From 887a8fc642b517955ff652bafa958c87e17aa0f4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 15 Jun 2018 14:27:14 +0200
Subject: [PATCH] API providing genme information
---
.../genomics/ReferenceGenomeController.java | 36 +++++++++
.../api/genomics/ReferenceGenomeRestImpl.java | 76 ++++++++++++++++++-
.../ReferenceGenomeControllerTest.java | 53 +++++++++++++
.../interfaces/IReferenceGenomeService.java | 18 ++---
4 files changed, 173 insertions(+), 10 deletions(-)
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 67b4a370f0..51342dd986 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 +1,6 @@
package lcsb.mapviewer.api.genomics;
+import java.util.List;
import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
@@ -32,4 +33,39 @@ public class ReferenceGenomeController extends BaseController {
) throws SecurityException, QueryException, ObjectNotFoundException {
return referenceGenomeController.getReferenceGenome(token, organism, type, version);
}
+
+ @RequestMapping(value = "/genomics/taxonomies/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeTaxonomies(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeTaxonomies(token);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeTaxonomyTypes(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeTypes(token, organism);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeVersion(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeVersions(token, organism, type);
+ }
+
+ @RequestMapping(value = "/genomics/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getDownloaded(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomes(token);
+ }
+
}
\ 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 9c1f782af4..b8be215211 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
@@ -2,8 +2,11 @@ package lcsb.mapviewer.api.genomics;
import java.io.FileNotFoundException;
import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.TreeMap;
import org.apache.log4j.Logger;
@@ -11,6 +14,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.api.QueryException;
@@ -71,7 +75,7 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
- return null;
+ return result;
}
private String getLocalUrl(String sourceUrl) {
@@ -102,4 +106,74 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
return result;
}
+ public List<Map<String, Object>> getReferenceGenomeTaxonomies(String token) throws QueryException {
+ try {
+ Set<MiriamData> organisms = new HashSet<>();
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
+ }
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MiriamData miriamData : organisms) {
+ result.add(createAnnotation(miriamData));
+ }
+ return result;
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining organism list", e);
+ }
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeTypes(String token, String organismId) throws QueryException {
+ try {
+ Set<MiriamData> organisms = new HashSet<>();
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
+ }
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MiriamData miriamData : organisms) {
+ if (miriamData.getResource().equals(organismId)) {
+ Map<String, Object> entry = new HashMap<>();
+ entry.put("type", ReferenceGenomeType.UCSC.toString());
+ result.add(entry);
+ }
+ }
+ return result;
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining organism list", e);
+ }
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeVersions(String token, String organismId, String type)
+ throws QueryException {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ List<String> versions;
+ try {
+ versions = referenceGenomeService.getAvailableGenomeVersions(genomeType, organism);
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining version list", e);
+ }
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (String string : versions) {
+ Map<String, Object> entry = new HashMap<>();
+ entry.put("version", string);
+ result.add(entry);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getReferenceGenomes(String token)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
+ result.add(genomeToMap(genome));
+ }
+ 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 4d9929a940..d1bb8e0b1f 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
@@ -1,8 +1,12 @@
package lcsb.mapviewer.api.genomics;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.util.List;
+import java.util.Map;
+
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
@@ -58,4 +62,53 @@ public class ReferenceGenomeControllerTest extends RestTestFunctions {
}
}
+ @Test
+ public void testGetReferenceGenomeTaxonomies() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getReferenceGenomeTaxonomies(token);
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetReferenceGenomeTypes() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getReferenceGenomeTypes(token,"9606");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetReferenceGenomeVersions() throws Exception {
+ try {
+ List<Map<String, Object>> result = referenceGenomeRestImpl.getReferenceGenomeVersions(token,"9606","UCSC");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAllDowloadedReferenceGenomes() throws Exception {
+ try {
+ List<?> result = referenceGenomeRestImpl.getReferenceGenomes(token);
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
}
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 419116d1d7..c87597d001 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -11,7 +11,7 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
/**
- * Service used to maintain referemce genome data.
+ * Service used to maintain reference genome data.
*
* @author Piotr Gawron
*
@@ -24,7 +24,7 @@ public interface IReferenceGenomeService {
* @param type
* {@link ReferenceGenomeType type} of reference genome
* @param organism
- * organism for which renference genome is added
+ * organism for which reference genome is added
* @param version
* version of the reference genome
* @param customUrl
@@ -35,7 +35,7 @@ public interface IReferenceGenomeService {
* thrown when url is invalid
* @throws ReferenceGenomeConnectorException
* thrown when reference genome already exists or there is problem
- * wirh adding genome
+ * with adding genome
*/
void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
@@ -49,7 +49,7 @@ public interface IReferenceGenomeService {
* @return list of available organisms
* @throws ReferenceGenomeConnectorException
* thrown when there is a problem with accessing information about
- * reference genoems
+ * reference genomes
*/
List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException;
@@ -64,7 +64,7 @@ public interface IReferenceGenomeService {
* @return list of available organisms
* @throws ReferenceGenomeConnectorException
* thrown when there is a problem with accessing information about
- * reference genoems
+ * reference genomes
*/
List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
throws ReferenceGenomeConnectorException;
@@ -83,9 +83,9 @@ public interface IReferenceGenomeService {
String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version);
/**
- * Returns list of all downladed reference genomes.
+ * Returns list of all downloaded reference genomes.
*
- * @return list of all downladed reference genomes
+ * @return list of all downloaded reference genomes
*/
List<ReferenceGenome> getDownloadedGenomes();
@@ -100,7 +100,7 @@ public interface IReferenceGenomeService {
void removeGenome(ReferenceGenome genome) throws IOException;
/**
- * Adds gene mapping to refernce genome.
+ * Adds gene mapping to reference genome.
*
* @param referenceGenome
* reference genome where we add mapping
@@ -113,7 +113,7 @@ public interface IReferenceGenomeService {
* @throws URISyntaxException
* thrown when url is invalid
* @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with manipulatinf information about
+ * thrown when there is a problem with manipulating information about
* reference genome
*/
void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
--
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