diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
index 607a26f3ba2166176d90aa00fa55c754a1d6c97f..ed4c5e5240cf5305eb7890d48e38ced44f6d7965 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -80,14 +80,16 @@ public class PermanentDatabaseLevelCache extends XmlParser implements PermanentD
@Override
public CacheQuery call() throws Exception {
- logger.debug("Query task call");
- dbUtils.createSessionForCurrentThread();
- logger.debug("Query task session started");
- CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
- logger.debug("Query task data retrieved");
- dbUtils.closeSessionForCurrentThread();
- logger.debug("Query task return");
- return entry;
+ logger.debug("Query task call");
+ try {
+ dbUtils.createSessionForCurrentThread();
+ logger.debug("Query task session started");
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+ logger.debug("Query task data retrieved");
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
}
}
@@ -227,26 +229,29 @@ public class PermanentDatabaseLevelCache extends XmlParser implements PermanentD
@Override
public CacheQuery call() throws Exception {
- logger.debug("Add task call");
- dbUtils.createSessionForCurrentThread();
- CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
-
- if (entry == null) {
- entry = new CacheQuery();
- entry.setQuery((String) query);
- entry.setAccessed(Calendar.getInstance());
- } else {
- entry.setAccessed(Calendar.getInstance());
- }
- entry.setValue(value);
- entry.setType(type);
- Calendar expires = Calendar.getInstance();
- expires.add(Calendar.DAY_OF_MONTH, type.getValidity());
- entry.setExpires(expires);
-
- getCacheQueryDao().add(entry);
- dbUtils.closeSessionForCurrentThread();
- return entry;
+ logger.debug("Add task call");
+ try {
+ dbUtils.createSessionForCurrentThread();
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+
+ if (entry == null) {
+ entry = new CacheQuery();
+ entry.setQuery((String) query);
+ entry.setAccessed(Calendar.getInstance());
+ } else {
+ entry.setAccessed(Calendar.getInstance());
+ }
+ entry.setValue(value);
+ entry.setType(type);
+ Calendar expires = Calendar.getInstance();
+ expires.add(Calendar.DAY_OF_MONTH, type.getValidity());
+ entry.setExpires(expires);
+
+ getCacheQueryDao().add(entry);
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
}
}
@@ -290,13 +295,16 @@ public class PermanentDatabaseLevelCache extends XmlParser implements PermanentD
@Override
public CacheQuery call() throws Exception {
logger.debug("Remove task call");
- dbUtils.createSessionForCurrentThread();
- CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
- if (entry != null) {
- getCacheQueryDao().delete(entry);
- }
- dbUtils.closeSessionForCurrentThread();
- return entry;
+ try {
+ dbUtils.createSessionForCurrentThread();
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+ if (entry != null) {
+ getCacheQueryDao().delete(entry);
+ }
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
index df03d1175cb14e1d072df7f3eb0649473bf1d2b6..014346e3767002a35cf441bd4f1532fa093961cd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -57,18 +57,18 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Homepage of drugbank.
*/
- static final String URL = "http://ctdbase.org/";
+ static final String URL = "https://ctdbase.org/";
/**
* URL to get a list of chemicals by disease id.
*/
- public static final String DISEASE_URL = "http://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+ public static final String DISEASE_URL = "https://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+ "type=disease&acc=MESH%3A";
/**
* URL to get a list of chemicals by gene id.
*/
- public static final String DISEASE_GENE_URL = "http://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+ public static final String DISEASE_GENE_URL = "https://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+ "d-1332398-e=5&view=disease&type=gene&assnType=curated&acc=";
/**
@@ -218,7 +218,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
}
}
- } catch (FileNotFoundException e) {
+ } catch (WrongResponseCodeIOException e) {
// it means that there are no results for this query
} catch (IOException e) {
throw new ChemicalSearchException("ctdbase service unavailable", e);
@@ -447,14 +447,14 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
if (entrez == null) {
invalidHgnc.add(md);
} else {
- String query = "http://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc=" + entrez.getResource();
+ String query = "https://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc=" + entrez.getResource();
String referencesPage = getWebPageContent(query);
Matcher matcher = pattern.matcher(referencesPage);
while (matcher.find()) {
idx.add(matcher.group(1));
}
for (String string : idx) {
- String query2 = "http://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=" + string;
+ String query2 = "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=" + string;
String referencesPage2 = getWebPageContent(query2);
String[] lines = referencesPage2.split("\n");
for (int i = 1; i < lines.length; i++) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index f917270d8a88f9da0a9c4f27bf0235caa230838f..0fbcd7a00e507a8d95cb43a2491c02a565fc1610 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -29,7 +29,7 @@ import lcsb.mapviewer.model.map.MiriamType;
/**
* This class is a backend to publically available pubmed API in
- * <a href="http://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
+ * <a href="https://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
*
* @author Piotr Gawron
*
@@ -57,6 +57,8 @@ public class PubmedParser extends CachableInterface implements IExternalService
*/
static final String SUPPORTED_VERSION = "5.2.2";
+ static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
+
/**
* Connector used for accessing data from miriam registry.
*/
@@ -131,7 +133,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
result = new Article();
try {
- String url = "http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query="
+ String url = API_URL+"search/resulttype=core&query="
+ java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
String content = getWebPageContent(url);
@@ -261,7 +263,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
@Override
public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central", "http://europepmc.org/RestfulWebService");
+ ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central", "https://europepmc.org/RestfulWebService");
GeneralCacheInterface cacheCopy = getCache();
this.setCache(null);
@@ -292,7 +294,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
*/
public String getApiVersion() throws PubmedSearchException {
try {
- String url = "http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query=src%3Amed+ext_id%3A23644949";
+ String url = API_URL+"search/resulttype=core&query=src%3Amed+ext_id%3A23644949";
String content = getWebPageContent(url);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index f3dfdc8aead7a80f6cafce1724e6470a638175f0..07692f2bf2b14a16a8667aafc10c6b81f7897694 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -29,7 +29,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This class is responsible for connecting to
- * <a href="http://rest.ensembl.org">Ensembl API</a> and annotate elements with
+ * <a href="https://rest.ensembl.org">Ensembl API</a> and annotate elements with
* information taken from this service.
*
*
@@ -46,7 +46,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
/**
* Url address of ensembl restful service.
*/
- private static final String REST_SERVICE_URL = "http://rest.ensembl.org/xrefs/id/";
+ private static final String REST_SERVICE_URL = "https://rest.ensembl.org/xrefs/id/";
/**
* Suffix that is needed for getting proper result using
@@ -57,7 +57,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
/**
* Url used for retrieving version of the restful API.
*/
- private static final String REST_SERVICE_VERSION_URL = "http://rest.ensembl.org/info/rest?content-type=text/xml";
+ private static final String REST_SERVICE_VERSION_URL = "https://rest.ensembl.org/info/rest?content-type=text/xml";
/**
* Default constructor.
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index c4e5cb7b25e514eaadeaea0a43e33c695fe6c45b..a542728437b4eba270c3abad9439ccca70c5a25e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.BioEntity;
@@ -29,7 +30,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This class is responsible for connecting to
- * <a href="http://rest.genenames.org/">HGNC restfull API</a> and annotate
+ * <a href="https://rest.genenames.org/">HGNC restfull API</a> and annotate
* elements with information taken from this service.
*
*
@@ -40,7 +41,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
/**
* Address of HGNC API that should be used for retrieving data.
*/
- private static final String REST_API_URL = "http://rest.genenames.org/fetch/";
+ private static final String REST_API_URL = "https://rest.genenames.org/fetch/";
/**
* Default constructor.
@@ -231,6 +232,8 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
}
}
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn(prefix + "Cannot find information for element.");
} catch (Exception e) {
throw new AnnotatorException(e);
}
@@ -314,7 +317,10 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
}
return result;
- } catch (Exception e) {
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn("No HGNC data found for id: "+miriamData);
+ return new ArrayList<>();
+ } catch (Exception e) {
throw new AnnotatorException(e);
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 3e26f3006a7d190ec35450ba5f9c388cc2d4e8af..c006d49ed4106d58c1323c1bf5dcd930001bcf36 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -43,7 +43,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
/**
* Address of annotation rest service for reactions.
*/
- private static final String REACTION_ANNOTATION_URL_PREFIX = "http://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
+ private static final String REACTION_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
/**
* Class used for some simple operations on {@link BioEntity} elements.
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 997494bd6562f088eb1fd2a0ce46aa3f15912f6b..332354bed41576191fcd66fc72d10f5f8e4eacf1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -134,7 +134,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
* @return url to uniprot restfull API about uniprot entry
*/
private String getUniprotUrl(String uniprotId) {
- return "http://www.uniprot.org/uniprot/" + uniprotId + ".txt";
+ return "https://www.uniprot.org/uniprot/" + uniprotId + ".txt";
}
/**
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
index f03eb92e179fd32c00e3ac5686e069374d0d8a32..38fa0393ed9e2677e5b5c76870cff9bfc3b8bba8 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -551,7 +551,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
// remove info about single publication from cache (so we will have to
// download it)
chemicalParser.getCache().removeByQuery(
- "http://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=4802115", chemicalParser.getCacheType());
+ "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=4802115", chemicalParser.getCacheType());
// disallow to use cache for first query (it will be directly about drug),
// so parser will have to parse results taking data from cache (or