diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
index 84d2a479626c345beca3fd0d74f7ddbaacee88d5..a7539637a939f934cee8754e7657ba66e5476d9f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
@@ -14,7 +14,6 @@ import org.apache.log4j.Logger;
import org.w3c.dom.Node;
import com.google.gson.Gson;
-import com.google.gson.internal.StringMap;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
@@ -191,11 +190,11 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* @return name of {@link MeSH} entry
*/
private String getName(Map<?, ?> gsonObject) {
- StringMap<?> descriptorTag = (StringMap<?>) gsonObject.get("DescriptorName");
+ Map<?, ?> descriptorTag = (Map<?, ?>) gsonObject.get("DescriptorName");
if (descriptorTag == null) {
- descriptorTag = (StringMap<?>) gsonObject.get("SupplementalRecordName");
+ descriptorTag = (Map<?, ?>) gsonObject.get("SupplementalRecordName");
}
- return (String) (((StringMap<?>) descriptorTag.get("String")).get("t"));
+ return (String) (((Map<?, ?>) descriptorTag.get("String")).get("t"));
}
/**
@@ -206,9 +205,9 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* @return id of {@link MeSH} entry
*/
private String getId(Map<?, ?> gsonObject) {
- StringMap<?> descriptorTag = (StringMap<?>) gsonObject.get("DescriptorUI");
+ Map<?, ?> descriptorTag = (Map<?, ?>) gsonObject.get("DescriptorUI");
if (descriptorTag == null) {
- descriptorTag = (StringMap<?>) gsonObject.get("SupplementalRecordUI");
+ descriptorTag = (Map<?, ?>) gsonObject.get("SupplementalRecordUI");
}
return (String) descriptorTag.get("t");
}
@@ -221,7 +220,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* @return description of {@link MeSH} entry
*/
private String getDescription(Map<?, ?> gsonObject) {
- StringMap<?> concepts = (StringMap<?>) gsonObject.get("_generated");
+ Map<?, ?> concepts = (Map<?, ?>) gsonObject.get("_generated");
return (String) concepts.get("PreferredConceptScopeNote");
}
@@ -234,14 +233,14 @@ public class MeSHParser extends CachableInterface implements IExternalService {
*/
private Set<String> getSynonyms(Map<?, ?> gsonObject) {
Set<String> synonyms = new HashSet<>();
- StringMap<?> concepts = (StringMap<?>) gsonObject.get("ConceptList");
+ Map<?, ?> concepts = (Map<?, ?>) gsonObject.get("ConceptList");
ArrayList<?> conceptList = (ArrayList<?>) concepts.get("Concept");
for (Object object : conceptList) {
- StringMap<?> concept = (StringMap<?>) object;
- ArrayList<?> termList = (ArrayList<?>) ((StringMap<?>) concept.get("TermList")).get("Term");
+ Map<?, ?> concept = (Map<?, ?>) object;
+ ArrayList<?> termList = (ArrayList<?>) ((Map<?, ?>) concept.get("TermList")).get("Term");
for (Object object2 : termList) {
- StringMap<?> term = (StringMap<?>) object2;
- StringMap<?> synonym = (StringMap<?>) term.get("String");
+ Map<?, ?> term = (Map<?, ?>) object2;
+ Map<?, ?> synonym = (Map<?, ?>) term.get("String");
synonyms.add((String) synonym.get("t"));
}
@@ -317,11 +316,11 @@ public class MeSHParser extends CachableInterface implements IExternalService {
private Set<MiriamData> getIdsBySynonymQuery(Map<?, ?> gsonObject) {
Set<MiriamData> result = new HashSet<>();
- StringMap<?> hits = (StringMap<?>) gsonObject.get("hits");
+ Map<?, ?> hits = (Map<?, ?>) gsonObject.get("hits");
ArrayList<?> hitsList = (ArrayList<?>) hits.get("hits");
for (Object object : hitsList) {
- StringMap<?> hit = (StringMap<?>) object;
- String id = (String) hit.get("_id");
+ Map<?, ?> hit = (Map<?, ?>) object;
+ String id = (String) hit.get("_id");
result.add(new MiriamData(MiriamType.MESH_2012, id));
}
return result;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index f3fa31a4bed15dc2f5057380933c4a84afc12e91..c4a6196a75c36d3ce66f18772eef3e1e9e6f6f7a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -9,7 +9,6 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import com.google.gson.Gson;
-import com.google.gson.internal.StringMap;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -61,29 +60,29 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
*/
private XmlSerializer<Go> goSerializer;
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(GO_TERM_CACHE_PREFIX)) {
- String term = name.substring(GO_TERM_CACHE_PREFIX.length());
- MiriamData md = createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, term);
- result = goSerializer.objectToString(getGoElement(md));
- } else if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else {
- throw new InvalidArgumentException("Don't know what to do with query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException | GoSearchException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(GO_TERM_CACHE_PREFIX)) {
+ String term = name.substring(GO_TERM_CACHE_PREFIX.length());
+ MiriamData md = createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, term);
+ result = goSerializer.objectToString(getGoElement(md));
+ } else if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (IOException | GoSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
/**
* Default constructor. Initializes structures used for transforming {@link Go}
@@ -150,11 +149,11 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
}
List<?> objects = (List<?>) gsonObject.get("results");
- StringMap<?> object = (StringMap<?>) objects.get(0);
+ Map<?, ?> object = (Map<?, ?>) objects.get(0);
result.setGoTerm((String) object.get("id"));
result.setCommonName((String) object.get("name"));
- StringMap<?> descr = (StringMap<?>) object.get("definition");
+ Map<?, ?> descr = (Map<?, ?>) object.get("definition");
if (descr != null) {
result.setDescription((String) descr.get("text"));
}
@@ -174,7 +173,8 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
try {
Compartment compartment = new Compartment("some_id");
- compartment.addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
+ compartment
+ .addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
annotateElement(compartment);
if (compartment.getFullName() == null || compartment.getFullName().equals("")) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
index aacd382a99dbf0822b7bc02b8d18922915c979d0..e270ab1b642d56ed2115b71bc5fbbb63a40e21fa 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
@@ -21,7 +21,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
index bc77268d3851b5454f58e74c1e9a2fc4fdba2cf8..f7540997deea79dd6a65c61568043131ec342458 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
@@ -20,7 +20,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
diff --git a/pom.xml b/pom.xml
index 44ae9949613bca16da19a6180ab7be58e9890ca9..4483ada9080945d59d00357c71622fe57685e467 100644
--- a/pom.xml
+++ b/pom.xml
@@ -65,6 +65,9 @@
<cglib.version>3.2.8</cglib.version>
+ <gson.version>2.8.5</gson.version>
+
+
<primafaces.version>4.0</primafaces.version>
<primafaces.themes.version>1.0.8</primafaces.themes.version>
@@ -92,8 +95,6 @@
<jsbml.version>1.4</jsbml.version>
- <gson.version>2.2.2</gson.version>
-
<chebi-ws.version>2.3.2</chebi-ws.version>