From eb4c81021d4e5cd2d1c6872d2ea643c940f35a85 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 29 Oct 2019 15:15:19 +0100
Subject: [PATCH] list of converters is resolved based on spring components
---
converter-CellDesigner/pom.xml | 7 +++++++
.../celldesigner/CellDesignerXmlParser.java | 2 ++
.../model/sbgnml/SbgnmlXmlConverter.java | 2 ++
.../converter/model/sbml/SbmlParser.java | 2 ++
.../lcsb/mapviewer/wikipathway/GpmlParser.java | 2 ++
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 16 +++++-----------
.../lcsb/mapviewer/api/SpringRestApiConfig.java | 2 +-
.../lcsb/mapviewer/api/BaseRestImplTest.java | 14 +++++++++++++-
8 files changed, 34 insertions(+), 13 deletions(-)
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 6c63f5a768..733ba83e10 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -67,6 +67,13 @@
<scope>compile</scope>
</dependency>
+ <!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context</artifactId>
+ <version>${springframework.version}</version>
+ </dependency>
+
</dependencies>
</project>
\ No newline at end of file
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index c6386575d6..34aaa538dc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -11,6 +11,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
import org.apache.xerces.parsers.DOMParser;
+import org.springframework.stereotype.Component;
import org.w3c.dom.*;
import lcsb.mapviewer.common.*;
@@ -55,6 +56,7 @@ import lcsb.mapviewer.model.map.species.Element;
* @author Piotr Gawron
*
*/
+@Component
public class CellDesignerXmlParser extends Converter {
/**
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 95ed20c123..892dab8549 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
@@ -9,12 +9,14 @@ import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.core.LogEvent;
import org.sbgn.SbgnUtil;
import org.sbgn.bindings.Sbgn;
+import org.springframework.stereotype.Component;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.model.map.model.Model;
+@Component
public class SbgnmlXmlConverter extends Converter {
@Override
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 1e47dc8e3b..9e0bd55f28 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
@@ -13,6 +13,7 @@ import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.springframework.stereotype.Component;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
@@ -33,6 +34,7 @@ import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+@Component
public class SbmlParser extends Converter {
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
index 964b5e026f..796d4a006e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
@@ -5,6 +5,7 @@ import java.io.IOException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Component;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.converter.*;
@@ -13,6 +14,7 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
import lcsb.mapviewer.wikipathway.XML.ModelToGPML;
+@Component
public class GpmlParser extends Converter {
Logger logger = LogManager.getLogger();
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 ec0ab44c31..5ab4674620 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -23,9 +23,6 @@ import lcsb.mapviewer.annotation.services.*;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.*;
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;
import lcsb.mapviewer.model.map.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -33,7 +30,6 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.annotator.*;
import lcsb.mapviewer.services.interfaces.*;
import lcsb.mapviewer.services.search.ElementMatcher;
-import lcsb.mapviewer.wikipathway.GpmlParser;
@Transactional
public abstract class BaseRestImpl {
@@ -61,6 +57,9 @@ public abstract class BaseRestImpl {
@Autowired
private PubmedParser pubmedParser;
+ @Autowired
+ private List<Converter> modelConverters;
+
private ElementMatcher elementMatcher = new ElementMatcher();
private Transformer mathMlTransformer;
@@ -162,7 +161,7 @@ public abstract class BaseRestImpl {
* @param modelId
* list of model identifiers separated by "," or '*' when all models
* should be returned
- * @throws QueryException
+ * @throws QueryException
*/
protected List<Model> getModels(String projectId, String modelId) throws QueryException {
Model model = modelService.getLastModelByProjectId(projectId);
@@ -319,12 +318,7 @@ public abstract class BaseRestImpl {
}
protected List<Converter> getModelConverters() {
- List<Converter> result = new ArrayList<>();
- result.add(new CellDesignerXmlParser());
- result.add(new SbgnmlXmlConverter());
- result.add(new SbmlParser());
- result.add(new GpmlParser());
- return result;
+ return modelConverters;
}
protected String getFirstValue(List<Object> list) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java b/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
index 2836562969..57b92597b0 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/SpringRestApiConfig.java
@@ -8,7 +8,7 @@ import lcsb.mapviewer.services.SpringServiceConfig;
@Configuration
@EnableWebMvc
@Import({ SpringServiceConfig.class })
-@ComponentScan(basePackages = { "lcsb.mapviewer.api" })
+@ComponentScan(basePackages = { "lcsb.mapviewer" })
public class SpringRestApiConfig {
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
index 77e415ea34..84d9f956a0 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java
@@ -15,16 +15,21 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.api.projects.ProjectRestImpl;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.user.annotator.AnnotatorData;
public class BaseRestImplTest extends RestTestFunctions {
- Logger logger = LogManager.getLogger(BaseRestImplTest.class);
+ Logger logger = LogManager.getLogger();
@Autowired
MiriamConnector mc;
+ @Autowired
+ ProjectRestImpl restImpl;
+
@Autowired
PubmedParser pubmedParser;
@@ -107,4 +112,11 @@ public class BaseRestImplTest extends RestTestFunctions {
Integer x = controller.parseInteger(null);
assertNull(x);
}
+
+ @Test
+ public void testGetConverters() throws Exception {
+ List<Converter> list = restImpl.getModelConverters();
+ assertTrue(list.size() > 0);
+ }
+
}
--
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