From 38b4f2958435942ecc31bc9231fefa7096fb5806 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 1 Aug 2017 10:43:59 +0200
Subject: [PATCH] common cache interface extracted for mirnas, drugs,
chemicals|
---
.../services/search/db/DbSearchService.java | 48 +++++++++++++++++
.../search/db/chemical/ChemicalService.java | 35 +------------
.../services/search/db/drug/DrugService.java | 52 +------------------
.../search/db/mirna/MiRNAService.java | 34 +-----------
4 files changed, 54 insertions(+), 115 deletions(-)
create mode 100644 service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java
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 0000000000..43bdc10b27
--- /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 7ada8d540a..94eaaef9c4 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 584dfa0811..c220c2a4c1 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 57ccbb24e6..136a102242 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);
- }
- }
- }
-
- }
-
}
--
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