent's locationURI is not a valid URI
* @throws NullPointerException
* if the parent {@link SBMLDocument}'s locationURI is not set.
*/
public Model getReferencedModel() throws XMLStreamException, IOException, URISyntaxException {
if(getSBMLDocument().isSetLocationURI()) {
// Cut off the file-name of the containing document here:
String absolutePath = getSBMLDocument().getLocationURI().substring(0, getSBMLDocument().getLocationURI().lastIndexOf("/"));
return getReferencedModel(new URI(absolutePath));
} else {
throw new NullPointerException(
"The containing model's location is not set. Either set it, or use the getReferencedModel(URI)-variant");
}
}
/**
* Finds the absolute URI of the source-file specified: If the source is
* specified through a relative path, will try to use the containing
* SBMLDocument's {@link SBMLDocument#getLocationURI} to turn it into an
* absolute URI in the current context.
*
* The actual source is not changed in the process
*
* @return The absolute URI to the source
* ({@link ExternalModelDefinition#getSource}) of this
* ExternalModelDefinition
* @throws URISyntaxException
* @throws MalformedURLException
*/
public URI getAbsoluteSourceURI() throws URISyntaxException, MalformedURLException {
if(getSBMLDocument().isSetLocationURI()) {
// Cut off the file-name of the containing document here:
String absolutePath = getSBMLDocument().getLocationURI().substring(0, getSBMLDocument().getLocationURI().lastIndexOf("/"));
return getAbsoluteSourceURI(new URI(absolutePath));
} else {
throw new NullPointerException(
"The containing model's location is not set. Either set it, or use the getReferencedModel(URI)-variant");
}
}
/**
* Finds the absolute URI of the source-file specified: If the source is
* specified through a relative path, will try to use the given
* absoluteContainingURI to turn it into an absolute URI in the current
* context.
*
* The actual source is not changed in the process
*
* @param absoluteContainingURI
* absolute URI to the directory containing the
* file that defines this (needed to resolve local
* references)
* @return The absolute URI to the source
* ({@link ExternalModelDefinition#getSource}) of this
* ExternalModelDefinition
* @throws MalformedURLException
* @throws URISyntaxException
*/
public URI getAbsoluteSourceURI(URI absoluteContainingURI) throws MalformedURLException, URISyntaxException {
URI sourceURI;
String completionOfAbsoluteContainingURI =
absoluteContainingURI.toString().endsWith("/") ? "" : "/";
URL sourceUrl;
try {
// the source itself is a valid URL: do not need absoluteContainingURI
sourceUrl = new URL(new URI(source).toString());
} catch (MalformedURLException e) {
// the source itself is not a valid URL: it is relative
StringBuilder workingURI = new StringBuilder();
if (!new File(source).isAbsolute()) {
workingURI.append(absoluteContainingURI);
workingURI.append(completionOfAbsoluteContainingURI);
} else {
workingURI.append("file:");
String completionOfPrefix = source.startsWith("/") ? "" : "/";
workingURI.append(completionOfPrefix);
}
workingURI.append(source);
sourceUrl = new URL(workingURI.toString());
}
sourceURI = sourceUrl.toURI();
return sourceURI;
}
}
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