diff --git a/CHANGELOG b/CHANGELOG
index 23f682142be771adf7bdd821d793d104544ec423..58f8734fe19016b816bff246dcf1330e6a4dbec9 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -3,6 +3,16 @@ minerva (12.0.0) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Dec 2017 16:00:00 +0200
+minerva (11.0.7) stable; urgency=medium
+ * Bug fix: redirection added when anonymous tries to access secured map
+ * Bug fix: loading time of custom overlays is reduced
+ * Bug fix: there should be no problem with symlink when upgrading debian
+ package
+ * Bug fix: number of services changed API address to https: pmceurope
+ (pubmed), uniprot, ensembl, hgnc, recon, ctd database
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Jan 2018 16:00:00 +0200
+
minerva (11.0.6) stable; urgency=medium
* Bug fix: fix a bug when entering invalid mirna id
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 08c0fabbfe8fa51f82996ee01cbe73c63facd78b..986b24bc69cd2ba2108e176e2b59129f321b5adb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -45,29 +45,29 @@ public class PermanentDatabaseLevelCache extends XmlParser
/**
* This class represents new thread task for quering database.
- *
+ *
* @author Piotr Gawron
- *
+ *
*/
private final class QueryTask implements Callable<CacheQuery> {
/**
* Identifier of cached entry.
- *
+ *
* @see CacheQuery#query
*/
private String query;
/**
* Type of cached entry.
- *
+ *
* @see CacheQuery#type
*/
private CacheType type;
/**
* Default constructor.
- *
+ *
* @param query
* {@link #query}
* @param type
@@ -79,45 +79,47 @@ public class PermanentDatabaseLevelCache extends XmlParser
this.type = type;
}
- @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;
- }
+ @Override
+ public CacheQuery call() throws Exception {
+ 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();
+ }
+ }
}
/**
* This class represents new thread task for refreshing element in db.
- *
+ *
* @author Piotr Gawron
- *
+ *
*/
private final class RefreshTask implements Callable<CacheQuery> {
/**
* Identifier of cached entry.
- *
+ *
* @see CacheQuery#query
*/
private String query;
/**
* Type of cached entry.
- *
+ *
* @see CacheQuery#type
*/
private CacheType type;
/**
* Default constructor.
- *
+ *
* @param query
* {@link #query}
* @param type
@@ -183,42 +185,42 @@ public class PermanentDatabaseLevelCache extends XmlParser
/**
* This class represents new thread task for adding entry to database.
- *
+ *
* @author Piotr Gawron
- *
+ *
*/
private final class AddTask implements Callable<CacheQuery> {
/**
* Identifier of cached entry.
- *
+ *
* @see CacheQuery#query
*/
private String query;
/**
* Type of cached entry.
- *
+ *
* @see CacheQuery#type
*/
private CacheType type;
/**
* Value to cache.
- *
+ *
* @see CacheQuery#value
*/
private String value;
/**
* How long should the entry be valid in days.
- *
+ *
*/
private int validDays;
/**
* Default constructor.
- *
+ *
* @param query
* {@link #query}
* @param type
@@ -234,57 +236,60 @@ public class PermanentDatabaseLevelCache extends XmlParser
this.validDays = validDays;
}
- @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, validDays);
- entry.setExpires(expires);
-
- getCacheQueryDao().add(entry);
- dbUtils.closeSessionForCurrentThread();
- return entry;
- }
+ @Override
+ public CacheQuery call() throws Exception {
+ 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, validDays());
+ entry.setExpires(expires);
+
+ getCacheQueryDao().add(entry);
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
}
/**
* This class represents new thread task for removing entry from database.
- *
+ *
* @author Piotr Gawron
- *
+ *
*/
private final class RemoveTask implements Callable<CacheQuery> {
/**
* Identifier of cached entry.
- *
+ *
* @see CacheQuery#query
*/
private String query;
/**
* Type of cached entry.
- *
+ *
* @see CacheQuery#type
*/
private CacheType type;
/**
* Default constructor.
- *
+ *
* @param query
* {@link #query}
* @param type
@@ -296,25 +301,28 @@ public class PermanentDatabaseLevelCache extends XmlParser
this.type = type;
}
- @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;
- }
+ @Override
+ public CacheQuery call() throws Exception {
+ logger.debug("Remove task call");
+ try {
+ dbUtils.createSessionForCurrentThread();
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+ if (entry != null) {
+ getCacheQueryDao().delete(entry);
+ }
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
}
/**
* This class represents new thread task for invalidating entry in database.
- *
+ *
* @author Piotr Gawron
- *
+ *
*/
private final class InvalidateTask implements Callable<CacheQuery> {
@@ -330,7 +338,7 @@ public class PermanentDatabaseLevelCache extends XmlParser
/**
* Default constructor.
- *
+ *
* @param query
* {@link #query}
* @param type
@@ -529,7 +537,7 @@ public class PermanentDatabaseLevelCache extends XmlParser
/**
* Executes and returns result of the task provided in the parameter. This
* method is blocking (it's waiting for the results).
- *
+ *
* @param task
* task to be executed
* @return value returned by the task
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
index c03944fd8fb1507836139a32d05ffcde9b3864d3..5f468f1ad11eb4a49bf8d5599622191751bfe16a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
@@ -20,8 +20,8 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
/**
- * This class helps to download webpages. The pages are downloaded in separate
- * thred, due to the fact that sometimes java socket can hang (related JVM bug:
+ * This class helps to download web pages. The pages are downloaded in separate
+ * thread, due to the fact that sometimes java socket can hang (related JVM bug:
* https://bugs.openjdk.java.net/browse/JDK-8075484 ).
*
* @author Piotr Gawron
@@ -40,13 +40,13 @@ public class WebPageDownloader {
/**
* Hard timeout (threads are terminated) of http connection that access data
- * across internet.
+ * across Internet.
*/
private static final int HTTP_CONNECTION_TIMEOUT_SEC = 120;
/**
* How much time should the thread sleep before another try to access the
- * webpage that thrown INTERNAL SERVER ERROR http response.
+ * web page that thrown INTERNAL SERVER ERROR http response.
*/
private static final int HTTP_INTERNAL_ERROR_RECONNECT_SLEEP_TIME = 2000;
@@ -55,15 +55,15 @@ public class WebPageDownloader {
* receiving INTERNAL SERVER ERROR http response.
*/
private static final int HTTP_INTERNAL_ERROR_RECONNECT_TIMES = 2;
-
-
-
+
+
+
/**
- * Returns content of the webpage identified by url using GET.
+ * Returns content of the web page identified by url.
*
* @param accessUrl
- * url of a webpage
- * @return content of the webpage identified by url
+ * url of a web page
+ * @return content of the web page identified by url
* @throws IOException
* thrown when there is any problem with accessing webpage
*/
@@ -71,18 +71,18 @@ public class WebPageDownloader {
return getFromNetwork(accessUrl, "GET", null);
}
-
+
/**
- * Returns content of the webpage identified by url. The HTTP query is done
+ * Returns content of the webpage identified by url. The HTTP query is done
* using the provided POST if postData is not null.
- *
- *
+ *
+ *
* @param accessUrl
* url of a webpage
* @param httpRequestMethod
* type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
* @param data
- * string to be sent in the body of the
+ * string to be sent in the body of the
* @return content of the webpage identified by url
* @throws IOException
* thrown when there is any problem with accessing webpage
@@ -90,7 +90,7 @@ public class WebPageDownloader {
public String getFromNetwork(String accessUrl, String httpRequestMethod, String data) throws IOException {
/**
- * Tasks that retrieves content from webpage
+ * Tasks that retrieves content from web page
*
* @author Piotr Gawron
*
@@ -107,17 +107,17 @@ public class WebPageDownloader {
// connect to the server, if HTTP_INTERNAL_ERROR occurred then try to
// reconnect HTTP_INTERNAL_ERROR_RECONNECT_TIMES times
while (code == HttpURLConnection.HTTP_INTERNAL_ERROR || code == HttpURLConnection.HTTP_NOT_FOUND) {
- urlConn = openConnection(accessUrl);
+ urlConn = openConnection(accessUrl);
urlConn.addRequestProperty("User-Agent", "minerva-framework");
-
+
urlConn.setRequestMethod(httpRequestMethod);
- if (data != null) {
- urlConn.setDoOutput(true);
+ if (data != null) {
+ urlConn.setDoOutput(true);
DataOutputStream wr = new DataOutputStream(urlConn.getOutputStream());
wr.writeBytes(data);
- wr.close();
+ wr.close();
}
-
+
try {
urlConn.connect();
code = urlConn.getResponseCode();
@@ -174,7 +174,7 @@ public class WebPageDownloader {
* argument.
*
* @param accessUrl
- * url to the webpagae
+ * url to the web page
* @return {@link HttpURLConnection connection} to the url given in the
* argument
* @throws MalformedURLException
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 20351481b2d36412f64f2277bafa28ca1d9a6bdc..81d15a4530cfe77dae90131724c5513680f7b4ef 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -69,18 +69,18 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Home page of ctd database.
*/
- 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=";
/**
@@ -173,7 +173,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
private MeSHParser meshParser;
/**
- *
+ *
*/
public ChemicalParser() {
super(ChemicalParser.class);
@@ -252,7 +252,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Serializes list of chemicalId-chemicalName pairs.
- *
+ *
* @param chemicals
* list of objects to serialize
* @return serialized string
@@ -267,7 +267,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Deserializes list of chemicalId-chemicalName pairs.
- *
+ *
* @param chemicalNode
* string to deserialize
* @return list of chemicalId-chemicalName pairs
@@ -420,7 +420,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Method that creates chemical from a tab separated row from ctd database. Data
* looks like (line wrapping added for clarity):
- *
+ *
* <pre>
1. Disease Name Disease ID Direct Evidence Inference Network Inference Score Reference Count
2. Drug-Induced Liver Injury MESH:D056486 1-(2-trifluoromethoxyphenyl)-2-nitroethanone|1,4-bis(2-(3,5-dichloropyridyloxy))benzene|
@@ -433,7 +433,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
pirinixic acid|Polyphenols|Polysaccharides|potassium chromate(VI)|propiconazole|Quercetin|resveratrol|rosiglitazone|Rotenone|
Streptozocin|Tetrachlorodibenzodioxin|titanium dioxide|Tretinoin|usnic acid|Valproic Acid|Vincristine|Zinc|zinc chloride 190.67 634
* </pre>
- *
+ *
* @param lineValues
* line split by tab separator
* @param chemID
@@ -480,7 +480,7 @@ 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="
+ 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);
@@ -488,7 +488,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
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 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");
@@ -535,7 +535,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Returns list of chemicals for given set of target genes related to the
* disease.
- *
+ *
* @param targets
* set of target genes
* @param diseaseMiriam
@@ -592,7 +592,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Return list of chemical names that interact with a target.
- *
+ *
* @param diseaseMiriam
* we want to get chemicals in context of the disease
* @param target
@@ -631,7 +631,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Returns list of chemicals that interact with a target.
- *
+ *
* @param target
* target for which we are looking for chemicals
* @param disease
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 851847b75d185a38b232e0edeefcd26a044e60e5..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
*
@@ -55,7 +55,9 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* Version of the remote API thnat is supported by this connecting class.
*/
- static final String SUPPORTED_VERSION = "5.2.1";
+ 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 27cd669cc89e4ef80fd72248a15226dfb7a12941..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.
*
*
@@ -41,12 +41,12 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
/**
* Version of the rest API that is supported by this annotator.
*/
- static final String SUPPORTED_VERSION = "6.1";
+ static final String SUPPORTED_VERSION = "6.2";
/**
- * Url address of ensembl restfull service.
+ * 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 4010497e526fa1ac097b6113b18f6f1235d2c928..b7cd593c8d99a78aeea7d1b947a28397df869160 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
@@ -16,6 +16,7 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.BioEntity;
@@ -31,7 +32,7 @@ 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.
*
*
@@ -43,7 +44,7 @@ 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/";
@Autowired
private MiriamConnector miriamConnector;
@@ -236,19 +237,21 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
}
- }
- }
- }
- }
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
- }
- }
+ }
+ }
+ }
+ }
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn(prefix + "Cannot find information for element.");
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
/**
* Creates query url for given {@link MiriamType#HGNC} identifier.
- *
+ *
* @param id
* {@link MiriamType#HGNC} identifier
* @return url to restful api webpage for given identifier
@@ -259,7 +262,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
/**
* Creates query url for given {@link MiriamType#HGNC_SYMBOL}.
- *
+ *
* @param name
* {@link MiriamType#HGNC_SYMBOL}
* @return url to restful api webpage for given hgnc symbol
@@ -271,7 +274,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
/**
* Converts {@link MiriamType#HGNC}/{@link MiriamType#HGNC_SYMBOL} identifier
* into list of {@link MiriamType#UNIPROT} identifiers.
- *
+ *
* @param miriamData
* {@link MiriamData} with {@link MiriamType#HGNC} identifier
* @return list of {@link MiriamData} with {@link MiriamType#UNIPROT}
@@ -301,38 +304,41 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
} else {
Node entry = getNode("doc", resultNode.getChildNodes());
- NodeList list = entry.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("arr")) {
- String type = getNodeAttr("name", node);
- if (type.equals("uniprot_ids")) {
- NodeList uniprotList = node.getChildNodes();
- for (int j = 0; j < uniprotList.getLength(); j++) {
- Node uniprotNode = uniprotList.item(j);
- if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
- if (uniprotNode.getNodeName().equals("str")) {
- result.add(new MiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
- }
- }
- }
- }
- }
- }
- }
- }
- return result;
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
+ NodeList list = entry.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("arr")) {
+ String type = getNodeAttr("name", node);
+ if (type.equals("uniprot_ids")) {
+ NodeList uniprotList = node.getChildNodes();
+ for (int j = 0; j < uniprotList.getLength(); j++) {
+ Node uniprotNode = uniprotList.item(j);
+ if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (uniprotNode.getNodeName().equals("str")) {
+ result.add(new MiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn("No HGNC data found for id: "+miriamData);
+ return new ArrayList<>();
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
}
/**
* Converts {@link MiriamType#HGNC} identifier into
* {@link MiriamType#HGNC_SYMBOL}.
- *
+ *
* @param miriamData
* {@link MiriamData} with {@link MiriamType#HGNC} identifier
* @return {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
@@ -381,7 +387,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
/**
* Returns <code>true</code> if the {@link MiriamData} given in the parameter is
* a valid {@link MiriamType#HGNC} or {@link MiriamType#HGNC_SYMBOL}.
- *
+ *
* @param md
* {@link MiriamData} to validate
* @return <code>true</code> if the {@link MiriamData} given in the parameter is
@@ -403,7 +409,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
/**
* Transforms HGNC symbol into {@link MiriamType#ENTREZ} identifier.
- *
+ *
* @param md
* hgnc symbol
* @return {@link MiriamType#ENTREZ} identifier for a given hgnc symbol
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 36e85c27dbde7245cabfc955df81540b5f293fa1..8b318a426b463aa72401a8eaf6c93e6d022e445e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -193,7 +193,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
}
}
-
+
@Test
public void testGetChemicalBySynonym() throws Exception {
try {
@@ -209,7 +209,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
}
}
-
+
@Test
public void testFindByInvalidIdFromChemicalList() throws Exception {
@@ -584,7 +584,7 @@ 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",
+ "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),
diff --git a/debian/template/postinst b/debian/template/postinst
index 44228b77f9db6a5d9d50ee43d4917a886fe73f9e..2f2c3863a88d87c25e0f49a67687296261a2a16e 100644
--- a/debian/template/postinst
+++ b/debian/template/postinst
@@ -64,7 +64,7 @@ case "$1" in
#availble when new war is deployed from debian package, so tomcat will catch SQL exception and stop deployment
invoke-rc.d $TOMCAT_PACKAGE stop || true
rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
- ln -s /usr/share/minerva/minerva.war /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
+ ln -sf /usr/share/minerva/minerva.war /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
invoke-rc.d $TOMCAT_PACKAGE start
;;
*)
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index 34f05f2b6725a81a42e0403dad51c5a388a024ec..c3b40206069b7aa812bba3f7df4999fd97bbcd54 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -175,6 +175,33 @@ GuiConnector.prototype.hideProcessing = function () {
$(self._processingDialog).dialog("close");
};
+GuiConnector.prototype.alert = function (error, redirectIfSecurityError) {
+ if (redirectIfSecurityError === undefined) {
+ redirectIfSecurityError = false;
+ }
+ if (redirectIfSecurityError && error instanceof SecurityError && ServerConnector.getSessionData().getLogin() === "anonymous") {
+ window.location.href = ServerConnector.getServerBaseUrl() + "login.xhtml?from=" + encodeURI(window.location.href);
+ } else {
+ var self = returnThisOrSingleton(this);
+ logger.error(error);
+ if (self._errorDialog === undefined) {
+ self._errorDialog = document.createElement("div");
+ self._errorDialogContent = document.createElement("div");
+ self._errorDialog.appendChild(self._errorDialogContent);
+ document.body.appendChild(self._errorDialog);
+ $(self._errorDialog).dialog({
+ classes: {
+ "ui-dialog": "ui-state-error"
+ },
+ modal: true,
+ title: "ERROR"
+ }).siblings('.ui-dialog-titlebar').css("background", "red");
+ }
+ self._errorDialogContent.innerHTML = self.getErrorMessageForError(error);
+ $(self._errorDialog).dialog("open");
+ }
+};
+
GuiConnector.prototype.getErrorMessageForError = function (error) {
var message = error;
if (message instanceof SecurityError) {
@@ -200,27 +227,6 @@ GuiConnector.prototype.getErrorMessageForError = function (error) {
return message;
};
-GuiConnector.prototype.alert = function (error) {
- var self = returnThisOrSingleton(this);
- logger.error(error);
- if (self._errorDialog === undefined) {
- self._errorDialog = document.createElement("div");
- self._errorDialogContent = document.createElement("div");
- self._errorDialog.appendChild(self._errorDialogContent);
- document.body.appendChild(self._errorDialog);
- $(self._errorDialog).dialog({
- classes: {
- "ui-dialog": "ui-state-error"
- },
- modal: true,
- title: "ERROR"
- }).siblings('.ui-dialog-titlebar').css("background", "red");
- }
- self._errorDialogContent.innerHTML = self.getErrorMessageForError(error);
- $(self._errorDialog).dialog("open");
-
-};
-
GuiConnector.prototype.info = function (message) {
var self = returnThisOrSingleton(this);
if (self._infoDialog === undefined) {
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index 9c743127841a5697b4725329b25ad589302997dc..fd53d158f8fde5b329803cefb433c6bb179b17bf 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -1,268 +1,293 @@
-"use strict";
-
-require("./mocha-config");
-
-var minerva = require('../../main/js/minerva');
-var ServerConnectorMock = require('./ServerConnector-mock');
-var ProxyAccessPlugin = require('./plugin/ProxyAccessPlugin');
-
-var chai = require('chai');
-var assert = chai.assert;
-var logger = require('./logger');
-
-describe('minerva global', function () {
- beforeEach(function () {
- global.ServerConnector = undefined;
- });
-
- afterEach(function () {
- global.ServerConnector = ServerConnectorMock;
- });
-
- describe('create', function () {
- it('default', function () {
- var options = null;
- return ServerConnectorMock.getProject().then(function (project) {
- options = helper.createCustomMapOptions(project);
-
- return minerva.create(options);
- }).then(function (result) {
- assert.ok(result);
- assert.equal(logger.getWarnings().length, 0);
- return result.destroy();
- });
- });
- it('invalid projectId', function () {
- var options = {
- projectId: "unknownId",
- element: testDiv
- };
- return minerva.create(options).then(function () {
- assert.ok(false);
- }, function (error) {
- assert.ok(error.message.indexOf("Project with given id doesn't exist") >= 0);
- });
- });
- it('with overview', function () {
- helper.setUrl("http://test/?id=complex_model_with_images");
- var customMap;
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createOptions(project);
-
- return minerva.create(options);
- }).then(function (result) {
- customMap = result;
- assert.ok(result);
- assert.equal(logger.getWarnings().length, 0);
- var showOverviewButton = document.getElementsByName("showOverviewButton")[0];
- return showOverviewButton.onclick();
- }).then(function () {
- return customMap.destroy();
- });
- });
- });
-
-
- it("showComments", function () {
- var options = null;
- var map ;
- return ServerConnectorMock.getProject().then(function (project) {
- options = helper.createCustomMapOptions(project);
- return minerva.create(options);
- }).then(function (result) {
- map = result;
- var commentCheckbox = document.getElementsByName("commentCheckbox")[0];
- commentCheckbox.checked = true;
- return commentCheckbox.onclick();
- }).then(function () {
- assert.ok(ServerConnectorMock.getSessionData(options.getProject()).getShowComments());
- return map.destroy();
- });
- });
-
- describe("constructor", function () {
-
- it("with GET zoom param", function () {
- helper.setUrl("http://test/?zoom=5");
- var options;
- return ServerConnectorMock.getProject().then(function (project) {
- options = helper.createCustomMapOptions(project);
- return minerva.create(options);
- }).then(function (result) {
- var sessionData = ServerConnectorMock.getSessionData(options.getProject());
- assert.equal(sessionData.getZoomLevel(options.getProject().getModel()), 5);
- return result.destroy();
- });
- });
-
- it("with GET coordinates param", function () {
- helper.setUrl("http://test/?x=5&y=6");
- var options;
- return ServerConnectorMock.getProject().then(function (project) {
- options = helper.createCustomMapOptions(project);
- return minerva.create(options);
- }).then(function (result) {
- var center = ServerConnectorMock.getSessionData(options.getProject()).getCenter(options.getProject().getModel());
- assert.ok(center instanceof google.maps.Point);
- assert.equal(center.x, 5);
- assert.equal(center.y, 6);
- return result.destroy();
- });
- });
-
- it("simple", function () {
- var options = {
- projectId: "sample",
- element: testDiv
- };
- return minerva.create(options).then(function (result) {
- assert.ok(result);
- result.destroy();
- });
- });
- });
-
- it('create with layout', function () {
- var layout, project, plugin, map;
- return ServerConnectorMock.getProject().then(function (result) {
- project = result;
- var options = helper.createCustomMapOptions(project);
-
- plugin = new ProxyAccessPlugin({});
- options.getPlugins().push(plugin);
-
- layout = project.getModel().getLayouts()[1];
-
- helper.setUrl("http://test/?layout=" + layout.getName());
-
- return minerva.create(options);
- }).then(function (result) {
- map = result;
- assert.ok(result);
- // input file is not available so it's the background
- return plugin.getMinervaPluginProxy().project.map.getVisibleDataOverlays();
- }).then(function (visibleDataOverlays) {
- // input file is available so it's not the background file but overlay
- assert.equal(visibleDataOverlays.length, 0);
- assert.equal(ServerConnectorMock.getSessionData(project).getSelectedBackgroundOverlay(), layout.getId());
- assert.equal(logger.getWarnings().length, 0);
- return map.destroy();
- });
- });
-
- it('create with layout from session data', function () {
- var layout;
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createCustomMapOptions(project);
-
- layout = project.getModel().getLayouts()[1];
-
- ServerConnectorMock.getSessionData(project).setSelectedBackgroundOverlay(layout.getId());
-
- return minerva.create(options);
- }).then(function (result) {
- assert.equal(ServerConnectorMock.getSessionData().getSelectedBackgroundOverlay(), layout.getId());
- return result.destroy();
- });
- });
-
- it('create with layout 2', function () {
- helper.setUrl("http://test/?layout=xxx");
- var globalObject, plugin;
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createCustomMapOptions(project);
- plugin = new ProxyAccessPlugin();
- options.getPlugins().push(plugin);
- return minerva.create(options);
- }).then(function (result) {
- globalObject = result;
- assert.ok(result);
- return plugin.getMinervaPluginProxy().project.map.getVisibleDataOverlays();
- }).then(function (visibleDataOverlays) {
- // input file is available so it's not the background file but overlay
- assert.equal(visibleDataOverlays.length, 1);
- assert.equal(logger.getWarnings().length, 0);
- return globalObject.destroy();
- });
- });
-
- it('create with search overlay and GET search param', function () {
- helper.setUrl("http://test/?search=s1");
-
- var globalObject, plugin;
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createCustomMapOptions(project);
- plugin = new ProxyAccessPlugin();
- options.getPlugins().push(plugin);
- return minerva.create(options);
- }).then(function (result) {
- globalObject = result;
- return plugin.getMinervaPluginProxy().project.map.getHighlightedBioEntities("search");
- }).then(function (elements) {
- assert.ok(elements.length > 0);
- return globalObject.destroy();
- });
- });
-
- it('create with show submodel GET param', function () {
- helper.setUrl("http://test/?submap=15781");
-
- var project = helper.createProject();
- project.getModel().setId(15781);
-
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createCustomMapOptions(project);
-
- return minerva.create(options);
- }).then(function (result) {
- return result.destroy();
- });
- });
-
- it("constructor with touch enabled", function () {
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createCustomMapOptions(project);
- options.setCustomTouchInterface(true);
- return minerva.create(options).then(function (result) {
- assert.ok(result);
- return result.destroy();
- });
- });
- });
-
-
- it('create Export', function () {
- var options = null;
- return ServerConnectorMock.getProject().then(function (project) {
- options = helper.createCustomMapOptions(project);
-
- return minerva.createExport(options);
- }).then(function (result) {
- assert.ok(result);
- assert.equal(logger.getWarnings().length, 0);
- });
- });
-
- it('create Admin', function () {
- var options = null;
- return ServerConnectorMock.getProject().then(function (project) {
- options = helper.createCustomMapOptions(project);
-
- return minerva.createAdmin(options);
- }).then(function (result) {
- assert.ok(result);
- assert.equal(logger.getWarnings().length, 0);
- result.destroy();
- });
- });
- it('getProject', function () {
- return ServerConnectorMock.getProject().then(function (project) {
- var options = helper.createCustomMapOptions(project);
- return minerva.create(options);
- }).then(function (result) {
- assert.equal(result.getProject().getProjectId(), "sample");
- return result.destroy();
- });
- });
-
-});
+"use strict";
+
+require("./mocha-config");
+
+var Alias = require('../../main/js/map/data/Alias');
+var minerva = require('../../main/js/minerva');
+var Project = require('../../main/js/map/data/Project');
+var GuiConnectorMock = require('./GuiConnector-mock');
+var SecurityError = require('../../main/js/SecurityError');
+var ServerConnectorMock = require('./ServerConnector-mock');
+var ProxyAccessPlugin = require('./plugin/ProxyAccessPlugin');
+
+var chai = require('chai');
+var assert = chai.assert;
+var logger = require('./logger');
+
+describe('minerva global', function () {
+ beforeEach(function () {
+ global.ServerConnector = undefined;
+ });
+
+ afterEach(function () {
+ global.ServerConnector = ServerConnectorMock;
+ });
+
+ describe('create', function() {
+ it('default', function() {
+ var options = null;
+ return ServerConnectorMock.getProject().then(function(project) {
+ options = helper.createCustomMapOptions(project);
+
+ return minerva.create(options);
+ }).then(function(result) {
+ assert.ok(result);
+ assert.equal(logger.getWarnings().length, 0);
+ return result.destroy();
+ });
+ });
+ it('invalid projectId', function() {
+ var options = {
+ projectId: "unknownId",
+ element: testDiv
+ };
+ return minerva.create(options).then(function () {
+ assert.ok(false);
+ }, function (error) {
+ assert.ok(error.message.indexOf("Project with given id doesn't exist") >= 0);
+ });
+ });
+ it('with overview', function () {
+ helper.setUrl("http://test/?id=complex_model_with_images");
+ var customMap;
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createOptions(project);
+
+ return minerva.create(options);
+ }).then(function (result) {
+ customMap = result;
+ assert.ok(result);
+ assert.equal(logger.getWarnings().length, 0);
+ var showOverviewButton = document.getElementsByName("showOverviewButton")[0];
+ return showOverviewButton.onclick();
+ }).then(function () {
+ return customMap.destroy();
+ });
+ });
+ });
+
+
+ it("showComments", function() {
+ var options = null;
+ var map ;
+ return ServerConnectorMock.getProject().then(function (project) {
+ options = helper.createCustomMapOptions(project);
+ return minerva.create(options);
+ }).then(function (result) {
+ map = result;
+ var commentCheckbox = document.getElementsByName("commentCheckbox")[0];
+ commentCheckbox.checked = true;
+ return commentCheckbox.onclick();
+ }).then(function() {
+ assert.ok(ServerConnectorMock.getSessionData(options.getProject()).getShowComments());
+ return map.destroy();
+ });
+ });
+
+ describe("constructor", function () {
+
+ it("with GET zoom param", function () {
+ helper.setUrl("http://test/?zoom=5");
+ var options;
+ return ServerConnectorMock.getProject().then(function (project) {
+ options = helper.createCustomMapOptions(project);
+ return minerva.create(options);
+ }).then(function (result) {
+ var sessionData = ServerConnectorMock.getSessionData(options.getProject());
+ assert.equal(sessionData.getZoomLevel(options.getProject().getModel()), 5);
+ return result.destroy();
+ });
+ });
+
+ it("with GET coordinates param", function () {
+ helper.setUrl("http://test/?x=5&y=6");
+ var options;
+ return ServerConnectorMock.getProject().then(function (project) {
+ options = helper.createCustomMapOptions(project);
+ return minerva.create(options);
+ }).then(function (result) {
+ var center = ServerConnectorMock.getSessionData(options.getProject()).getCenter(options.getProject().getModel());
+ assert.ok(center instanceof google.maps.Point);
+ assert.equal(center.x, 5);
+ assert.equal(center.y, 6);
+ return result.destroy();
+ });
+ });
+
+ it("simple", function () {
+ var options = {
+ projectId: "sample",
+ element: testDiv
+ };
+ return minerva.create(options).then(function (result) {
+ assert.ok(result);
+ result.destroy();
+ });
+ });
+ });
+
+ it('create with layout', function () {
+ var layout, project, plugin, map;
+ return ServerConnectorMock.getProject().then(function (result) {
+ project = result;
+ var options = helper.createCustomMapOptions(project);
+
+ plugin = new ProxyAccessPlugin({});
+ options.getPlugins().push(plugin);
+
+ layout = project.getModel().getLayouts()[1];
+
+ helper.setUrl("http://test/?layout=" + layout.getName());
+
+ return minerva.create(options);
+ }).then(function (result) {
+ map = result;
+ assert.ok(result);
+ // input file is not available so it's the background
+ return plugin.getMinervaPluginProxy().project.map.getVisibleDataOverlays();
+ }).then(function (visibleDataOverlays) {
+ // input file is available so it's not the background file but overlay
+ assert.equal(visibleDataOverlays.length, 0);
+ assert.equal(ServerConnectorMock.getSessionData(project).getSelectedBackgroundOverlay(), layout.getId());
+ assert.equal(logger.getWarnings().length, 0);
+ return map.destroy();
+ });
+ });
+
+ it('create restricted map', function () {
+ var originalFunction = ServerConnectorMock.getProject;
+ ServerConnectorMock.getProject=function(){
+ return Promise.reject(new SecurityError("Access denied."));
+ };
+ helper.setUrl("http://test/?id=restricted_sample");
+ var options = {
+ element: testDiv,
+ mapDiv: testDiv,
+ configuration: helper.getConfiguration()
+ };
+
+ return minerva.create(options).then(function (map) {
+ assert.equal(null, map);
+ }).catch(function (e) {
+ assert.ok(e.message.indexOf("Access denied") >= 0);
+ }).finally(function(){
+ ServerConnectorMock.getProject = originalFunction;
+ });
+ });
+
+ it('create with layout from session data', function() {
+ var layout;
+ return ServerConnectorMock.getProject().then(function(project) {
+ var options = helper.createCustomMapOptions(project);
+
+ layout = project.getModel().getLayouts()[1];
+
+ ServerConnectorMock.getSessionData(project).setSelectedBackgroundOverlay(layout.getId());
+
+ return minerva.create(options);
+ }).then(function (result) {
+ assert.equal(ServerConnectorMock.getSessionData().getSelectedBackgroundOverlay(), layout.getId());
+ return result.destroy();
+ });
+ });
+
+ it('create with layout 2', function () {
+ helper.setUrl("http://test/?layout=xxx");
+ var globalObject, plugin;
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ plugin = new ProxyAccessPlugin();
+ options.getPlugins().push(plugin);
+ return minerva.create(options);
+ }).then(function (result) {
+ globalObject = result;
+ assert.ok(result);
+ return plugin.getMinervaPluginProxy().project.map.getVisibleDataOverlays();
+ }).then(function (visibleDataOverlays) {
+ // input file is available so it's not the background file but overlay
+ assert.equal(visibleDataOverlays.length, 1);
+ assert.equal(logger.getWarnings().length, 0);
+ return globalObject.destroy();
+ });
+ });
+
+ it('create with search overlay and GET search param', function () {
+ helper.setUrl("http://test/?search=s1");
+
+ var globalObject, plugin;
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ plugin = new ProxyAccessPlugin();
+ options.getPlugins().push(plugin);
+ return minerva.create(options);
+ }).then(function (result) {
+ globalObject = result;
+ return plugin.getMinervaPluginProxy().project.map.getHighlightedBioEntities("search");
+ }).then(function (elements) {
+ assert.ok(elements.length > 0);
+ return globalObject.destroy();
+ });
+ });
+
+ it('create with show submodel GET param', function () {
+ helper.setUrl("http://test/?submap=15781");
+
+ var project = helper.createProject();
+ project.getModel().setId(15781);
+
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+
+ return minerva.create(options);
+ }).then(function (result) {
+ return result.destroy();
+ });
+ });
+
+ it("constructor with touch enabled", function () {
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ options.setCustomTouchInterface(true);
+ return minerva.create(options).then(function(result) {
+ assert.ok(result);
+ return result.destroy();
+ });
+ });
+ });
+
+
+ it('create Export', function () {
+ var options = null;
+ return ServerConnectorMock.getProject().then(function (project) {
+ options = helper.createCustomMapOptions(project);
+
+ return minerva.createExport(options);
+ }).then(function (result) {
+ assert.ok(result);
+ assert.equal(logger.getWarnings().length, 0);
+ });
+ });
+
+ it('create Admin', function () {
+ var options = null;
+ return ServerConnectorMock.getProject().then(function (project) {
+ options = helper.createCustomMapOptions(project);
+
+ return minerva.createAdmin(options);
+ }).then(function (result) {
+ assert.ok(result);
+ assert.equal(logger.getWarnings().length, 0);
+ result.destroy();
+ });
+ });
+ it('getProject', function () {
+ return ServerConnectorMock.getProject().then(function (project) {
+ var options = helper.createCustomMapOptions(project);
+ return minerva.create(options);
+ }).then(function (result) {
+ assert.equal(result.getProject().getProjectId(), "sample");
+ return result.destroy();
+ });
+ });
+
+});
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
index 672b1feca43b0fdcc3d2ceae6e0fd1cf974e6614..acb3b4612a6dce1f24b2671530cd8ec2e95ea777 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
@@ -34,7 +34,7 @@ import lcsb.mapviewer.model.user.User;
@Entity
public class Layout implements Serializable {
/**
- *
+ *
*/
private static final long serialVersionUID = 1L;
@@ -143,7 +143,7 @@ public class Layout implements Serializable {
/**
* Constructor that initializes object with basic parameters.
- *
+ *
* @param title
* title of the layout
* @param directory
@@ -159,7 +159,7 @@ public class Layout implements Serializable {
/**
* Constructor that initializes object with the copy of the data from parameter.
- *
+ *
* @param layout
* from this object the data will be initialized
*/
@@ -180,7 +180,7 @@ public class Layout implements Serializable {
/**
* Prepares a copy of layout.
- *
+ *
* @return copy of layout
*/
public Layout copy() {
@@ -398,7 +398,7 @@ public class Layout implements Serializable {
/**
* When this layout is connected to the top model in complex models then this
* method adds layout of a submodel.
- *
+ *
* @param layout
* layout of a submodel
*/
@@ -409,7 +409,7 @@ public class Layout implements Serializable {
/**
* Sets {@link #model}.
- *
+ *
* @param model
* new {@link #model} value
*/
diff --git a/persist/src/db/11.0.7/fix_db_20180118.sql b/persist/src/db/11.0.7/fix_db_20180118.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/11.0.7/fix_db_20180118.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
index 02afc0199a9e39022bc90935372407560d5c4b3b..c6b2da557941c4337a9178d4a4da31b5c2177218 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
@@ -3,11 +3,13 @@ package lcsb.mapviewer.persist.dao;
import java.util.List;
import org.apache.log4j.Logger;
+import org.hibernate.Query;
import org.hibernate.Session;
import org.hibernate.criterion.Projections;
import org.hibernate.criterion.Restrictions;
import org.springframework.beans.factory.annotation.Autowired;
+import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.persist.DbUtils;
/**
@@ -21,273 +23,302 @@ import lcsb.mapviewer.persist.DbUtils;
*/
public abstract class BaseDao<T> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(BaseDao.class);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(BaseDao.class);
- /**
- * Sometimes objects have a flag that indicate that the object was removed
- * from the system (but is still there because of foreign keys etc). This
- * column determines the name of the column. If its set to null then such
- * column doesn't exist.
- */
- private String removableColumn = null;
+ /**
+ * Sometimes objects have a flag that indicate that the object was removed from
+ * the system (but is still there because of foreign keys etc). This column
+ * determines the name of the column. If its set to null then such column
+ * doesn't exist.
+ */
+ private String removableColumn = null;
- /**
- * Class of the object that DAO works on.
- */
- private Class<? extends T> clazz;
+ /**
+ * Class of the object that DAO works on.
+ */
+ private Class<? extends T> clazz;
- /**
- * Default constructor.
- *
- * @param theClass
- * class of the object that DAO will work on
- */
- public BaseDao(Class<? extends T> theClass) {
- this.clazz = theClass;
- }
+ /**
+ * Default constructor.
+ *
+ * @param theClass
+ * class of the object that DAO will work on
+ */
+ public BaseDao(Class<? extends T> theClass) {
+ this.clazz = theClass;
+ }
- /**
- * Default constructor.
- *
- * @param theClass
- * class of the object that DAO will work on
- * @param removableColumn
- * determines the column in the object table that indicates if object
- * should be considered as removed or not (see also:
- * {@link #removableColumn}.
- *
- */
- public BaseDao(Class<? extends T> theClass, String removableColumn) {
- this(theClass);
- this.removableColumn = removableColumn;
- }
+ /**
+ * Default constructor.
+ *
+ * @param theClass
+ * class of the object that DAO will work on
+ * @param removableColumn
+ * determines the column in the object table that indicates if object
+ * should be considered as removed or not (see also:
+ * {@link #removableColumn}.
+ *
+ */
+ public BaseDao(Class<? extends T> theClass, String removableColumn) {
+ this(theClass);
+ this.removableColumn = removableColumn;
+ }
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
- /**
- * Adds object to the database.
- *
- * @param object
- * object to add to database
- */
- public void add(T object) {
- getSession().save(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
+ /**
+ * Adds object to the database.
+ *
+ * @param object
+ * object to add to database
+ */
+ public void add(T object) {
+ getSession().save(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
- /**
- * Flush connection with database.
- */
- public void flush() {
- getSession().flush();
- }
+ /**
+ * Flush connection with database.
+ */
+ public void flush() {
+ getSession().flush();
+ }
- /**
- * Commit current transaction.
- */
- public void commit() {
- if (!dbUtils.isCustomSessionForCurrentThread()) {
- logger.warn("Manual commit with spring managed session!", new Exception());
- }
+ /**
+ * Commit current transaction.
+ */
+ public void commit() {
+ if (!dbUtils.isCustomSessionForCurrentThread()) {
+ logger.warn("Manual commit with spring managed session!", new Exception());
+ }
- getSession().getTransaction().commit();
- getSession().beginTransaction();
- }
+ getSession().getTransaction().commit();
+ getSession().beginTransaction();
+ }
- /**
- * Returns current session.
- *
- * @return session for current thread
- */
- protected Session getSession() {
- return dbUtils.getSessionForCurrentThread();
- }
+ /**
+ * Returns current session.
+ *
+ * @return session for current thread
+ */
+ protected Session getSession() {
+ return dbUtils.getSessionForCurrentThread();
+ }
- /**
- * Update object in the database.
- *
- * @param object
- * object to be updated
- */
- public void update(T object) {
- getSession().update(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
+ /**
+ * Update object in the database.
+ *
+ * @param object
+ * object to be updated
+ */
+ public void update(T object) {
+ getSession().update(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
- /**
- * Removes object from the database.
- *
- * @param object
- * object to be removed from database
- */
- public void delete(T object) {
- getSession().delete(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
+ /**
+ * Removes object from the database.
+ *
+ * @param object
+ * object to be removed from database
+ */
+ public void delete(T object) {
+ getSession().delete(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
- /**
- * "Disconnects" object with the element in database. From this point on we
- * cannot update/delete it in the database.
- *
- * @param object
- * object that should be evicted
- */
- public void evict(T object) {
- getSession().evict(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
+ /**
+ * "Disconnects" object with the element in database. From this point on we
+ * cannot update/delete it in the database.
+ *
+ * @param object
+ * object that should be evicted
+ */
+ public void evict(T object) {
+ getSession().evict(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
- /**
- * Returns number of elements in the table for this object.
- *
- * @return number of all elements in database
- */
- public long getCount() {
- if (removableColumn == null) {
- return (Long) getSession().createCriteria(this.clazz).setProjection(Projections.rowCount()).uniqueResult();
- } else {
- return (Long) getSession().createCriteria(this.clazz).add(Restrictions.eq(removableColumn, false)).setProjection(Projections.rowCount()).uniqueResult();
- }
- }
+ /**
+ * Returns number of elements in the table for this object.
+ *
+ * @return number of all elements in database
+ */
+ public long getCount() {
+ if (removableColumn == null) {
+ return (Long) getSession().createCriteria(this.clazz).setProjection(Projections.rowCount()).uniqueResult();
+ } else {
+ return (Long) getSession().createCriteria(this.clazz).add(Restrictions.eq(removableColumn, false))
+ .setProjection(Projections.rowCount()).uniqueResult();
+ }
+ }
- /**
- * Returns an element that has a key parameter equal to value. If there is
- * more than one element than one of them will be returned. If there is no
- * such element then <code>null</code> is returned.
- *
- * @param key
- * which parameter will filter the data
- * @param value
- * what must be the value of parameter key
- * @return element that fulfill T.key=value criteria
- */
- @SuppressWarnings("unchecked")
- protected T getByParameter(String key, Object value) {
- List<?> list = getSession()
- .createQuery(" from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant()).setParameter("param_val", value)
- .list();
- if (list.size() == 0) {
- return null;
- } else {
- return (T) list.get(0);
- }
- }
+ /**
+ * Returns an element that has a key parameter equal to value. If there is more
+ * than one element than one of them will be returned. If there is no such
+ * element then <code>null</code> is returned.
+ *
+ * @param key
+ * which parameter will filter the data
+ * @param value
+ * what must be the value of parameter key
+ * @return element that fulfill T.key=value criteria
+ */
+ @SuppressWarnings("unchecked")
+ protected T getByParameter(String key, Object value) {
+ List<?> list = getSession()
+ .createQuery(
+ " from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant())
+ .setParameter("param_val", value).list();
+ if (list.size() == 0) {
+ return null;
+ } else {
+ return (T) list.get(0);
+ }
+ }
- /**
- * Returns the list of elements that havae a key parameter equal to value.
- *
- * @param key
- * which parameter will filter the data
- * @param value
- * what must be the value of parameter key
- * @return list of elements that fulfill T.key=value criteria
- */
- @SuppressWarnings("unchecked")
- protected List<T> getElementsByParameter(String key, Object value) {
- List<?> list = getSession()
- .createQuery(" from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant()).setParameter("param_val", value)
- .list();
- return (List<T>) list;
- }
+ /**
+ * Returns the list of elements that have a key parameter equal to value.
+ *
+ * @param key
+ * which parameter will filter the data
+ * @param value
+ * what must be the value of parameter key
+ * @return list of elements that fulfill T.key=value criteria
+ */
+ @SuppressWarnings("unchecked")
+ protected List<T> getElementsByParameter(String key, Object value) {
+ List<?> list = getSession()
+ .createQuery(
+ " from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant())
+ .setParameter("param_val", value).list();
+ return (List<T>) list;
+ }
- /**
- * Returns element with the id given as parameter.
- *
- * @param id
- * database identifier
- * @return object width identifier given as parameter
- */
- @SuppressWarnings("unchecked")
- public T getById(int id) {
- List<?> list = getSession().createQuery(" from " + this.clazz.getSimpleName() + " where id=? " + removableAndStatemant()).setParameter(0, id).list();
- if (list.size() == 0) {
- return null;
- } else {
- return (T) list.get(0);
- }
- }
+ @SuppressWarnings("unchecked")
+ protected List<T> getElementsByParameters(List<Pair<String, Object>> params) {
+ String queryString = " from " + this.clazz.getSimpleName() + " where ";
+ boolean firstParam = true;
+ for (Pair<String, Object> param : params) {
+ String key = param.getLeft();
+ if (!firstParam) {
+ queryString += " AND ";
+ }
+ queryString += key + " = :param_val_" + key + " ";
- /**
- * Returns list of all object in db.
- *
- * @return list of all object in db
- */
- @SuppressWarnings("unchecked")
- public List<T> getAll() {
- List<?> list = getSession().createQuery(" from " + this.clazz.getSimpleName() + " " + removableStatemant()).list();
- return (List<T>) list;
- }
+ firstParam = false;
+ }
+ queryString += removableAndStatemant();
+ Query query = getSession().createQuery(queryString);
+ for (Pair<String, Object> param : params) {
+ String key = param.getLeft();
+ Object value = param.getRight();
+ query = query.setParameter("param_val_" + key, value);
+ }
+ List<?> list = query.list();
+ return (List<T>) list;
+ }
- /**
- * Removes all elements from the database.
- */
- public void clearTable() {
- String stringQuery = "DELETE FROM " + this.clazz.getSimpleName();
- getSession().createQuery(stringQuery).executeUpdate();
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
+ /**
+ * Returns element with the id given as parameter.
+ *
+ * @param id
+ * database identifier
+ * @return object width identifier given as parameter
+ */
+ @SuppressWarnings("unchecked")
+ public T getById(int id) {
+ List<?> list = getSession()
+ .createQuery(" from " + this.clazz.getSimpleName() + " where id=? " + removableAndStatemant())
+ .setParameter(0, id).list();
+ if (list.size() == 0) {
+ return null;
+ } else {
+ return (T) list.get(0);
+ }
+ }
- /**
- * Refresh object with the new data taken from database.
- *
- * @param object
- * object to be refreshed
- */
- public void refresh(Object object) {
- getSession().refresh(object);
- }
+ /**
+ * Returns list of all object in db.
+ *
+ * @return list of all object in db
+ */
+ @SuppressWarnings("unchecked")
+ public List<T> getAll() {
+ List<?> list = getSession().createQuery(" from " + this.clazz.getSimpleName() + " " + removableStatemant()).list();
+ return (List<T>) list;
+ }
- /**
- * @return the clazz
- */
- protected Class<? extends T> getClazz() {
- return clazz;
- }
+ /**
+ * Removes all elements from the database.
+ */
+ public void clearTable() {
+ String stringQuery = "DELETE FROM " + this.clazz.getSimpleName();
+ getSession().createQuery(stringQuery).executeUpdate();
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
- /**
- * Returns part of HQL statement responsible for {@link #removableColumn}.
- *
- * @return part of HQL statement responsible for {@link #removableColumn}.
- */
- protected String removableAndStatemant() {
- if (removableColumn == null) {
- return "";
- } else {
- return " AND " + removableColumn + " = false ";
- }
- }
+ /**
+ * Refresh object with the new data taken from database.
+ *
+ * @param object
+ * object to be refreshed
+ */
+ public void refresh(Object object) {
+ getSession().refresh(object);
+ }
- /**
- * Returns part of HQL statement responsible for {@link #removableColumn}
- * (without sql AND).
- *
- * @return part of HQL statement responsible for {@link #removableColumn}
- * (without sql AND).
- */
- protected String removableStatemant() {
- if (removableColumn == null) {
- return "";
- } else {
- return " WHERE " + removableColumn + " = false ";
- }
- }
+ /**
+ * @return the clazz
+ */
+ protected Class<? extends T> getClazz() {
+ return clazz;
+ }
+
+ /**
+ * Returns part of HQL statement responsible for {@link #removableColumn}.
+ *
+ * @return part of HQL statement responsible for {@link #removableColumn}.
+ */
+ protected String removableAndStatemant() {
+ if (removableColumn == null) {
+ return "";
+ } else {
+ return " AND " + removableColumn + " = false ";
+ }
+ }
+
+ /**
+ * Returns part of HQL statement responsible for {@link #removableColumn}
+ * (without sql AND).
+ *
+ * @return part of HQL statement responsible for {@link #removableColumn}
+ * (without sql AND).
+ */
+ protected String removableStatemant() {
+ if (removableColumn == null) {
+ return "";
+ } else {
+ return " WHERE " + removableColumn + " = false ";
+ }
+ }
}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
index 11fb912fdff420b04c871a2f3979c9c9a3742a6a..e464248cdda8d07df887438b05d64d76336474f2 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
@@ -1,86 +1,101 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.hibernate.Criteria;
-import org.hibernate.criterion.Projections;
-import org.hibernate.criterion.Restrictions;
-
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link Layout} class.
- *
- * @author Piotr Gawron
- *
- */
-public class LayoutDao extends BaseDao<Layout> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayoutDao.class);
-
- /**
- * Default constructor.
- */
- public LayoutDao() {
- super(Layout.class);
- }
-
- /**
- * Lists layouts for the model.
- *
- * @param model
- * for this model layouts will be listed
- * @return list of layouts for the model
- */
- public List<Layout> getLayoutsByModel(Model model) {
- List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
- for (Layout layout : layouts) {
- refresh(layout);
- }
- return layouts;
- }
-
- /**
- * Return number of layouts created by the user.
- *
- * @param user
- * the user
- * @return number of layouts created by the user
- */
- public long getCountByUser(User user) {
- Criteria crit = getSession().createCriteria(this.getClazz());
- crit.setProjection(Projections.rowCount());
- crit.add(Restrictions.eq("creator", user));
- crit.createAlias("model", "m");
- crit.add(Restrictions.sizeLe("m.parentModels", 0));
- return (Long) crit.uniqueResult();
- }
-
- /**
- * Returns layout identified by name and model.
- *
- * @param model
- * model where the layouts lay on
- * @param name
- * name of the layout
- * @return layout
- */
- public Layout getLayoutByName(Model model, String name) {
- List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
- for (Layout layout : layouts) {
- refresh(layout);
- if (layout.getTitle().equals(name)) {
- return layout;
- }
- }
- return null;
- }
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.hibernate.Criteria;
+import org.hibernate.criterion.Projections;
+import org.hibernate.criterion.Restrictions;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link Layout} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LayoutDao extends BaseDao<Layout> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayoutDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public LayoutDao() {
+ super(Layout.class);
+ }
+
+ /**
+ * Lists layouts for the model.
+ *
+ * @param model
+ * for this model layouts will be listed
+ * @return list of layouts for the model
+ */
+ public List<Layout> getLayoutsByModel(Model model) {
+ List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
+ for (Layout layout : layouts) {
+ refresh(layout);
+ }
+ return layouts;
+ }
+
+ public List<Layout> getLayoutsByModel(Model model, User creator, Boolean isPublic) {
+ List<Pair<String, Object>> params = new ArrayList<>();
+ params.add(new Pair<String, Object>("model_iddb", model.getId()));
+ if (isPublic != null) {
+ params.add(new Pair<String, Object>("publicLayout", isPublic));
+ }
+ if (creator != null) {
+ params.add(new Pair<String, Object>("creator_iddb", creator.getId()));
+ }
+ List<Layout> layouts = getElementsByParameters(params);
+ return layouts;
+ }
+
+ /**
+ * Return number of layouts created by the user.
+ *
+ * @param user
+ * the user
+ * @return number of layouts created by the user
+ */
+ public long getCountByUser(User user) {
+ Criteria crit = getSession().createCriteria(this.getClazz());
+ crit.setProjection(Projections.rowCount());
+ crit.add(Restrictions.eq("creator", user));
+ crit.createAlias("model", "m");
+ crit.add(Restrictions.sizeLe("m.parentModels", 0));
+ return (Long) crit.uniqueResult();
+ }
+
+ /**
+ * Returns layout identified by name and model.
+ *
+ * @param model
+ * model where the layouts lay on
+ * @param name
+ * name of the layout
+ * @return layout
+ */
+ public Layout getLayoutByName(Model model, String name) {
+ List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
+ for (Layout layout : layouts) {
+ refresh(layout);
+ if (layout.getTitle().equals(name)) {
+ return layout;
+ }
+ }
+ return null;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index ddc1e5f3bcd551a012a6e360d367029ab974f488..53762ae79f0123483f6d6c1eaa8ba46052fb9de8 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -107,7 +107,7 @@ public class LayoutService implements ILayoutService {
/**
* Service used to access logs.
- *
+ *
* @see ILogService
*/
@Autowired
@@ -171,31 +171,14 @@ public class LayoutService implements ILayoutService {
}
@Override
- public List<LayoutView> getCustomLayouts(Model model, User user, Boolean publicOverlay, User creator) {
+ public List<LayoutView> getCustomLayouts(Model model, User user) {
List<LayoutView> result = new ArrayList<>();
if (model == null || user == null) {
return result;
}
- List<Layout> layouts = layoutDao.getLayoutsByModel(model);
+ List<Layout> layouts = layoutDao.getLayoutsByModel(model, user, false);
for (Layout layout : layouts) {
- boolean toAdd = true;
- if (creator != null) {
- if (layout.getCreator() == null) {
- toAdd = false;
- } else if (!layout.getCreator().getId().equals(creator.getId())) {
- toAdd = false;
- }
- }
- if (publicOverlay != null) {
- if (!publicOverlay.equals(layout.isPublicLayout())) {
- toAdd = false;
- }
- }
- if (toAdd) {
- if (userCanViewOverlay(layout, user)) {
- result.add(layoutViewFactory.create(layout));
- }
- }
+ result.add(layoutViewFactory.create(layout));
}
Collections.sort(result, LayoutView.ID_COMPARATOR);
return result;
@@ -648,7 +631,7 @@ public class LayoutService implements ILayoutService {
/**
* Sends notification email that layout was removed.
- *
+ *
* @param projectId
* identifier of the project
* @param layoutName
@@ -667,7 +650,7 @@ public class LayoutService implements ILayoutService {
/**
* Sends notification email that layout was generated.
- *
+ *
* @param params
* list of {@link CreateLayoutParams params} used for layout creation
* @param schemas
@@ -706,7 +689,7 @@ public class LayoutService implements ILayoutService {
/**
* Prepares table with statistics about coloring.
- *
+ *
* @param schemas
* schemas that were used for coloring
* @param scr
@@ -738,7 +721,7 @@ public class LayoutService implements ILayoutService {
* {@link ColorSchema} sometimes contains merged value from few rows. This
* method split single {@link ColorSchema} object to simple flat objects that
* can be serialiazed in a simple tab separated file.
- *
+ *
* @param originalSchema
* original {@link ColorSchema} objcet that we want to spli into flat
* objects
@@ -763,7 +746,7 @@ public class LayoutService implements ILayoutService {
/**
* Prepares tab separated {@link String} represenation of {@link ColorSchema}.
- *
+ *
* @param columns
* columns that should be outputed in the result String
* @param schema
@@ -791,7 +774,7 @@ public class LayoutService implements ILayoutService {
/**
* Returns String representing data of {@link GenericColorSchema} that should
* appear in a given {@link ColorSchemaColumn}.
- *
+ *
* @param schema
* object for which data will be returned
* @param column
@@ -846,7 +829,7 @@ public class LayoutService implements ILayoutService {
/**
* Returns String representing data of {@link GeneVariationColorSchema} that
* should appear in a given {@link ColorSchemaColumn}.
- *
+ *
* @param schema
* object for which data will be returned
* @param column
@@ -921,7 +904,7 @@ public class LayoutService implements ILayoutService {
/**
* Returns byte array containing data from original input file that was used to
* generate the layout.
- *
+ *
* @param layoutId
* identifier of layout for which we want to retrieve original file
* data
diff --git a/web/src/main/webapp/index.xhtml b/web/src/main/webapp/index.xhtml
index 7dd60ad0c641af31c616d06de5529e70948704bd..4173a0d9b725208930f7bba7f48de251ed0d5583 100644
--- a/web/src/main/webapp/index.xhtml
+++ b/web/src/main/webapp/index.xhtml
@@ -38,7 +38,7 @@ function initMap(){
customMap = result;
document.title = result.getProject().getName();
}).catch(function(rejectReason){
- minerva.GuiConnector.alert(rejectReason);
+ minerva.GuiConnector.alert(rejectReason, true);
});
}