From a45c50b50c5da5ef35a1a85f29386ec0fa6487db Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 19 Nov 2018 13:15:06 +0100
Subject: [PATCH] warnings are passed to the sbgn file
---
.../model/sbgnml/SbgnmlXmlConverter.java | 141 +++++++++++-------
.../model/sbgnml/SbgnmlXmlExporter.java | 1 -
.../model/sbgnml/CellDesignerToSbgnTest.java | 101 +++++++------
3 files changed, 146 insertions(+), 97 deletions(-)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
index 3618c14e95..08174a6e20 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
@@ -5,11 +5,22 @@ package lcsb.mapviewer.converter.model.sbgnml;
import java.io.File;
import java.io.FileInputStream;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.io.OutputStream;
import javax.xml.bind.JAXBException;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.apache.tools.ant.filters.StringInputStream;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Sbgn;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
@@ -18,67 +29,95 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Sbgn;
-
/**
* @author Michał Kuźma
*
*/
public class SbgnmlXmlConverter implements IConverter {
+ Logger logger = Logger.getLogger(SbgnmlXmlConverter.class);
+
+ @Override
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+ SbgnmlXmlParser parser = new SbgnmlXmlParser();
+ return parser.createModel(params);
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws InconsistentModelException, ConverterException {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ Sbgn exportedData;
+ StringBuilder notes = new StringBuilder("");
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
+ exportedData = exporter.toSbgnml(model);
+ if (!appender.getWarnings().isEmpty()) {
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ notes.append("\n" + ((String) event.getMessage()));
+ }
+ }
+ }
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ try {
+ File tempFile = File.createTempFile("sbgnmlExportTempFile", ".tmp");
+ InputStream result;
+ SbgnUtil.writeToFile(exportedData, tempFile);
+ try (FileInputStream inputStream = new FileInputStream(tempFile)) {
+ String xml = IOUtils.toString(inputStream, "UTF-8");
+ if (notes.length() > 0) {
+ int position = xml.indexOf("<map language");
+ if (position < 0) {
+ throw new ConverterException("problematic output sbgn. Cannot find map tag");
+ }
+ String notesNode = "<notes><html:body xmlns:html=\"http://www.w3.org/1999/xhtml\">" +
+ StringEscapeUtils.escapeXml(notes.toString()) + "\n</html:body></notes> ";
+ xml = xml.substring(0, position) + notesNode + xml.substring(position, xml.length());
+ }
+ result = new StringInputStream(xml);
+ }
+ return result;
+ } catch (IOException e) {
+ throw new ConverterException(e);
+ } catch (JAXBException e) {
+ throw new ConverterException(e);
+ }
+ }
- @Override
- public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
- SbgnmlXmlParser parser = new SbgnmlXmlParser();
- return parser.createModel(params);
- }
+ @Override
+ public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, ConverterException {
+ InputStream inputStream = exportModelToInputStream(model);
- @Override
- public InputStream exportModelToInputStream(Model model) throws InconsistentModelException, ConverterException {
- SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
- Sbgn exportedData = exporter.toSbgnml(model);
- File tempFile;
- try {
- tempFile = File.createTempFile("sbgnmlExportTempFile", ".tmp");
- SbgnUtil.writeToFile(exportedData, tempFile);
- InputStream result = new FileInputStream(tempFile);
- return result;
- } catch (IOException e) {
- throw new ConverterException(e);
- } catch (JAXBException e) {
- throw new ConverterException(e);
- }
- }
+ try {
+ File exportedFile = new File(filePath);
+ if (exportedFile.getParentFile() != null) {
+ exportedFile.getParentFile().mkdirs();
+ }
+ OutputStream outputStream = new FileOutputStream(exportedFile);
+ IOUtils.copy(inputStream, outputStream);
+ outputStream.close();
- @Override
- public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, ConverterException {
- SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
- Sbgn exportedData = exporter.toSbgnml(model);
- File exportedFile = new File(filePath);
- if (exportedFile.getParentFile() != null) {
- exportedFile.getParentFile().mkdirs();
- }
- try {
- SbgnUtil.writeToFile(exportedData, exportedFile);
- } catch (JAXBException e) {
- throw new ConverterException(e);
- }
- return exportedFile;
- }
+ return exportedFile;
+ } catch (IOException e) {
+ throw new ConverterException(e);
+ }
+ }
- @Override
- public String getCommonName() {
- return "SBGN-ML";
- }
+ @Override
+ public String getCommonName() {
+ return "SBGN-ML";
+ }
- @Override
- public MimeType getMimeType() {
- return MimeType.TEXT;
- }
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.TEXT;
+ }
- @Override
- public String getFileExtension() {
- return "sbgn";
- }
+ @Override
+ public String getFileExtension() {
+ return "sbgn";
+ }
}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 0015b30511..824664c47b 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -187,7 +187,6 @@ public class SbgnmlXmlExporter {
}
sbgnData.setMap(map);
-
return sbgnData;
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
index bc4b09114b..edaea41e34 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
@@ -1,7 +1,11 @@
package lcsb.mapviewer.converter.model.sbgnml;
+import static org.junit.Assert.assertTrue;
+
import java.io.File;
+import java.io.FileInputStream;
+import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
@@ -13,50 +17,57 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
public class CellDesignerToSbgnTest {
- Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSample() throws Exception {
- try {
- IConverter converter = new CellDesignerXmlParser();
- IConverter converter2 = new SbgnmlXmlConverter();
-
- Model model;
- model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
-
- String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
- converter2.exportModelToFile(model, output);
- new File(output).delete();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSample2() throws Exception {
- try {
- IConverter converter = new CellDesignerXmlParser();
- IConverter converter2 = new SbgnmlXmlConverter();
-
- Model model;
- model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
-
- String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
- converter2.exportModelToFile(model, output);
- new File(output).delete();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSample() throws Exception {
+ try {
+ IConverter converter = new CellDesignerXmlParser();
+ IConverter converter2 = new SbgnmlXmlConverter();
+
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
+
+ String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+ converter2.exportModelToFile(model, output);
+
+ try (FileInputStream inputStream = new FileInputStream(output)) {
+ String everything = IOUtils.toString(inputStream, "UTF-8");
+ assertTrue("Warnings are not exported into sbgn", everything.contains("Element type is not supported"));
+ }
+ converter2.createModel(new ConverterParams().filename(output));
+
+ new File(output).delete();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSample2() throws Exception {
+ try {
+ IConverter converter = new CellDesignerXmlParser();
+ IConverter converter2 = new SbgnmlXmlConverter();
+
+ Model model;
+ model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
+
+ String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+ converter2.exportModelToFile(model, output);
+ new File(output).delete();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
--
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