diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index bcd7da6eec806623c261579cb2fc62fa658f1f60..fcf44102362777f98200ed90612f1a7c2173dc4d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -17,7 +17,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
import lcsb.mapviewer.model.map.compartment.Compartment;
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java b/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
index 38920e1caed5f00fc4017059749400b3a141f9e0..8e55dbd35a707a07aa425b9c166fb372d61f951e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
@@ -3,7 +3,11 @@ package lcsb.mapviewer.commands;
import org.apache.log4j.Logger;
public class SemanticZoomLevelMatcher {
- Logger logger = Logger.getLogger(SemanticZoomLevelMatcher.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SemanticZoomLevelMatcher.class);
/**
* Checks if level belongs to the range defined in
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 57882b31944b9b09f93db81038093d919c383396..56071ddde9682e481a222acbb34b1021b3363bad 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -33,7 +33,11 @@ import lcsb.mapviewer.services.view.AnnotationView;
@Transactional(value = "txManager")
public abstract class BaseRestImpl {
- Logger logger = Logger.getLogger(BaseRestImpl.class);
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(BaseRestImpl.class);
@Autowired
private IModelService modelService;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
index 0d79586f926aa1a0cae0f6dc42ef10b649002536..8b4e0560e0a125cd69f1b7e2cb29b18c2378e795 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
@@ -6,7 +6,6 @@ import java.util.Map;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.services.view.AnnotationView;
import lcsb.mapviewer.services.view.OverviewImageView;
public class ProjectMetaData implements Serializable {
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 41af2e14c2428ce1486c00498ab8f8ef756260e7..a64ef7f781d081252867ed3badc89b2f645c2a27 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
@@ -62,7 +62,6 @@ import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index 949e985122aed64db0eb3d0fc23e3daddfd472a5..25c714b01695187487c30f571f98fa7d8dccb02f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -36,7 +36,6 @@ public class ChemicalRestImpl extends BaseRestImpl {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private Logger logger = Logger.getLogger(ChemicalRestImpl.class);
@Autowired
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index b566144f91d2f600e98b483ae143341ffb7c644f..a08a985d71237383216c776d64c2277356d19b05 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -22,7 +22,6 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.drug.IDrugService;
@@ -35,16 +34,16 @@ public class DrugRestImpl extends BaseRestImpl {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(DrugRestImpl.class);
+ private Logger logger = Logger.getLogger(DrugRestImpl.class);
@Autowired
- private IDrugService drugService;
+ private IDrugService drugService;
@Autowired
- private IModelService modelService;
+ private IModelService modelService;
@Autowired
- private IUserService userService;
+ private IUserService userService;
public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
AuthenticationToken authenticationToken = userService.getToken(token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
index 1d9f8fc7e6000f1e153f183877355f224b98fd99..3f0352abf05e0f668a86f494d30b1cd9b164e3a9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
@@ -33,13 +32,10 @@ public class MiRnaRestImpl extends BaseRestImpl {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(MiRnaRestImpl.class);
+ private Logger logger = Logger.getLogger(MiRnaRestImpl.class);
@Autowired
- private IMiRNAService miRnaService;
-
- @Autowired
- private ElementMatcher elementMatcher;
+ private IMiRNAService miRnaService;
public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
AuthenticationToken authenticationToken = getUserService().getToken(token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index 931996af49b4f8c57035a5431f87e3caaca41b65..c30f92abc8903929a1c1ddabb55d9fca647f7acf 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -19,8 +19,6 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ElementModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 1bab83b85dc597cfe316707de11b67229d6f8ed5..ace3974815517e448e1de1e8908cd432a6c0854f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.api.projects.models.publications;
import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
@@ -33,7 +31,6 @@ import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
index 86df7fbcaae28d378d477b192b7d459c7fa929a4..32b1acd9ede8099f67a72ad949d864f29c081051 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
@@ -16,8 +16,6 @@ import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
-import lcsb.mapviewer.annotation.data.ChemicalDirectEvidenceTest;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index b70b7bd0e6242fb11c95bfa3ffa91b5509224d1a..0a7a3244eacb3dc3dba1a2e3aa793323d4d9fc38 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -28,6 +28,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
/**
* Default class logger.
*/
+ @SuppressWarnings("unused")
private final Logger logger = Logger.getLogger(SearchResultFactory.class);
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java
new file mode 100644
index 0000000000000000000000000000000000000000..43bdc10b273b2dae5058ab2cf180b02bac634abf
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java
@@ -0,0 +1,48 @@
+package lcsb.mapviewer.services.search.db;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargettingStructure;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+@Transactional(value = "txManager")
+public abstract class DbSearchService {
+
+ /**
+ * Service accessing
+ * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ protected void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
+ Set<MiriamData> result = new HashSet<>();
+ result.addAll(targettingStructure.getSources());
+ for (Target target : targettingStructure.getTargets()) {
+ result.addAll(target.getGenes());
+ result.addAll(target.getReferences());
+
+ }
+
+ for (MiriamData miriamData : result) {
+ if (MiriamType.PUBMED.equals(miriamData.getDataType())) {
+ try {
+ pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
+ } catch (NumberFormatException | PubmedSearchException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
+
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
index 7ada8d540a60128a2b971d5fbdf54f7d30ac57ff..94eaaef9c453f396703f1b202b8d475d9a936906 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
@@ -17,12 +17,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargettingStructure;
import lcsb.mapviewer.annotation.services.ChemicalParser;
import lcsb.mapviewer.annotation.services.ChemicalSearchException;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -38,6 +34,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about chemicals.
@@ -46,7 +43,7 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
*
*/
@Transactional(value = "txManager")
-public class ChemicalService implements IChemicalService {
+public class ChemicalService extends DbSearchService implements IChemicalService {
/**
* Default class logger.
@@ -70,13 +67,6 @@ public class ChemicalService implements IChemicalService {
@Autowired
private HgncAnnotator hgncAnnotator;
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
/**
* Service that manages search history.
*/
@@ -323,25 +313,4 @@ public class ChemicalService implements IChemicalService {
}
}
- private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index 584dfa0811af34460401f681e91418800cd9bf05..c220c2a4c102b82ea351dadb4c272f68aaad35e0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -13,12 +13,9 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargettingStructure;
import lcsb.mapviewer.annotation.services.ChEMBLParser;
import lcsb.mapviewer.annotation.services.DrugSearchException;
import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -33,6 +30,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about drugs.
@@ -41,7 +39,7 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
*
*/
@Transactional(value = "txManager")
-public class DrugService implements IDrugService {
+public class DrugService extends DbSearchService implements IDrugService {
/**
* Default class logger.
@@ -67,13 +65,6 @@ public class DrugService implements IDrugService {
@Autowired
private HgncAnnotator hgncAnnotator;
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
/**
* Service that manages search history.
*/
@@ -348,23 +339,6 @@ public class DrugService implements IDrugService {
this.searchHistoryService = searchHistoryService;
}
- /**
- * @return the pubmedParser
- * @see #pubmedParser
- */
- public PubmedParser getPubmedParser() {
- return pubmedParser;
- }
-
- /**
- * @param pubmedParser
- * the pubmedParser to set
- * @see #pubmedParser
- */
- public void setPubmedParser(PubmedParser pubmedParser) {
- this.pubmedParser = pubmedParser;
- }
-
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
logger.debug("Caching drug queries...");
@@ -410,26 +384,4 @@ public class DrugService implements IDrugService {
}
}
}
-
- private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
index 57ccbb24e684aa05fd347e39cc442cfdd3125d8a..136a1022424a2a323b18978ef40fa64aca9b8645 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
@@ -15,11 +15,8 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.MiRNA;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargettingStructure;
import lcsb.mapviewer.annotation.services.MiRNAParser;
import lcsb.mapviewer.annotation.services.MiRNASearchException;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -34,6 +31,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about che.
@@ -42,7 +40,7 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
*
*/
@Transactional(value = "txManager")
-public class MiRNAService implements IMiRNAService {
+public class MiRNAService extends DbSearchService implements IMiRNAService {
/**
* Default class logger.
@@ -68,13 +66,6 @@ public class MiRNAService implements IMiRNAService {
@Autowired
private ISearchHistoryService searchHistoryService;
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
/**
* Default constructor.
*/
@@ -243,25 +234,4 @@ public class MiRNAService implements IMiRNAService {
}
}
- private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
-
}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
index cbc0cd46bce3da8c5ad5b1dc17a07292cf92ff38..de78f41fcc601f02c197278c77d4208869803382 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
@@ -1,19 +1,6 @@
package lcsb.mapviewer.bean;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.view.ConfigurationView;
-import lcsb.mapviewer.services.view.ConfigurationViewFactory;
-import lcsb.mapviewer.services.view.ProjectView;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
@@ -21,15 +8,21 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.view.ConfigurationViewFactory;
+
public class ConfigurationBeanTest extends WebTestFunctions {
- ConfigurationBean cBean;
- UserBean uBean;
- String oldValue;
- User user2;
+ ConfigurationBean cBean;
+ UserBean uBean;
+ String oldValue;
+ User user2;
@Autowired
- ConfigurationViewFactory configurationViewFactory;
+ ConfigurationViewFactory configurationViewFactory;
@Before
public void setUp() throws Exception {