From 02b19ddbe05ed2148b30f559524f60e86599aed1 Mon Sep 17 00:00:00 2001
From: sherzinger <sascha.herzinger@uni.lu>
Date: Tue, 19 Feb 2019 09:02:50 +0100
Subject: [PATCH] refactored rest-api module to use new converter class
---
.../main/java/lcsb/mapviewer/common/XmlParser.java | 2 +-
.../main/java/lcsb/mapviewer/api/BaseRestImpl.java | 13 +++++--------
.../api/configuration/ConfigurationRestImpl.java | 6 +++---
.../mapviewer/api/convert/ConvertRestImpl.java | 14 +++++++-------
.../mapviewer/api/projects/ProjectRestImpl.java | 6 ++----
.../api/projects/models/ModelRestImpl.java | 2 +-
6 files changed, 19 insertions(+), 24 deletions(-)
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 9a163309bc..ce34cdefa4 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -222,7 +222,7 @@ final public class XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- private static Document getXmlDocumentFromString(final String text, boolean validate) throws InvalidXmlSchemaException {
+ public static Document getXmlDocumentFromString(final String text, boolean validate) throws InvalidXmlSchemaException {
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(text));
try {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index e7b443111d..59ea4f1820 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -31,14 +31,11 @@ import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.converter.model.sbml.SbmlParser;
@@ -322,8 +319,8 @@ public abstract class BaseRestImpl {
this.projectService = projectService;
}
- protected IConverter getModelParser(String handlerClass) throws QueryException {
- for (IConverter converter : getModelConverters()) {
+ protected Converter getModelParser(String handlerClass) throws QueryException {
+ for (Converter converter : getModelConverters()) {
if (converter.getClass().getCanonicalName().equals(handlerClass)) {
return converter;
}
@@ -331,8 +328,8 @@ public abstract class BaseRestImpl {
throw new QueryException("Unknown handlerClass: " + handlerClass);
}
- protected List<IConverter> getModelConverters() {
- List<IConverter> result = new ArrayList<>();
+ protected List<Converter> getModelConverters() {
+ List<Converter> result = new ArrayList<>();
result.add(new CellDesignerXmlParser());
result.add(new SbgnmlXmlConverter());
result.add(new SbmlParser());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 3030964b4d..171eb6ceec 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -20,7 +20,7 @@ import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.model.graphics.MapCanvasType;
@@ -117,11 +117,11 @@ public class ConfigurationRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
verifyToken(token);
- List<IConverter> converters = getModelConverters();
+ List<Converter> converters = getModelConverters();
List<Map<String, Object>> result = new ArrayList<>();
- for (IConverter converter : converters) {
+ for (Converter converter : converters) {
Map<String, Object> row = new TreeMap<>();
row.put("name", converter.getCommonName());
row.put("handler", converter.getClass().getCanonicalName());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
index 9d8a7d1152..c68685a48b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java
@@ -24,7 +24,7 @@ import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.DrawingException;
@@ -49,8 +49,8 @@ public class ConvertRestImpl extends BaseRestImpl {
ConverterParams params = createConvertParams(input);
Model model = getModelParserByNameOrClass(fromFormat).createModel(params);
- IConverter exporter = getModelParserByNameOrClass(toFormat);
- return IOUtils.toString(exporter.exportModelToInputStream(model));
+ Converter exporter = getModelParserByNameOrClass(toFormat);
+ return IOUtils.toString(exporter.model2InputStream(model));
}
public ByteArrayOutputStream converToImage(String token, String fromFormat, String toFormat, String input,
@@ -82,7 +82,7 @@ public class ConvertRestImpl extends BaseRestImpl {
List<Object> converters = new ArrayList<>();
- for (IConverter converter: getModelConverters()) {
+ for (Converter converter: getModelConverters()) {
List<String> names = new ArrayList<>();
names.add(removeWhiteSpaces(converter.getCommonName()));
@@ -119,7 +119,7 @@ public class ConvertRestImpl extends BaseRestImpl {
return info;
}
- private IConverter getModelParserByNameOrClass(String id) throws QueryException {
+ private Converter getModelParserByNameOrClass(String id) throws QueryException {
try {
return getModelParserByName(id);
} catch (QueryException e) {
@@ -131,8 +131,8 @@ public class ConvertRestImpl extends BaseRestImpl {
return str.replace(' ', '_');
}
- private IConverter getModelParserByName(String name) throws QueryException {
- for (IConverter converter : getModelConverters()) {
+ private Converter getModelParserByName(String name) throws QueryException {
+ for (Converter converter : getModelConverters()) {
if (removeWhiteSpaces(converter.getCommonName()).equals(name)) {
return converter;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 1da0a9b526..2f334b9deb 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.api.projects;
import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.Serializable;
import java.security.MessageDigest;
@@ -16,7 +15,6 @@ import java.util.Set;
import java.util.TreeMap;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.util.MultiValueMap;
@@ -31,7 +29,7 @@ import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
@@ -379,7 +377,7 @@ public class ProjectRestImpl extends BaseRestImpl {
if (parserClass == null) {
throw new QueryException("parser is obligatory");
}
- IConverter parser = getModelParser(parserClass);
+ Converter parser = getModelParser(parserClass);
List<ZipEntryFile> zipEntries = extractZipEntries(data);
params.complex(zipEntries.size() > 0);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index 2632a23fbd..2c21e157e2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -244,7 +244,7 @@ public class ModelRestImpl extends BaseRestImpl {
}
Converter parser = getModelParser(handlerClass);
- InputStream is = parser.exportModelToInputStream(part);
+ InputStream is = parser.model2InputStream(part);
String fileExtension = parser.getFileExtension();
--
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