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It is not understandable why the Eclipse plugin for git did not push all
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changes with the last commit. Here is another attempt.
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@draeger
draeger committed Oct 10, 2016
1 parent d1b417d commit fa911e4
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Showing 28 changed files with 1,665 additions and 611 deletions.
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920 changes: 920 additions & 0 deletions res/kgml/hsa00010.xml
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217 changes: 129 additions & 88 deletions src/main/java/edu/ucsd/sbrg/escher/EscherConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,9 @@
import java.util.ResourceBundle;
import java.util.logging.Logger;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.stream.XMLStreamException;
import javax.xml.transform.TransformerException;
Expand All @@ -43,6 +45,7 @@
import org.sbml.jsbml.TidySBMLWriter;
import org.xml.sax.SAXException;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.fge.jsonschema.core.exceptions.ProcessingException;
Expand All @@ -56,48 +59,41 @@
import de.zbit.util.Utils;
import de.zbit.util.prefs.KeyProvider;
import de.zbit.util.prefs.SBProperties;
import edu.ucsd.sbrg.escher.converters.Escher2SBGN;
import edu.ucsd.sbrg.escher.converters.Escher2SBML;
import edu.ucsd.sbrg.escher.converters.Escher2Standard;
import edu.ucsd.sbrg.escher.converters.SBGN2Escher;
import edu.ucsd.sbrg.escher.converters.SBML2Escher;
import edu.ucsd.sbrg.escher.converter.Escher2SBGN;
import edu.ucsd.sbrg.escher.converter.Escher2SBML;
import edu.ucsd.sbrg.escher.converter.Escher2Standard;
import edu.ucsd.sbrg.escher.converter.SBGN2Escher;
import edu.ucsd.sbrg.escher.converter.SBML2Escher;
import edu.ucsd.sbrg.escher.gui.EscherConverterUI;
import edu.ucsd.sbrg.escher.model.EscherMap;
import edu.ucsd.sbrg.escher.utilities.EscherIOOptions;
import edu.ucsd.sbrg.escher.utilities.EscherOptions;
import edu.ucsd.sbrg.escher.utilities.EscherOptions.InputFormat;
import edu.ucsd.sbrg.escher.utilities.EscherOptions.OutputFormat;
import edu.ucsd.sbrg.escher.utilities.Validator;
import edu.ucsd.sbrg.escher.util.EscherIOOptions;
import edu.ucsd.sbrg.escher.util.EscherOptions;
import edu.ucsd.sbrg.escher.util.Validator;
import edu.ucsd.sbrg.escher.util.EscherOptions.InputFormat;
import edu.ucsd.sbrg.escher.util.EscherOptions.OutputFormat;

/**
* @author Andreas Dräger, Devesh Khandelwal
* @author Andreas Dräger
* @author Devesh Khandelwal
*/
public class EscherConverter extends Launcher {

/**
* Localization support.
*/
private static final transient ResourceBundle
baseBundle =
ResourceManager.getBundle("Messages");
private static final transient ResourceBundle baseBundle = ResourceManager.getBundle("edu.ucsd.sbrg.escher.Messages");
/**
* Localization support.
*/
private static final transient ResourceBundle
bundle =
ResourceManager.getBundle("Messages");
private static final transient ResourceBundle bundle = ResourceManager.getBundle("edu.ucsd.sbrg.escher.Messages");
/**
* A {@link Logger} for this class.
*/
private static final Logger
logger =
Logger.getLogger(EscherConverter.class.getName());
private static final Logger logger = Logger.getLogger(EscherConverter.class.getName());
/**
* Generated serial version identifier.
*/
private static final long
serialVersionUID =
9037698164025548416L;
private static final long serialVersionUID = 9037698164025548416L;


/**
Expand Down Expand Up @@ -208,13 +204,31 @@ public static <T> T convert(File input, Class<? extends T> format,
* @throws IOException Thrown if there are problems in reading the {@code input} file.
*/
public static EscherMap parseEscherJson(File input) throws IOException {
ObjectMapper objectMapper = edu.ucsd.sbrg.escher.utilities.Utils.getObjectMapper();

logger.info(format(bundle.getString("EscherConverter.readingFile"), input));

EscherMap map = parseEscherJson(new FileInputStream(input));

logger.info(format(bundle.getString("EscherConverter.readingDone"), input));

return map;
}


/**
* Parses an {@link InputStream} that represents an Escher JSON file into an
* {@link EscherMap} instance using Jackson.
*
* @param stream
* @return
* @throws IOException
* @throws JsonProcessingException
*/
public static EscherMap parseEscherJson(InputStream stream)
throws IOException, JsonProcessingException {
ObjectMapper objectMapper = edu.ucsd.sbrg.escher.util.Utils.getObjectMapper();
// An Escher array contains meta-info about the map as the first object and the actual map as
// second map.
JsonNode escherJson = objectMapper.readTree(input);
JsonNode escherJson = objectMapper.readTree(stream);
// Meta-info.
EscherMap meta = objectMapper.treeToValue(escherJson.get(0), EscherMap.class);
// Layout map (nodes, reactions, text labels and canvas info).
Expand All @@ -228,9 +242,6 @@ public static EscherMap parseEscherJson(File input) throws IOException {
map.setURL(meta.getURL());

map.processMap();

logger.info(format(bundle.getString("EscherConverter.readingDone"), input));

return map;
}

Expand Down Expand Up @@ -311,8 +322,7 @@ public void batchProcess(File input, File output, SBProperties properties)
if (output.isDirectory()) {
String fName = input.getName();
fName = FileTools.removeFileExtension(fName) + ".xml";
output =
new File(Utils.ensureSlash(output.getAbsolutePath()) + fName);
output = new File(Utils.ensureSlash(output.getAbsolutePath()) + fName);
}
properties.put(InputFormat.class.getSimpleName(), InputFormat.Escher);
convert(input, output, properties);
Expand Down Expand Up @@ -344,9 +354,7 @@ else if (SBFileFilter.isSBGNFile(input)) {
output.getAbsolutePath()));
}
for (File file : input.listFiles()) {
File
target =
new File(
File target = new File(
Utils.ensureSlash(output.getAbsolutePath()) + input.getName());
batchProcess(file, target, properties);
}
Expand Down Expand Up @@ -421,8 +429,8 @@ public void convert(File input, File output, SBProperties properties)
throws IOException, ParseException,
XMLStreamException, SBMLException, JAXBException, SAXException,
ParserConfigurationException, TransformerException {
OutputFormat format = OutputFormat.valueOf(properties.getProperty(EscherOptions.FORMAT));
InputFormat inputFormat = InputFormat.valueOf(properties.get(InputFormat.class.getSimpleName()));
OutputFormat outputFormat = OutputFormat.valueOf(properties.getProperty(EscherOptions.FORMAT));

logger.warning(bundle.getString("ValidationStart"));
if (!validateInput(input, inputFormat)) {
Expand All @@ -437,49 +445,49 @@ public void convert(File input, File output, SBProperties properties)
boolean success = false;

// Check output format.
switch (format) {
switch (outputFormat) {

case SBML:
SBMLDocument doc = convert(input, SBMLDocument.class, properties);
TidySBMLWriter.write(doc, output, System.getProperty("app.name"),
getVersionNumber(), ' ', (short) 2);
success = true;
break;
case SBML:
SBMLDocument doc = convert(input, SBMLDocument.class, properties);
TidySBMLWriter.write(doc, output, System.getProperty("app.name"),
getVersionNumber(), ' ', (short) 2);
success = true;
break;

case SBGN:
Sbgn sbgn = convert(input, Sbgn.class, properties);
SbgnUtil.writeToFile(sbgn, output);
success = true;
break;

case Escher:
// Check input format.
switch (inputFormat) {

case SBGN:
Sbgn sbgn = convert(input, Sbgn.class, properties);
SbgnUtil.writeToFile(sbgn, output);
EscherMap map = parseSBGNML(input, properties);
writeEscherJson(map, output);
success = true;
break;

case Escher:
// Check input format.
switch (inputFormat) {

case SBGN:
EscherMap map = convert(SbgnUtil.readFromFile(input), properties);
writeEscherJson(map, output);
success = true;
break;

case SBML:
if (properties.getBooleanProperty(EscherOptions.EXTRACT_COBRA)) {
extractCobraModel(input);
}
List<EscherMap> maps = convert(SBMLReader.read(input), properties);
writeEscherJson(maps, output);
success = true;
break;

case Escher:
logger.info(bundle.getString("InputOutputFormatIdentical"));
break;
case SBML:
if (properties.getBooleanProperty(EscherOptions.EXTRACT_COBRA)) {
extractCobraModel(input);
}
List<EscherMap> maps = convert(SBMLReader.read(input), properties);
writeEscherJson(maps, output);
success = true;
break;

default:
logger.severe(bundle.getString("UnsupportedFormat"));
case Escher:
logger.info(bundle.getString("InputOutputFormatIdentical"));
break;
}
break;

default:
logger.severe(bundle.getString("UnsupportedFormat"));
break;
}

if (success) {
Expand All @@ -489,6 +497,34 @@ public void convert(File input, File output, SBProperties properties)
}


/**
* @param input
* @param properties
* @return
* @throws JAXBException
*/
public static EscherMap parseSBGNML(File input, SBProperties properties) throws JAXBException {
return convert(SbgnUtil.readFromFile(input), properties);
}

/**
*
* @param is
* @param properties
* @return
* @throws JAXBException
*/
public static EscherMap parseSBGNML(InputStream is, SBProperties properties) throws JAXBException {
JAXBContext context = JAXBContext.newInstance("org.sbgn.bindings");
Unmarshaller unmarshaller = context.createUnmarshaller();

// Now read from "is" and put the result in "sbgn"
Sbgn sbgnDoc = (Sbgn) unmarshaller.unmarshal(is);

return convert(sbgnDoc, properties);
}


/**
* Extracts CoBRA from {@link SBMLDocument} if it is FBC compliant. cobrapy must be present for
* this.
Expand All @@ -512,8 +548,7 @@ public static boolean extractCobraModel(File file) throws IOException, XMLStream
command = new String[]{"python3", "-c", "\"print('yo');from cobra import io;"
+ "io.save_json_model(model=io.read_sbml_model('" + file
.getAbsolutePath() + "'), file_name='" + file
.getAbsolutePath() + ".json" + "');print('yo')\"",
"> /temp/log"};
.getAbsolutePath() + ".json" + "');print('yo')\"", "> /temp/log"};
// command = new String[] {"/usr/local/bin/python3", "-c", "\"print('yo')\""};
command = new String[] {"python3"};
Process p;
Expand All @@ -522,8 +557,8 @@ public static boolean extractCobraModel(File file) throws IOException, XMLStream
p = Runtime.getRuntime().exec(command);
p.waitFor();
if (p.exitValue() == 0) {
logger.info(format(bundle.getString("SBMLFBCExtractionSuccessful"), file
.getAbsolutePath(), file.getAbsolutePath()));
logger.info(format(bundle.getString("SBMLFBCExtractionSuccessful"),
file.getAbsolutePath(), file.getAbsolutePath()));
InputStream is = p.getErrorStream();
is = p.getInputStream();
OutputStream os = p.getOutputStream();
Expand Down Expand Up @@ -574,17 +609,17 @@ private boolean validateInput(File input, InputFormat inputFormat) throws IOExce

// Call appropriate validator according to input format.
switch (inputFormat) {
case SBGN:
logger.info(bundle.getString("ValidatingSBGN"));
return validator.validateSbgnml(input);
case SBGN:
logger.info(bundle.getString("ValidatingSBGN"));
return validator.validateSbgnml(input);

case SBML:
logger.info(bundle.getString("ValidatingSBML"));
return validator.validateSbmlLE(input);
case SBML:
logger.info(bundle.getString("ValidatingSBML"));
return validator.validateSbmlLE(input);

case Escher:
logger.info(bundle.getString("ValidatingEscher"));
return validator.validateEscher(input);
case Escher:
logger.info(bundle.getString("ValidatingEscher"));
return validator.validateEscher(input);

}
return false;
Expand All @@ -598,7 +633,7 @@ private boolean validateInput(File input, InputFormat inputFormat) throws IOExce
* @param output Output file to write to.
* @throws IOException Thrown if there are problems in reading the {@code input} file(s).
*/
private void writeEscherJson(EscherMap map, File output) throws IOException {
public static void writeEscherJson(EscherMap map, File output) throws IOException {
// An Escher array contains meta-info about the map as the first object and the actual map as
// second map. That's why we need an array of size 2.
List<EscherMap> mapList = new ArrayList<>(2);
Expand All @@ -620,8 +655,7 @@ private void writeEscherJson(EscherMap map, File output) throws IOException {

mapList.add(map);

edu.ucsd.sbrg.escher.utilities.Utils.getObjectMapper().writeValue(output, mapList);

edu.ucsd.sbrg.escher.util.Utils.getObjectMapper().writeValue(output, mapList);
}


Expand All @@ -631,7 +665,7 @@ private void writeEscherJson(EscherMap map, File output) throws IOException {
* @param mapList List of Escher maps to serialize.
* @param output Directory to create files in.
*/
private void writeEscherJson(List<EscherMap> mapList, File output) {
public static void writeEscherJson(List<EscherMap> mapList, File output) {
try {
if (mapList.size() == 0) {
// SBML file has no layout.
Expand All @@ -649,8 +683,15 @@ private void writeEscherJson(List<EscherMap> mapList, File output) {
}
else {
// Write all maps to their own file.
mapList.forEach(map -> {
File file = new File(Utils.ensureSlash(output.getPath()) + map.getId() + ".json");
for (EscherMap map : mapList) {
File file;
if ((mapList.size() > 1) || (output.exists() && output.isDirectory())) {
file = new File(Utils.ensureSlash(output.getPath()) + map.getId() + ".json");
} else if (SBFileFilter.isJSONFile(output)) {
file = output;
} else {
file = new File(output.getAbsolutePath() + ".json");
}
try {
if (!file.exists()) {
file.getParentFile().mkdirs();
Expand All @@ -660,7 +701,7 @@ private void writeEscherJson(List<EscherMap> mapList, File output) {
} catch (IOException e) {
logger.severe(format(bundle.getString("FileIOError"), file.getAbsolutePath()));
}
});
}
}
}
catch (IOException e) {
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/edu/ucsd/sbrg/escher/converter/Escher2SBGN.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
* <http://www.gnu.org/licenses/lgpl-3.0-standalone.html>.
* ---------------------------------------------------------------------
*/
package edu.ucsd.sbrg.escher.converters;
package edu.ucsd.sbrg.escher.converter;

import de.zbit.graph.io.def.SBGNProperties;
import de.zbit.graph.io.def.SBGNProperties.ArcType;
Expand Down Expand Up @@ -56,7 +56,7 @@ public class Escher2SBGN extends Escher2Standard<Sbgn> {
*/
public static final ResourceBundle
bundle =
ResourceManager.getBundle("Messages");
ResourceManager.getBundle("edu.ucsd.sbrg.escher.Messages");
/**
* The SBGN map builder.
*/
Expand Down
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