From cd8676d94aeaede447bc5d55ea55a52fe54689a5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Wed, 19 Mar 2025 08:53:56 +0100
Subject: [PATCH] export to sbgn could generate notes without schema
---
CHANGELOG | 1 +
.../model/sbgnml/SbgnmlXmlConverter.java | 73 ++++++++-----------
.../model/sbgnml/SbgnmlXmlExporter.java | 2 +-
.../lcsb/mapviewer/converter/Converter.java | 48 ++++++------
4 files changed, 52 insertions(+), 72 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 619737659d..92f2c18966 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -23,6 +23,7 @@ minerva (19.0.0~alpha.0) stable; urgency=medium
* Bug fix: when removing project the layer texts/rectangles/ovals were not
removed
* Bug fix: index.html has been cached but should not (#2210)
+ * Bug fix: export to SBGN-ML could generate invalid notes node for the file
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 18 Sep 2024 13:00:00 +0200
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 7d132fdae4..20445f8986 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
@@ -1,11 +1,19 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.util.Arrays;
-import java.util.List;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.MinervaLoggerAppender;
+import lcsb.mapviewer.converter.Converter;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.modelutils.map.LogFormatter;
+import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Sbgn;
+import org.springframework.stereotype.Component;
+import org.w3c.dom.Document;
import javax.xml.XMLConstants;
import javax.xml.parsers.DocumentBuilderFactory;
@@ -18,30 +26,17 @@ import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
-
-import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Sbgn;
-import org.springframework.stereotype.Component;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.modelutils.map.LogFormatter;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.Collections;
+import java.util.List;
@Component
public class SbgnmlXmlConverter extends Converter {
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger();
+ private final NotesConverter notesConverter = new NotesConverter();
@Override
public Model createModel(final ConverterParams params) throws InvalidInputDataExecption, ConverterException {
@@ -72,13 +67,13 @@ public class SbgnmlXmlConverter extends Converter {
Templates template = factory
.newTemplates(new StreamSource(classLoader.getResourceAsStream("rename_id_list_attribute.xsl")));
- Transformer xformer = template.newTransformer();
+ Transformer transformer = template.newTransformer();
ByteArrayOutputStream output = new ByteArrayOutputStream();
Source source = new StreamSource(inputStream);
Result result = new StreamResult(output);
- xformer.transform(source, result);
+ transformer.transform(source, result);
return inputStream2File(output.toInputStream());
} catch (final Exception e) {
@@ -96,13 +91,14 @@ public class SbgnmlXmlConverter extends Converter {
exportedData = exporter.toSbgnml(model);
if (!appender.getWarnings().isEmpty()) {
for (final String entry : new LogFormatter().createFormattedWarnings(appender.getWarnings())) {
- notes.append("\n" + entry);
+ notes.append("\n").append(entry);
}
}
} finally {
MinervaLoggerAppender.unregisterLogEventStorage(appender);
}
try {
+ exportedData.setNotes(notesConverter.createNotesNode(notes.toString()));
ByteArrayOutputStream baos = new ByteArrayOutputStream();
SbgnUtil.writeTo(exportedData, baos);
@@ -113,23 +109,12 @@ public class SbgnmlXmlConverter extends Converter {
.newDocumentBuilder()
.parse(baos.toInputStream());
- if (notes.length() > 0) {
- Element bodyNode = input.createElement("body");
- bodyNode.setAttribute("xmlns", "http://www.w3.org/1999/xhtml");
- bodyNode.setTextContent(notes.toString());
-
- Element notesNode = input.createElement("notes");
- notesNode.appendChild(bodyNode);
-
- input.getFirstChild().insertBefore(notesNode, input.getFirstChild().getFirstChild());
- }
-
TransformerFactory transformerFactory = TransformerFactory.newInstance();
transformerFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
- Transformer xformer = transformerFactory.newTransformer();
- xformer.setOutputProperty(OutputKeys.INDENT, "yes");
+ Transformer transformer = transformerFactory.newTransformer();
+ transformer.setOutputProperty(OutputKeys.INDENT, "yes");
StringWriter output = new StringWriter();
- xformer.transform(new DOMSource(input), new StreamResult(output));
+ transformer.transform(new DOMSource(input), new StreamResult(output));
return output.toString();
} catch (final Exception e) {
@@ -149,7 +134,7 @@ public class SbgnmlXmlConverter extends Converter {
@Override
public List<String> getFileExtensions() {
- return Arrays.asList("sbgn");
+ return Collections.singletonList("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 8584db5f3c..4bd341bd11 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
@@ -178,7 +178,7 @@ public class SbgnmlXmlExporter {
* Transforms model into SBGN-ML xml.
*
* @param model model that should be transformed
- * @return SBGM-ML xml string for the model
+ * @return SBGN-ML xml string for the model
*/
public Sbgn toSbgnml(final Model model) throws ConverterException {
// Reset global variables
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/Converter.java b/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
index b7a3575529..a3a40b1fdf 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
@@ -1,5 +1,12 @@
package lcsb.mapviewer.converter;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import org.apache.commons.io.FileUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
@@ -9,29 +16,22 @@ import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.UUID;
-import org.apache.commons.io.FileUtils;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-
/**
* Interface used for reading data from file and putting it into {@link Model}
* object.
- *
+ *
* @author Piotr Gawron
- *
*/
public abstract class Converter {
+ protected static final Logger logger = LogManager.getLogger();
+
/**
* Parse input source and transforms it into a model object.
- *
- * @param params
- * input params used for reading data
+ *
+ * @param params input params used for reading data
* @return model obtained from input source
- * @throws InvalidInputDataExecption
- * thrown when input parameters are invalid
+ * @throws InvalidInputDataExecption thrown when input parameters are invalid
*/
public abstract Model createModel(final ConverterParams params) throws InvalidInputDataExecption, ConverterException;
@@ -39,8 +39,7 @@ public abstract class Converter {
* Generate String representation of the model. Traditionally often XML but can
* be any other format as well.
*
- * @param model
- * The MINERVA ${@link Model} to be serialized
+ * @param model The MINERVA ${@link Model} to be serialized
* @return The translated Model
*/
public abstract String model2String(final Model model) throws InconsistentModelException, ConverterException;
@@ -68,12 +67,10 @@ public abstract class Converter {
/**
* Export model to {@link InputStream}.
- *
- * @param model
- * model to be exported
+ *
+ * @param model model to be exported
* @return {@link InputStream} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
+ * @throws InconsistentModelException thrown when given model is inconsistent and unable to be exported
*/
public InputStream model2InputStream(final Model model)
throws InconsistentModelException, ConverterException {
@@ -83,14 +80,11 @@ public abstract class Converter {
/**
* Export model to {@link File}.
- *
- * @param model
- * model to be exported
- * @param filePath
- * exported file path
+ *
+ * @param model model to be exported
+ * @param filePath exported file path
* @return {@link File} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
+ * @throws InconsistentModelException thrown when given model is inconsistent and unable to be exported
*/
public File model2File(final Model model, final String filePath)
throws InconsistentModelException, IOException, ConverterException {
--
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