From 387d759759311b27097345ef57caf7d6e69f33c4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 11 Jan 2018 13:11:59 +0100
Subject: [PATCH] sbml parser is available via rest API
---
converter-sbml/pom.xml | 41 +++++++++++--------
.../converter/model/sbml/SbmlParser.java | 2 +-
model-command/pom.xml | 1 -
rest-api/pom.xml | 6 +++
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 22 ++++++----
.../configuration/ConfigurationRestImpl.java | 9 ++--
6 files changed, 48 insertions(+), 33 deletions(-)
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index 6fc10f0b45..278f035aad 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -16,16 +16,20 @@
</properties>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jar-plugin</artifactId>
- <version>2.3</version>
- <configuration>
- <excludes>
- <exclude>**/log4j.properties</exclude>
- </excludes>
- </configuration>
- </plugin>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.3</version>
+ <configuration>
+ <excludes>
+ <exclude>**/log4j.properties</exclude>
+ </excludes>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
<dependencies>
@@ -37,7 +41,16 @@
<artifactId>model</artifactId>
<version>1.0</version>
</dependency>
-
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model-command</artifactId>
+ <version>1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-CellDesigner</artifactId>
+ <version>1.0</version>
+ </dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
@@ -72,12 +85,6 @@
<version>1.0</version>
<scope>test</scope>
</dependency>
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-CellDesigner</artifactId>
- <version>1.0</version>
- <scope>test</scope>
- </dependency>
</dependencies>
</project>
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index b72c589162..938ad9a799 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -231,7 +231,7 @@ public class SbmlParser implements IConverter {
fileWriter.write(exportedString);
fileWriter.flush();
fileWriter.close();
- return null;
+ return file;
}
@Override
diff --git a/model-command/pom.xml b/model-command/pom.xml
index d827b05db5..5d559371b4 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -25,7 +25,6 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>1.0</version>
- <scope>test</scope>
</dependency>
<dependency>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index 43e369a82a..a25a71c338 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -26,6 +26,12 @@
<version>1.0</version>
</dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-sbml</artifactId>
+ <version>1.0</version>
+ </dependency>
+
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>jsr311-api</artifactId>
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 0f82683334..d0dc1002f7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -21,6 +21,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
+import lcsb.mapviewer.converter.model.sbml.SbmlParser;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -287,15 +288,20 @@ public abstract class BaseRestImpl {
}
protected IConverter getModelParser(String handlerClass) throws QueryException {
- IConverter parser;
- if (SbgnmlXmlConverter.class.getCanonicalName().equals(handlerClass)) {
- parser = new SbgnmlXmlConverter();
- } else if (CellDesignerXmlParser.class.getCanonicalName().equals(handlerClass)) {
- parser = new CellDesignerXmlParser();
- } else {
- throw new QueryException("Unknown handlerClass: " + handlerClass);
+ for (IConverter converter : getModelConverters()) {
+ if (converter.getClass().getCanonicalName().equals(handlerClass)) {
+ return converter;
+ }
}
- return parser;
+ throw new QueryException("Unknown handlerClass: " + handlerClass);
+ }
+
+ protected List<IConverter> getModelConverters() {
+ List<IConverter> result = new ArrayList<>();
+ result.add(new CellDesignerXmlParser());
+ result.add(new SbgnmlXmlConverter());
+ result.add(new SbmlParser());
+ return result;
}
protected String getFirstValue(List<Object> list) {
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 e6a8df1e5c..7c41b7d650 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
@@ -16,12 +16,11 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.ImageGenerators;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -38,7 +37,7 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaType;
import lcsb.mapviewer.services.view.ConfigurationView;
@Transactional(value = "txManager")
-public class ConfigurationRestImpl {
+public class ConfigurationRestImpl extends BaseRestImpl {
/**
* Default class logger.
*/
@@ -113,9 +112,7 @@ public class ConfigurationRestImpl {
public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
userService.getToken(token);
- List<IConverter> converters = new ArrayList<>();
- converters.add(new CellDesignerXmlParser());
- converters.add(new SbgnmlXmlConverter());
+ List<IConverter> converters = getModelConverters();
List<Map<String, Object>> result = new ArrayList<>();
--
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