From e4aca2f4201c9bf5eddfbc2344efc9a825b20fdf Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 11 Apr 2018 14:20:37 +0200
Subject: [PATCH] ReferenceGenomeView class removed
---
.../genomics/ReferenceGenomeController.java | 28 +--
.../api/genomics/ReferenceGenomeRestImpl.java | 69 ++++++-
.../ReferenceGenomeControllerTest.java | 3 +-
.../services/impl/ReferenceGenomeService.java | 20 +-
.../interfaces/IReferenceGenomeService.java | 12 +-
.../view/ReferenceGenomeGeneMappingView.java | 125 -----------
...ReferenceGenomeGeneMappingViewFactory.java | 59 ------
.../services/view/ReferenceGenomeView.java | 194 ------------------
.../view/ReferenceGenomeViewFactory.java | 68 ------
.../resources/applicationContext-service.xml | 3 -
.../mapviewer/services/view/AllViewTests.java | 2 -
...renceGenomeGeneMappingViewFactoryTest.java | 55 -----
.../view/ReferenceGenomeViewFactoryTest.java | 55 -----
13 files changed, 85 insertions(+), 608 deletions(-)
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingView.java
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactory.java
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeView.java
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactory.java
delete mode 100644 service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactoryTest.java
delete mode 100644 service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactoryTest.java
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index 80caa2d0fd..67b4a370f0 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.api.genomics;
+import java.util.Map;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.CookieValue;
@@ -8,26 +10,26 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
+import javassist.tools.rmi.ObjectNotFoundException;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.view.ReferenceGenomeView;
@RestController
public class ReferenceGenomeController extends BaseController {
- @Autowired
- private ReferenceGenomeRestImpl referenceGenomeController;
+ @Autowired
+ private ReferenceGenomeRestImpl referenceGenomeController;
- @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}/", method = { RequestMethod.GET },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public ReferenceGenomeView getDrugsByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type, //
- @PathVariable(value = "version") String version//
- ) throws SecurityException, QueryException {
- return referenceGenomeController.getReferenceGenome(token, organism, type, version);
- }
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getGenomesByQuery(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type, //
+ @PathVariable(value = "version") String version//
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenome(token, organism, type, version);
+ }
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
index e517c1eaad..9c1f782af4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
@@ -1,19 +1,29 @@
package lcsb.mapviewer.api.genomics;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
+import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-import lcsb.mapviewer.services.view.ReferenceGenomeView;
@Transactional(value = "txManager")
-public class ReferenceGenomeRestImpl {
+public class ReferenceGenomeRestImpl extends BaseRestImpl {
/**
* Default class logger.
@@ -27,25 +37,68 @@ public class ReferenceGenomeRestImpl {
@Autowired
private IReferenceGenomeService referenceGenomeService;
- public ReferenceGenomeView getReferenceGenome(String token, String organismId, String type, String version)
- throws SecurityException, QueryException {
+ @Autowired
+ private BigFileCache bigFileCache;
+
+ public Map<String, Object> getReferenceGenome(String token, String organismId, String type, String version)
+ throws SecurityException, QueryException, ObjectNotFoundException {
MiriamData organism = null;
if (organismId != null && !organismId.isEmpty()) {
organism = new MiriamData(MiriamType.TAXONOMY, organismId);
} else {
throw new QueryException("Unknown taxonomy organism: " + organismId);
}
- ReferenceGenomeView result = null;
try {
ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
version = version.replaceAll("\\*", "");
- result = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version, token);
- if (result == null) {
- throw new QueryException("Cannot find requested reference genome");
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version,
+ token);
+ if (genome == null) {
+ throw new ObjectNotFoundException("Cannot find requested reference genome");
}
+ return genomeToMap(genome);
} catch (IllegalArgumentException e) {
throw new QueryException("Cannot find type: " + type);
}
+ }
+
+ private Map<String, Object> genomeToMap(ReferenceGenome genome) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("organism", super.createAnnotation(genome.getOrganism()));
+ result.put("version", genome.getVersion());
+ result.put("downloadProgress", genome.getDownloadProgress());
+ result.put("sourceUrl", genome.getSourceUrl());
+ result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
+ result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
+
+ return null;
+ }
+
+ private String getLocalUrl(String sourceUrl) {
+ String url = null;
+ try {
+ url = "../" + bigFileCache.getLocalPathForFile(sourceUrl);
+ } catch (FileNotFoundException e) {
+ logger.warn("Cannot find local file", e);
+ }
+ return url;
+ }
+
+ private List<Map<String, Object>> geneMappingToMaps(List<ReferenceGenomeGeneMapping> geneMapping) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ReferenceGenomeGeneMapping referenceGenomeGeneMapping : geneMapping) {
+ result.add(geneMappingToMap(referenceGenomeGeneMapping));
+ }
+
+ return result;
+ }
+
+ private Map<String, Object> geneMappingToMap(ReferenceGenomeGeneMapping mapping) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("downloadProgress", mapping.getDownloadProgress());
+ result.put("localUrl", getLocalUrl(mapping.getSourceUrl()));
+ result.put("sourceUrl", mapping.getSourceUrl());
+ result.put("name", mapping.getName());
return result;
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
index cc820e0780..4d9929a940 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
@@ -10,6 +10,7 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
+import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
@@ -49,7 +50,7 @@ public class ReferenceGenomeControllerTest extends RestTestFunctions {
try {
referenceGenomeRestImpl.getReferenceGenome(token, "960000", "UCSC", "ver");
fail("Exception expected");
- } catch (QueryException e2) {
+ } catch (ObjectNotFoundException e2) {
assertTrue(e2.getMessage().contains("Cannot find requested reference genome"));
} catch (Exception e) {
e.printStackTrace();
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
index 07fc7be059..b3bc006549 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -21,8 +21,6 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
-import lcsb.mapviewer.services.view.ReferenceGenomeView;
-import lcsb.mapviewer.services.view.ReferenceGenomeViewFactory;
/**
* Service managing reference genomes.
@@ -52,12 +50,6 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
@Autowired
private ReferenceGenomeDao referenceGenomeDao;
- /**
- * Factory that creates {@link ReferenceGenomeView}.
- */
- @Autowired
- private ReferenceGenomeViewFactory factory;
-
@Override
public void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
@@ -140,21 +132,15 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
}
@Override
- public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType,
- String version) {
+ public ReferenceGenome getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType,
+ String version, String authenticationToken) {
List<ReferenceGenome> list = referenceGenomeDao.getByType(genomeType);
for (ReferenceGenome referenceGenome : list) {
if (referenceGenome.getOrganism().equals(miriamData) && referenceGenome.getVersion().equals(version)) {
- return factory.create(referenceGenome);
+ return referenceGenome;
}
}
return null;
}
- @Override
- public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType,
- String version, String authenticationToken) {
- return this.getReferenceGenomeViewByParams(organism, genomeType, version);
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
index 1857baf300..419116d1d7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -9,7 +9,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.services.view.ReferenceGenomeView;
/**
* Service used to maintain referemce genome data.
@@ -131,7 +130,7 @@ public interface IReferenceGenomeService {
void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
/**
- * Returns {@link ReferenceGenomeView} for specific reference genome.
+ * Returns {@link ReferenceGenome} for specific reference genome.
*
* @param organism
* organism of reference genome
@@ -139,11 +138,8 @@ public interface IReferenceGenomeService {
* reference genome type
* @param version
* version of the reference genome
- * @return {@link ReferenceGenomeView} for specific reference genome
+ * @return {@link ReferenceGenome} for specific reference genome
*/
- ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType,
- String version);
-
- ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType,
- String version, String authenticationToken);
+ ReferenceGenome getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
+ String authenticationToken);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingView.java b/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingView.java
deleted file mode 100644
index f7c5284cb1..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingView.java
+++ /dev/null
@@ -1,125 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-
-/**
- * View representation of the {@link ReferenceGenome}.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeGeneMappingView extends AbstractView<ReferenceGenomeGeneMapping> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * {@link ReferenceGenomeGeneMapping#name}.
- */
- private String name;
-
- /**
- * Url from which reference genome was downloaded.
- */
- private String sourceUrl;
-
- /**
- * Local url where reference genome file can be accessed.
- */
- private String localUrl;
-
- /**
- * Progess of downloading process (100 means file is downloaded).
- */
- private double downloadProgress;
-
- /**
- * Default constructor.
- *
- * @param object
- * {@link ReferenceGenome} which this view should visualize
- */
- protected ReferenceGenomeGeneMappingView(ReferenceGenomeGeneMapping object) {
- super(object);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected ReferenceGenomeGeneMappingView() {
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the sourceUrl
- * @see #sourceUrl
- */
- public String getSourceUrl() {
- return sourceUrl;
- }
-
- /**
- * @param sourceUrl
- * the sourceUrl to set
- * @see #sourceUrl
- */
- public void setSourceUrl(String sourceUrl) {
- this.sourceUrl = sourceUrl;
- }
-
- /**
- * @return the localUrl
- * @see #localUrl
- */
- public String getLocalUrl() {
- return localUrl;
- }
-
- /**
- * @param localUrl
- * the localUrl to set
- * @see #localUrl
- */
- public void setLocalUrl(String localUrl) {
- this.localUrl = localUrl;
- }
-
- /**
- * @return the downloadProgress
- * @see #downloadProgress
- */
- public double getDownloadProgress() {
- return downloadProgress;
- }
-
- /**
- * @param downloadProgress
- * the downloadProgress to set
- * @see #downloadProgress
- */
- public void setDownloadProgress(double downloadProgress) {
- this.downloadProgress = downloadProgress;
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactory.java
deleted file mode 100644
index 9eabc77f2f..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactory.java
+++ /dev/null
@@ -1,59 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.FileNotFoundException;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.cache.BigFileCache;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-
-/**
- * Factory class for {@link AnnotationView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeGeneMappingViewFactory extends AbstractViewFactory<ReferenceGenomeGeneMapping, ReferenceGenomeGeneMappingView> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ReferenceGenomeGeneMappingViewFactory.class);
-
- /**
- * Service that allows to access big files (reference genome is stored as a
- * big file on the server).
- */
- @Autowired
- private BigFileCache bigFileCache;
-
- @Override
- public ReferenceGenomeGeneMappingView create(ReferenceGenomeGeneMapping object) {
- ReferenceGenomeGeneMappingView result = new ReferenceGenomeGeneMappingView();
- result.setDownloadProgress(object.getDownloadProgress());
- try {
- result.setLocalUrl("../" + bigFileCache.getLocalPathForFile(object.getSourceUrl()));
- } catch (FileNotFoundException e) {
- result.setLocalUrl(null);
- }
- result.setSourceUrl(object.getSourceUrl());
- result.setName(object.getName());
- return result;
- }
-
- @Override
- public String createGson(ReferenceGenomeGeneMappingView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public ReferenceGenomeGeneMapping viewToObject(ReferenceGenomeGeneMappingView view) {
- throw new NotImplementedException();
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeView.java b/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeView.java
deleted file mode 100644
index 9ab0d68a2a..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeView.java
+++ /dev/null
@@ -1,194 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-
-/**
- * View representation of the {@link ReferenceGenome}.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeView extends AbstractView<ReferenceGenome> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * {@link ReferenceGenome#organism}.
- */
- private MiriamData organism;
-
- /**
- * {@link ReferenceGenome#type}.
- */
- private ReferenceGenomeType type;
-
- /**
- * {@link ReferenceGenome#version}.
- */
- private String version;
-
- /**
- * Progress of download process (100 means that file is complete).
- */
- private double downloadProgress;
-
- /**
- * Url from which reference genome file was downloaded.
- */
- private String sourceUrl;
-
- /**
- * Url to local copy of reference genome file.
- */
- private String localUrl;
-
- /**
- * List of gene mappings for reference genome.
- */
- private List<ReferenceGenomeGeneMappingView> geneMapping = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param object
- * {@link ReferenceGenome} which this view should visualize
- */
- protected ReferenceGenomeView(ReferenceGenome object) {
- super(object);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected ReferenceGenomeView() {
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public MiriamData getOrganism() {
- return organism;
- }
-
- /**
- * @param organism
- * the organism to set
- * @see #organism
- */
- public void setOrganism(MiriamData organism) {
- this.organism = organism;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public ReferenceGenomeType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(ReferenceGenomeType type) {
- this.type = type;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * @return the downloadProgress
- * @see #downloadProgress
- */
- public double getDownloadProgress() {
- return downloadProgress;
- }
-
- /**
- * @param downloadProgress
- * the downloadProgress to set
- * @see #downloadProgress
- */
- public void setDownloadProgress(double downloadProgress) {
- this.downloadProgress = downloadProgress;
- }
-
- /**
- * @return the sourceUrl
- * @see #sourceUrl
- */
- public String getSourceUrl() {
- return sourceUrl;
- }
-
- /**
- * @param sourceUrl
- * the sourceUrl to set
- * @see #sourceUrl
- */
- public void setSourceUrl(String sourceUrl) {
- this.sourceUrl = sourceUrl;
- }
-
- /**
- * @return the localUrl
- * @see #localUrl
- */
- public String getLocalUrl() {
- return localUrl;
- }
-
- /**
- * @param localUrl
- * the localUrl to set
- * @see #localUrl
- */
- public void setLocalUrl(String localUrl) {
- this.localUrl = localUrl;
- }
-
- /**
- * @return the geneMapping
- * @see #geneMapping
- */
- public List<ReferenceGenomeGeneMappingView> getGeneMapping() {
- return geneMapping;
- }
-
- /**
- * @param geneMapping
- * the geneMapping to set
- * @see #geneMapping
- */
- public void setGeneMapping(List<ReferenceGenomeGeneMappingView> geneMapping) {
- this.geneMapping = geneMapping;
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactory.java
deleted file mode 100644
index c85ad828df..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactory.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.FileNotFoundException;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.cache.BigFileCache;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-
-/**
- * Factory class for {@link AnnotationView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeViewFactory extends AbstractViewFactory<ReferenceGenome, ReferenceGenomeView> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReferenceGenomeViewFactory.class);
-
- /**
- * Access point for big files.
- */
- @Autowired
- private BigFileCache bigFileCache;
-
- /**
- * Factory that creates readable gene mappings.
- */
- @Autowired
- private ReferenceGenomeGeneMappingViewFactory referenceGenomeGeneMappingViewFactory;
-
- @Override
- public ReferenceGenomeView create(ReferenceGenome object) {
- ReferenceGenomeView result = new ReferenceGenomeView();
- result.setDownloadProgress(object.getDownloadProgress());
- result.setGeneMapping(referenceGenomeGeneMappingViewFactory.createList(object.getGeneMapping()));
- try {
- result.setLocalUrl("../" + bigFileCache.getLocalPathForFile(object.getSourceUrl()));
- } catch (FileNotFoundException e) {
- logger.warn("Cannot find local file", e);
- result.setLocalUrl(null);
- }
- result.setOrganism(object.getOrganism());
- result.setSourceUrl(object.getSourceUrl());
- result.setType(object.getType());
- result.setVersion(object.getVersion());
- return result;
- }
-
- @Override
- public String createGson(ReferenceGenomeView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public ReferenceGenome viewToObject(ReferenceGenomeView view) {
- throw new NotImplementedException();
- }
-
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index e259fea970..ab4eb9ada7 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -45,9 +45,6 @@
<bean id="PasswordEncoder" class="lcsb.mapviewer.services.impl.Md5PasswordEncoder"/>
<!-- View factories -->
- <bean id="ReferenceGenomeViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeViewFactory"/>
- <bean id="ReferenceGenomeGeneMappingViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeGeneMappingViewFactory"/>
-
<bean id="FullAliasViewFactory" class="lcsb.mapviewer.services.search.data.FullAliasViewFactory"/>
<bean id="FullReactionViewFactory" class="lcsb.mapviewer.services.search.data.FullReactionViewFactory"/>
<bean id="LightAliasViewFactory" class="lcsb.mapviewer.services.search.data.LightAliasViewFactory"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
index 3497bf17ae..ce60a5e13e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
@@ -6,8 +6,6 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ FrameworkVersionViewTest.class, //
- ReferenceGenomeViewFactoryTest.class, //
- ReferenceGenomeGeneMappingViewFactoryTest.class, //
})
public class AllViewTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactoryTest.java
deleted file mode 100644
index 6ad7e4e64b..0000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeGeneMappingViewFactoryTest.java
+++ /dev/null
@@ -1,55 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-public class ReferenceGenomeGeneMappingViewFactoryTest extends ServiceTestFunctions {
-
- @Autowired
- ReferenceGenomeGeneMappingViewFactory factory;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- ReferenceGenomeGeneMapping referenceGenome = new ReferenceGenomeGeneMapping();
- Object object = factory.create(referenceGenome);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateGson() throws Exception {
- try {
- ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
- ReferenceGenomeGeneMappingView object = factory.create(mapping);
- assertNotNull(factory.createGson(object));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactoryTest.java
deleted file mode 100644
index 9a2eb39ee5..0000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/ReferenceGenomeViewFactoryTest.java
+++ /dev/null
@@ -1,55 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-public class ReferenceGenomeViewFactoryTest extends ServiceTestFunctions {
-
- @Autowired
- ReferenceGenomeViewFactory factory;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- ReferenceGenome referenceGenome = new ReferenceGenome();
- Object object = factory.create(referenceGenome);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateGson() throws Exception {
- try {
- ReferenceGenome referenceGenome = new ReferenceGenome();
- ReferenceGenomeView object = factory.create(referenceGenome);
- assertNotNull(factory.createGson(object));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
--
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