/*******************************************************************************
* Copyright 2006 - 2014 Vienna University of Technology,
* Department of Software Technology and Interactive Systems, IFS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and limitations under the License.
******************************************************************************/
package eu.scape_project.planning.services.taverna.parser;
import java.io.InputStream;
import java.util.HashMap;
import java.util.Map;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import org.dom4j.XPath;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import eu.scape_project.planning.xml.ProjectImporter;
import eu.scape_project.planning.xml.SchemaResolver;
import eu.scape_project.planning.xml.ValidatingParserFactory;
/**
* Parser for t2flow files.
*/
public class T2FlowParser {
private static Logger log = LoggerFactory.getLogger(T2FlowParser.class);
protected static final String SCHEMA_LOCATION = "data/schemas/";
protected static final Map<String, String> T2FLOW_NAMESPACE_MAP = new HashMap<String, String>();
/**
* Component profiles.
*/
public enum ComponentProfile {
MigrationAction("http://scape-project.eu/component/profile/migrationaction"),
Characterisation("http://scape-project.eu/component/profile/characterisation"),
QA("http://scape-project.eu/component/profile/qa"),
ExecutablePlan("http://scape-project.eu/component/profile/executableplan"),
NoProfile("");
private final String uri;
/**
* Creates a component profile based on the provided URI.
*
* @param uri
* the URI of the profile
*/
ComponentProfile(String uri) {
this.uri = uri;
}
@Override
public String toString() {
return uri;
}
/**
* Returns the ComponentProfile corresponding to the provided text.
*
* @param text
* the text of the ComponentProfile
* @return the ComponentProfile
*/
public static ComponentProfile fromString(String text) {
if (text != null) {
for (ComponentProfile b : ComponentProfile.values()) {
if (text.equalsIgnoreCase(b.toString())) {
return b;
}
}
}
throw new IllegalArgumentException("No constant with text " + text + " found");
}
}
/**
* The parsed document.
*/
private Document doc = null;
/**
* Creates a T2FlowParser from the inputstream.
*
* @param t2flow
* the inputstream to parse
* @return the parser
* @throws TavernaParserException
* if the parser could not be initialized
*/
public static T2FlowParser createParser(InputStream t2flow) throws TavernaParserException {
T2FlowParser parser = new T2FlowParser();
parser.initialise(t2flow);
return parser;
}
/**
* Initialises the parser by reading the the t2flow from the input stream
* and parsing it.
*
* @param t2flow
* the t2flow
* @throws TavernaParserException
* if the parser could not be initialized
*/
protected void initialise(InputStream t2flow) throws TavernaParserException {
log.debug("Parsing inputstream");
T2FLOW_NAMESPACE_MAP.put("t2f", "http://taverna.sf.net/2008/xml/t2flow");
ValidatingParserFactory vpf = new ValidatingParserFactory();
try {
SAXParser parser = vpf.getValidatingParser();
parser.setProperty(ValidatingParserFactory.JAXP_SCHEMA_SOURCE, ProjectImporter.TAVERNA_SCHEMA_URI);
SAXReader reader = new SAXReader(parser.getXMLReader());
reader.setValidation(false);
SchemaResolver schemaResolver = new SchemaResolver();
schemaResolver.addSchemaLocation(ProjectImporter.TAVERNA_SCHEMA_URI, SCHEMA_LOCATION
+ ProjectImporter.TAVERNA_SCHEMA);
reader.setEntityResolver(schemaResolver);
doc = reader.read(t2flow);
} catch (DocumentException e) {
log.error("Error initialising T2FlowParser: {}", e.getMessage());
throw new TavernaParserException("Error parsing workflow.", e);
} catch (ParserConfigurationException e) {
log.error("Error initialising T2FlowParser: {}", e.getMessage());
throw new TavernaParserException("Error parsing workflow.", e);
} catch (SAXException e) {
log.error("Error initialising T2FlowParser: {}", e.getMessage());
throw new TavernaParserException("Error parsing workflow.", e);
}
}
/**
* Reads the ID annotation of the t2flow.
*
* @return the id the workflow adheres to
* @throws TavernaParserException
*/
public String getId() throws TavernaParserException {
log.debug("Extracting profile ID");
XPath xpath = DocumentHelper.createXPath("/t2f:workflow/t2f:dataflow[@role='top']/@id");
xpath.setNamespaceURIs(T2FLOW_NAMESPACE_MAP);
Node node = xpath.selectSingleNode(doc);
if (node == null) {
return null;
}
return node.getText();
}
/**
* Reads the name annotation of the t2flow.
*
* @return the name of the workflow
* @throws TavernaParserException
*/
public String getName() throws TavernaParserException {
log.debug("Extracting workflow name");
XPath xpath = DocumentHelper
.createXPath("/t2f:workflow/t2f:dataflow[@role='top']/t2f:annotations/*/*/*/*/annotationBean[@class='net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle']/text");
xpath.setNamespaceURIs(T2FLOW_NAMESPACE_MAP);
Node node = xpath.selectSingleNode(doc);
if (node == null) {
return null;
}
return node.getText();
}
/**
* Reads the description annotation of the t2flow.
*
* @return the description of the workflow
* @throws TavernaParserException
*/
public String getDescription() throws TavernaParserException {
log.debug("Extracting workflow description");
XPath xpath = DocumentHelper
.createXPath("/t2f:workflow/t2f:dataflow[@role='top']/t2f:annotations/*/*/*/*/annotationBean[@class='net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription']/text");
xpath.setNamespaceURIs(T2FLOW_NAMESPACE_MAP);
Node node = xpath.selectSingleNode(doc);
if (node == null) {
return null;
}
return node.getText();
}
/**
* Reads the author annotation of the t2flow.
*
* @return the author of the workflow
* @throws TavernaParserException
*/
public String getAuthor() throws TavernaParserException {
log.debug("Extracting workflow author");
XPath xpath = DocumentHelper
.createXPath("/t2f:workflow/t2f:dataflow[@role='top']/t2f:annotations/*/*/*/*/annotationBean[@class='net.sf.taverna.t2.annotation.annotationbeans.Author']/text");
xpath.setNamespaceURIs(T2FLOW_NAMESPACE_MAP);
Node node = xpath.selectSingleNode(doc);
if (node == null) {
return null;
}
return node.getText();
}
// -------- Getter/Setter --------
public Document getDoc() {
return doc;
}
}