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Commit c6573caf authored by Sascha Herzinger's avatar Sascha Herzinger
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Making XmlParser a utility class

parent c169b7ac
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1 merge request!644Refactored IConverter and XmlParser across project
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commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+ 40
− 73
View file @ c6573caf
......@@ -31,7 +31,6 @@ import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
/**
......@@ -40,7 +39,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
* @author Piotr Gawron
*
*/
public class XmlParser {
final public class XmlParser {
/**
* Default class logger.
......@@ -53,38 +52,35 @@ public class XmlParser {
private static final int HEX_BASE = 16;
/**
* {@link DocumentBuilderFactory} used to create {@link DocumentBuilder} objects
* that will manipulate xml nodes.
* {@link DocumentBuilder} objects that will manipulate xml nodes.
*/
private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
private static DocumentBuilderFactory nonValidateDocumentBuilderFactory;
private static DocumentBuilder validatedDocumentBuilder;
private static DocumentBuilder nonValidatedDocumentBuilder;
static {
nonValidateDocumentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilderFactory nonValidateDocumentBuilderFactory = DocumentBuilderFactory.newInstance();
nonValidateDocumentBuilderFactory.setNamespaceAware(false);
nonValidateDocumentBuilderFactory.setValidating(false);
try {
nonValidateDocumentBuilderFactory.setFeature("http://xml.org/sax/features/namespaces", false);
nonValidateDocumentBuilderFactory.setFeature("http://xml.org/sax/features/validation", false);
nonValidateDocumentBuilderFactory.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar",
false);
nonValidateDocumentBuilderFactory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",
false);
nonValidateDocumentBuilderFactory.setFeature(
"http://xml.org/sax/features/namespaces", false);
nonValidateDocumentBuilderFactory.setFeature(
"http://xml.org/sax/features/validation", false);
nonValidateDocumentBuilderFactory.setFeature(
"http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
nonValidateDocumentBuilderFactory.setFeature(
"http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
nonValidatedDocumentBuilder = nonValidateDocumentBuilderFactory.newDocumentBuilder();
validatedDocumentBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
} catch (ParserConfigurationException e) {
logger.error(e, e);
}
}
/**
* DOM document builder used for xml transformations.
*/
private DocumentBuilder validatedDocumentBuilder;
private DocumentBuilder nonValidatedDocumentBuilder;
/**
* Default constructor that prevents from instantiation of the class.
* private constructor. This class has no state and contains only static utility methods.
*/
protected XmlParser() {
private XmlParser() {
}
/**
......@@ -98,7 +94,7 @@ public class XmlParser {
* @return node from nodes list with the tagName name, <b>null</b> if such node
* doesn't exist
*/
protected Node getNode(final String tagName, final NodeList nodes) {
public static Node getNode(final String tagName, final NodeList nodes) {
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
......@@ -121,7 +117,7 @@ public class XmlParser {
* @return node from nodes list with the tagName name, <b>null</b> if such node
* doesn't exist
*/
protected Node getNode(final String tagName, final Node parentNode) {
public static Node getNode(final String tagName, final Node parentNode) {
return getNode(tagName, parentNode.getChildNodes());
}
......@@ -135,7 +131,7 @@ public class XmlParser {
* list of input nodes
* @return list of nodes with 'tagName' name
*/
protected List<Node> getNodes(final String tagName, final NodeList nodes) {
public static List<Node> getNodes(final String tagName, final NodeList nodes) {
List<Node> result = new ArrayList<Node>();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
......@@ -157,7 +153,7 @@ public class XmlParser {
* @return the value of node attribute, empty string("") if attribute doesn't
* exist
*/
protected String getNodeAttr(final String attrName, final Node node) {
public static String getNodeAttr(final String attrName, final Node node) {
NamedNodeMap attrs = node.getAttributes();
for (int y = 0; y < attrs.getLength(); y++) {
Node attr = attrs.item(y);
......@@ -177,7 +173,7 @@ public class XmlParser {
* @return the text value of node or empty string ("") if the text could be
* found.
*/
protected String getNodeValue(final Node node) {
static String getNodeValue(final Node node) {
if (node == null) {
return "";
}
......@@ -200,44 +196,16 @@ public class XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
protected Document getXmlDocumentFromInputSource(final InputSource stream, boolean validate)
static Document getXmlDocumentFromInputSource(final InputSource stream, boolean validate)
throws InvalidXmlSchemaException {
try {
DocumentBuilder db = getDocumentBuilder(validate);
synchronized (db) { // DocumentBuilder cannot parse few objects at the
// same time
return db.parse(stream);
}
} catch (SAXException e) {
throw new InvalidXmlSchemaException("Problem with xml parser", e);
} catch (IOException e) {
throw new InvalidXmlSchemaException("Problem with xml parser", e);
}
}
/**
* Return proper document builder.
*
* @param validate
* - should the document builder validate input xml or not
* @return
*/
private DocumentBuilder getDocumentBuilder(boolean validate) {
try {
if (validate) {
if (validatedDocumentBuilder == null) {
validatedDocumentBuilder = documentBuilderFactory.newDocumentBuilder();
}
return validatedDocumentBuilder;
return validatedDocumentBuilder.parse(stream);
} else {
if (nonValidatedDocumentBuilder == null) {
nonValidatedDocumentBuilder = nonValidateDocumentBuilderFactory.newDocumentBuilder();
}
return nonValidatedDocumentBuilder;
return nonValidatedDocumentBuilder.parse(stream);
}
} catch (ParserConfigurationException e) {
throw new InvalidStateException("Problem with xml parser");
} catch (SAXException | IOException e) {
throw new InvalidXmlSchemaException("Problem with xml parser", e);
}
}
......@@ -254,7 +222,7 @@ public class XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
protected Document getXmlDocumentFromString(final String text, boolean validate) throws InvalidXmlSchemaException {
private static Document getXmlDocumentFromString(final String text, boolean validate) throws InvalidXmlSchemaException {
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(text));
try {
......@@ -274,7 +242,7 @@ public class XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
public static Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
return getXmlDocumentFromString(text, true);
}
......@@ -285,7 +253,7 @@ public class XmlParser {
* node that should be transformed into xml string
* @return string representation of the xml node
*/
protected String nodeToString(final Node node) {
static String nodeToString(final Node node) {
return nodeToString(node, false);
}
......@@ -298,7 +266,7 @@ public class XmlParser {
* should the top level node exist in the output
* @return string representation of the xml node
*/
protected String nodeToString(final Node node, final boolean includeHeadNode) {
static String nodeToString(final Node node, final boolean includeHeadNode) {
if (node == null) {
return null;
}
......@@ -331,7 +299,7 @@ public class XmlParser {
* string representing color
* @return Color object for the fiven string
*/
protected Color stringToColor(final String color) {
static Color stringToColor(final String color) {
try {
String alpha = color.substring(0, 2);
Color tmp = new Color(hexToInteger(color.substring(2)));
......@@ -348,7 +316,7 @@ public class XmlParser {
* string representation in hex base
* @return Integer value of the hex string
*/
private Integer hexToInteger(String hexString) {
static Integer hexToInteger(String hexString) {
return Integer.valueOf(hexString, HEX_BASE);
}
......@@ -359,7 +327,7 @@ public class XmlParser {
* color that should be converted into string
* @return hex string representation of the color
*/
protected String colorToString(final Color color) {
static String colorToString(final Color color) {
return String.format("%08X", color.getRGB());
}
......@@ -372,7 +340,7 @@ public class XmlParser {
* @throws IOException
* thrown when there are some problems with a file
*/
protected String fileToString(final String fileName) throws IOException {
static String fileToString(final String fileName) throws IOException {
BufferedReader reader = new BufferedReader(new FileReader(fileName));
String line = null;
StringBuilder stringBuilder = new StringBuilder();
......@@ -397,11 +365,10 @@ public class XmlParser {
* @throws IOException
* thrown if there are some problems with input stream
*/
protected String inputStreamToString(final InputStream inputStream) throws IOException {
static String inputStreamToString(final InputStream inputStream) throws IOException {
StringWriter writer = new StringWriter();
IOUtils.copy(inputStream, writer, "UTF-8");
String result = writer.toString();
return result;
return writer.toString();
}
/**
......@@ -411,7 +378,7 @@ public class XmlParser {
* string to be escaped
* @return escaped string, ready to be used in xml
*/
protected String escapeXml(final String string) {
public static String escapeXml(final String string) {
if (string == null) {
return null;
}
......@@ -419,7 +386,7 @@ public class XmlParser {
return StringEscapeUtils.escapeXml10(string).replaceAll("\n", "&#10;").replace("\r", "&#13;");
}
public List<Node> getAllNotNecessirellyDirectChild(String tagName, Node root) {
private static List<Node> getAllNotNecessirellyDirectChild(String tagName, Node root) {
List<Node> result = new ArrayList<>();
for (int x = 0; x < root.getChildNodes().getLength(); x++) {
Node node = root.getChildNodes().item(x);
......
commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
+ 48
− 50
View file @ c6573caf
......@@ -38,8 +38,6 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
public class XmlParserTest {
Logger logger = Logger.getLogger(XmlParserTest.class);
XmlParser parser = new XmlParser();
@Before
public void setUp() throws Exception {
}
......@@ -53,11 +51,11 @@ public class XmlParserTest {
try {
String strColor = "ffcbcd09";
Color c = parser.stringToColor(strColor);
String resultString = parser.colorToString(c);
Color c = XmlParser.stringToColor(strColor);
String resultString = XmlParser.colorToString(c);
assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
Color c2 = parser.stringToColor(resultString);
Color c2 = XmlParser.stringToColor(resultString);
assertEquals(c.getRed(), c2.getRed());
assertEquals(c.getGreen(), c2.getGreen());
......@@ -73,7 +71,7 @@ public class XmlParserTest {
try {
String strColor = "hello world";
parser.stringToColor(strColor);
XmlParser.stringToColor(strColor);
fail("Exception expected");
} catch (InvalidArgumentException e) {
} catch (Exception e) {
......@@ -87,11 +85,11 @@ public class XmlParserTest {
try {
String strColor = "fecbcd09";
Color c = parser.stringToColor(strColor);
String resultString = parser.colorToString(c);
Color c = XmlParser.stringToColor(strColor);
String resultString = XmlParser.colorToString(c);
assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
Color c2 = parser.stringToColor(resultString);
Color c2 = XmlParser.stringToColor(resultString);
assertEquals(c.getRed(), c2.getRed());
assertEquals(c.getGreen(), c2.getGreen());
......@@ -106,7 +104,7 @@ public class XmlParserTest {
@Test
public void testGetXmlDocumentFromString() throws Exception {
try {
Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
Document validDoc = XmlParser.getXmlDocumentFromString("<node>test</node>");
assertNotNull(validDoc);
} catch (Exception e) {
e.printStackTrace();
......@@ -119,8 +117,8 @@ public class XmlParserTest {
public void testNodeToString() throws Exception {
try {
String xml = "<test_node>test_x</test_node>";
Document validDoc = parser.getXmlDocumentFromString(xml);
String str = parser.nodeToString(validDoc);
Document validDoc = XmlParser.getXmlDocumentFromString(xml);
String str = XmlParser.nodeToString(validDoc);
assertEquals(xml.trim(), str.trim());
} catch (Exception e) {
e.printStackTrace();
......@@ -132,7 +130,7 @@ public class XmlParserTest {
@Test
public void testEmptyNodeToString() throws Exception {
try {
String str = parser.nodeToString(null);
String str = XmlParser.nodeToString(null);
assertNull(str);
} catch (Exception e) {
e.printStackTrace();
......@@ -145,8 +143,8 @@ public class XmlParserTest {
public void testNodeToStringWithHeader() throws Exception {
try {
String xml = "<test_node>test_x</test_node>";
Document validDoc = parser.getXmlDocumentFromString(xml);
String str = parser.nodeToString(validDoc, true);
Document validDoc = XmlParser.getXmlDocumentFromString(xml);
String str = XmlParser.nodeToString(validDoc, true);
assertTrue(str.contains(xml));
} catch (Exception e) {
e.printStackTrace();
......@@ -180,7 +178,7 @@ public class XmlParserTest {
;
Element el = new Tmp();
root.appendChild(el);
assertNotNull(parser.nodeToString(root, true));
assertNotNull(XmlParser.nodeToString(root, true));
} catch (Exception e) {
e.printStackTrace();
throw e;
......@@ -190,7 +188,7 @@ public class XmlParserTest {
@Test
public void testGetXmlDocumentFromInvalidString() throws Exception {
try {
parser.getXmlDocumentFromString("<node>test<node>");
XmlParser.getXmlDocumentFromString("<node>test<node>");
fail("Exception expected");
} catch (InvalidXmlSchemaException e) {
} catch (Exception e) {
......@@ -203,7 +201,7 @@ public class XmlParserTest {
@Test
public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
try {
parser.getXmlDocumentFromInputSource(new InputSource(), true);
XmlParser.getXmlDocumentFromInputSource(new InputSource(), true);
fail("Exception expected");
} catch (InvalidXmlSchemaException e) {
} catch (Exception e) {
......@@ -216,7 +214,7 @@ public class XmlParserTest {
@Test
public void testEscapeXml() throws Exception {
try {
String str = parser.escapeXml("<xml>node</xml>");
String str = XmlParser.escapeXml("<xml>node</xml>");
assertFalse(str.contains("<"));
} catch (Exception e) {
e.printStackTrace();
......@@ -228,7 +226,7 @@ public class XmlParserTest {
@Test
public void testEscapeNullXml() throws Exception {
try {
String str = parser.escapeXml(null);
String str = XmlParser.escapeXml(null);
assertNull(str);
} catch (Exception e) {
e.printStackTrace();
......@@ -240,7 +238,7 @@ public class XmlParserTest {
@Test
public void testFileToString() throws Exception {
try {
String str = parser.fileToString("testFiles/test.txt");
String str = XmlParser.fileToString("testFiles/test.txt");
assertTrue(str.contains("test"));
assertTrue(str.contains("file"));
assertTrue(str.contains("with some content"));
......@@ -255,7 +253,7 @@ public class XmlParserTest {
public void testInputStreamToString() throws Exception {
try {
InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
String str = parser.inputStreamToString(stream);
String str = XmlParser.inputStreamToString(stream);
assertEquals("stream string", str);
} catch (Exception e) {
e.printStackTrace();
......@@ -267,9 +265,9 @@ public class XmlParserTest {
@Test
public void testGetNodeValue() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node>content</node>");
Node node = parser.getNode("node", document);
String str = parser.getNodeValue(node);
Document document = XmlParser.getXmlDocumentFromString("<node>content</node>");
Node node = XmlParser.getNode("node", document);
String str = XmlParser.getNodeValue(node);
assertEquals("content", str);
} catch (Exception e) {
e.printStackTrace();
......@@ -281,7 +279,7 @@ public class XmlParserTest {
@Test
public void testGetNodeValue2() throws Exception {
try {
String str = parser.getNodeValue(null);
String str = XmlParser.getNodeValue(null);
assertEquals("", str);
} catch (Exception e) {
e.printStackTrace();
......@@ -293,9 +291,9 @@ public class XmlParserTest {
@Test
public void testGetNodeValue3() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node></node>");
Node node = parser.getNode("node", document);
String str = parser.getNodeValue(node);
Document document = XmlParser.getXmlDocumentFromString("<node></node>");
Node node = XmlParser.getNode("node", document);
String str = XmlParser.getNodeValue(node);
assertEquals("", str);
} catch (Exception e) {
e.printStackTrace();
......@@ -307,9 +305,9 @@ public class XmlParserTest {
@Test
public void testGetNodeValue4() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
Node node = parser.getNode("node", document);
String str = parser.getNodeValue(node);
Document document = XmlParser.getXmlDocumentFromString("<node><subnode/></node>");
Node node = XmlParser.getNode("node", document);
String str = XmlParser.getNodeValue(node);
assertEquals("", str);
} catch (Exception e) {
e.printStackTrace();
......@@ -321,7 +319,7 @@ public class XmlParserTest {
@Test
public void testInputStreamToStringThrowsException() throws Exception {
try {
parser.inputStreamToString(new InputStream() {
XmlParser.inputStreamToString(new InputStream() {
@Override
public int read() throws IOException {
throw new IOException();
......@@ -339,7 +337,7 @@ public class XmlParserTest {
@Test
public void testFileToStringThrowsException() throws Exception {
try {
parser.fileToString("testFiles/unknown file.txt");
XmlParser.fileToString("testFiles/unknown file.txt");
fail("Exception expected");
} catch (IOException e) {
} catch (Exception e) {
......@@ -352,11 +350,11 @@ public class XmlParserTest {
@Test
public void testGetNodeAttr() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
Node node = parser.getNode("node", document);
String str = parser.getNodeAttr("attr", node);
Document document = XmlParser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
Node node = XmlParser.getNode("node", document);
String str = XmlParser.getNodeAttr("attr", node);
assertEquals("val", str);
str = parser.getNodeAttr("attr2", node);
str = XmlParser.getNodeAttr("attr2", node);
assertEquals("", str);
} catch (Exception e) {
e.printStackTrace();
......@@ -368,9 +366,9 @@ public class XmlParserTest {
@Test
public void testGetNodes() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
Node node = parser.getNode("node", document);
List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
Document document = XmlParser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
Node node = XmlParser.getNode("node", document);
List<Node> nodes = XmlParser.getNodes("subnode", node.getChildNodes());
assertEquals(2, nodes.size());
} catch (Exception e) {
e.printStackTrace();
......@@ -382,9 +380,9 @@ public class XmlParserTest {
@Test
public void testGetNode() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
Node node = parser.getNode("node", document);
Node child = parser.getNode("other", node.getChildNodes());
Document document = XmlParser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
Node node = XmlParser.getNode("node", document);
Node child = XmlParser.getNode("other", node.getChildNodes());
assertNotNull(child);
} catch (Exception e) {
e.printStackTrace();
......@@ -396,9 +394,9 @@ public class XmlParserTest {
@Test
public void testGetNode2() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
Node node = parser.getNode("node", document);
Node child = parser.getNode("other2", node.getChildNodes());
Document document = XmlParser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
Node node = XmlParser.getNode("node", document);
Node child = XmlParser.getNode("other2", node.getChildNodes());
assertNull(child);
} catch (Exception e) {
e.printStackTrace();
......@@ -410,9 +408,9 @@ public class XmlParserTest {
@Test
public void testGetNode3() throws Exception {
try {
Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
Node node = parser.getNode("node", document);
Node child = parser.getNode("other2", node.getChildNodes());
Document document = XmlParser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
Node node = XmlParser.getNode("node", document);
Node child = XmlParser.getNode("other2", node.getChildNodes());
assertNull(child);
} catch (Exception e) {
e.printStackTrace();
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+ 26
− 49
View file @ c6573caf
......@@ -2,14 +2,10 @@ package lcsb.mapviewer.converter.model.celldesigner;
import java.awt.geom.Line2D;
import java.awt.geom.Rectangle2D;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import lcsb.mapviewer.common.XmlParser;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
......@@ -22,10 +18,9 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
......@@ -62,9 +57,9 @@ import lcsb.mapviewer.model.map.species.Species;
* cases:
* <ul>
* <li>CellDesigner xml -> our model. To perform this action
* {@link #createModel(Params)} method should be called.</li>
* {@link Converter#createModel(ConverterParams)}} method should be called.</li>
* <li>our model -> CellDesigner xml. To perform this action
* {@link #toXml(Model)} method should be called.</li>
* {@link #model2Xml(Model)} method should be called.</li>
* </ul>
* <p/>
* CellDEsigner format is the extension of <a href="http://sbml.org">SBML</a>.
......@@ -75,7 +70,7 @@ import lcsb.mapviewer.model.map.species.Species;
* @author Piotr Gawron
*
*/
public class CellDesignerXmlParser extends XmlParser implements IConverter {
public class CellDesignerXmlParser extends Converter {
/**
* Default class logger.
......@@ -137,20 +132,20 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
NodeList root = doc.getChildNodes();
// Navigate down the hierarchy to get to the CEO node
Node sbmlNode = getNode("SBML", root);
Node sbmlNode = XmlParser.getNode("SBML", root);
if (sbmlNode == null) {
throw new InvalidInputDataExecption("No SBML node");
}
Node modelNode = getNode("model", sbmlNode.getChildNodes());
Node modelNode = XmlParser.getNode("model", sbmlNode.getChildNodes());
if (modelNode == null) {
throw new InvalidInputDataExecption("No model node in SBML");
}
// we ignore metaid - it's useless and obstruct data model
// model.setMetaId(getNodeAttr("metaId", modelNode));
model.setIdModel(getNodeAttr("id", modelNode));
// model.setMetaId(XmlParser.getNodeAttr("metaId", modelNode));
model.setIdModel(XmlParser.getNodeAttr("id", modelNode));
Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
Node compartmentNode = XmlParser.getNode("listOfCompartments", modelNode.getChildNodes());
if (compartmentNode != null) {
List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser
.parseXmlCompartmentCollection(compartmentNode);
......@@ -159,7 +154,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
InternalModelSpeciesData modelData = new InternalModelSpeciesData();
Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
Node speciesNode = XmlParser.getNode("listOfSpecies", modelNode.getChildNodes());
if (speciesNode != null) {
List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
.parseSbmlSpeciesCollection(speciesNode);
......@@ -209,7 +204,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
model.addParameters(parameterParser.parseXmlParameterCollection(parametersNode));
}
Node annotationNode = getNode("annotation", modelNode.getChildNodes());
Node annotationNode = XmlParser.getNode("annotation", modelNode.getChildNodes());
if (annotationNode == null) {
throw new InvalidInputDataExecption("No annotation node in SBML/model");
}
......@@ -357,7 +352,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
CellDesignerElementCollection elements) throws InvalidXmlSchemaException {
SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
Node extensionNode = getNode("celldesigner:extension", annotationNode.getChildNodes());
Node extensionNode = XmlParser.getNode("celldesigner:extension", annotationNode.getChildNodes());
if (extensionNode == null) {
throw new InvalidXmlSchemaException("No celldesigner:extension node in SBML/model/annotation");
}
......@@ -380,8 +375,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
// model.setVersion(getNodeValue(node));
continue;
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:modelDisplay")) {
model.setWidth(getNodeAttr("sizeX", node));
model.setHeight(getNodeAttr("sizeY", node));
model.setWidth(XmlParser.getNodeAttr("sizeX", node));
model.setHeight(XmlParser.getNodeAttr("sizeY", node));
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfSpeciesAliases")) {
listofSpeciesAlias = node;
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfComplexSpeciesAliases")) {
......@@ -468,8 +463,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
if (includedSpecies != null) {
parseAnnotationAliasesConnections(model, getNode("celldesigner:listOfSpeciesAliases", nodes));
parseAnnotationComplexAliasesConnections(model, getNode("celldesigner:listOfComplexSpeciesAliases", nodes));
parseAnnotationAliasesConnections(model, XmlParser.getNode("celldesigner:listOfSpeciesAliases", nodes));
parseAnnotationComplexAliasesConnections(model, XmlParser.getNode("celldesigner:listOfComplexSpeciesAliases", nodes));
}
if (listOfGroups != null) {
......@@ -496,8 +491,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
String aliasId = getNodeAttr("id", node);
String complexId = getNodeAttr("complexSpeciesAlias", node);
String aliasId = XmlParser.getNodeAttr("id", node);
String complexId = XmlParser.getNodeAttr("complexSpeciesAlias", node);
Complex alias = model.getElementByElementId(aliasId);
if (alias == null) {
throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
......@@ -534,8 +529,8 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
String aliasId = getNodeAttr("id", node);
String complexId = getNodeAttr("complexSpeciesAlias", node);
String aliasId = XmlParser.getNodeAttr("id", node);
String complexId = XmlParser.getNodeAttr("complexSpeciesAlias", node);
Element alias = model.getElementByElementId(aliasId);
if (alias == null) {
throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
......@@ -555,8 +550,9 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
}
public String toXml(Model model) throws InconsistentModelException {
return toXml(model, true);
@Override
public String model2Xml(Model model) throws InconsistentModelException {
return model2Xml(model, true);
}
/**
......@@ -569,7 +565,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
* thrown when then model is invalid
* @throws InconsistentModelException
*/
public String toXml(Model model, boolean appendWarnings) throws InconsistentModelException {
public String model2Xml(Model model, boolean appendWarnings) throws InconsistentModelException {
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
try {
Logger.getRootLogger().addAppender(appender);
......@@ -606,7 +602,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
if (model.getNotes() != null || !appender.getWarnings().isEmpty()) {
result.append("<notes>");
if (model.getNotes() != null) {
result.append(escapeXml(model.getNotes()));
result.append(XmlParser.escapeXml(model.getNotes()));
}
if (appendWarnings) {
for (LoggingEvent event : appender.getWarnings()) {
......@@ -679,25 +675,6 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
return result.toString();
}
@Override
public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
String exportedString = toXml(model);
InputStream inputStream = new ByteArrayInputStream(exportedString.getBytes());
return inputStream;
}
@Override
public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, IOException {
File file = new File(filePath);
String exportedString = toXml(model);
FileWriter fileWriter = new FileWriter(file);
fileWriter.write(exportedString);
fileWriter.flush();
fileWriter.close();
return file;
}
@Override
public String getCommonName() {
return "CellDesigner SBML";
......
converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
+ 7
− 7
View file @ c6573caf
......@@ -24,7 +24,7 @@ import lcsb.mapviewer.model.map.MiriamType;
* @author Piotr Gawron
*
*/
public class XmlAnnotationParser extends XmlParser {
public class XmlAnnotationParser {
/**
* Deafult logger.
......@@ -51,7 +51,7 @@ public class XmlAnnotationParser extends XmlParser {
*/
public Set<MiriamData> parse(String data) throws InvalidXmlSchemaException {
// start from creating a DOM parser and parse the whole document
Document doc = getXmlDocumentFromString(data);
Document doc = XmlParser.getXmlDocumentFromString(data);
NodeList root = doc.getChildNodes();
......@@ -69,7 +69,7 @@ public class XmlAnnotationParser extends XmlParser {
* thrown when there is a problem with xml
*/
public Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
Node rdf = getNode("rdf:RDF", root);
Node rdf = XmlParser.getNode("rdf:RDF", root);
return parseRdfNode(rdf);
}
......@@ -85,7 +85,7 @@ public class XmlAnnotationParser extends XmlParser {
public Set<MiriamData> parseRdfNode(Node rdf) throws InvalidXmlSchemaException {
Set<MiriamData> miriamDataSet = new HashSet<>();
if (rdf != null) {
Node description = getNode("rdf:Description", rdf.getChildNodes());
Node description = XmlParser.getNode("rdf:Description", rdf.getChildNodes());
if (description != null) {
NodeList list = description.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
......@@ -125,14 +125,14 @@ public class XmlAnnotationParser extends XmlParser {
NodeList list = node.getChildNodes();
String relationTypeString = node.getNodeName();
MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
Node bag = getNode("rdf:Bag", list);
Node bag = XmlParser.getNode("rdf:Bag", list);
if (bag == null) {
throw new InvalidXmlSchemaException("No rdf:Bag node found");
}
list = bag.getChildNodes();
List<Node> nodes = getNodes("rdf:li", list);
List<Node> nodes = XmlParser.getNodes("rdf:li", list);
for (Node li : nodes) {
String dataTypeUri = getNodeAttr("rdf:resource", li);
String dataTypeUri = XmlParser.getNodeAttr("rdf:resource", li);
if (dataTypeUri == null || dataTypeUri.isEmpty()) {
throw new InvalidXmlSchemaException("rdf:li does not have a rdf:resource attribute");
}
......
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