diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs
index 4c28b1a898a0f0bc507b93f8f5393d172709fe73..4824b8026319a8fb303971008a7d59a816d58bd6 100644
--- a/.settings/org.eclipse.core.resources.prefs
+++ b/.settings/org.eclipse.core.resources.prefs
@@ -1,4 +1,2 @@
eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding//src/test/java=UTF-8
encoding/<project>=UTF-8
diff --git a/CellDesigner-plugin/src/main/resources/empty.txt b/CellDesigner-plugin/src/main/resources/empty.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e45f025b4e3a8b4af265accb372955b7774d589f
--- /dev/null
+++ b/CellDesigner-plugin/src/main/resources/empty.txt
@@ -0,0 +1 @@
+EMPTY file to force git to push the folder
\ No newline at end of file
diff --git a/README.md b/README.md
index ebefb9ef5ec76f5bf38e152f5aca93d1c6982b9f..861648d99c5e64126470d7438abf13c19892bd67 100644
--- a/README.md
+++ b/README.md
@@ -98,6 +98,16 @@ curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" http://pg-sandbox.uni.lu/mine
```
#### (sub)Maps
+* List of (sub)maps in a project
+ * URL: `/projects/{projectId}/models/`
+ * Method: GET
+ * Parameters:
+ * `projectId` - identifier of the project
+ * Example:
+```
+curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxxxx" "http://pg-sandbox.uni.lu/minerva/api/projects/pdmap_dec15/models/"
+```
+
* Download map as a model file (ie. in CellDesigner format)
* URL: `/projects/{projectId}/models/{modelId}:downloadModel`
* Method: GET
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
index 697ad02a904a580178ce464bb012bce957264988..e8e58449730796316d63035ba6726cad84e9cc1b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
@@ -112,11 +112,15 @@ public class Drug implements Serializable, TargettingStructure {
for (Target t : targets) {
if (t.getSource() != null) {
result.append(t.getSource().getResource() + "|" + t.getName() + "|" + t.getGenes());
+ } else {
+ result.append("N/A |" + t.getName() + "|" + t.getGenes());
}
- result.append("\nReferences:");
+ result.append(" (References:");
for (MiriamData md : t.getReferences()) {
- result.append(md.getResource());
+ result.append(md.getResource() + ",");
}
+ result.append(")+\n");
+
}
return result.toString();
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 7cae5de69da970c92262fe42c47ea5c0be0d4203..45c6daa1ebe3375bfb63983866742ab91bd960b3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.annotation.services;
import java.io.IOException;
import java.net.URLEncoder;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -111,11 +112,6 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
@Autowired
private HgncAnnotator hgncAnnotator;
- /**
- * Object used to access information about organism taxonomy.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
/**
* Default constructor.
@@ -180,7 +176,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("organism")) {
// node with information abou organism
- target.setOrganism(taxonomyBackend.getByName(node.getTextContent()));
+ target.setOrganism(getTaxonomyBackend().getByName(node.getTextContent()));
} else if (node.getNodeName().equalsIgnoreCase("pref_name")) {
// node with information about name
target.setName(node.getTextContent());
@@ -541,9 +537,9 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
@Override
- public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
- List<Drug> result = new ArrayList<Drug>();
- List<MiriamData> uniprotData = new ArrayList<MiriamData>();
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ List<MiriamData> uniprotData = new ArrayList<>();
if (MiriamType.HGNC_SYMBOL.equals(target.getDataType())) {
try {
uniprotData = hgncAnnotator.hgncToUniprot(target);
@@ -561,7 +557,10 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
logger.warn("Too many uniprot ids. Only first will be taken");
}
try {
- String page = getWebPageContent(URL_TARGET_FROM_UNIPROT + uniprotData.get(0).getResource());
+ String url = URL_TARGET_FROM_UNIPROT + uniprotData.get(0).getResource();
+ logger.debug(url);
+
+ String page = getWebPageContent(url);
Set<String> drugNames = new HashSet<>();
Document document = getXmlDocumentFromString(page);
@@ -573,14 +572,17 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
Node node = nodeList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("target")) {
- Node chemblTargetIdNode = getNode("target_chembl_id", node);
- MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
- List<Drug> drugs = getDrugsByChemblTarget(targetMiriam);
- for (Drug drug : drugs) {
- // don't add duplicates
- if (!drugNames.contains(drug.getName())) {
- drugNames.add(drug.getName());
- result.add(drug);
+ String organismName = getNode("organism", node).getTextContent();
+ if (organismMatch(organismName, organisms)) {
+ Node chemblTargetIdNode = getNode("target_chembl_id", node);
+ MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
+ List<Drug> drugs = getDrugsByChemblTarget(targetMiriam);
+ for (Drug drug : drugs) {
+ // don't add duplicates
+ if (!drugNames.contains(drug.getName())) {
+ drugNames.add(drug.getName());
+ result.add(drug);
+ }
}
}
}
@@ -597,6 +599,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
+
/**
* Returns list of drugs found by target identified in the paramter.
*
@@ -664,23 +667,6 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
super.setWebPageDownloader(webPageDownloader);
}
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- protected TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- protected void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
/**
* @return the hgncAnnotator
* @see #hgncAnnotator
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 74e38ec3bfe6defa7e5fe0c90198a253b4d56a3c..df03d1175cb14e1d072df7f3eb0649473bf1d2b6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -12,6 +12,7 @@ import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.apache.commons.lang3.SerializationException;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Node;
@@ -353,8 +354,12 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
// look for chemical in the cache
Node chemicalNode = super.getCacheNode(getIdentifier(diseaseID, chemicalId));
if (chemicalNode != null && chemicalNode.hasChildNodes()) {
- result = chemicalSerializer.xmlToObject(chemicalNode);
- return result;
+ try {
+ result = chemicalSerializer.xmlToObject(chemicalNode);
+ return result;
+ } catch (SerializationException e) {
+ logger.error(e, e);
+ }
}
try {
String diseaseQuery = DISEASE_URL + diseaseID.getResource();
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
index 64d4f11adc23464be114a36f4f4eb37902a1f814..5e8ca1b99ace1e532f9a70cf9ab6648713e14031 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
@@ -6,10 +6,14 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
/**
* Abstract class with some functionalities used by class accessing drug
@@ -20,11 +24,22 @@ import lcsb.mapviewer.model.map.MiriamData;
*/
public abstract class DrugAnnotation extends CachableInterface {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(DrugAnnotation.class);
+
/**
* Object that allows to serialize {@link Drug} elements into xml string and
* deserialize xml into {@link Drug} objects.
*/
- private XmlSerializer<Drug> drugSerializer;
+ private XmlSerializer<Drug> drugSerializer;
+
+ /**
+ * Object used to access information about organism taxonomy.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
/**
* Default constructor. Initializes structures used for transforming
@@ -54,12 +69,28 @@ public abstract class DrugAnnotation extends CachableInterface {
*
* @param target
* {@link MiriamData} describing target
+ * @param organisms
+ * list of organisms to which results should be limited (when no
+ * organisms defined filtering will be turned off)
* @return list of drugs
* @throws DrugSearchException
* thrown when there are problems with finding drug
*/
- public abstract List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException;
+ public abstract List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) throws DrugSearchException;
+
+ /**
+ * Returns list of drugs that target protein.
+ *
+ * @param target
+ * {@link MiriamData} describing target
+ * @return list of drugs
+ * @throws DrugSearchException
+ * thrown when there are problems with finding drug
+ */
+ public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
+ return getDrugListByTarget(target, new ArrayList<>());
+ }
/**
* Returns list of drugs that target at least one protein from the parameter
@@ -67,11 +98,14 @@ public abstract class DrugAnnotation extends CachableInterface {
*
* @param targets
* list of {@link MiriamData} describing targets
+ * @param organisms
+ * list of organisms to which results should be limited (when no
+ * organisms defined filtering will be turned off)
* @return list of drugs
* @throws DrugSearchException
* thrown when there are problems with connection to drug database
*/
- public List<Drug> getDrugListByTargets(Collection<MiriamData> targets) throws DrugSearchException {
+ public List<Drug> getDrugListByTargets(Collection<MiriamData> targets, Collection<MiriamData> organisms) throws DrugSearchException {
List<Drug> result = new ArrayList<Drug>();
Set<String> set = new HashSet<String>();
Set<MiriamData> searchedResult = new HashSet<MiriamData>();
@@ -80,7 +114,7 @@ public abstract class DrugAnnotation extends CachableInterface {
continue;
}
searchedResult.add(md);
- List<Drug> drugs = getDrugListByTarget(md);
+ List<Drug> drugs = getDrugListByTarget(md, organisms);
for (Drug drug : drugs) {
if (!set.contains(drug.getSources().get(0).getResource())) {
result.add(drug);
@@ -93,6 +127,20 @@ public abstract class DrugAnnotation extends CachableInterface {
return result;
}
+ /**
+ * Returns list of drugs that target at least one protein from the parameter
+ * list.
+ *
+ * @param targets
+ * list of {@link MiriamData} describing targets
+ * @return list of drugs
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to drug database
+ */
+ public List<Drug> getDrugListByTargets(Collection<MiriamData> targets) throws DrugSearchException {
+ return getDrugListByTargets(targets, new ArrayList<>());
+ }
+
/**
* @return the drugSerializer
* @see #drugSerializer
@@ -110,4 +158,46 @@ public abstract class DrugAnnotation extends CachableInterface {
this.drugSerializer = drugSerializer;
}
+ /**
+ * Checks if organism name matches list of organisms.
+ *
+ * @param organismName
+ * name of the organism (should be something recognizable by
+ * {@link MiriamType#TAXONOMY} db).
+ * @param organisms
+ * list of organisms
+ * @return <code>false</code> if organisName couldn't be found in organisms
+ * list. If organismName is null or empty or list of organisms is
+ * empty true will be returned
+ */
+ protected boolean organismMatch(String organismName, Collection<MiriamData> organisms) {
+ if (organismName == null || organismName.isEmpty() || organisms.size() == 0) {
+ return true;
+ }
+ try {
+ MiriamData organism = taxonomyBackend.getByName(organismName);
+ return organisms.contains(organism);
+ } catch (TaxonomySearchException e) {
+ logger.error("Problem with taxonomy search for: " + organismName, e);
+ return true;
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index cb9b4ac8032611e54f010bf40c662521b5f111be..de70f2f49512d700cc2a4348d59833f1168a960d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -1,8 +1,10 @@
package lcsb.mapviewer.annotation.services;
import java.io.IOException;
+import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -107,12 +109,6 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
*/
private Pattern targetPattern = Pattern.compile("(?<=\"/biodb/bio_entities/)([\\s\\S]*?)(?=\")");
- /**
- * Object used to access information about organism taxonomy.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
/**
* Default constructor.
*/
@@ -305,79 +301,41 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
List<Target> getTargetsForDrug(String page) throws DrugSearchException {
List<Target> result = new ArrayList<>();
try {
- int i, j;
+ int pageStart;
Target target = new Target();
target.setType(TargetType.SINGLE_PROTEIN);
- i = page.indexOf("<div class=\"target well well");
+ pageStart = page.indexOf("<div class=\"target well well");
int end = page.indexOf("<div class=\"enzyme well well");
if (end < 0) {
- end = page.indexOf("<tr id=\"comments\">");
+ end = page.indexOf("<div class=\"carrier well well");
if (end < 0) {
- end = page.length() - 1;
+ end = page.indexOf("<div class=\"transporter well well");
+
+ if (end < 0) {
+ end = page.indexOf("<tr id=\"comments\">");
+ if (end < 0) {
+ end = page.length() - 1;
+ }
+ }
}
}
- i = page.indexOf("Details</a></div>", i);
- while (i > 0 && i < end) {
- int kindIndex = page.indexOf("<dt>Kind</dt><dd>", i);
- kindIndex += "<dt>Kind</dt><dd>".length();
- int endKindIndex = page.indexOf("</dd>", kindIndex);
- String type = "";
- if (kindIndex > 0 && endKindIndex > kindIndex) {
- type = page.substring(kindIndex, endKindIndex);
+ pageStart = page.indexOf("Details</a></div>", pageStart);
+ while (pageStart > 0 && pageStart < end) {
+ int targetStart = page.indexOf("</div><strong>", pageStart);
+ int nextTargetStart = page.indexOf("</div><strong>", targetStart + 1);
+ if (nextTargetStart < 0) {
+ nextTargetStart = end;
}
- if (type.trim().equalsIgnoreCase("Protein")) {
- i = page.indexOf("/biodb/polypeptides/", i);
- i += "/biodb/polypeptides/".length();
- target = new Target();
- target.setType(TargetType.SINGLE_PROTEIN);
-
- // Getting ID && Name
- j = page.indexOf('"', i);
- String uniprotId = page.substring(i, j);
- MiriamData uniprotTarget = new MiriamData(MiriamType.UNIPROT, uniprotId);
- MiriamData hgncTarget = uniprotAnnotator.uniProtToHgnc(uniprotTarget);
- if (hgncTarget != null) {
- target.addGene(hgncTarget);
- } else {
- target.addGene(uniprotTarget);
- }
- i = j + 2;
- j = page.indexOf("</", i);
- String name = StringEscapeUtils.unescapeHtml4(page.substring(i, j));
- target.setName(name);
-
- // Getting Organism
- i = page.indexOf("Organism</dt><dd>", i);
- i = i + "Organism</dt><dd>".length();
- j = page.indexOf("</dd>", i);
- target.setOrganism(taxonomyBackend.getByName(page.substring(i, j)));
-
- // Getting References
- i = page.indexOf("<strong>References</strong>", i);
- if (i > 0 && i < end) {
- int nextI = Math.min(page.indexOf("Details</a></div>", i), end);
- if (nextI < 0) {
- nextI = end;
- }
- target.addReferences(getPubmedFromRef(page.substring(i, nextI)));
- i = nextI;
- } else {
- i = end;
- }
+ target = parseTarget(page.substring(targetStart, nextTargetStart));
+ if (target != null) {
result.add(target);
- } else {
- i = kindIndex;
- logger.warn("Unknown target type: " + type + ". Skipping.");
- int nextI = Math.min(page.indexOf("Details</a></div>", i), end);
- if (nextI < 0) {
- nextI = end;
- }
- i = nextI;
}
+ pageStart = nextTargetStart;
+
}
} catch (TaxonomySearchException e) {
throw new DrugSearchException("Problem with finidng information about organism", e);
@@ -387,6 +345,67 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
return result;
}
+ /**
+ * Parse html info about target into {@link Target} structure.
+ *
+ * @param htmlPage
+ * string with html content
+ * @return {@link Target} for given html content
+ * @throws UniprotSearchException
+ * thrown when there is a problem with accessing uniprot db
+ * @throws TaxonomySearchException
+ * thrown when there is a problem with accessing taxonomy db
+ */
+ protected Target parseTarget(String htmlPage) throws UniprotSearchException, TaxonomySearchException {
+ int kindIndex = htmlPage.indexOf("<dt>Kind</dt><dd>");
+ kindIndex += "<dt>Kind</dt><dd>".length();
+ int endKindIndex = htmlPage.indexOf("</dd>");
+ String type = "";
+ if (kindIndex > 0 && endKindIndex > kindIndex) {
+ type = htmlPage.substring(kindIndex, endKindIndex);
+ }
+ if (type.trim().equalsIgnoreCase("Protein")) {
+ int uniprotIdStart = htmlPage.indexOf("/biodb/polypeptides/") + "/biodb/polypeptides/".length();
+ Target result = new Target();
+ result.setType(TargetType.SINGLE_PROTEIN);
+
+ // Getting ID && Name
+ int uniprotIdEnd = htmlPage.indexOf('"', uniprotIdStart);
+ String uniprotId = htmlPage.substring(uniprotIdStart, uniprotIdEnd);
+ MiriamData uniprotTarget = new MiriamData(MiriamType.UNIPROT, uniprotId);
+ MiriamData hgncTarget = uniprotAnnotator.uniProtToHgnc(uniprotTarget);
+ if (hgncTarget != null) {
+ result.addGene(hgncTarget);
+ } else {
+ result.addGene(uniprotTarget);
+ }
+
+ int nameStart = uniprotIdEnd + 2;
+ int nameEnd = htmlPage.indexOf("</", uniprotIdStart);
+ String name = StringEscapeUtils.unescapeHtml4(htmlPage.substring(nameStart, nameEnd));
+ result.setName(name);
+
+ // Getting Organism
+ int organismStart = htmlPage.indexOf("Organism</dt><dd>", nameEnd) + "Organism</dt><dd>".length();
+ int organismEnd = htmlPage.indexOf("</dd>", organismStart);
+ result.setOrganism(getTaxonomyBackend().getByName(htmlPage.substring(organismStart, organismEnd)));
+
+ // Getting References
+ int referencesStart = htmlPage.indexOf("<strong>References</strong>", organismEnd);
+ if (referencesStart > 0) {
+ int referencesEnd = Math.min(htmlPage.indexOf("Details</a></div>", referencesStart), htmlPage.length());
+ if (referencesEnd < 0) {
+ referencesEnd = htmlPage.length();
+ }
+ result.addReferences(getPubmedFromRef(htmlPage.substring(referencesStart, referencesEnd)));
+ }
+ return result;
+ } else {
+ logger.warn("Unknown target type: " + type + ". Skipping.");
+ return null;
+ }
+ }
+
/**
* Finds information about drug in drugbank database.
*
@@ -414,6 +433,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
result = new Drug();
result.addSource(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK, tmp));
result.setName(super.cleanHtml(findNameInText(inputLine)));
+ break;
}
}
@@ -435,6 +455,10 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
result.setBloodBrainBarrier(getBloodBrainBarrier(page));
result.setApproved(getApproved(page));
+
+ if (!nameMatch(result, name)) {
+ result = null;
+ }
}
} catch (IOException e) {
throw new DrugSearchException(e);
@@ -442,6 +466,35 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
return result;
}
+ /**
+ * Check if drug data mateches with the search name.
+ *
+ * @param drug
+ * drug to be checked
+ * @param name
+ * name of the drug that we were looking for
+ * @return true if if drug data matches with the search name
+ */
+ private boolean nameMatch(Drug drug, String name) {
+ Set<String> foundNames = new HashSet<>();
+ foundNames.add(drug.getName());
+ foundNames.addAll(drug.getSynonyms());
+ foundNames.addAll(drug.getBrandNames());
+ String lowerCaseName;
+ try {
+ lowerCaseName = java.net.URLDecoder.decode(name, "UTF-8").toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ } catch (UnsupportedEncodingException e) {
+ lowerCaseName = name.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ }
+ for (String string : foundNames) {
+ String query = string.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ if (query.contains(lowerCaseName)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
/**
* Finds blood brain barrier info about drug in the webpage content.
*
@@ -554,40 +607,51 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
}
@Override
- public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
- List<Drug> result = new ArrayList<Drug>();
- if (target == null) {
+ public List<Drug> getDrugListByTarget(MiriamData targetMiriamData, Collection<MiriamData> organisms) throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ if (targetMiriamData == null) {
return result;
}
- if (!(MiriamType.HGNC_SYMBOL.equals(target.getDataType()))) {
+ if (!(MiriamType.HGNC_SYMBOL.equals(targetMiriamData.getDataType()))) {
throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL + " type is accepted");
}
- String url = URL_TARGETS + target.getResource();
+ String url = URL_TARGETS + targetMiriamData.getResource();
- String page;
try {
- page = getWebPageContent(url);
- } catch (IOException e) {
- throw new DrugSearchException("Cannot access drug database", e);
- }
+ String page = getWebPageContent(url);
- Set<String> drugNames = new HashSet<String>();
+ Set<String> drugNames = new HashSet<>();
- Matcher matcher = targetPattern.matcher(page);
- while (matcher.find()) {
- String drugbankTargetId = matcher.group(0);
- drugNames.addAll(getDrugNamesForTarget(new MiriamData(MiriamType.DRUGBANK_TARGET_V4, drugbankTargetId), target));
- }
- for (String string : drugNames) {
- Drug drug = findDrug(string);
- if (drug == null) {
- logger.warn("Cannot find drug that should be there: " + string);
- } else {
- result.add(drug);
+ Matcher matcher = targetPattern.matcher(page);
+ while (matcher.find()) {
+ String drugbankTargetId = matcher.group(0);
+ drugNames.addAll(getDrugNamesForTarget(new MiriamData(MiriamType.DRUGBANK_TARGET_V4, drugbankTargetId), targetMiriamData, organisms));
+ }
+ for (String string : drugNames) {
+ Drug drug = findDrug(string);
+ if (drug == null) {
+ logger.warn("Cannot find drug that should be there: " + string);
+ } else {
+ boolean targets = false;
+ for (Target target : drug.getTargets()) {
+ for (MiriamData gene : target.getGenes()) {
+ if (gene.equals(targetMiriamData)) {
+ targets = true;
+ }
+ }
+ }
+ if (targets) {
+ result.add(drug);
+ } else {
+ logger.debug("Skipping drug that doesn't target required target. Drug name: " + drug.getName() + "; target: " + targetMiriamData);
+ }
+ }
}
- }
- return result;
+ return result;
+ } catch (IOException e) {
+ throw new DrugSearchException("Cannot access drug database", e);
+ }
}
/**
@@ -600,32 +664,36 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
* identifier of the target using {@link MiriamType#HGNC_SYMBOL},
* used for verification if the target really points to proper
* protein/gene
+ * @param organisms
+ * list of organisms to which results should be limited (when no
+ * organisms defined filtering will be turned off)
* @return list of drugs that target this target
* @throws DrugSearchException
* thrown when there are problems with connection to DrugBank
* database
*/
- private Set<String> getDrugNamesForTarget(MiriamData drugbankTarget, MiriamData hgncTarget) throws DrugSearchException {
+ private Set<String> getDrugNamesForTarget(MiriamData drugbankTarget, MiriamData hgncTarget, Collection<MiriamData> organisms) throws DrugSearchException {
if (!MiriamType.DRUGBANK_TARGET_V4.equals(drugbankTarget.getDataType())) {
throw new InvalidArgumentException("drugbankTarget must be of type: " + MiriamType.DRUGBANK_TARGET_V4);
}
try {
- Set<String> drugNames = new HashSet<String>();
+ Set<String> drugNames = new HashSet<>();
+ String url = URL_TARGET_DETAIL + drugbankTarget.getResource();
- String page = getWebPageContent(URL_TARGET_DETAIL + drugbankTarget.getResource());
+ String page = getWebPageContent(url);
- int id = page.indexOf("<th>DrugBank ID</th>");
- if (id < 0) {
+ int idPosition = page.indexOf("<th>DrugBank ID</th>");
+ if (idPosition < 0) {
throw new DrugSearchException("Problematic web page for target: " + drugbankTarget + "(" + hgncTarget + ")");
}
- int i = page.indexOf("/polypeptides/");
+ int protienLinkPosition = page.indexOf("/polypeptides/");
// sometimes there might not be an element
- if (i >= 0) {
- i = i + "/polypeptides/".length(); // 20;
- int j = page.indexOf('"', i);
- String uniprotId = page.substring(i, j);
+ if (protienLinkPosition >= 0) {
+ protienLinkPosition = protienLinkPosition + "/polypeptides/".length(); // 20;
+ int j = page.indexOf('"', protienLinkPosition);
+ String uniprotId = page.substring(protienLinkPosition, j);
MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId);
MiriamData hgncMiriam = uniprotAnnotator.uniProtToHgnc(uniprotMiriam);
if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
@@ -638,7 +706,18 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
return drugNames;
}
- Matcher matcher = drugNamePattern.matcher(page.substring(id));
+ int organismPosition = page.indexOf("Organism<");
+ if (organismPosition >= 0) {
+ int organismStart = page.indexOf("<td>", organismPosition) + "<td>".length();
+ int organismEnd = page.indexOf("<", organismStart + 1);
+ String organismName = page.substring(organismStart, organismEnd);
+ if (!organismMatch(organismName, organisms)) {
+ logger.debug("Organism doesn't match. Found" + organismName + ". Expected: " + organisms);
+ return drugNames;
+ }
+ }
+
+ Matcher matcher = drugNamePattern.matcher(page.substring(idPosition));
while (matcher.find()) {
drugNames.add(matcher.group(1));
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index 7c28ab4f17f65dc43031067f609509afd2d17ed2..84761857a50fbc4efc25089dc24a2445fd8e7350 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -19,9 +19,9 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * Interface that allows to annotate {@link BioEntity elements} in the
- * system. Different implementation use different resources to perform
- * annotation. They can annotate different types of elements.
+ * Interface that allows to annotate {@link BioEntity elements} in the system.
+ * Different implementation use different resources to perform annotation. They
+ * can annotate different types of elements.
*
* @author Piotr Gawron
*
@@ -31,7 +31,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Default class logger.
*/
- private final Logger logger = Logger.getLogger(ElementAnnotator.class);
+ private final Logger logger = Logger.getLogger(ElementAnnotator.class);
/**
* List of classes that can be annotated by this {@link IElementAnnotator
@@ -42,7 +42,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Should be this annotator used as a default annotator.
*/
- private boolean isDefault = false;
+ private boolean isDefault = false;
/**
* Default constructor.
@@ -61,8 +61,7 @@ public abstract class ElementAnnotator extends CachableInterface {
if (BioEntity.class.isAssignableFrom(validClass)) {
addValidClass((Class<? extends BioEntity>) validClass);
} else {
- throw new InvalidArgumentException(
- "Cannot pass class of type: " + validClass + ". Only classes extending " + BioEntity.class + " are accepted.");
+ throw new InvalidArgumentException("Cannot pass class of type: " + validClass + ". Only classes extending " + BioEntity.class + " are accepted.");
}
}
this.isDefault = isDefault;
@@ -193,7 +192,7 @@ public abstract class ElementAnnotator extends CachableInterface {
List<String> sortedSynonyms = new ArrayList<>();
sortedSynonyms.addAll(synonyms);
Collections.sort(sortedSynonyms);
-
+
element.setSynonyms(sortedSynonyms);
} else {
logger.warn(prefix + "Synonyms don't match: \"" + synonyms + "\", \"" + element.getSynonyms() + "\"");
@@ -227,10 +226,12 @@ public abstract class ElementAnnotator extends CachableInterface {
* value to set
*/
protected void setDescription(BioEntity element, String description) {
- if (element.getNotes() == null || element.getNotes().equals("") || element.getNotes().equals(description)) {
- element.setNotes(description);
- } else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
- element.setNotes(element.getNotes() + "\n" + description);
+ if (description != null) {
+ if (element.getNotes() == null || element.getNotes().equals("") || element.getNotes().equals(description)) {
+ element.setNotes(description);
+ } else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
+ element.setNotes(element.getNotes() + "\n" + description);
+ }
}
}
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 4ac8160718ce1fe15a0f85b6cabbaed1ee1351f7..27cd669cc89e4ef80fd72248a15226dfb7a12941 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
@@ -41,7 +41,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
/**
* Version of the rest API that is supported by this annotator.
*/
- static final String SUPPORTED_VERSION = "6.0";
+ static final String SUPPORTED_VERSION = "6.1";
/**
* Url address of ensembl restfull service.
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 c740c3f3fa0e9fae5d47100b87491e9eb4935292..e4a7a7f4a1d3bcc2424bf920836d942e82385420 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
@@ -140,7 +140,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
result = new Go();
}
- String accessUrl = getMc().getUrlString(md) + "&format=oboxml";
+ String accessUrl = "https://www.ebi.ac.uk/QuickGO-Old/GTerm?id=" + md.getResource() + "&format=oboxml";
try {
String tmp = getWebPageContent(accessUrl);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index cb0f6f29cabaf8446a498780297f37051675ab39..90b26f72ff4c3f6524a35975e7ed10abda0e9bde 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -694,6 +694,34 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
}
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
+ assertNotNull(drugs);
+ assertEquals("No drugs for this organisms should be found", 0, drugs.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testFindDrugsByRepeatingHgncTargets() throws Exception {
try {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
index d80c1c51c617a8802e68cd0eb1cb8b27f6925997..45ca75b80eaba935ebe495c9ddcd5ba7bb905e94 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.assertEquals;
+import java.util.Collection;
import java.util.List;
import org.apache.log4j.Logger;
@@ -47,7 +48,7 @@ public class DrugAnnotationTest extends AnnotationTestFunctions {
}
@Override
- public List<Drug> getDrugListByTarget(MiriamData target) {
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) {
// TODO Auto-generated method stub
return null;
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index fd9c324da1ea09802c52807d9d464f1da6af730e..92e47385e96e2b236654cd938046a279d230d407 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -92,7 +92,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
@Test
- public void test3FindDrug() throws Exception {
+ public void testFindRapamycin() throws Exception {
try {
// finding synonym
Drug rapamycinDrug = drugBankHTMLParser.findDrug("Rapamycin");
@@ -100,8 +100,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
assertEquals("Sirolimus", rapamycinDrug.getName());
assertEquals("DB00877", rapamycinDrug.getSources().get(0).getResource());
assertTrue(rapamycinDrug.getBloodBrainBarrier().equalsIgnoreCase("NO"));
- boolean res = rapamycinDrug.getDescription().contains(
- "A macrolide compound obtained from Streptomyces hygroscopicus that acts by selectively blocking the transcriptional activation of cytokines thereby inhibiting cytokine production. It is bioactive only when bound to immunophilins. Sirolimus is a potent immunosuppressant and possesses both antifungal and antineoplastic properties. [PubChem]");
+ boolean res = rapamycinDrug.getDescription().contains("A macrolide compound obtained from Streptomyces");
assertTrue(res);
assertEquals(3, rapamycinDrug.getTargets().size());
@@ -197,18 +196,6 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
- // at some point this search threw exception
- @Test
- public void testFindDrugKainicAcid() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("kainic acid");
- assertNotNull(test);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testFindDrugAmantadineWithBrandNames() throws Exception {
try {
@@ -302,6 +289,76 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testFindDrugByTFTarget() throws Exception {
+ try {
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "TF"));
+ assertNotNull(drugs);
+ for (Drug drug : drugs) {
+ assertFalse(drug.getName().equalsIgnoreCase("Iron saccharate"));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindAluminiumByName() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("Aluminium");
+ assertTrue(drug.getName().equalsIgnoreCase("Aluminium"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindBIIB054ByName() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("BIIB054");
+ if (drug != null) {
+ // check if are not pointint to BIIB021
+ assertFalse(drug.getSources().get(0).getResource().equalsIgnoreCase("DB12359"));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"), organisms);
+ assertNotNull(drugs);
+ assertEquals("No drugs for this organisms should be found", 0, drugs.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"), organisms);
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testFindDrugByInvalidTarget() throws Exception {
try {
@@ -438,12 +495,30 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
@Test
public void testFindIbuprofen() throws Exception {
try {
- Drug test = drugBankHTMLParser.findDrug("Ibuprofen");
- assertNotNull(test);
- assertEquals("Ibuprofen", test.getName());
- assertEquals("DB01050", test.getSources().get(0).getResource());
- assertNotNull(test.getDescription());
- assertEquals(8, test.getTargets().size());
+ Drug drug = drugBankHTMLParser.findDrug("Ibuprofen");
+ assertNotNull(drug);
+ assertEquals("Ibuprofen", drug.getName());
+ assertEquals("DB01050", drug.getSources().get(0).getResource());
+ assertNotNull(drug.getDescription());
+ assertTrue(drug.getTargets().size() >= 8);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindIronSaccharate() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("Iron saccharate");
+ assertNotNull(drug);
+ MiriamData tfProtein = new MiriamData(MiriamType.HGNC_SYMBOL, "TF");
+ for (Target target : drug.getTargets()) {
+ for (MiriamData md : target.getGenes()) {
+ assertFalse("TF is a carrier, not a target", md.equals(tfProtein));
+ }
+ }
} catch (Exception e) {
e.printStackTrace();
@@ -683,4 +758,13 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
assertEquals(uniprotAnnotator, parser.getUniprotAnnotator());
}
+ @Test
+ public void parseTarget() throws Exception {
+ String content = super.readFile("testFiles/drugbank/target-html-part.html");
+ Target target = drugBankHTMLParser.parseTarget(content);
+ assertNotNull(target);
+ assertEquals(2, target.getReferences().size());
+ assertEquals("Galactoside O-acetyltransferase", target.getName());
+ }
+
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
index a02974da7d865847f035cc1e0541374f4a667b8d..1dac8112d686798431180401071b4f4eb5eefaf0 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
@@ -85,6 +85,14 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
assertEquals(0, getWarnings().size());
}
+ @Test
+ public void testSetEmptyDescription() {
+ GenericProtein species = new GenericProtein("id");
+ species.setNotes("X");
+ annotator.setDescription(species, null);
+ assertEquals("X", species.getNotes());
+ }
+
@Test
public void testSetNotMatchingIchi() {
Ion species = new Ion("id");
diff --git a/annotation/testFiles/drugbank/target-html-part.html b/annotation/testFiles/drugbank/target-html-part.html
new file mode 100644
index 0000000000000000000000000000000000000000..904b85d584b169214b805142c54bcfe4808355a3
--- /dev/null
+++ b/annotation/testFiles/drugbank/target-html-part.html
@@ -0,0 +1 @@
+</div><strong>1. <a href="/biodb/polypeptides/P07464">Galactoside O-acetyltransferase</a></strong></div><div class="panel-body"><dl class="dl-horizontal"><dt>Kind</dt><dd>Protein</dd><dt>Organism</dt><dd>Escherichia coli (strain K12)</dd><dt>Pharmacological action</dt><dd><strong class="label label-warning">unknown</strong></dd></dl><dl class="dl-horizontal"><dt>General Function:</dt><dd>Galactoside o-acetyltransferase activity</dd><dt>Specific Function:</dt><dd>May assist cellular detoxification by acetylating non-metabolizable pyranosides, thereby preventing their reentry into the cell.</dd><dt>Gene Name:</dt><dd>lacA</dd><dt>Uniprot ID:</dt><dd><a target="_blank" class="wishart-link-out" href="http://www.uniprot.org/uniprot/P07464">P07464 <span class="glyphicon glyphicon-new-window"> </span></a></dd><dt>Uniprot Name:</dt><dd>Galactoside O-acetyltransferase</dd><dt>Molecular Weight:</dt><dd>22798.89 Da</dd></dl><h5><strong>References</strong></h5><blockquote class="references"><ol class="cite-this-references"><li id="reference-A1713">Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [<a target="_blank" class="wishart-link-out" href="http://www.ncbi.nlm.nih.gov/pubmed/17139284">PubMed:17139284 <span class="glyphicon glyphicon-new-window"> </span></a>] </li><li id="reference-A1715">Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [<a target="_blank" class="wishart-link-out" href="http://www.ncbi.nlm.nih.gov/pubmed/17016423">PubMed:17016423 <span class="glyphicon glyphicon-new-window"> </span></a>] </li></ol></blockquote></div></div><div class="panel panel-default" id="BE0000574"><div class="panel-heading"><div class="pull-right"><a class="btn btn-primary btn-xs" href="/biodb/polypeptides/P04035"><span class="glyphicon glyphicon-list"> </span> Details</a>
\ No newline at end of file
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 4df8104320ccd3743bcbc57472b3bd42ccc85d28..451deb265f68c530d378655394d234e67e1cec2a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -190,7 +190,10 @@ public class XmlParser {
*/
protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
try {
- return db.parse(stream);
+ synchronized (db) { // DocumentBuilder cannot parse few objects at the
+ // same time
+ return db.parse(stream);
+ }
} catch (SAXException e) {
throw new InvalidXmlSchemaException("Problem with xml parser", e);
} catch (IOException e) {
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
index f76dce4edb7f08ab22821bdf6633a1e4a7bff89a..f78e460818ca7672354874b712036e714d35a789 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -1,6 +1,8 @@
package lcsb.mapviewer.common.geometry;
import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -56,4 +58,17 @@ public class ColorParser {
Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
}
}
+
+ /**
+ * Converts color into list of atributes.
+ *
+ * @param color color to convert
+ * @return map with list of color attributes
+ */
+ public Map<String, Object> colorToMap(Color color) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("alpha", color.getAlpha());
+ result.put("rgb", color.getRGB());
+ return result;
+ }
}
diff --git a/converter-CellDesigner/src/main/resources/empty.txt b/converter-CellDesigner/src/main/resources/empty.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e45f025b4e3a8b4af265accb372955b7774d589f
--- /dev/null
+++ b/converter-CellDesigner/src/main/resources/empty.txt
@@ -0,0 +1 @@
+EMPTY file to force git to push the folder
\ No newline at end of file
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index 036d3b221f8cdf631b18cf7b2a5c5c09f1f50541..fcf44102362777f98200ed90612f1a7c2173dc4d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -68,7 +68,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*
*/
public abstract class AbstractImageGenerator {
-
+
/**
* Class that allows to check if element is visible (or transparent) when
* drawing. It's used to filter out invisible elements when drawing
@@ -205,6 +205,8 @@ public abstract class AbstractImageGenerator {
*/
private Color maxColor = Color.BLACK;
+ private Color simpleColor = Color.BLACK;
+
/**
* @param scale
* scale to set
@@ -533,6 +535,10 @@ public abstract class AbstractImageGenerator {
return maxColor;
}
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
/**
* Returns {@link Color} that should be used for drawing overlays with
* minimum value.
@@ -566,6 +572,17 @@ public abstract class AbstractImageGenerator {
return this;
}
+ /**
+ * @param simpleColor
+ * simpleColor to set
+ * @return object with all parameters
+ * @see #simpleColor
+ */
+ public Params simpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ return this;
+ }
+
/**
* @return the sbgn
* @see #sbgn
@@ -585,6 +602,12 @@ public abstract class AbstractImageGenerator {
return this;
}
+ public Params colorExtractor(ColorExtractor colorExtractor) {
+ return minColor(colorExtractor.getMinColor()).//
+ maxColor(colorExtractor.getMaxColor()).//
+ simpleColor(colorExtractor.getSimpleColor());
+ }
+
}
/**
@@ -653,7 +676,7 @@ public abstract class AbstractImageGenerator {
this.level = params.getLevel();
this.scale = params.getScale();
- colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor());
+ colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
// set border frame extended by a margin
border = new Rectangle2D.Double(
diff --git a/converter-graphics/src/main/resources/empty.txt b/converter-graphics/src/main/resources/empty.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e45f025b4e3a8b4af265accb372955b7774d589f
--- /dev/null
+++ b/converter-graphics/src/main/resources/empty.txt
@@ -0,0 +1 @@
+EMPTY file to force git to push the folder
\ No newline at end of file
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index 59f4964c758ef2dd761a65abd1d6196885e54d99..13aac7e4274322704c0f9a06b4f4c245a59a844d 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -26,7 +26,7 @@ public class ConverterTest {
@Test
public void test() {
try {
- ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED, Color.BLUE);
new BioEntityConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
new BioEntityConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
new BioEntityConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
index 206b3f332fb0d63ef640fdf71e63047a057b906b..68060ae78364070ca6f49d320a3be1e10cb31bc1 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
@@ -27,7 +27,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class BioEntityConverterImplTest {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@AfterClass
public static void tearDownAfterClass() throws Exception {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index 1bdacdc9d7ea94ec4328ca4f6305873286000a4a..3b8f0499b32142579e6ae3bd38d58823a2b4bea4 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class SpeciesConverterTest {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index f5f24088412eedb983923420f2cb1cac7a9f5ea6..6c54f92d23fed16523dfe9f89515ff52b7483d2b 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -40,7 +40,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class ReactionConverterTest extends GraphicsTestFunctions {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/frontend-js/.settings/org.eclipse.core.resources.prefs b/frontend-js/.settings/org.eclipse.core.resources.prefs
index 4c28b1a898a0f0bc507b93f8f5393d172709fe73..4824b8026319a8fb303971008a7d59a816d58bd6 100644
--- a/frontend-js/.settings/org.eclipse.core.resources.prefs
+++ b/frontend-js/.settings/org.eclipse.core.resources.prefs
@@ -1,4 +1,2 @@
eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding//src/test/java=UTF-8
encoding/<project>=UTF-8
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index 20ef80f885b05cda5c056edb2ab4d064f6ef5e35..727a2b54e03f78686e3312f28d23b53758f6aab9 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -137,13 +137,12 @@
border-right: 1px solid #9DE1F8;
}
-.legendBox {
+.minerva-legend {
position: absolute;
bottom: 10px;
right: 10px;
box-shadow: 0 3px 20px #999999;
border-top: 6px solid #017DA7;
- padding-top: 15px;
}
.searchPanel {
@@ -227,16 +226,6 @@
transition: all 0.4s ease-in-out 0s;
}
-.leftPanelClass {
- display: table-cell;
- position: relative;
- float: left;
- border: none;
- background-color: #ffffff;
- width: 357px;
- height: 100%;
-}
-
/* twitter typeahead */
.tt-query /* UPDATE: newer versions use tt-input instead of tt-query */
{
@@ -397,4 +386,95 @@ table.minerva-window-drug-table, table.minerva-window-drug-table th,
table.minerva-window-drug-table td {
padding: 2px;
border: 1px solid black;
+}
+
+.minerva-left-panel {
+ display: table-cell;
+ position: relative;
+ float: left;
+ border: none;
+ background-color: #ffffff;
+ width: 357px;
+ height: 100%;
+}
+
+.minerva-left-panel .minerva-help-button {
+ position: absolute;
+ top: 35px;
+ right: 35px;
+ width: 18px;
+}
+
+.minerva-left-panel .minerva-label, .minerva-element-info-div .minerva-label
+ {
+ font-weight: 900;
+ line-height: 24px;
+}
+
+.minerva-annotation-row-odd {
+ padding: 5px;
+ background-color: #EAEAEA;
+}
+
+.minerva-annotation-row-even {
+ padding: 5px;
+ background-color: #ffffff;
+}
+
+.minerva-overview-button {
+ color: #FFFFFF;
+ height: 36px;
+ line-height: 35px;
+ padding: 0 18px;
+ margin: 0;
+ border: none;
+ background-color: #017DA7;
+ font-size: 13px;
+ font-weight: 900;
+ border-right: 1px solid #9DE1F8;
+ cursor: pointer;
+ transition: background-color 0.4s ease-in-out 0s;
+}
+
+.minerva-overview-button:hover {
+ background-color: #01536D;
+ transition: background-color 0.4s ease-in-out 0s;
+}
+
+.minerva-top-checkbox-div {
+ height: 36px;
+ vertical-align: top;
+ font-size: 13px;
+ font-weight: 900;
+ color: #ffffff;
+ display: inline;
+ width: auto;
+ float: left;
+ text-align: left;
+ padding: 0 0 0 15px;
+ margin: 0;
+}
+
+.minerva-top-checkbox-div label {
+ padding: 0 15px 0 5px;
+ font-size: 11px;
+ line-height: 35px;
+ display: inline;
+ float: left;
+}
+
+.minerva-top-checkbox-div input {
+ margin-top: 12px;
+ display: inline;
+ float: left;
+}
+
+.minerva-overlay-dialog div[style*="display: table-cell"] {
+ padding: 2px;
+ vertical-align: top;
+}
+
+.minerva-open-submap-button {
+ padding: 2px;
+ margin: 2px;
}
\ No newline at end of file
diff --git a/frontend-js/src/main/js/ConfigurationType.js b/frontend-js/src/main/js/ConfigurationType.js
index defc30720f30b40ee06e0236b61d8fd0fe4954b5..aa792f821a083b1e4dfbb66bbb720ca43a89ff2f 100644
--- a/frontend-js/src/main/js/ConfigurationType.js
+++ b/frontend-js/src/main/js/ConfigurationType.js
@@ -8,6 +8,7 @@ var ConfigurationType = {
LEGEND_FILES : "LEGEND_FILES",
MIN_COLOR_VAL : "MIN_COLOR_VAL",
MAX_COLOR_VAL : "MAX_COLOR_VAL",
+ SIMPLE_COLOR_VAL : "SIMPLE_COLOR_VAL",
SEARCH_DISTANCE : "SEARCH_DISTANCE",
USER_MANUAL_FILE : "USER_MANUAL_FILE",
};
diff --git a/frontend-js/src/main/js/Functions.js b/frontend-js/src/main/js/Functions.js
index 14e71695de597639a821311fe11c0355169ccb25..c2594abb1575f2dc79df84ec36093fc7b7c2b701 100644
--- a/frontend-js/src/main/js/Functions.js
+++ b/frontend-js/src/main/js/Functions.js
@@ -170,17 +170,23 @@ Functions.overlayToColor = function(elementOverlay) {
if (elementOverlay === null || elementOverlay === undefined) {
return Promise.reject("elementOverlay cannot be null!");
} else if (elementOverlay.color !== undefined && elementOverlay.color !== null) {
- return Promise.resolve(self.intToColorString(elementOverlay.color.value));
- } else if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
+ return Promise.resolve(self.intToColorString(elementOverlay.color.rgb));
+ } else {
var ratio = 0;
var promiseColor = null;
- if (elementOverlay.value < 0) {
- ratio = -elementOverlay.value;
- promiseColor = ServerConnector.getMinOverlayColorInt();
+ if (elementOverlay.value !== undefined && elementOverlay.value !== null) {
+ if (elementOverlay.value < 0) {
+ ratio = -elementOverlay.value;
+ promiseColor = ServerConnector.getMinOverlayColorInt();
+ } else {
+ ratio = elementOverlay.value;
+ promiseColor = ServerConnector.getMaxOverlayColorInt();
+ }
} else {
- ratio = elementOverlay.value;
- promiseColor = ServerConnector.getMaxOverlayColorInt();
+ ratio = 1;
+ promiseColor = ServerConnector.getSimpleOverlayColorInt();
}
+
return promiseColor.then(function(color) {
ratio = 1 - ratio;
@@ -207,8 +213,6 @@ Functions.overlayToColor = function(elementOverlay) {
color = red | green | blue;
return self.intToColorString(color);
});
- } else {
- return Promise.reject("elementOverlay doesn't have neither color nor value set!");
}
};
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index e391ef730155f466ce161a34e66b823a4ce4cc13..e51c5b6b697fda9026ec54db304a36b194e7ae37 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -28,6 +28,17 @@ GuiConnector.yPos = 0;
GuiConnector.init = function() {
var self = this;
+ if (!String.prototype.endsWith) {
+ String.prototype.endsWith = function(pattern) {
+ var d = this.length - pattern.length;
+ return d >= 0 && this.lastIndexOf(pattern) === d;
+ };
+ }
+ var isIE = /* @cc_on!@ */false || !!document.documentMode;
+
+ if (isIE) {
+ alert("This webpage works well with Chrome, Firefox and Safari.");
+ }
// bootstrap tab initialization
$("ul.nav-tabs a").click(function(e) {
e.preventDefault();
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 98798955d4ee3490de9e7670627cc097cf20089a..88b8109a4d4e84649e92eba0f963f543d44feb37 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -21,6 +21,7 @@ var InvalidCredentialsError = require('./InvalidCredentialsError');
var LayoutAlias = require('./map/data/LayoutAlias');
var LayoutData = require('./map/data/LayoutData');
var LayoutReaction = require('./map/data/LayoutReaction');
+var MapModel = require('./map/data/MapModel');
var MiRna = require('./map/data/MiRna');
var NetworkError = require('./NetworkError');
var Project = require('./map/data/Project');
@@ -62,6 +63,24 @@ ServerConnector.getMinOverlayColorInt = function() {
});
};
+ServerConnector.getSimpleOverlayColorInt = function() {
+ var self = this;
+ var userColor;
+ return self.getLoggedUser().then(function(user) {
+ userColor = user.getSimpleColor();
+ return self.getConfigurationParam(ConfigurationType.SIMPLE_COLOR_VAL);
+ }).then(function(systemSimpleColor) {
+ var color = userColor;
+ if (userColor === null || userColor === undefined || userColor === "") {
+ color = systemSimpleColor;
+ }
+ color = parseInt(color, 16);
+ /* jslint bitwise: true */
+ color = (color & 0xFFFFFF);
+ return color;
+ });
+};
+
ServerConnector.getMaxOverlayColorInt = function() {
var self = this;
var userColor;
@@ -606,6 +625,23 @@ ServerConnector.getConfigurationParam = function(paramId) {
});
};
+ServerConnector.getModels = function(projectId) {
+ var queryParams = {};
+ var filterParams = {};
+ var project;
+ var self = this;
+ return self.getProjectId(projectId).then(function(result) {
+ queryParams.projectId = result;
+ return self.readFile(self.getModelsUrl(queryParams, filterParams));
+ }).then(function(content) {
+ var models = [];
+ var parsedJson = JSON.parse(content);
+ for (var i = 0; i < parsedJson.length; i++) {
+ models.push(new MapModel(parsedJson[i]));
+ }
+ return models;
+ });
+};
ServerConnector.getProject = function(projectId) {
var queryParams = {};
var filterParams = {};
@@ -616,6 +652,9 @@ ServerConnector.getProject = function(projectId) {
return self.readFile(self.getProjectsUrl(queryParams, filterParams));
}).then(function(content) {
project = new Project(content);
+ return self.getModels(projectId);
+ }).then(function(models) {
+ project.setModel(models[0]);
return self.getOverlays(projectId);
}).then(function(overlays) {
project.getModel().addLayouts(overlays);
diff --git a/frontend-js/src/main/js/gui/ContextMenu.js b/frontend-js/src/main/js/gui/ContextMenu.js
index 80d2ed8064b8ea7e2b6680b56392eddb2bd4485e..420598dfe77cc82dd727406192805b3fa06cdf94 100644
--- a/frontend-js/src/main/js/gui/ContextMenu.js
+++ b/frontend-js/src/main/js/gui/ContextMenu.js
@@ -129,7 +129,7 @@ ContextMenu.prototype.createExportAsModelSubmenu = function() {
});
var submenu = new SubMenu({
element : li,
- name : "Export as model",
+ name : "Export as map",
customMap : self.getMap()
});
diff --git a/frontend-js/src/main/js/gui/Panel.js b/frontend-js/src/main/js/gui/Panel.js
index 01694ae6a03233188fca8f40598725b3c766f0a6..d4c85402ef7ad3016073ef23f540018e21145813 100644
--- a/frontend-js/src/main/js/gui/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -56,7 +56,7 @@ Panel.prototype.createHelpButton = function() {
var self = this;
var helpTipButton = Functions.createElement({
type : "button",
- style : "position: absolute; top:5px; right: 5px;width:18px",
+ className : "minerva-help-button",
content : '<span class="ui-icon ui-icon-help" style="margin-left: -0.5em;"/>',
});
helpTipButton.onclick = function() {
@@ -186,6 +186,10 @@ Panel.prototype.assignDialogOptions = function(div, params) {
dialog.dialog('option', 'modal', params[key]);
} else if (key === "buttons") {
dialog.dialog('option', 'buttons', params[key]);
+ } else if (key === "className") {
+ dialog.dialog('option', 'dialogClass', params[key]);
+ } else if (key === "title") {
+ dialog.dialog('option', 'title', params[key]);
} else {
throw new Error("Unknown dialog param: " + key + " - " + params[key]);
}
@@ -215,7 +219,8 @@ Panel.prototype.openDialog = function(content, options) {
close : function() {
contentDiv.style.display = "none";
$(this).dialog('destroy');
- }
+ },
+ dialogClass : options.className,
});
this.assignDialogOptions(div, options);
@@ -258,23 +263,26 @@ Panel.prototype.onresize = function() {
// compute the width (we can only compute it for visible elements)
var size = 100000;
- $(".pre-scrollable", self.getElement()).each(function(index, element) {
- if ($(element).is(":visible")) {
- size = Math.min(size, footerPosition - $(element).offset().top);
- }
- });
- if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
- size = Math.min(size, footerPosition - $(self.getElement()).offset().top);
- }
- if (size !== 100000) {
+ if ($(self.getElement()).is(":visible")) {
+
$(".pre-scrollable", self.getElement()).each(function(index, element) {
- $(element).css('max-height', size);
- $(element).css('height', size);
+ if ($(element).is(":visible")) {
+ size = Math.min(size, footerPosition - $(element).offset().top);
+ }
});
- }
- if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
- $(self.getElement()).css('max-height', size);
- $(self.getElement()).css('height', size);
+ if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
+ size = Math.min(size, footerPosition - $(self.getElement()).offset().top);
+ }
+ if (size !== 100000) {
+ $(".pre-scrollable", self.getElement()).each(function(index, element) {
+ $(element).css('max-height', size);
+ $(element).css('height', size);
+ });
+ }
+ if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
+ $(self.getElement()).css('max-height', size);
+ $(self.getElement()).css('height', size);
+ }
}
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
index c4d88d5c80e481bde40f40bdd27c1e0207b859f3..8507144de26b29a5772c6c48cd759cd7e7e6fd60 100644
--- a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
@@ -14,7 +14,7 @@ function AbstractPanel(params) {
Panel.call(this, params);
var self = this;
- this._initializeGui();
+ this._initializeGui(params.placeholder);
this.setOverlayDb(self.getMap().getOverlayByName(params.panelName));
this._createEventHandlers();
@@ -63,7 +63,7 @@ AbstractPanel.prototype._createEventHandlers = function() {
};
-AbstractPanel.prototype._initializeGui = function() {
+AbstractPanel.prototype._initializeGui = function(placeholder) {
var searchQueryDiv = Functions.createElement({
type : "div",
name : "searchQuery",
@@ -81,33 +81,38 @@ AbstractPanel.prototype._initializeGui = function() {
this.setControlElement(PanelControlElementType.SEARCH_LABEL, searchLabel);
var searchInputDiv = Functions.createElement({
- type : "div",
- style : "display:table"
+ type : "table",
});
searchQueryDiv.appendChild(searchInputDiv);
+
+ var searchInputRow = Functions.createElement({
+ type : "tr",
+ });
+ searchInputDiv.appendChild(searchInputRow);
+
var searchInputCell = Functions.createElement({
- type : "div",
- style : "display:table-cell"
+ type : "td",
});
- searchInputDiv.appendChild(searchInputCell);
+ searchInputRow.appendChild(searchInputCell);
var searchInput = Functions.createElement({
type : "input",
name : "searchInput",
className : "input-field typeahead"
});
+ if (placeholder !== undefined) {
+ searchInput.placeholder = placeholder;
+ }
searchInputCell.appendChild(searchInput);
this.setControlElement(PanelControlElementType.SEARCH_INPUT, searchInput);
var searchButtonCell = Functions.createElement({
- type : "div",
- style : "display:table-cell"
+ type : "td",
});
- searchInputDiv.appendChild(searchButtonCell);
+ searchInputRow.appendChild(searchButtonCell);
var searchButton = Functions.createElement({
type : "a",
- className : "searchButton",
content : '<img src="resources/images/icons/search.png"/>'
});
searchButton.href = "#";
@@ -259,7 +264,9 @@ AbstractPanel.prototype.createTargetRow = function(target, icon) {
iconColumn.style.verticalAlign = "middle";
iconColumn.style.textAlign = "center";
result.appendChild(iconColumn);
+ var submaps = [];
if (target.getTargetElements().length > 0) {
+ var submapAddedIds = [];
iconColumn.appendChild(guiUtils.createIcon(icon));
var checkbox = document.createElement('input');
checkbox.type = "checkbox";
@@ -270,6 +277,14 @@ AbstractPanel.prototype.createTargetRow = function(target, icon) {
};
iconColumn.appendChild(checkbox);
+ var elements = target.getTargetElements();
+ for (var i = 0; i < elements.length; i++) {
+ var elementId = elements[i].getModelId();
+ if (elementId !== self.getMap().getId() && !submapAddedIds[elementId]) {
+ submaps.push(elementId);
+ submapAddedIds[elementId] = true;
+ }
+ }
}
var descColumn = document.createElement("td");
@@ -283,6 +298,25 @@ AbstractPanel.prototype.createTargetRow = function(target, icon) {
descColumn.appendChild(guiUtils.createAnnotations("References: ", target.getReferences(), {
showType : false,
}));
+ if (submaps.length > 0) {
+ descColumn.appendChild(guiUtils.createLabel("Available in submaps: "));
+ for (i = 0; i < submaps.length; i++) {
+ var model = self.getMap().getSubmapById(submaps[i]).getModel();
+ var onclick = function() {
+ var id = model.getId();
+ return function() {
+ self.getMap().openSubmap(id);
+ }
+ }();
+ var button = Functions.createElement({
+ type : "button",
+ className : "minerva-open-submap-button",
+ content : model.getName(),
+ onclick : onclick,
+ });
+ descColumn.appendChild(button);
+ }
+ }
return result;
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
index 5db01ad841b2dc1dc8f7428376b5aba98ddfb968..cf773acd3bffa346f359b3b7b75b89102a20e36d 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
@@ -15,6 +15,7 @@ function ChemicalPanel(params) {
+ '<p>only curated associations between genes and chemicals with direct evidence to '
+ 'Parkinson Disease (<a href="http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300" target="_blank">D010300</a>) are displayed</p>'
+ '<p>separate multiple search by semicolon';
+ params.placeholder = "full chemical name (CTD)";
AbstractDbPanel.call(this, params);
diff --git a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
index 20a384be921a318c8d6965ec2d7b6c351b3ebaf1..a5f84ab26d2c22976ef5b5a4b967cdd467ac7660 100644
--- a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
@@ -13,6 +13,8 @@ function DrugPanel(params) {
params.helpTip = '<p>source: <a target="_drugbank" href="http://www.drugbank.ca/">DrugBank</a> and '
+ '<a target="_drugbank" href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></p>'
+ "<p>use of drug names, synonyms and brand names is supported<p>separate multiple search by semicolon</p>";
+ params.placeholder = "drug, synonym, brand name";
+
AbstractDbPanel.call(this, params);
}
DrugPanel.prototype = Object.create(AbstractDbPanel.prototype);
diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index b5a417fba5aefe83e9b3d9fd9c59e26a570bd121..c14a59f39dee736b78b145184ff2235606cf9643 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -17,6 +17,7 @@ function GenericSearchPanel(params) {
params.helpTip = "<p>search tab allows to search for particular elements or interactions in the map</p>"
+ "<p>perfect match tick box active: only terms with an exact match to the query will be returned</p>"
+ "<p>separate multiple search by semicolon</p>";
+ params.placeholder = "keyword";
AbstractDbPanel.call(this, params);
@@ -65,14 +66,15 @@ GenericSearchPanel.prototype.createReactionElement = function(reaction) {
var td = document.createElement("td");
result.appendChild(td);
- var div = guiUtils.createReactionElement(reaction);
+ var div = guiUtils.createReactionElement({
+ reaction : reaction
+ });
div.appendChild(guiUtils.createSeparator());
td.appendChild(div);
return result;
};
-
GenericSearchPanel.prototype.createAliasElement = function(alias, icon) {
var self = this;
var guiUtils = self.getGuiUtils();
@@ -80,7 +82,10 @@ GenericSearchPanel.prototype.createAliasElement = function(alias, icon) {
var result = document.createElement("tr");
var td = document.createElement("td");
result.appendChild(td);
- var div = guiUtils.createAliasElement(alias, icon);
+ var div = guiUtils.createAliasElement({
+ alias : alias,
+ icon : icon
+ });
div.appendChild(guiUtils.createSeparator());
td.appendChild(div);
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index f18f2b865d84e35015b5656314857b96e7ed6b29..c5c25e7d03ed6ba2d631d5eb242eaabe8ece8cfa 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -27,7 +27,7 @@ GuiUtils.prototype.getConfiguration = function() {
GuiUtils.prototype.createLabel = function(value) {
var result = document.createElement("span");
result.innerHTML = value;
- result.className = "searchDescriptionLabel";
+ result.className = "minerva-label";
return result;
};
@@ -135,6 +135,8 @@ GuiUtils.prototype.createAnnotationLink = function(annotation, showType) {
};
GuiUtils.prototype.createAnnotations = function(label, value, options) {
+ var self = this;
+
var inline = false;
if (options !== undefined) {
if (options.inline !== undefined) {
@@ -142,13 +144,14 @@ GuiUtils.prototype.createAnnotations = function(label, value, options) {
}
}
var result = document.createElement("div");
+ result.appendChild(self.createLabel(label));
if (value !== undefined && value.length > 0) {
- var self = this;
- result.appendChild(self.createLabel(label));
if (!inline) {
result.appendChild(self.createNewLine());
}
result.appendChild(self.createAnnotationList(value, options));
+ } else {
+ result.appendChild(self.createLabelText("No annotations"));
}
return result;
};
@@ -182,9 +185,9 @@ GuiUtils.prototype.createAnnotationList = function(annotations, options) {
var row = document.createElement("div");
row.style.height = "26px";
if (i % 2 === 0) {
- row.className = "annotationRowOdd";
+ row.className = "minerva-annotation-row-odd";
} else {
- row.className = "annotationRowEven";
+ row.className = "minerva-annotation-row-even";
}
var header = document.createElement("div");
header.style.width = "24px";
@@ -241,7 +244,6 @@ GuiUtils.prototype.createParamLine = function(label, value) {
var self = this;
result.appendChild(self.createLabel(label));
result.appendChild(self.createLabelText(value));
- result.appendChild(self.createNewLine());
}
return result;
};
@@ -263,8 +265,7 @@ GuiUtils.prototype.createArrayParamLine = function(label, value) {
if (value !== undefined && value.length > 0) {
var self = this;
result.appendChild(self.createLabel(label));
- result.appendChild(self.createLabelText(value.join(",")));
- result.appendChild(self.createNewLine());
+ result.appendChild(self.createLabelText(value.join(", ")));
}
return result;
};
@@ -303,19 +304,25 @@ GuiUtils.prototype.createTableRow = function(elements) {
return row;
};
-GuiUtils.prototype.createReactionElement = function(reaction) {
+GuiUtils.prototype.createReactionElement = function(params) {
+ var reaction = params.reaction;
+ var showTitle = ((params.showTitle === undefined) || params.showTitle);
var self = this;
var div = document.createElement("div");
- div.appendChild(self.createLabel("Reaction: " + reaction.getReactionId()));
- if (reaction.getModelId() !== self.getMap().getId()) {
- div.appendChild(self.createSubMapLink("In submodel: ", reaction.getModelId()));
+ if (showTitle) {
+ div.appendChild(self.createLabel("Reaction: " + reaction.getReactionId()));
+ if (reaction.getModelId() !== self.getMap().getId()) {
+ div.appendChild(self.createSubMapLink("In submodel: ", reaction.getModelId()));
+ }
}
if (reaction.getLinkedSubmodelId() !== null && reaction.getLinkedSubmodelId() !== undefined) {
div.appendChild(self.createSubMapLink("Associated submodel: ", reaction.getLinkedSubmodelId()));
}
- div.appendChild(self.createNewLine());
+ if (showTitle) {
+ div.appendChild(self.createNewLine());
+ }
div.appendChild(self.createParamLine("Type: ", reaction.getType()));
div.appendChild(self.createParamLine("Symbol: ", reaction.getSymbol()));
@@ -336,23 +343,29 @@ GuiUtils.prototype.createReactionElement = function(reaction) {
return div;
};
-GuiUtils.prototype.createAliasElement = function(alias, icon) {
+GuiUtils.prototype.createAliasElement = function(params) {
+ var alias = params.alias;
+ var icon = params.icon;
+ var showTitle = ((params.showTitle === undefined) || params.showTitle);
var self = this;
var div = document.createElement("div");
- if (icon !== undefined) {
- div.appendChild(this.createIcon(icon));
- }
+ if (showTitle) {
+ if (icon !== undefined) {
+ div.appendChild(this.createIcon(icon));
+ }
- div.appendChild(this.createParamLine(alias.getType() + ": ", alias.getName()));
- if (alias.getModelId() !== self.getMap().getId()) {
- div.appendChild(self.createSubMapLink("In submodel: ", alias.getModelId()));
+ div.appendChild(this.createParamLine(alias.getType() + ": ", alias.getName()));
+ if (alias.getModelId() !== self.getMap().getId()) {
+ div.appendChild(self.createSubMapLink("In submodel: ", alias.getModelId()));
+ }
}
-
if (alias.getLinkedSubmodelId() !== null && alias.getLinkedSubmodelId() !== undefined) {
div.appendChild(self.createSubMapLink("Associated submodel: ", alias.getLinkedSubmodelId()));
}
- div.appendChild(self.createNewLine(3));
+ if (showTitle) {
+ div.appendChild(self.createNewLine(3));
+ }
div.appendChild(self.createParamLine("Full name: ", alias.getFullName()));
div.appendChild(self.createParamLine("Symbol: ", alias.getSymbol()));
diff --git a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
index 25057e24cbab79b0d7f4aeab8e6e760d37e2c549..fe553ab1f70c2fad8f51b4989e9e637f37b62b97 100644
--- a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
@@ -84,6 +84,7 @@ LeftPanel.prototype._createPanelGui = function() {
name : "elementInfoDiv",
type : "div",
style : "background-color:#f3f3f3",
+ className : "minerva-element-info-div",
});
self.elementInfoDiv = elementInfoDiv;
@@ -187,6 +188,7 @@ LeftPanel.prototype.showElementDetails = function(element) {
div.innerHTML = self.prepareElementDetailsContent(bioEntity).innerHTML;
$(div).dialog("open");
$(div).dialog("option", "title", self.getElementTitle(bioEntity));
+ $(div).scrollTop(0);
});
} else {
$(div).dialog("close");
@@ -198,9 +200,15 @@ LeftPanel.prototype.prepareElementDetailsContent = function(bioEntity) {
var guiUtils = new GuiUtils(this.getMap().getConfiguration());
guiUtils.setMap(this.getMap());
if (bioEntity instanceof Reaction) {
- return guiUtils.createReactionElement(bioEntity);
+ return guiUtils.createReactionElement({
+ reaction : bioEntity,
+ showTitle : false,
+ });
} else if (bioEntity instanceof Alias) {
- return guiUtils.createAliasElement(bioEntity);
+ return guiUtils.createAliasElement({
+ alias : bioEntity,
+ showTitle : false,
+ });
} else if (bioEntity instanceof PointData) {
return Functions.createElement({
type : "div"
diff --git a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
index ae466919fd4a3994ce538f350e53f883cc76a16a..4cc29424ce41f56ce2d4e8af922f71db85bb63e3 100644
--- a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
@@ -13,6 +13,7 @@ function MiRnaPanel(params) {
params.helpTip = '<p>source: <a target="_mirtarbase" href="http://mirtarbase.mbc.nctu.edu.tw/">miRTarBase</a></p>'
+ '<p>use only mature sequence IDs according to <a target="_mirbase" href="http://www.mirbase.org">www.mirbase.org</a> (e.g., hsa-miR-125a-3p)</p>'
+ '<p>only targets with strong evidence as defined by miRTarBase are displayed<p>separate multiple search by semicolon</p>';
+ params.placeholder = "mature seq. ID (miRTarBase)";
AbstractDbPanel.call(this, params);
}
MiRnaPanel.prototype = Object.create(AbstractDbPanel.prototype);
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 9f64f2e1b9ea1371e404cc3fac833e9a745c33fe..750b0204fbffab3b17c7259789963e037479ce4f 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -161,9 +161,9 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
checkbox.checked = checked;
checkbox.onclick = function() {
if (this.checked) {
- return self.getMap().openDataOverlay(overlay.getId());
+ return self.getMap().openDataOverlay(overlay.getId()).then(null, GuiConnector.alert);
} else {
- return self.getMap().removeSelectedLayout(overlay.getId());
+ return self.getMap().removeSelectedLayout(overlay.getId()).then(null, GuiConnector.alert);
}
};
viewTd.appendChild(checkbox);
@@ -208,6 +208,7 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
editTd.appendChild(editButton);
result.appendChild(editTd);
}
+ result.title = overlay.getDescription();
return result;
};
@@ -215,13 +216,13 @@ OverlayPanel.prototype.openEditOverlayDialog = function(overlay) {
var self = this;
var guiUtils = self.getGuiUtils();
var content = document.createElement("fieldset");
- content.appendChild(guiUtils.createLabel("Name"));
var nameInput = guiUtils.createInputText(overlay.getName());
- content.appendChild(nameInput);
+ var row = guiUtils.createTableRow([ guiUtils.createLabel("Name: "), nameInput ]);
+ content.appendChild(row);
- content.appendChild(guiUtils.createLabel("Description"));
var descriptionInput = guiUtils.createTextArea(overlay.getDescription());
- content.appendChild(descriptionInput);
+ row = guiUtils.createTableRow([ guiUtils.createLabel("Description: "), descriptionInput ]);
+ content.appendChild(row);
var buttons = [ {
text : "SAVE",
@@ -260,6 +261,8 @@ OverlayPanel.prototype.openEditOverlayDialog = function(overlay) {
self.openDialog(content, {
id : overlay.getId(),
buttons : buttons,
+ title : "Data overlay: " + overlay.getName(),
+ className : "minerva-overlay-dialog",
});
};
@@ -282,59 +285,63 @@ OverlayPanel.prototype.refresh = function() {
}
return ServerConnector.getOverlays();
- }).then(function(customOverlays) {
+ }).then(
+ function(customOverlays) {
- var id = self.getMap().getGoogleMap().getMapTypeId().substring(2);
- selectedOverlay[id] = true;
+ var id = self.getMap().getGoogleMap().getMapTypeId().substring(2);
+ selectedOverlay[id] = true;
- self.clear();
+ self.clear();
- var generalOverlays = [];
- var overlay;
+ var generalOverlays = [];
+ var overlay;
- var overlays = self.getMap().getLayouts();
- for (var i = 0; i < overlays.length; i++) {
- overlay = overlays[i];
- if (overlay.getCreator() === undefined || overlay.getCreator() === "") {
- generalOverlays.push(overlay);
- }
- }
+ var overlays = self.getMap().getLayouts();
+ for (var i = 0; i < overlays.length; i++) {
+ overlay = overlays[i];
+ if (overlay.getCreator() === undefined || overlay.getCreator() === "") {
+ generalOverlays.push(overlay);
+ }
+ }
- var table = self.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
- table.appendChild(self.createTableHeader());
+ var table = self.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
+ table.appendChild(self.createTableHeader());
- var body = document.createElement("tbody");
- table.appendChild(body);
- for (i = 0; i < generalOverlays.length; i++) {
- overlay = generalOverlays[i];
- body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()]));
- }
+ var body = document.createElement("tbody");
+ table.appendChild(body);
+ for (i = 0; i < generalOverlays.length; i++) {
+ overlay = generalOverlays[i];
+ body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()]));
+ }
- var title = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
- var addButton = self.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
- if (user.getLogin() === "anonymous") {
- title.innerHTML = 'YOU ARE NOT LOGGED IN. PLEASE, <a href="#">LOG IN</a> TO UPLOAD AND VIEW CUSTOM OVERLAYS';
- $(title).find("a")[0].onclick = function() {
- return self.getParent().getLoginDialog().open();
- };
- addButton.style.display = "none";
- } else {
- title.innerHTML = self.getCustomOverlaysMessage();
- addButton.style.display = "block";
+ var title = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
+ var addButton = self.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
+ if (user.getLogin() === "anonymous") {
+ title.innerHTML = 'YOU ARE NOT LOGGED IN. PLEASE, <a href="#">LOG IN</a>'
+ + 'TO UPLOAD AND VIEW CUSTOM OVERLAYS<br/><center><button>LOGIN</button></center>';
+ var openLoginDialog = function() {
+ return self.getParent().getLoginDialog().open();
+ };
+ $(title).find("a")[0].onclick = openLoginDialog;
+ $(title).find("button")[0].onclick = openLoginDialog;
+ addButton.style.display = "none";
+ } else {
+ title.innerHTML = self.getCustomOverlaysMessage();
+ addButton.style.display = "block";
- table = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
- table.appendChild(self.createTableHeader(true));
+ table = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
+ table.appendChild(self.createTableHeader(true));
- body = document.createElement("tbody");
- table.appendChild(body);
- for (i = 0; i < customOverlays.length; i++) {
- overlay = customOverlays[i];
- body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()]));
- }
- }
+ body = document.createElement("tbody");
+ table.appendChild(body);
+ for (i = 0; i < customOverlays.length; i++) {
+ overlay = customOverlays[i];
+ body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()]));
+ }
+ }
- self.onresize();
- });
+ self.onresize();
+ });
};
OverlayPanel.prototype.setCustomOverlaysMessage = function(customOverlaysMessage) {
@@ -422,7 +429,7 @@ OverlayPanel.prototype.openAddOverlayDialog = function() {
content.appendChild(fileInput);
content.appendChild(guiUtils.createNewLine());
- content.appendChild(guiUtils.createLabel("Or provide list of elements here: "));
+ content.appendChild(guiUtils.createLabel("Or provide list of elements here (one per line): "));
content.appendChild(guiUtils.createNewLine());
contentInput = guiUtils.createTextArea();
content.appendChild(contentInput);
diff --git a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
index 79ba6d65c87e6cae67c9ccf7b5d459cde775bbcb..391ba195a7ff15e8676951f8a6988cb737df3f14 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
@@ -228,7 +228,9 @@ ProjectInfoPanel.prototype.refresh = function() {
projectNameText.innerHTML = project.getName();
projectVersionText.innerHTML = project.getVersion();
projectDescriptionText.innerHTML = project.getDescription();
- projectPublicationsText.innerHTML = project.getPublicationCount();
+ return ServerConnector.getProjectStatistics();
+ }).then(function(statistics) {
+ projectPublicationsText.innerHTML = statistics.getPublicationCount();
return ServerConnector.getLoggedUser();
}).then(function(user) {
self.showUserProfilePage(user);
@@ -304,7 +306,7 @@ ProjectInfoPanel.prototype._createUserDataTab = function() {
type : "span",
name : "emailValue"
});
- this.setControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT, emailText);
+ self.setControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT, emailText);
userDataDiv.appendChild(guiUtils.createTableRow([ emailLabel, emailText ]));
var centerTag = Functions.createElement({
@@ -318,8 +320,8 @@ ProjectInfoPanel.prototype._createUserDataTab = function() {
content : "LOGOUT"
});
centerTag.appendChild(logoutButton);
- this.setControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON, logoutButton);
- this.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
+ self.setControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON, logoutButton);
+ self.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
var loginTabDiv = Functions.createElement({
type : "div",
@@ -327,10 +329,14 @@ ProjectInfoPanel.prototype._createUserDataTab = function() {
className : "searchPanel",
style : "display:none",
content : '<h3><img src="./resources/images/profile.png" border="0" align="left"/>'
- + '<br/>User data</h3><br/>YOU ARE NOT LOGGED IN.'
+ + '<br/>User data</h3><br/>YOU ARE NOT LOGGED IN.<br/>' + '<center><button>LOGIN</button></center>',
});
- this.getElement().appendChild(loginTabDiv);
- this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_DIV, loginTabDiv);
+ $(loginTabDiv).find("button")[0].onclick = function() {
+ return self.getParent().getLoginDialog().open();
+ };
+
+ self.getElement().appendChild(loginTabDiv);
+ self.setControlElement(PanelControlElementType.USER_TAB_LOGIN_DIV, loginTabDiv);
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index 6cd57ed65f59b57d3a21bb05bf08b2a7c788c275..82882484556107073d65cc8dafe744b8654ae00b 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -64,51 +64,62 @@ PublicationListDialog.prototype._dataTableAjaxCall = function(data, callback) {
sortColumn : self.getColumnsDefinition()[data.order[0].column].name,
sortOrder : data.order[0].dir,
search : data.search.value,
- })
- .then(
- function(publicationList) {
- var out = [];
- var allElements = [];
- for (var i = 0; i < publicationList.data.length; i++) {
- var publication = publicationList.data[i].publication.article;
- var elements = publicationList.data[i].elements;
-
- var row = [];
- row[0] = "<a href='" + publication.link + "'>" + publication.id + "</a>";
- row[1] = publication.title;
- row[2] = publication.authors.join();
- row[3] = publication.journal;
- row[4] = publication.year;
- row[5] = "<div>";
- for (var j = 0; j < elements.length; j++) {
- row[5] += "<a name='" + elements[j].id + "' href='#'>" + elements[j].type + ":" + elements[j].id
- + "</a>, ";
- allElements.push(new IdentifiedElement(elements[j]));
- }
- row[5] += "</div>";
- out.push(row);
- }
- callback({
- draw : data.draw,
- recordsTotal : publicationList.totalSize,
- recordsFiltered : publicationList.filteredSize,
- data : out,
- });
- var promises = [];
- allElements.forEach(function(element) {
- promises.push(self.getMap().getSubmapById(element.getModelId()).getModel().getByIdentifiedElement(
- element, true).then(function(elementData) {
- var name = null;
- if (elementData instanceof Alias) {
- name = elementData.getName();
- } else if (elementData instanceof Reaction) {
- name = elementData.getReactionId();
- }
- $("a[name=" + elementData.getId() + "]", $(self.getElement())).html(name);
- }));
- });
- return Promise.all(promises);
- });
+ }).then(function(publicationList) {
+ var out = [];
+ var allElements = [];
+ for (var i = 0; i < publicationList.data.length; i++) {
+ var publication = publicationList.data[i].publication.article;
+ var elements = publicationList.data[i].elements;
+
+ var row = [];
+ row[0] = "<a href='" + publication.link + "'>" + publication.id + "</a>";
+ row[1] = publication.title;
+ row[2] = publication.authors.join();
+ row[3] = publication.journal;
+ row[4] = publication.year;
+ row[5] = "<div>";
+ for (var j = 0; j < elements.length; j++) {
+ row[5] += "<a name='" + elements[j].id + "' href='#'>" + elements[j].type + ":" + elements[j].id + "</a>, ";
+ allElements.push(new IdentifiedElement(elements[j]));
+ }
+ row[5] += "</div>";
+ out.push(row);
+ }
+ callback({
+ draw : data.draw,
+ recordsTotal : publicationList.totalSize,
+ recordsFiltered : publicationList.filteredSize,
+ data : out,
+ });
+ var promises = [];
+ allElements.forEach(function(element) {
+ var model = self.getMap().getSubmapById(element.getModelId()).getModel();
+ promises.push(model.getByIdentifiedElement(element, true).then(function(elementData) {
+ var name = null;
+ if (elementData instanceof Alias) {
+ name = elementData.getName();
+ } else if (elementData instanceof Reaction) {
+ name = elementData.getReactionId();
+ }
+ $("a[name=" + elementData.getId() + "]", $(self.getElement())).html(name);
+ var onclick = function() {
+ var searchOverlay = self.getMap().getOverlayByName("search");
+ var query;
+ if (element.getType() === "ALIAS") {
+ query = "element:" + element.getId();
+ } else {
+ query = "reaction:" + element.getId();
+ }
+ self.getMap().openSubmap(elementData.getModelId());
+ return searchOverlay.searchByQuery(query, true, true).then(function() {
+ $(self.getElement()).dialog("close");
+ }).then(null, GuiConnector.alert);
+ }
+ $("a[name=" + elementData.getId() + "]", $(self.getElement())).click(onclick);
+ }));
+ });
+ return Promise.all(promises);
+ });
};
PublicationListDialog.prototype.show = function() {
diff --git a/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js
index 2c6dd1d01175c4334b09e38afff3694948794be5..fd9775099dc73153100940b9447cbe81b7036017 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js
@@ -4,7 +4,7 @@ var Promise = require("bluebird");
/* exported logger */
-var AbstractGuiElement = require('../AbstractGuiElement');
+var Panel = require('../Panel');
var ChemicalPanel = require('./ChemicalPanel');
var DrugPanel = require('./DrugPanel');
var MiRnaPanel = require('./MiRnaPanel');
@@ -14,7 +14,8 @@ var Functions = require('../../Functions');
var logger = require('../../logger');
function SearchPanel(params) {
- AbstractGuiElement.call(this, params);
+ params.panelName = "global-search";
+ Panel.call(this, params);
var self = this;
this._tabIdCount = 0;
@@ -24,7 +25,7 @@ function SearchPanel(params) {
}
-SearchPanel.prototype = Object.create(AbstractGuiElement.prototype);
+SearchPanel.prototype = Object.create(Panel.prototype);
SearchPanel.prototype.constructor = SearchPanel;
SearchPanel.prototype._createPanelGui = function() {
diff --git a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
index c2d97a382de1e6442537821301fc4eb7f49f6bbd..2cc077f69fd8abf2e46f9c7ff7f9b4576981d163 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
@@ -46,13 +46,14 @@ SubmapPanel.prototype.createRow = function(model) {
var openTd = document.createElement("td");
if (model.getId() !== self.getMap().getId()) {
- var button = document.createElement("button");
var img = guiUtils.createIcon("icons/search.png");
- button.appendChild(img);
- button.onclick = function() {
+ var link = document.createElement("a");
+ link.href = "#";
+ link.onclick = function() {
self.getMap().openSubmap(model.getId());
};
- openTd.appendChild(button);
+ link.appendChild(img);
+ openTd.appendChild(link);
}
result.appendChild(openTd);
@@ -69,9 +70,11 @@ SubmapPanel.prototype.createTableHeader = function() {
nameTd.innerHTML = "Name";
row.appendChild(nameTd);
- var viewTd = document.createElement("th");
- viewTd.innerHTML = "View";
- row.appendChild(viewTd);
+ row.appendChild(Functions.createElement({
+ type : "th",
+ style : "width: 60px;",
+ content : "View"
+ }));
result.appendChild(row);
return result;
@@ -125,10 +128,14 @@ SubmapPanel.prototype.createTable = function(models, type) {
result.appendChild(table);
table.appendChild(self.createTableHeader());
+ var tableBody = Functions.createElement({
+ type : "tbody",
+ });
+ table.appendChild(tableBody);
+
for (var i = 0; i < models.length; i++) {
- table.appendChild(self.createRow(models[i]));
+ tableBody.appendChild(self.createRow(models[i]));
}
-
return result;
};
diff --git a/frontend-js/src/main/js/gui/topMenu/TopMenu.js b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
index af684e2a404a5b4a4fd22333096a77e8261e91ad..cd80bd94f685681a1b457fa460fef4e6ebeeb845 100644
--- a/frontend-js/src/main/js/gui/topMenu/TopMenu.js
+++ b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
@@ -69,9 +69,9 @@ TopMenu.prototype._createGui = function() {
var showOverviewButton = Functions.createElement({
type : "button",
- className : "overview_button",
+ className : "minerva-overview-button",
name : "showOverviewButton",
- content : "<i class='fa fa-sitemap' style='font-size:18px; font-weight:400; padding-right:10px;'/>SHOW OVERVIEW",
+ content : "<i class='fa fa-sitemap' style='font-size:18px; font-weight:400; padding-right:10px;'></i><span >SHOW OVERVIEW</span>",
style : "display:none",
});
showOverviewDiv.appendChild(showOverviewButton);
@@ -85,7 +85,7 @@ TopMenu.prototype._createGui = function() {
var div4checkboxes = Functions.createElement({
type : "div",
- className : "div4checkboxes",
+ className : "minerva-top-checkbox-div",
});
rightHeaderMenuDiv.appendChild(div4checkboxes);
@@ -117,7 +117,7 @@ TopMenu.prototype._createGui = function() {
var refreshCommentButton = Functions.createElement({
type : "button",
- className : "overview_button",
+ className : "minerva-overview-button",
name : "refreshCommentButton",
content : "<i class='fa fa-refresh' style='font-size:21px; font-weight:400;'></i>",
style : "display:none",
@@ -127,7 +127,7 @@ TopMenu.prototype._createGui = function() {
var clearButton = Functions.createElement({
type : "button",
- className : "overview_button",
+ className : "minerva-overview-button",
name : "clearButton",
content : "<i class='fa fa-times' style='font-size:18px; font-weight:300; padding-right:10px;'></i>CLEAR",
});
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index b2af8d23694c21c81f4677e476285575e75434b1..10cc77ed9362755a3ff84256833118259b58f1df 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -604,7 +604,7 @@ AbstractCustomMap.prototype._showSelectedLayout = function(layoutId, index, leng
startX : startX,
endX : endX,
onClick : [ function() {
- return self._openInfoWindowForIdentifiedElement(element, surface.getGoogleMarker());
+ return self._openInfoWindowForAlias(aliasData, surface.getGoogleMarker());
}, function() {
return self.getTopMap().callListeners("onBioEntityClick", element);
} ]
@@ -625,7 +625,7 @@ AbstractCustomMap.prototype._showSelectedLayout = function(layoutId, index, leng
reaction : reactionData,
map : self,
onClick : [ function() {
- return self._openInfoWindowForIdentifiedElement(element, surface.getGoogleMarker());
+ return self._openInfoWindowForReaction(reactionData, surface.getGoogleMarker());
}, function() {
return self.getTopMap().callListeners("onBioEntityClick", element);
} ],
@@ -673,7 +673,7 @@ AbstractCustomMap.prototype._openInfoWindowForAlias = function(alias, googleMark
var infoWindow = this.getAliasInfoWindowById(alias.getId());
if (infoWindow !== null && infoWindow !== undefined) {
if (!infoWindow.isOpened()) {
- infoWindow.open();
+ infoWindow.open(googleMarker);
} else {
logger.warn("Info window for alias: " + alias.getId() + " is already opened");
}
@@ -731,28 +731,6 @@ AbstractCustomMap.prototype._refreshInfoWindows = function() {
return Promise.all(promises);
};
-/**
- * Opens {@link AbstractInfoWindow} for a marker.
- *
- * @param marker
- * marker for which we are opening window
- */
-AbstractCustomMap.prototype._openInfoWindowForIdentifiedElement = function(element, googleMarker) {
- var self = this;
- if (element.getType() === "ALIAS") {
- return self.getModel().getByIdentifiedElement(element).then(function(alias) {
- return self._openInfoWindowForAlias(alias, googleMarker);
- });
- } else if (element.getType() === "POINT") {
- return self._openInfoWindowForPoint(new PointData(element), googleMarker);
- } else if (element.getType() === "REACTION") {
- return self.getModel().getByIdentifiedElement(element).then(function(reaction) {
- return self._openInfoWindowForReaction(reaction, googleMarker);
- });
- } else {
- throw new Error("Unknown element type: " + element.getType());
- }
-};
/**
* Opens {@link ReactionInfoWindow} for given reaction identifier.
@@ -765,7 +743,7 @@ AbstractCustomMap.prototype._openInfoWindowForReaction = function(reaction, goog
var self = this;
if (infoWindow !== null && infoWindow !== undefined) {
if (!infoWindow.isOpened()) {
- infoWindow.open();
+ infoWindow.open(googleMarker);
} else {
logger.warn("Info window for reaction: " + reaction.getId() + " is already opened");
}
@@ -791,7 +769,7 @@ AbstractCustomMap.prototype._openInfoWindowForPoint = function(pointData, google
var infoWindow = this.getPointInfoWindowById(pointData.getId());
if (infoWindow !== null && infoWindow !== undefined) {
if (!infoWindow.isOpened()) {
- infoWindow.open();
+ infoWindow.open(googleMarker);
} else {
logger.warn("Info window for point: " + pointData.getId() + " is already opened");
}
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 0e01282e60f3618470eb463fc29119c3b838e3fc..0ad9cc8620eaeeb7886d310f8cc178f3ceb9571d 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -16,6 +16,7 @@ var ControlType = require('./ControlType');
var CustomMapOptions = require('./CustomMapOptions');
var IdentifiedElement = require('./data/IdentifiedElement');
var LayoutData = require('./data/LayoutData');
+var PointData = require('./data/PointData');
var PointMarker = require('./marker/PointMarker');
var Reaction = require('./data/Reaction');
var ReactionMarker = require('./marker/ReactionMarker');
@@ -1316,4 +1317,28 @@ CustomMap.prototype.createSurfaceForDbOverlay = function(element, dbOverlay) {
}
};
+/**
+ * Opens {@link AbstractInfoWindow} for a marker.
+ *
+ * @param marker
+ * marker for which we are opening window
+ */
+CustomMap.prototype._openInfoWindowForIdentifiedElement = function(element, googleMarker) {
+ var self = this;
+ var submap = self.getSubmapById(element.getModelId());
+ if (element.getType() === "ALIAS") {
+ return submap.getModel().getByIdentifiedElement(element).then(function(alias) {
+ return submap._openInfoWindowForAlias(alias, googleMarker);
+ });
+ } else if (element.getType() === "POINT") {
+ return submap._openInfoWindowForPoint(new PointData(element), googleMarker);
+ } else if (element.getType() === "REACTION") {
+ return submap.getModel().getByIdentifiedElement(element).then(function(reaction) {
+ return submap._openInfoWindowForReaction(reaction, googleMarker);
+ });
+ } else {
+ throw new Error("Unknown element type: " + element.getType());
+ }
+};
+
module.exports = CustomMap;
diff --git a/frontend-js/src/main/js/map/Submap.js b/frontend-js/src/main/js/map/Submap.js
index 0a5e1df5d5930dad25aea669ba06cee9ad347c41..ea36bbea10d201196e5516b7b2abf9a66e7d5607 100644
--- a/frontend-js/src/main/js/map/Submap.js
+++ b/frontend-js/src/main/js/map/Submap.js
@@ -1,5 +1,7 @@
"use strict";
+/* exported logger */
+
var logger = require('../logger');
var AbstractCustomMap = require('./AbstractCustomMap');
var CustomMapOptions = require('./CustomMapOptions');
@@ -62,11 +64,18 @@ Submap.prototype.open = function(htmlTag) {
mapDiv.style.height = "100%";
contentDiv.appendChild(mapDiv);
- $(self.htmlTag).dialog("open");
- $(self.htmlTag).dialog('option', 'title', self.getModel().getName());
+ $(self.htmlTag).dialog({
+ title : self.getModel().getName(),
+ width : Math.floor(window.innerWidth * 2 / 3),
+ height : Math.floor(window.innerHeight * 2 / 3),
+ position : {
+ my : "center",
+ at : "center",
+ of : $(self.getTopMap().getElement()),
+ },
+ });
- $(self.htmlTag).dialog("option", "width", Math.floor(window.innerWidth * 2 / 3));
- $(self.htmlTag).dialog("option", "height", Math.floor(window.innerHeight * 2 / 3));
+ $(self.htmlTag).dialog("open");
self.setGoogleMap(new google.maps.Map(mapDiv, mapOptions));
self._createMapChangedCallbacks();
@@ -99,7 +108,6 @@ Submap.prototype.open = function(htmlTag) {
self.initialized = true;
} else {
$(self.htmlTag).dialog("open");
-
}
};
@@ -110,26 +118,6 @@ Submap.prototype.openDataOverlay = function(identifier) {
}
};
-Submap.prototype.loadSubmapConfiguration = function() {
- var self = this;
- var onConfigurationReload = function() {
- var submodelFound = false;
- for (var i = 0; i < self.getTopMap().configuration.SUBMODELS.length && (!submodelFound); i++) {
- if (self.getTopMap().configuration.SUBMODELS[i].getId() === self.getId()) {
- self.configuration = self.getTopMap().configuration.SUBMODELS[i];
- submodelFound = true;
- }
- }
- if (!submodelFound) {
- throw "Cannot find configuration for submodel " + self.getId();
- }
- logger.debug("Submodel config reloaded: " + self.getId());
- };
-
- onConfigurationReload();
- this.getTopMap().configuration.addListener("onreload", onConfigurationReload);
-};
-
Submap.prototype.getTopMap = function() {
return this.getCustomMap();
};
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index 8abcdd1b5265bc3c8432ce6b75c092cc4cdeb505..85c8b64da14a8553eceaf4cf340c7ba1c023a057 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -5,6 +5,8 @@ var ObjectWithListeners = require('../../ObjectWithListeners');
var Annotation = require("./Annotation");
var Model = require('./MapModel');
+var logger = require('../../logger');
+
function Project(data) {
// call super constructor
ObjectWithListeners.call(this);
@@ -53,8 +55,6 @@ Project.prototype.loadFromData = function(data) {
this.setOrganism(data.organism);
this.setPublicationCount(data.publicationCount);
- this.setModel(new Model(data.map));
-
this.callListeners("onreload");
}
};
diff --git a/frontend-js/src/main/js/map/data/ProjectStatistics.js b/frontend-js/src/main/js/map/data/ProjectStatistics.js
index d905df46d6122a4f7b4b30f4360a90da862f0bba..e30fe8b0cbb34f7021b6e3fabec5dd60cc5bda45 100644
--- a/frontend-js/src/main/js/map/data/ProjectStatistics.js
+++ b/frontend-js/src/main/js/map/data/ProjectStatistics.js
@@ -12,6 +12,7 @@ function ProjectStatistics(data, configuration) {
this.setReactionAnnotations(data.reactionAnnotations, configuration);
this.setElementAnnotations(data.elementAnnotations, configuration);
+ this.setPublicationCount(data.publications, configuration);
}
ProjectStatistics.prototype = Object.create(ObjectWithListeners.prototype);
@@ -49,4 +50,11 @@ ProjectStatistics.prototype.getElementAnnotations = function() {
return this._elementAnnotations;
};
+ProjectStatistics.prototype.setPublicationCount = function(count) {
+ this._publicationsCount = count;
+};
+ProjectStatistics.prototype.getPublicationCount = function() {
+ return this._publicationsCount;
+};
+
module.exports = ProjectStatistics;
diff --git a/frontend-js/src/main/js/map/data/User.js b/frontend-js/src/main/js/map/data/User.js
index 48398247f9155faaaee8a27c86a6e1ded54e4ed3..cd41f7d7f9760ec82f889fe2618259a19fc1c792 100644
--- a/frontend-js/src/main/js/map/data/User.js
+++ b/frontend-js/src/main/js/map/data/User.js
@@ -13,6 +13,7 @@ function User(javaObject) {
this.setPrivileges(javaObject.privileges);
this.setMinColor(javaObject.minColor);
this.setMaxColor(javaObject.maxColor);
+ this.setSimpleColor(javaObject.simpleColor);
}
User.prototype.setLogin = function(login) {
@@ -63,6 +64,14 @@ User.prototype.getMinColor = function() {
return this._minColor;
};
+User.prototype.setSimpleColor = function(simpleColor) {
+ this._simpleColor = simpleColor;
+};
+
+User.prototype.getSimpleColor = function() {
+ return this._simpleColor;
+};
+
User.prototype.setMaxColor = function(maxColor) {
this._maxColor = maxColor;
};
diff --git a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
index 219bb87a6a290c07eb508c4df0a181bf132db807..bea8fbcd5f13470f77968f373a273b9cf7818a32 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
@@ -131,6 +131,7 @@ AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = functio
});
} else {
return new Promise(function(resolve) {
+ var drugNames = [];
var result = [];
var queries = self.getQueries();
for (var i = 0; i < queries.length; i++) {
@@ -144,8 +145,9 @@ AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = functio
for (var k = 0; k < targets.length; k++) {
var elements = targets[k].getTargetElements();
for (var l = 0; l < elements.length; l++) {
- if (element.equals(elements[l])) {
+ if (element.equals(elements[l]) && drugNames[drug.getName()] === undefined) {
result.push(drug);
+ drugNames[drug.getName()] = true;
}
}
}
diff --git a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
index 4a8d7b2b58163fef9b6d66e2d86e1f80a379e5a6..d657fd6bceeb294d0f01cd2440652bce567ba8d7 100644
--- a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
+++ b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
@@ -15,6 +15,9 @@ function AbstractOverlayElement(params) {
self.registerListenerType("onClick");
self.setCustomMap(params.map);
+ if (params.element !== undefined && params.element !== null) {
+ self.setIdentifiedElement(params.element);
+ }
self._googleMapObjects = [];
if (params.onClick !== undefined) {
@@ -42,7 +45,7 @@ AbstractOverlayElement.prototype.getBounds = function() {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
bounds.extend(this.getGoogleMapObjects()[i].getBounds().getSouthWest());
bounds.extend(this.getGoogleMapObjects()[i].getBounds().getNorthEast());
- }
+ }
return bounds;
};
@@ -96,6 +99,10 @@ AbstractOverlayElement.prototype.getIdentifiedElement = function() {
return this._identifiedElement;
};
+AbstractOverlayElement.prototype.getModelId = function() {
+ return this.getIdentifiedElement().getModelId();
+};
+
AbstractOverlayElement.prototype.updateIdentifiedElement = function(identifiedElement) {
if (identifiedElement.getColor() !== undefined) {
this.setColor(identifiedElement.getColor());
@@ -106,6 +113,18 @@ AbstractOverlayElement.prototype.setIdentifiedElement = function(identifiedEleme
this._identifiedElement = identifiedElement;
};
+AbstractOverlayElement.prototype.getBounds = function() {
+ var self = this;
+ var bounds = new google.maps.LatLngBounds();
+ for (var i = 0; i < self.getGoogleMapObjects().length; i++) {
+ var elementBounds = self.getGoogleMapObjects()[i].getBounds();
+ bounds.extend(elementBounds.getNorthEast());
+ bounds.extend(elementBounds.getSouthWest());
+ }
+
+ return bounds;
+};
+
/**
* Returns {@link AbstractCustomMap} where surface is located.
*
diff --git a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
index c20b3693b97aae709a9af3502508464d1e1163d8..e807019a6f9036c35e5b01b0f11f8e609005d31d 100644
--- a/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AbstractInfoWindow.js
@@ -1,5 +1,7 @@
"use strict";
+var Promise = require("bluebird");
+
var logger = require('../../logger');
var Functions = require('../../Functions');
@@ -32,19 +34,17 @@ function AbstractInfoWindow(params) {
var onOverlayFullViewChanged = function(e) {
var self = e.object;
// first change the content of the element
- return self.update().then(
- function() {
- if (e.newVal) {
- var element = new IdentifiedElement({
- objectId : self.getElementId(),
- modelId : self.getCustomMap().getId(),
- type : self.getElementType()
- });
-
- return self.getCustomMap().getTopMap().retrieveOverlayDetailDataForElement(element,
- self.getOverlayFullViewArray());
- }
+ return self.update().then(function() {
+ if (e.newVal) {
+ var element = new IdentifiedElement({
+ objectId : self.getElementId(),
+ modelId : self.getCustomMap().getId(),
+ type : self.getElementType()
});
+ var topMap = self.getCustomMap().getTopMap();
+ return topMap.retrieveOverlayDetailDataForElement(element, self.getOverlayFullViewArray());
+ }
+ });
};
@@ -121,12 +121,15 @@ AbstractInfoWindow.prototype.isOpened = function() {
/**
* Opens Info Window.
*/
-AbstractInfoWindow.prototype.open = function() {
+AbstractInfoWindow.prototype.open = function(newMarker) {
var self = this;
if (self.googleInfowindow === null) {
logger.warn("Cannot open window.");
return;
}
+ if (newMarker !== undefined) {
+ self.setGoogleMarker(newMarker);
+ }
self.googleInfowindow.open(self.getCustomMap().getGoogleMap(), self.getGoogleMarker());
return self.update().then(function() {
@@ -222,7 +225,11 @@ AbstractInfoWindow.prototype.createOverlayInfoDiv = function(overlay, data) {
* @returns {String} with a div for drug overlay information
*/
AbstractInfoWindow.prototype._createDrugInfoDiv = function(overlay, data) {
- return this._createTargetInfoDiv(overlay, data, "Interacting drugs");
+ return this._createTargetInfoDiv({
+ overlay : overlay,
+ data : data,
+ name : "Interacting drugs"
+ });
};
/**
@@ -408,7 +415,11 @@ AbstractInfoWindow.prototype.update = function() {
return this._updateContent();
};
-AbstractInfoWindow.prototype._createTargetInfoDiv = function(overlay, data, name) {
+AbstractInfoWindow.prototype._createTargetInfoDiv = function(params) {
+ var overlay = params.overlay;
+ var data = params.data;
+ var name = params.name;
+
var self = this;
var result = document.createElement("div");
@@ -472,6 +483,11 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
table.appendChild(header);
var row;
+ var onclick = function() {
+ // ';' enforces single query (in case there are ',' characters in the name)
+ return overlay.searchByQuery(this.innerHTML + ";");
+ };
+
var count = 0;
for ( var searchId in data) {
if (data.hasOwnProperty(searchId)) {
@@ -491,10 +507,18 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
}
}
}
- row.appendChild(Functions.createElement({
+ var link = Functions.createElement({
+ type : "a",
+ onclick : onclick,
+ href : "#",
+ content : nameContent,
+ });
+
+ var nameTd = Functions.createElement({
type : "td",
- content : nameContent
- }));
+ });
+ nameTd.appendChild(link);
+ row.appendChild(nameTd);
var referencesCell = Functions.createElement({
type : "td",
@@ -550,7 +574,11 @@ AbstractInfoWindow.prototype.getGuiUtils = function() {
* @returns DOM element with a div for comment overlay information
*/
AbstractInfoWindow.prototype._createChemicalInfoDiv = function(overlay, data) {
- return this._createTargetInfoDiv(overlay, data, "Interacting chemicals");
+ return this._createTargetInfoDiv({
+ overlay : overlay,
+ data : data,
+ name : "Interacting chemicals",
+ });
};
/**
@@ -561,7 +589,11 @@ AbstractInfoWindow.prototype._createChemicalInfoDiv = function(overlay, data) {
* @returns DOM element with a div for comment overlay information
*/
AbstractInfoWindow.prototype._createMiRnaInfoDiv = function(overlay, data) {
- return this._createTargetInfoDiv(overlay, data, "Interacting Micro RNAs");
+ return this._createTargetInfoDiv({
+ overlay : overlay,
+ data : data,
+ name : "Interacting Micro RNAs"
+ });
};
/**
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 94de429a75952adccd697d6c1bf4222f05d9c99c..f84281272aa732bf0a147b5856f517e54f7e5425 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -84,7 +84,7 @@ function createDivStructure(element) {
var leftPanelDiv = functions.createElement({
type : "div",
name : "leftPanelDiv",
- className : "leftPanelClass",
+ className : "minerva-left-panel",
});
element.appendChild(leftPanelDiv);
var rightPanelDiv = functions.createElement({
@@ -116,7 +116,7 @@ function createDivStructure(element) {
var legendDiv = functions.createElement({
type : "div",
name : "legendDiv",
- className : "legendBox",
+ className : "minerva-legend",
style : "display:none",
});
rightPanelContainerDiv.appendChild(legendDiv);
diff --git a/frontend-js/src/test/js/Export-test.js b/frontend-js/src/test/js/Export-test.js
index b58d6fca71246a0c0a62557156cf296066c4e244..f3ca1655401c87e20568d97e6619e4ca7afcfcf9 100644
--- a/frontend-js/src/test/js/Export-test.js
+++ b/frontend-js/src/test/js/Export-test.js
@@ -1,6 +1,7 @@
"use strict";
/* exported logger */
+/* exported assert */
var Export = require('../../main/js/Export');
var logger = require('./logger');
diff --git a/frontend-js/src/test/js/Functions-test.js b/frontend-js/src/test/js/Functions-test.js
index 9595bf326be87b4c7f0e38f96f486ccd0a68cf7f..7951eb34d46a18abd620131c1aa744acc1faae8a 100644
--- a/frontend-js/src/test/js/Functions-test.js
+++ b/frontend-js/src/test/js/Functions-test.js
@@ -200,9 +200,7 @@ describe('functions', function() {
it('overlayToColor with invalid arg 2', function() {
return functions.overlayToColor({}).then(function(colorString) {
- throw new Error('Promise was unexpectedly fulfilled. Result: ' + colorString);
- }, function rejected(error) {
- assert.ok(error.indexOf("elementOverlay doesn't have neither color nor value set") >= 0);
+ assert.ok(colorString);
});
});
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index cb575f3384c06e952ffdc550afeecff86a8a2011..730bca8fa4bf409b466d4fc8e62d3f2e90c18eac 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -2,11 +2,14 @@
require("./mocha-config.js");
+var Promise = require("bluebird");
+
var HttpStatus = require('http-status-codes');
var Alias = require('../../main/js/map/data/Alias');
var Configuration = require('../../main/js/Configuration');
var LayoutAlias = require('../../main/js/map/data/LayoutAlias');
+var MapModel = require('../../main/js/map/data/MapModel');
var NetworkError = require('../../main/js/NetworkError');
var Project = require('../../main/js/map/data/Project');
var Reaction = require('../../main/js/map/data/Reaction');
@@ -32,6 +35,13 @@ describe('ServerConnector', function() {
});
});
+ it('getModels', function() {
+ return ServerConnector.getModels("sample").then(function(models) {
+ assert.equal(1, models.length);
+ assert.ok(models[0] instanceof MapModel);
+ });
+ });
+
it('getPublications', function() {
return ServerConnector.getPublications().then(function(result) {
assert.equal(result.totalSize, 1);
diff --git a/frontend-js/src/test/js/google-map-mock.js b/frontend-js/src/test/js/google-map-mock.js
index 82a07a1d2c995d455b0eeaa5db90bb80e00cd332..9db90a0a3a54e0ad45053aa394fcd35148c1086f 100644
--- a/frontend-js/src/test/js/google-map-mock.js
+++ b/frontend-js/src/test/js/google-map-mock.js
@@ -80,29 +80,32 @@ var google = {
getNorthEast : function() {
return data.ne;
},
+ getCenter : function() {
+ return new google.maps.LatLng((data.ne.lat() + data.sw.lat()) / 2, (data.ne.lng() + data.sw.lng()) / 2);
+ },
isEmpty : function() {
- return ne === sw || (data.ne.lat() === sw.lat() && data.ne.lng() === sw.lng());
+ return data.ne === data.sw || (data.ne.lat() === data.sw.lat() && data.ne.lng() === data.sw.lng());
},
extend : function(arg) {
if (data.sw === undefined) {
- data.sw = arg;
+ data.sw = new google.maps.LatLng(arg.lat(), arg.lng());
} else {
if (arg.lng() < data.sw.lng()) {
data.sw.longitude = arg.lng();
}
if (arg.lat() < data.sw.lat()) {
- data.sw.longitude = arg.lng();
+ data.sw.latitude = arg.lat();
}
}
if (data.ne === undefined) {
- data.ne = arg;
+ data.ne = new google.maps.LatLng(arg.lat(), arg.lng());
} else {
if (arg.lng() > data.ne.lng()) {
data.ne.longitude = arg.lng();
}
if (arg.lat() > data.ne.lat()) {
- data.ne.longitude = arg.lng();
+ data.ne.latitude = arg.lat();
}
}
},
@@ -206,6 +209,7 @@ var google = {
},
fitBounds : function(bounds) {
this.setBounds(bounds);
+ this.setCenter(bounds.getCenter());
},
};
},
diff --git a/frontend-js/src/test/js/gui/OverviewDialog-test.js b/frontend-js/src/test/js/gui/OverviewDialog-test.js
index f38ec2696df1b51fd8ef8380b736ced13285ad12..02fd8ab3ae0fc51989d32cce3beb388b34976e03 100644
--- a/frontend-js/src/test/js/gui/OverviewDialog-test.js
+++ b/frontend-js/src/test/js/gui/OverviewDialog-test.js
@@ -15,8 +15,8 @@ var logger = require('../logger');
describe('OverviewDialog', function() {
it('open image', function() {
- return ServerConnector.readFile("testFiles/projectWithImages.json").then(function(fileContent) {
- var project = new Project(JSON.parse(fileContent));
+ helper.setUrl("http://test/?id=complex_model_with_images");
+ return ServerConnector.getProject().then(function(project) {
var options = helper.createOptions(project);
var map = new CustomMap(options);
@@ -31,8 +31,8 @@ describe('OverviewDialog', function() {
});
it('open invalid image', function() {
- return ServerConnector.readFile("testFiles/projectWithImages.json").then(function(fileContent) {
- var project = new Project(JSON.parse(fileContent));
+ helper.setUrl("http://test/?id=complex_model_with_images");
+ return ServerConnector.getProject().then(function(project) {
var options = helper.createOptions(project);
var map = new CustomMap(options);
@@ -48,8 +48,8 @@ describe('OverviewDialog', function() {
describe('openLink', function() {
it('link to map', function() {
- return ServerConnector.readFile("testFiles/projectWithImages.json").then(function(fileContent) {
- var project = new Project(JSON.parse(fileContent));
+ helper.setUrl("http://test/?id=complex_model_with_images");
+ return ServerConnector.getProject().then(function(project) {
var options = helper.createOptions(project);
var map = new CustomMap(options);
diff --git a/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js b/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js
index 75d5339b0557fa02c03926b295f6047a3a7cfc67..75339099c76ac7063ab79982aaf18916154a4af4 100644
--- a/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/AbstractPanel-test.js
@@ -31,26 +31,36 @@ describe('AbstractDbPanel', function() {
describe('createTargetRow', function() {
it('target with elements', function() {
var div = document.createElement("div");
- var map = helper.createCustomMap();
- map.registerDbOverlay(helper.createSearchDbOverlay(map));
+ helper.setUrl("http://test/?id=complex_model_with_submaps");
+ var map;
- var panel = new AbstractDbPanel({
- element : div,
- customMap : map,
- panelName : "search",
- });
+ return ServerConnector.getProject().then(function(project) {
+ map = helper.createCustomMap(project);
+ map.registerDbOverlay(helper.createSearchDbOverlay(map));
+
+ var panel = new AbstractDbPanel({
+ element : div,
+ customMap : map,
+ panelName : "search",
+ });
- var target = new Target({
- targetElements : [ {
- id : 329168,
- modelId : 15781,
- type : "ALIAS"
- } ],
- references : [],
- targetParticipants : [],
+ var target = new Target({
+ targetElements : [ {
+ id : 345337,
+ modelId : 16731,
+ type : "ALIAS"
+ }, {
+ id : 345338,
+ modelId : 16731,
+ type : "ALIAS"
+ } ],
+ references : [],
+ targetParticipants : [],
+ });
+ var htmlTag = panel.createTargetRow(target, "empty.png");
+ assert.ok(htmlTag);
+ assert.equal(1, $(".minerva-open-submap-button", $(htmlTag)).length)
});
- var htmlTag = panel.createTargetRow(target, "empty.png");
- assert.ok(htmlTag);
});
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
index 0b096d11d03720499b37f0a277fe2d4430b16b41..c57e0c966530bbb71dca0fb2d9a65e65eccdf773 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
@@ -48,7 +48,9 @@ describe('GuiUtils', function() {
var guiUtils = new GuiUtils();
guiUtils.setMap(map);
- var aliasDiv = guiUtils.createAliasElement(alias);
+ var aliasDiv = guiUtils.createAliasElement({
+ alias : alias
+ });
assert.ok(aliasDiv.innerHTML);
});
@@ -61,7 +63,7 @@ describe('GuiUtils', function() {
var res = guiUtils.createLabelText();
assert.notOk(res.innerHTML);
});
-
+
it('createSubMapLink', function() {
var map = helper.createCustomMap();
@@ -71,7 +73,6 @@ describe('GuiUtils', function() {
var res = guiUtils.createSubMapLink("TEST", map.getId());
assert.ok(res.innerHTML);
});
-
it('createPostTranslationalModifications', function() {
var alias = helper.createAlias();
@@ -104,12 +105,14 @@ describe('GuiUtils', function() {
var guiUtils = new GuiUtils();
guiUtils.setMap(map);
-
+
var reaction = helper.createReaction(map);
var reactionType = "XX TYPE";
reaction.setType(reactionType);
- assert.ok(guiUtils.createReactionElement(reaction).innerHTML.indexOf(reactionType) >= 0);
+ assert.ok(guiUtils.createReactionElement({
+ reaction : reaction
+ }).innerHTML.indexOf(reactionType) >= 0);
});
});
@@ -123,10 +126,14 @@ describe('GuiUtils', function() {
var alias = helper.createAlias(map);
alias.setFullName("xxx");
- assert.ok(guiUtils.createAliasElement(alias).innerHTML.indexOf("Full name") >= 0);
+ assert.ok(guiUtils.createAliasElement({
+ alias : alias
+ }).innerHTML.indexOf("Full name") >= 0);
alias.setFullName("");
- assert.ok(guiUtils.createAliasElement(alias).innerHTML.indexOf("Full name") === -1);
+ assert.ok(guiUtils.createAliasElement({
+ alias : alias
+ }).innerHTML.indexOf("Full name") === -1);
});
});
diff --git a/frontend-js/src/test/js/map/AbstractCustomMap-test.js b/frontend-js/src/test/js/map/AbstractCustomMap-test.js
index 9cb8fd652fe4cf8fae027a151c54f4972e2ce6d9..178bbea0fa09cf46f300e4e2efce9a3a2637a043 100644
--- a/frontend-js/src/test/js/map/AbstractCustomMap-test.js
+++ b/frontend-js/src/test/js/map/AbstractCustomMap-test.js
@@ -3,6 +3,7 @@
var Promise = require("bluebird");
var AliasMarker = require('../../../main/js/map/marker/AliasMarker');
+var AliasSurface = require('../../../main/js/map/surface/AliasSurface');
var AbstractCustomMap = require('../../../main/js/map/AbstractCustomMap');
var PointData = require('../../../main/js/map/data/PointData');
var PointMarker = require('../../../main/js/map/marker/PointMarker');
@@ -281,83 +282,6 @@ describe('AbstractCustomMap', function() {
});
- describe("_openInfoWindowForIdentifiedElement", function() {
- it("for AliasMarker", function() {
- var map;
- var alias, marker;
- return ServerConnector.getProject().then(function(project) {
- map = helper.createCustomMap(project);
- return map.getModel().getAliasById(329171);
- }).then(function(result) {
- alias = result;
-
- var identifiedElement = new IdentifiedElement(alias);
- identifiedElement.setIcon("empty.png");
-
- marker = new AliasMarker({
- element : identifiedElement,
- map : map
- });
-
- return marker.init();
- }).then(function() {
- assert.equal(null, map.getAliasInfoWindowById(alias.getId()));
- return map._openInfoWindowForIdentifiedElement(marker).then(function() {
- assert.ok(map.getAliasInfoWindowById(alias.getId()));
- });
- });
-
- });
- it("for ReactionMarker", function() {
- var map;
- var reaction, marker;
- return ServerConnector.getProject().then(function(project) {
- map = helper.createCustomMap(project);
- return map.getModel().getReactionById(153510);
- }).then(function(result) {
- reaction = result;
-
- marker = new ReactionMarker({
- element : new IdentifiedElement(reaction),
- map : map
- });
- return marker.init();
- }).then(function() {
- assert.equal(null, map.getReactionInfoWindowById(reaction.getId()));
- return map._openInfoWindowForIdentifiedElement(marker);
- }).then(function() {
- assert.ok(map.getReactionInfoWindowById(reaction.getId()));
- });
-
- });
- it("for PointMarker", function() {
-
- var mockObject = helper.createAbstractCustomMap();
-
- mockObject.getTopMap = function() {
- return mockObject;
- };
- mockObject.getOverlayDataForPoint = function() {
- return Promise.resolve([]);
- };
-
- var point = new google.maps.Point(2, 3.45);
- var pointData = new PointData(point, 15781);
-
- var pointMarker = new PointMarker({
- element : new IdentifiedElement(pointData),
- map : mockObject
- });
-
- return pointMarker.init().then(function() {
- assert.equal(null, mockObject.getPointInfoWindowById(pointData.getId()));
- return mockObject._openInfoWindowForIdentifiedElement(pointMarker.getIdentifiedElement());
- }).then(function() {
- assert.ok(mockObject.getPointInfoWindowById(pointData.getId()));
- });
- });
- });
-
it("_openInfoWindowForReaction", function() {
var mockObject = helper.createAbstractCustomMap();
@@ -387,4 +311,31 @@ describe('AbstractCustomMap', function() {
assert.ok(map.isDebug());
});
+ it("fitBounds", function() {
+ var map = helper.createCustomMap();
+ var alias = helper.createAlias(map);
+ var ie = new IdentifiedElement(alias);
+ var marker = new AliasMarker({
+ map : map,
+ element : ie
+ });
+ var surface = new AliasSurface({
+ map : map,
+ element : ie,
+ gmapObj : new google.maps.Rectangle({
+ map : map.getGoogleMap(),
+ bounds : new google.maps.LatLngBounds(new google.maps.LatLng(0, 0), new google.maps.LatLng(0.5, 1)),
+ })
+ });
+
+ var markers = [ marker, surface ];
+ return marker.init().then(function() {
+
+ var center = map.getGoogleMap().getCenter();
+ map.fitBounds(markers);
+ var center2 = map.getGoogleMap().getCenter();
+ assert.ok(center.lat() !== center2.lat() || center.lng() !== center2.lng());
+ })
+ });
+
});
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index 3f2bbadec5fa92d7d7bc588ee50ea60fed2193d2..3c434c3198f62fb471c0981e85acc049982341f4 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -4,11 +4,15 @@ var Promise = require("bluebird");
require("../mocha-config.js");
+var AliasMarker = require('../../../main/js/map/marker/AliasMarker');
var AliasSurface = require('../../../main/js/map/surface/AliasSurface');
var Comment = require('../../../main/js/map/data/Comment');
var CustomMap = require('../../../main/js/map/CustomMap');
var IdentifiedElement = require('../../../main/js/map/data/IdentifiedElement');
var MapContextMenu = require('../../../main/js/gui/MapContextMenu');
+var PointData = require('../../../main/js/map/data/PointData');
+var PointMarker = require('../../../main/js/map/marker/PointMarker');
+var ReactionMarker = require('../../../main/js/map/marker/ReactionMarker');
var ReactionSurface = require('../../../main/js/map/surface/ReactionSurface');
var SelectionContextMenu = require('../../../main/js/gui/SelectionContextMenu');
@@ -900,4 +904,78 @@ describe('CustomMap', function() {
});
+ describe("_openInfoWindowForIdentifiedElement", function() {
+ it("for AliasMarker", function() {
+ var map;
+ var alias, marker;
+ return ServerConnector.getProject().then(function(project) {
+ map = helper.createCustomMap(project);
+ return map.getModel().getAliasById(329171);
+ }).then(function(result) {
+ alias = result;
+
+ var identifiedElement = new IdentifiedElement(alias);
+ identifiedElement.setIcon("empty.png");
+
+ marker = new AliasMarker({
+ element : identifiedElement,
+ map : map
+ });
+
+ return marker.init();
+ }).then(function() {
+ assert.equal(null, map.getAliasInfoWindowById(alias.getId()));
+ return map._openInfoWindowForIdentifiedElement(marker).then(function() {
+ assert.ok(map.getAliasInfoWindowById(alias.getId()));
+ });
+ });
+
+ });
+ it("for ReactionMarker", function() {
+ var map;
+ var reaction, marker;
+ return ServerConnector.getProject().then(function(project) {
+ map = helper.createCustomMap(project);
+ return map.getModel().getReactionById(153510);
+ }).then(function(result) {
+ reaction = result;
+
+ marker = new ReactionMarker({
+ element : new IdentifiedElement(reaction),
+ map : map
+ });
+ return marker.init();
+ }).then(function() {
+ assert.equal(null, map.getReactionInfoWindowById(reaction.getId()));
+ return map._openInfoWindowForIdentifiedElement(marker);
+ }).then(function() {
+ assert.ok(map.getReactionInfoWindowById(reaction.getId()));
+ });
+
+ });
+ it("for PointMarker", function() {
+
+ var mockObject = helper.createCustomMap();
+
+ mockObject.getOverlayDataForPoint = function() {
+ return Promise.resolve([]);
+ };
+
+ var point = new google.maps.Point(2, 3.45);
+ var pointData = new PointData(point, mockObject.getId());
+
+ var pointMarker = new PointMarker({
+ element : new IdentifiedElement(pointData),
+ map : mockObject
+ });
+
+ return pointMarker.init().then(function() {
+ assert.equal(null, mockObject.getPointInfoWindowById(pointData.getId()));
+ return mockObject._openInfoWindowForIdentifiedElement(pointMarker.getIdentifiedElement());
+ }).then(function() {
+ assert.ok(mockObject.getPointInfoWindowById(pointData.getId()));
+ });
+ });
+ });
+
});
diff --git a/frontend-js/src/test/js/map/data/Project-test.js b/frontend-js/src/test/js/map/data/Project-test.js
index 169244b48a1131b378b33f36307fc6e0fd9efd62..e2857d6e12091c92a1132fc01f45f5e7cbf5881b 100644
--- a/frontend-js/src/test/js/map/data/Project-test.js
+++ b/frontend-js/src/test/js/map/data/Project-test.js
@@ -8,70 +8,38 @@ var chai = require('chai');
var assert = chai.assert;
describe('Project', function() {
- it("contructor", function() {
- return ServerConnector.readFile("testFiles/project.json").then(function(res) {
- var project = new Project(res);
- assert.ok(project);
-
- assert.equal(project.getVersion(), "0");
- assert.equal(project.getId(), 14898);
- assert.equal(project.getName(), "UNKNOWN DISEASE MAP");
- assert.equal(project.getProjectId(), "sample");
- assert.equal(project.getDescription(), "");
- assert.deepEqual(project.getOverviewImages(), []);
-
- var model = project.getModel();
- assert.equal(model.getName(), "UNKNOWN DISEASE MAP2");
- assert.equal(model.getId(), 15781);
- assert.equal(model.getTileSize(), 256);
- assert.equal(model.getWidth(), 1305);
- assert.equal(model.getHeight(), 473);
- assert.equal(model.getMinZoom(), 2);
- assert.equal(model.getMaxZoom(), 5);
- assert.equal(model.getLayoutsData().length, 3);
-
- assert.equal(model.getCenterLatLng().lat(), 79.18277721779353);
- assert.equal(model.getCenterLatLng().lng(), -135.06093781915757);
- assert.equal(model.getTopLeftLatLng().lat(), 85.05112877980659);
- assert.equal(model.getTopLeftLatLng().lng(), -180.0);
- assert.equal(model.getBottomRightLatLng().lat(), 81.26928406550978);
- assert.equal(model.getBottomRightLatLng().lng(), -90.0);
-
- assert.equal(logger.getWarnings().length, 0);
+ describe("constructor", function() {
+ it("default", function() {
+ return ServerConnector.readFile("testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&").then(function(res) {
+ var project = new Project(res);
+ assert.ok(project);
+
+ assert.equal(project.getVersion(), "0");
+ assert.equal(project.getId(), 14898);
+ assert.equal(project.getName(), "UNKNOWN DISEASE MAP");
+ assert.equal(project.getProjectId(), "sample");
+ assert.equal(project.getDescription(), "");
+ assert.deepEqual(project.getOverviewImages(), []);
+
+ assert.equal(logger.getWarnings().length, 0);
+ });
});
- });
- it("contructor from Project obj", function() {
- return ServerConnector.readFile("testFiles/project.json").then(function(res) {
- var tmpProject = new Project(res);
-
- var project = new Project(tmpProject);
- assert.ok(project);
-
- assert.equal(project.getVersion(), "0");
- assert.equal(project.getId(), 14898);
- assert.equal(project.getName(), "UNKNOWN DISEASE MAP");
- assert.equal(project.getProjectId(), "sample");
- assert.equal(project.getDescription(), "");
- assert.deepEqual(project.getOverviewImages(), []);
-
- var model = project.getModel();
- assert.equal(model.getName(), "UNKNOWN DISEASE MAP2");
- assert.equal(model.getId(), 15781);
- assert.equal(model.getTileSize(), 256);
- assert.equal(model.getWidth(), 1305);
- assert.equal(model.getHeight(), 473);
- assert.equal(model.getMinZoom(), 2);
- assert.equal(model.getMaxZoom(), 5);
- assert.equal(model.getLayoutsData().length, 3);
-
- assert.equal(model.getCenterLatLng().lat(), 79.18277721779353);
- assert.equal(model.getCenterLatLng().lng(), -135.06093781915757);
- assert.equal(model.getTopLeftLatLng().lat(), 85.05112877980659);
- assert.equal(model.getTopLeftLatLng().lng(), -180.0);
- assert.equal(model.getBottomRightLatLng().lat(), 81.26928406550978);
- assert.equal(model.getBottomRightLatLng().lng(), -90.0);
-
- assert.equal(logger.getWarnings().length, 0);
+ it("from Project obj", function() {
+ return ServerConnector.readFile("testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&").then(function(res) {
+ var tmpProject = new Project(res);
+
+ var project = new Project(tmpProject);
+ assert.ok(project);
+
+ assert.equal(project.getVersion(), "0");
+ assert.equal(project.getId(), 14898);
+ assert.equal(project.getName(), "UNKNOWN DISEASE MAP");
+ assert.equal(project.getProjectId(), "sample");
+ assert.equal(project.getDescription(), "");
+ assert.deepEqual(project.getOverviewImages(), []);
+
+ assert.equal(logger.getWarnings().length, 0);
+ });
});
});
});
diff --git a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
index afea449132adc624f75f1540bfeed7d844da90b9..8559d76ad1ff18fff31471ed623829383214dd22 100644
--- a/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
+++ b/frontend-js/src/test/js/map/window/AliasInfoWindow-test.js
@@ -125,6 +125,32 @@ describe('AliasInfoWindow', function() {
});
});
+ it("createChemicalOverlayInfoDiv", function() {
+ var map, ie, aliasWindow, oc;
+ return ServerConnector.getProject().then(function(project) {
+ map = helper.createCustomMap(project);
+
+ oc = helper.createChemicalDbOverlay(map);
+
+ ie = new IdentifiedElement({
+ id : 329170,
+ modelId : map.getId(),
+ type : "ALIAS"
+ });
+
+ return map.getModel().getByIdentifiedElement(ie, true);
+ }).then(function(alias) {
+ aliasWindow = new AliasInfoWindow({
+ alias : alias,
+ map : map
+ });
+ return oc.getDetailDataByIdentifiedElement(ie, true);
+ }).then(function(data) {
+ var overlayDiv = aliasWindow.createOverlayInfoDiv(oc, data);
+ assert.ok(functions.isDomElement(overlayDiv));
+ });
+ });
+
it("createCommentOverlayInfoDiv", function() {
var map = helper.createCustomMap();
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index 9425790ab9708720eff2d41940ace5093fffc956..6d989ae49367d46f79e121cd6197df6d322d0d2f 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -55,8 +55,8 @@ describe('minerva global', function() {
});
it('create with overview', function() {
- return ServerConnectorMock.readFile("testFiles/projectWithImages.json").then(function(fileContent) {
- var project = new Project(JSON.parse(fileContent));
+ helper.setUrl("http://test/?id=complex_model_with_images");
+ return ServerConnectorMock.getProject().then(function(project) {
var options = helper.createOptions(project);
return minerva.create(options);
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..f71a795beacd84a38018bf292dc4d7906885f882
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/models/all/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"version":null,"name":"main","idObject":19397,"tileSize":256,"width":495,"height":357,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17987,"modelId":19397,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":17988,"modelId":19397,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":17989,"modelId":19397,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty0","creator":"","inputDataAvailable":"false"}],"submodels":[{"version":null,"name":"s3","idObject":19399,"tileSize":256,"width":421,"height":315,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17978,"modelId":19399,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested3","creator":"","inputDataAvailable":"false"},{"idObject":17979,"modelId":19399,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal3","creator":"","inputDataAvailable":"false"},{"idObject":17980,"modelId":19399,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty3","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.19139766235872,"lng":-135.10688836104512},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.06362505154212,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s2","idObject":19400,"tileSize":256,"width":451,"height":253,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17984,"modelId":19400,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested2","creator":"","inputDataAvailable":"false"},{"idObject":17985,"modelId":19400,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal2","creator":"","inputDataAvailable":"false"},{"idObject":17986,"modelId":19400,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty2","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.19006423440219,"lng":-135.09977827050997},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":78.0903352323621,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s1","idObject":19398,"tileSize":256,"width":571,"height":276,"minZoom":2,"maxZoom":4,"layouts":[{"idObject":17981,"modelId":19398,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested1","creator":"","inputDataAvailable":"false"},{"idObject":17982,"modelId":19398,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal1","creator":"","inputDataAvailable":"false"},{"idObject":17983,"modelId":19398,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty1","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.18613072613702,"lng":-135.07880910683014},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":79.44906929997262,"lng":-90.0},"submodelType":"PATHWAY"}],"centerLatLng":{"lat":79.18840067864828,"lng":-135.0909090909091},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.71754541589858,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s3","idObject":19399,"tileSize":256,"width":421,"height":315,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17978,"modelId":19399,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested3","creator":"","inputDataAvailable":"false"},{"idObject":17979,"modelId":19399,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal3","creator":"","inputDataAvailable":"false"},{"idObject":17980,"modelId":19399,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty3","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.19139766235872,"lng":-135.10688836104512},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.06362505154212,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s2","idObject":19400,"tileSize":256,"width":451,"height":253,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17984,"modelId":19400,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested2","creator":"","inputDataAvailable":"false"},{"idObject":17985,"modelId":19400,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal2","creator":"","inputDataAvailable":"false"},{"idObject":17986,"modelId":19400,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty2","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.19006423440219,"lng":-135.09977827050997},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":78.0903352323621,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s1","idObject":19398,"tileSize":256,"width":571,"height":276,"minZoom":2,"maxZoom":4,"layouts":[{"idObject":17981,"modelId":19398,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested1","creator":"","inputDataAvailable":"false"},{"idObject":17982,"modelId":19398,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal1","creator":"","inputDataAvailable":"false"},{"idObject":17983,"modelId":19398,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty1","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.18613072613702,"lng":-135.07880910683014},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":79.44906929997262,"lng":-90.0},"submodelType":"UNKNOWN"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..0e57e7d5d1106a9458b581f9737c13c30df655a7
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/statistics/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"reactionAnnotations":{"UNKNOWN":0,"MI_R_BASE_SEQUENCE":0,"WORM_BASE":0,"COG":0,"HGNC":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"CHEBI":0,"DRUGBANK_TARGET_V4":0,"KEGG_ORTHOLOGY":0,"KEGG_COMPOUND":0,"PUBMED":0,"PHARM":0,"CAS":0,"REFSEQ":0,"WIKIPATHWAYS":0,"UNIPROT_ISOFORM":0,"OMIM":0,"UNIGENE":0,"TOXICOGENOMIC_CHEMICAL":0,"MESH_2012":0,"WIKIPEDIA":0,"HGNC_SYMBOL":0,"ENTREZ":0,"MI_R_BASE_MATURE_SEQUENCE":0,"CHEMBL_COMPOUND":0,"MGD":0,"PANTHER":0,"GO":0,"UNIPROT":0,"SGD":0,"WIKIDATA":0,"CCDS":0,"PUBCHEM":0,"EC":0,"HMDB":0,"INTERPRO":0,"DRUGBANK":0,"KEGG_PATHWAY":0,"TAXONOMY":0,"ENSEMBL_PLANTS":0,"TAIR_LOCUS":0,"KEGG_GENES":0,"REACTOME":0,"ENSEMBL":0,"KEGG_REACTION":0,"PUBCHEM_SUBSTANCE":0,"CHEMSPIDER":0,"PFAM":0,"CHEMBL_TARGET":0},"elementAnnotations":{"UNKNOWN":0,"MI_R_BASE_SEQUENCE":0,"WORM_BASE":0,"COG":0,"HGNC":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"CHEBI":0,"DRUGBANK_TARGET_V4":0,"KEGG_ORTHOLOGY":0,"KEGG_COMPOUND":0,"PUBMED":0,"PHARM":0,"CAS":0,"REFSEQ":0,"WIKIPATHWAYS":0,"UNIPROT_ISOFORM":0,"OMIM":0,"UNIGENE":0,"TOXICOGENOMIC_CHEMICAL":0,"MESH_2012":0,"WIKIPEDIA":0,"HGNC_SYMBOL":0,"ENTREZ":0,"MI_R_BASE_MATURE_SEQUENCE":0,"CHEMBL_COMPOUND":0,"MGD":0,"PANTHER":0,"GO":0,"UNIPROT":0,"SGD":0,"WIKIDATA":0,"CCDS":0,"PUBCHEM":0,"EC":0,"HMDB":0,"INTERPRO":0,"DRUGBANK":0,"KEGG_PATHWAY":0,"TAXONOMY":0,"ENSEMBL_PLANTS":0,"TAIR_LOCUS":0,"KEGG_GENES":0,"REACTOME":0,"ENSEMBL":0,"KEGG_REACTION":0,"PUBCHEM_SUBSTANCE":0,"CHEMSPIDER":0,"PFAM":0,"CHEMBL_TARGET":0},"publications":0}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID&
index e8518f0cb3b6d40abeee366be090671826e24444..9693fbe4938f164fba86283f3d950368e5bfc432 100644
--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_images/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"version":"0","disease":null,"organism":null,"idObject":18115,"name":"UNKNOWN DISEASE MAP","projectId":"complex_model_with_images","description":"","map":{"version":null,"name":"main","idObject":19397,"tileSize":256,"width":495,"height":357,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17987,"modelId":19397,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":17988,"modelId":19397,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":17989,"modelId":19397,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty0","creator":"","inputDataAvailable":"false"}],"submodels":[{"version":null,"name":"s3","idObject":19399,"tileSize":256,"width":421,"height":315,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17978,"modelId":19399,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested3","creator":"","inputDataAvailable":"false"},{"idObject":17979,"modelId":19399,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal3","creator":"","inputDataAvailable":"false"},{"idObject":17980,"modelId":19399,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty3","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.19139766235872,"lng":-135.10688836104512},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.06362505154212,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s2","idObject":19400,"tileSize":256,"width":451,"height":253,"minZoom":2,"maxZoom":3,"layouts":[{"idObject":17984,"modelId":19400,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested2","creator":"","inputDataAvailable":"false"},{"idObject":17985,"modelId":19400,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal2","creator":"","inputDataAvailable":"false"},{"idObject":17986,"modelId":19400,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty2","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.19006423440219,"lng":-135.09977827050997},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":78.0903352323621,"lng":-90.0},"submodelType":"UNKNOWN"},{"version":null,"name":"s1","idObject":19398,"tileSize":256,"width":571,"height":276,"minZoom":2,"maxZoom":4,"layouts":[{"idObject":17981,"modelId":19398,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested1","creator":"","inputDataAvailable":"false"},{"idObject":17982,"modelId":19398,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal1","creator":"","inputDataAvailable":"false"},{"idObject":17983,"modelId":19398,"name":"Empty","description":null,"status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty1","creator":"","inputDataAvailable":"false"}],"submodels":[],"centerLatLng":{"lat":79.18613072613702,"lng":-135.07880910683014},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":79.44906929997262,"lng":-90.0},"submodelType":"PATHWAY"}],"centerLatLng":{"lat":79.18840067864828,"lng":-135.0909090909091},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.71754541589858,"lng":-90.0},"submodelType":"UNKNOWN"},"publicationCount":0,"overviewImageViews":[{"idObject":1261,"filename":"fbdbe43de73fe38f62889b89cb863adb/sub_image.png","width":963,"height":639,"links":[{"idObject":2369,"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":1,"latLng":{"lat":84.89177465079632,"lng":-161.8181818181818},"modelLinkId":19397,"imageLinkId":null,"query":null,"type":"OverviewModelLink"}]},{"idObject":1262,"filename":"fbdbe43de73fe38f62889b89cb863adb/test.png","width":963,"height":639,"links":[{"idObject":2370,"polygon":[{"x":10.0,"y":10.0},{"x":100.0,"y":10.0},{"x":100.0,"y":100.0},{"x":10.0,"y":100.0}],"zoomLevel":null,"latLng":null,"modelLinkId":null,"imageLinkId":1261,"query":null,"type":"OverviewImageLink"},{"idObject":2371,"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":0,"latLng":{"lat":84.89177465079632,"lng":-178.1818181818182},"modelLinkId":19397,"imageLinkId":null,"query":null,"type":"OverviewModelLink"}]}],"topOverviewImage":{"idObject":1262,"filename":"fbdbe43de73fe38f62889b89cb863adb/test.png","width":963,"height":639,"links":[{"idObject":2370,"polygon":[{"x":10.0,"y":10.0},{"x":100.0,"y":10.0},{"x":100.0,"y":100.0},{"x":10.0,"y":100.0}],"zoomLevel":null,"latLng":null,"modelLinkId":null,"imageLinkId":1261,"query":null,"type":"OverviewImageLink"},{"idObject":2371,"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":0,"latLng":{"lat":84.89177465079632,"lng":-178.1818181818182},"modelLinkId":19397,"imageLinkId":null,"query":null,"type":"OverviewModelLink"}]}}
\ No newline at end of file
+{"version":"0","disease":null,"organism":null,"idObject":18115,"name":"UNKNOWN DISEASE MAP","projectId":"complex_model_with_images","description":"","overviewImageViews":[{"idObject":1261,"filename":"fbdbe43de73fe38f62889b89cb863adb/sub_image.png","width":963,"height":639,"links":[{"idObject":2369,"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":1,"latLng":{"lat":84.89177465079632,"lng":-161.8181818181818},"modelLinkId":19397,"imageLinkId":null,"query":null,"type":"OverviewModelLink"}]},{"idObject":1262,"filename":"fbdbe43de73fe38f62889b89cb863adb/test.png","width":963,"height":639,"links":[{"idObject":2370,"polygon":[{"x":10.0,"y":10.0},{"x":100.0,"y":10.0},{"x":100.0,"y":100.0},{"x":10.0,"y":100.0}],"zoomLevel":null,"latLng":null,"modelLinkId":null,"imageLinkId":1261,"query":null,"type":"OverviewImageLink"},{"idObject":2371,"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":0,"latLng":{"lat":84.89177465079632,"lng":-178.1818181818182},"modelLinkId":19397,"imageLinkId":null,"query":null,"type":"OverviewModelLink"}]}],"topOverviewImage":{"idObject":1262,"filename":"fbdbe43de73fe38f62889b89cb863adb/test.png","width":963,"height":639,"links":[{"idObject":2370,"polygon":[{"x":10.0,"y":10.0},{"x":100.0,"y":10.0},{"x":100.0,"y":100.0},{"x":10.0,"y":100.0}],"zoomLevel":null,"latLng":null,"modelLinkId":null,"imageLinkId":1261,"query":null,"type":"OverviewImageLink"},{"idObject":2371,"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":0,"latLng":{"lat":84.89177465079632,"lng":-178.1818181818182},"modelLinkId":19397,"imageLinkId":null,"query":null,"type":"OverviewModelLink"}]}}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..19fa38ecdf18b5a74896e1113d84f726663b9f9b
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/models/all/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"version":null,"name":"main","idObject":16728,"tileSize":256,"width":515,"height":362,"minZoom":2,"maxZoom":4,"layouts":[{"idObject":14959,"modelId":16728,"name":"Pathways and compartments","description":null,"status":"Not available","progress":"0.00","directory":"0e6072e4c8d73a05d8bd8ec873761725/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":14960,"modelId":16728,"name":"Network","description":null,"status":"Not available","progress":"0.00","directory":"0e6072e4c8d73a05d8bd8ec873761725/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":14961,"modelId":16728,"name":"Empty","description":null,"status":"Not 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diff --git a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/complex_model_with_submaps/token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/drug_target_sample/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/drug_target_sample/models/all/token=MOCK_TOKEN_ID&
new file mode 100644
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@@ -0,0 +1 @@
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diff --git a/frontend-js/testFiles/apiCalls/projects/drug_target_sample/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/drug_target_sample/token=MOCK_TOKEN_ID&
index 685f9b480c96e79a9b15dcbc156de9be0b8e0d01..d75e17d06d3be7226cd2b024dec6fa18a18ddc46 100644
--- a/frontend-js/testFiles/apiCalls/projects/drug_target_sample/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/drug_target_sample/token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/empty/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/empty/models/all/token=MOCK_TOKEN_ID&
new file mode 100644
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diff --git a/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID&
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--- a/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/empty/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329170&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329170&token=MOCK_TOKEN_ID&
new file mode 100644
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID&
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+++ b/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"reactionAnnotations":{"SGD":0,"HGNC_SYMBOL":0,"GO":0,"MI_R_BASE_SEQUENCE":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"REACTOME":2,"ENSEMBL":0,"OMIM":0,"CHEBI":0,"KEGG_COMPOUND":0,"DRUGBANK":0,"UNIGENE":0,"KEGG_ORTHOLOGY":0,"CHEMBL_TARGET":0,"WORM_BASE":0,"ENSEMBL_PLANTS":0,"REFSEQ":0,"ENTREZ":0,"UNKNOWN":0,"MI_R_BASE_MATURE_SEQUENCE":0,"UNIPROT_ISOFORM":0,"COG":0,"TAXONOMY":0,"KEGG_REACTION":0,"TOXICOGENOMIC_CHEMICAL":0,"CHEMSPIDER":0,"TAIR_LOCUS":0,"UNIPROT":0,"PHARM":0,"CCDS":0,"HGNC":0,"WIKIPEDIA":0,"HMDB":0,"PANTHER":0,"WIKIDATA":0,"PUBCHEM_SUBSTANCE":0,"CAS":0,"KEGG_PATHWAY":0,"MGD":0,"PUBMED":1,"CHEMBL_COMPOUND":0,"PFAM":0,"MESH_2012":0,"EC":0,"PUBCHEM":0,"DRUGBANK_TARGET_V4":0,"WIKIPATHWAYS":0,"INTERPRO":0,"KEGG_GENES":0},"elementAnnotations":{"SGD":0,"HGNC_SYMBOL":0,"GO":0,"MI_R_BASE_SEQUENCE":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"REACTOME":4,"ENSEMBL":0,"OMIM":0,"CHEBI":0,"KEGG_COMPOUND":0,"DRUGBANK":0,"UNIGENE":0,"KEGG_ORTHOLOGY":0,"CHEMBL_TARGET":0,"WORM_BASE":0,"ENSEMBL_PLANTS":0,"REFSEQ":5,"ENTREZ":2,"UNKNOWN":0,"MI_R_BASE_MATURE_SEQUENCE":0,"UNIPROT_ISOFORM":0,"COG":0,"TAXONOMY":0,"KEGG_REACTION":0,"TOXICOGENOMIC_CHEMICAL":0,"CHEMSPIDER":0,"TAIR_LOCUS":0,"UNIPROT":0,"PHARM":1,"CCDS":0,"HGNC":1,"WIKIPEDIA":0,"HMDB":0,"PANTHER":0,"WIKIDATA":0,"PUBCHEM_SUBSTANCE":0,"CAS":0,"KEGG_PATHWAY":0,"MGD":0,"PUBMED":0,"CHEMBL_COMPOUND":0,"PFAM":0,"MESH_2012":0,"EC":0,"PUBCHEM":0,"DRUGBANK_TARGET_V4":0,"WIKIPATHWAYS":0,"INTERPRO":0,"KEGG_GENES":1}}
\ No newline at end of file
+{"reactionAnnotations":{"UNKNOWN":0,"MI_R_BASE_SEQUENCE":0,"WORM_BASE":0,"COG":0,"HGNC":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"CHEBI":0,"DRUGBANK_TARGET_V4":0,"KEGG_ORTHOLOGY":0,"KEGG_COMPOUND":0,"PUBMED":1,"PHARM":0,"CAS":0,"REFSEQ":0,"WIKIPATHWAYS":0,"UNIPROT_ISOFORM":0,"OMIM":0,"UNIGENE":0,"TOXICOGENOMIC_CHEMICAL":0,"MESH_2012":0,"WIKIPEDIA":0,"HGNC_SYMBOL":0,"ENTREZ":0,"MI_R_BASE_MATURE_SEQUENCE":0,"CHEMBL_COMPOUND":0,"MGD":0,"PANTHER":0,"GO":0,"UNIPROT":0,"SGD":0,"WIKIDATA":0,"CCDS":0,"PUBCHEM":0,"EC":0,"HMDB":0,"INTERPRO":0,"DRUGBANK":0,"KEGG_PATHWAY":0,"TAXONOMY":0,"ENSEMBL_PLANTS":0,"TAIR_LOCUS":0,"KEGG_GENES":0,"REACTOME":2,"ENSEMBL":0,"KEGG_REACTION":0,"PUBCHEM_SUBSTANCE":0,"CHEMSPIDER":0,"PFAM":0,"CHEMBL_TARGET":0},"elementAnnotations":{"UNKNOWN":0,"MI_R_BASE_SEQUENCE":0,"WORM_BASE":0,"COG":0,"HGNC":1,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"CHEBI":0,"DRUGBANK_TARGET_V4":0,"KEGG_ORTHOLOGY":0,"KEGG_COMPOUND":0,"PUBMED":0,"PHARM":1,"CAS":0,"REFSEQ":5,"WIKIPATHWAYS":0,"UNIPROT_ISOFORM":0,"OMIM":0,"UNIGENE":0,"TOXICOGENOMIC_CHEMICAL":0,"MESH_2012":0,"WIKIPEDIA":0,"HGNC_SYMBOL":0,"ENTREZ":2,"MI_R_BASE_MATURE_SEQUENCE":0,"CHEMBL_COMPOUND":0,"MGD":0,"PANTHER":0,"GO":0,"UNIPROT":0,"SGD":0,"WIKIDATA":0,"CCDS":0,"PUBCHEM":0,"EC":0,"HMDB":0,"INTERPRO":0,"DRUGBANK":0,"KEGG_PATHWAY":0,"TAXONOMY":0,"ENSEMBL_PLANTS":0,"TAIR_LOCUS":0,"KEGG_GENES":1,"REACTOME":4,"ENSEMBL":0,"KEGG_REACTION":0,"PUBCHEM_SUBSTANCE":0,"CHEMSPIDER":0,"PFAM":0,"CHEMBL_TARGET":0},"publications":1}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&
index de46921fd2d951aa249b764d214c912789761b19..2854eb409636931a81242b5c1ea33fbc3b784969 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"version":"0","disease":{"resource":"D010300","link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","id":1104479,"type":"MESH_2012"},"organism":{"resource":"1570291","link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","id":1104480,"type":"TAXONOMY"},"idObject":14898,"name":"UNKNOWN DISEASE MAP","projectId":"sample","description":"","map":{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":15781,"tileSize":256,"width":1305,"height":473,"minZoom":2,"maxZoom":5,"layouts":[{"idObject":14081,"modelId":15781,"name":"Pathways and compartments","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":14082,"modelId":15781,"name":"Network","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":14083,"modelId":15781,"name":"Empty","description":"","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false"},{"idObject":18076,"modelId":15781,"name":"C:\\fakepath\\test.txt","description":"xxx","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18076","creator":"","inputDataAvailable":"true"},{"idObject":18077,"modelId":15781,"name":"xxx","description":"yyy","status":"OK","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18077","creator":"","inputDataAvailable":"true"}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0},"submodelType":"UNKNOWN"},"publicationCount":1,"overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
+{"version":"0","disease":{"resource":"D010300","link":"http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300","id":1104479,"type":"MESH_2012"},"organism":{"resource":"1570291","link":"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1570291","id":1104480,"type":"TAXONOMY"},"idObject":14898,"name":"UNKNOWN DISEASE MAP","projectId":"sample","description":"","overviewImageViews":[],"topOverviewImage":null}
\ No newline at end of file
diff --git a/frontend-js/testFiles/project.json b/frontend-js/testFiles/project.json
deleted file mode 100644
index fa052d1df622691b47b04d680c0f29b38e866157..0000000000000000000000000000000000000000
--- a/frontend-js/testFiles/project.json
+++ /dev/null
@@ -1 +0,0 @@
-{"version":"0","idObject":14898,"name":"UNKNOWN DISEASE MAP","projectId":"sample","description":"","map":{"name":"UNKNOWN DISEASE MAP2","idObject":15781,"tileSize":256,"width":1305,"height":473,"minZoom":2,"maxZoom":5,"layouts":[{"modelId":15781,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false","idObject":14081},{"modelId":15781,"name":"Network","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false","idObject":14082},{"modelId":15781,"name":"Empty","status":"Not available","progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false","idObject":14083}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0}},"overviewImageViews":[]}
\ No newline at end of file
diff --git a/frontend-js/testFiles/projectWithImages.json b/frontend-js/testFiles/projectWithImages.json
deleted file mode 100644
index b989ec48df62f47ce57be130dd7028861f6240a5..0000000000000000000000000000000000000000
--- a/frontend-js/testFiles/projectWithImages.json
+++ /dev/null
@@ -1 +0,0 @@
-{"version":"0","idObject":18115,"name":"UNKNOWN DISEASE MAP","projectId":"complex_model_with_images","description":"","map":{"name":"main","idObject":19397,"tileSize":256,"width":495,"height":357,"minZoom":2,"maxZoom":3,"layouts":[{"modelId":19397,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested0","creator":"","inputDataAvailable":"false","idObject":17987},{"modelId":19397,"name":"Network","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal0","creator":"","inputDataAvailable":"false","idObject":17988},{"modelId":19397,"name":"Empty","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty0","creator":"","inputDataAvailable":"false","idObject":17989}],"submodels":[{"name":"s2","idObject":19400,"tileSize":256,"width":451,"height":253,"minZoom":2,"maxZoom":3,"layouts":[{"modelId":19400,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested2","creator":"","inputDataAvailable":"false","idObject":17984},{"modelId":19400,"name":"Network","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal2","creator":"","inputDataAvailable":"false","idObject":17985},{"modelId":19400,"name":"Empty","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty2","creator":"","inputDataAvailable":"false","idObject":17986}],"submodels":[],"centerLatLng":{"lat":79.19006423440219,"lng":-135.09977827050997},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":78.0903352323621,"lng":-90.0}},{"name":"s3","idObject":19399,"tileSize":256,"width":421,"height":315,"minZoom":2,"maxZoom":3,"layouts":[{"modelId":19399,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested3","creator":"","inputDataAvailable":"false","idObject":17978},{"modelId":19399,"name":"Network","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal3","creator":"","inputDataAvailable":"false","idObject":17979},{"modelId":19399,"name":"Empty","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty3","creator":"","inputDataAvailable":"false","idObject":17980}],"submodels":[],"centerLatLng":{"lat":79.19139766235872,"lng":-135.10688836104512},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.06362505154212,"lng":-90.0}},{"name":"s1","idObject":19398,"tileSize":256,"width":571,"height":276,"minZoom":2,"maxZoom":4,"layouts":[{"modelId":19398,"name":"Pathways and compartments","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_nested1","creator":"","inputDataAvailable":"false","idObject":17981},{"modelId":19398,"name":"Network","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_normal1","creator":"","inputDataAvailable":"false","idObject":17982},{"modelId":19398,"name":"Empty","status":"Not available","progress":"0.00","directory":"fbdbe43de73fe38f62889b89cb863adb/_empty1","creator":"","inputDataAvailable":"false","idObject":17983}],"submodels":[],"centerLatLng":{"lat":79.18613072613702,"lng":-135.07880910683014},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":79.44906929997262,"lng":-90.0}}],"centerLatLng":{"lat":79.18840067864828,"lng":-135.0909090909091},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":74.71754541589858,"lng":-90.0}},"overviewImageViews":[{"filename":"fbdbe43de73fe38f62889b89cb863adb/sub_image.png","width":963,"height":639,"links":[{"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":1,"latLng":{"lat":84.89177465079632,"lng":-161.8181818181818},"modelLinkId":19397,"type":"OverviewModelLink","idObject":2369}],"idObject":1261},{"filename":"fbdbe43de73fe38f62889b89cb863adb/test.png","width":963,"height":639,"links":[{"polygon":[{"x":10.0,"y":10.0},{"x":100.0,"y":10.0},{"x":100.0,"y":100.0},{"x":10.0,"y":100.0}],"imageLinkId":1261,"type":"OverviewImageLink","idObject":2370},{"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":0,"latLng":{"lat":84.89177465079632,"lng":-178.1818181818182},"modelLinkId":19397,"type":"OverviewModelLink","idObject":2371}],"idObject":1262}],"topOverviewImage":{"filename":"fbdbe43de73fe38f62889b89cb863adb/test.png","width":963,"height":639,"links":[{"polygon":[{"x":10.0,"y":10.0},{"x":100.0,"y":10.0},{"x":100.0,"y":100.0},{"x":10.0,"y":100.0}],"imageLinkId":1261,"type":"OverviewImageLink","idObject":2370},{"polygon":[{"x":200.0,"y":200.0},{"x":200.0,"y":400.0},{"x":400.0,"y":400.0},{"x":400.0,"y":200.0}],"zoomLevel":0,"latLng":{"lat":84.89177465079632,"lng":-178.1818181818182},"modelLinkId":19397,"type":"OverviewModelLink","idObject":2371}],"idObject":1262}}
\ No newline at end of file
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
index 891434f015e8b5a93073963b4f34532f7317c20f..64a211a66469f91641e9b2555a2a4d5af16eb6a4 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
@@ -26,7 +26,7 @@ public class ClearColorModelCommand extends ModelCommand {
*/
public ClearColorModelCommand(Model model) {
super(model);
- colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE));
+ colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE, Color.WHITE));
}
@Override
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
index 1a6d5d5d31976885404440319dab3dc8e4304507..0638978854921b447bdf5ec20ae3cff3865c5cff 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
@@ -24,6 +24,8 @@ public class ColorExtractor {
*/
private Color maxColor;
+ private Color simpleColor;
+
/**
* Default constructor.
*
@@ -34,12 +36,13 @@ public class ColorExtractor {
* Color that should be used for max values of
* {@link ColorSchema#value}
*/
- public ColorExtractor(Color minColor, Color maxColor) {
- if (minColor == null || maxColor == null) {
+ public ColorExtractor(Color minColor, Color maxColor, Color simpleColor) {
+ if (minColor == null || maxColor == null || simpleColor == null) {
throw new InvalidArgumentException("Parameters cannot be null");
}
this.minColor = minColor;
this.maxColor = maxColor;
+ this.simpleColor = simpleColor;
}
/**
@@ -53,6 +56,8 @@ public class ColorExtractor {
public Color getNormalizedColor(ColorSchema colorSchema) {
if (colorSchema.getColor() != null) {
return colorSchema.getColor();
+ } else if (colorSchema.getValue() == null) {
+ return simpleColor;
} else {
return getColorForValue(colorSchema.getValue());
}
@@ -93,4 +98,8 @@ public class ColorExtractor {
public Color getMaxColor() {
return maxColor;
}
+
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java b/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
index 38920e1caed5f00fc4017059749400b3a141f9e0..8e55dbd35a707a07aa425b9c166fb372d61f951e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SemanticZoomLevelMatcher.java
@@ -3,7 +3,11 @@ package lcsb.mapviewer.commands;
import org.apache.log4j.Logger;
public class SemanticZoomLevelMatcher {
- Logger logger = Logger.getLogger(SemanticZoomLevelMatcher.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SemanticZoomLevelMatcher.class);
/**
* Checks if level belongs to the range defined in
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 14d934650b6eec46884d8f889e27d8e8472fcbbc..8bc1cd05cba8f5a21e96fb2a700abbe6dcf54369 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -31,7 +31,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class ColorModelCommandTest extends CommandTestFunctions {
Logger logger = Logger.getLogger(ColorModelCommandTest.class);
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
index 71e8845ee329681ac3b0d57562ef0826288abc30..8ff0f95344526a7e9e12cd455af360f510d71a1d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java
@@ -126,7 +126,12 @@ public enum ConfigurationElementType {
/**
* Color used for positive overlay values.
*/
- MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR, false);
+ MAX_COLOR_VAL("Overlay color for postive values", "0000FF", ConfigurationElementEditType.COLOR, false),
+
+ /**
+ * Color used for undefined overlay values.
+ */
+ SIMPLE_COLOR_VAL("Overlay color when no values are defined", "00FF00", ConfigurationElementEditType.COLOR, false);
/**
* Default value of the configuration parameter (it will be used only when
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/User.java b/model/src/main/java/lcsb/mapviewer/model/user/User.java
index 3cc421f8f51a6d229836e00d244be48821b286f4..216c7837dbf52005d912857520f45af158284698 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -80,6 +80,13 @@ public class User implements Serializable {
*/
private Color maxColor;
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#SIMPLE_COLOR_VAL}. Used for coloring
+ * overlays without values and colors.
+ */
+ private Color simpleColor;
+
/**
* Is the user removed.
*/
@@ -309,4 +316,21 @@ public class User implements Serializable {
this.maxColor = maxColor;
}
+ /**
+ * @return the simpleColor
+ * @see #simpleColor
+ */
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
+ /**
+ * @param simpleColor
+ * the simpleColor to set
+ * @see #simpleColor
+ */
+ public void setSimpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ }
+
}
diff --git a/pathvisio/src/main/resources/empty.txt b/pathvisio/src/main/resources/empty.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e45f025b4e3a8b4af265accb372955b7774d589f
--- /dev/null
+++ b/pathvisio/src/main/resources/empty.txt
@@ -0,0 +1 @@
+EMPTY file to force git to push the folder
\ No newline at end of file
diff --git a/persist/src/db/11/fix_db_20170725.sql b/persist/src/db/11/fix_db_20170725.sql
new file mode 100644
index 0000000000000000000000000000000000000000..37a66ace4e369cad3a43817851e970acbd5eae04
--- /dev/null
+++ b/persist/src/db/11/fix_db_20170725.sql
@@ -0,0 +1,2 @@
+--simple color for coloring
+alter table user_table add column simplecolor bytea;
\ No newline at end of file
diff --git a/persist/src/db/11/fix_db_20170731.sql b/persist/src/db/11/fix_db_20170731.sql
new file mode 100644
index 0000000000000000000000000000000000000000..8e9c0ad40716340e825ff88d423c06d7ba536d9e
--- /dev/null
+++ b/persist/src/db/11/fix_db_20170731.sql
@@ -0,0 +1,2 @@
+--drugbank targets issue
+delete from cachequery where type in (select iddb from cache_type where classname = 'lcsb.mapviewer.annotation.services.DrugbankHTMLParser') and not query like 'http%';
diff --git a/quadTrees/src/main/resources/empty.txt b/quadTrees/src/main/resources/empty.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e45f025b4e3a8b4af265accb372955b7774d589f
--- /dev/null
+++ b/quadTrees/src/main/resources/empty.txt
@@ -0,0 +1 @@
+EMPTY file to force git to push the folder
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 7953a630b0d2524f8c4e3e7f80170b3e262ac62f..ac78d8b8d3665ee9c2839b91150ed323cc98d978 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.api;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -25,6 +26,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
@@ -32,11 +34,18 @@ import lcsb.mapviewer.services.view.AnnotationView;
@Transactional(value = "txManager")
public abstract class BaseRestImpl {
- Logger logger = Logger.getLogger(BaseRestImpl.class);
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(BaseRestImpl.class);
@Autowired
private IModelService modelService;
+ @Autowired
+ private IProjectService projectService;
+
@Autowired
private IUserService userService;
@@ -74,8 +83,8 @@ public abstract class BaseRestImpl {
};
protected Map<String, Object> createAnnotation(MiriamData annotation) {
- Map<String, Object> result = new HashMap<>();
if (annotation != null && annotation.getDataType() != null) {
+ Map<String, Object> result = new HashMap<>();
if (annotation.getDataType().getUris().size() > 0) {
try {
result.put("link", miriamConnector.getUrlString(annotation));
@@ -94,8 +103,10 @@ public abstract class BaseRestImpl {
result.put("type", annotation.getDataType().name());
result.put("resource", annotation.getResource());
result.put("id", annotation.getId());
+ return result;
+ } else {
+ throw new InvalidArgumentException("invalid miriam data: " + annotation);
}
- return result;
};
protected Map<String, Object> createAnnotation(AnnotationView annotation) {
@@ -200,6 +211,23 @@ public abstract class BaseRestImpl {
for (Target target : targets) {
result.add(prepareTarget(target, models));
}
+ result.sort(new Comparator<Map<String, Object>>() {
+
+ @Override
+ public int compare(Map<String, Object> o1, Map<String, Object> o2) {
+ List<?> targetedObjects1 = (List<?>) o1.get("targetElements");
+ List<?> targetedObjects2 = (List<?>) o2.get("targetElements");
+ Integer size1 = 0;
+ Integer size2 = 0;
+ if (targetedObjects1 != null) {
+ size1 = targetedObjects1.size();
+ }
+ if (targetedObjects2 != null) {
+ size2 = targetedObjects2.size();
+ }
+ return -size1.compareTo(size2);
+ }
+ });
return result;
}
@@ -238,5 +266,20 @@ public abstract class BaseRestImpl {
}
}
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
index 0d79586f926aa1a0cae0f6dc42ef10b649002536..58365826a5a547972bb6fe8a927ff2aa6c017c76 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
@@ -6,7 +6,6 @@ import java.util.Map;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.services.view.AnnotationView;
import lcsb.mapviewer.services.view.OverviewImageView;
public class ProjectMetaData implements Serializable {
@@ -48,10 +47,6 @@ public class ProjectMetaData implements Serializable {
*/
private String description;
- private ModelMetaData map;
-
- private Integer publicationCount;
-
/**
* List of overview images attached to this model.
*/
@@ -170,23 +165,6 @@ public class ProjectMetaData implements Serializable {
this.projectId = projectId;
}
- /**
- * @return the map
- * @see #map
- */
- public ModelMetaData getMap() {
- return map;
- }
-
- /**
- * @param map
- * the map to set
- * @see #map
- */
- public void setMap(ModelMetaData map) {
- this.map = map;
- }
-
/**
* @return the idObject
* @see #idObject
@@ -237,22 +215,4 @@ public class ProjectMetaData implements Serializable {
public void setOrganism(Map<String, Object> organism) {
this.organism = organism;
}
-
- /**
- * @return the publicationCount
- * @see #publicationCount
- */
- public Integer getPublicationCount() {
- return publicationCount;
- }
-
- /**
- * @param publicationCount
- * the publicationCount to set
- * @see #publicationCount
- */
- public void setPublicationCount(Integer publicationCount) {
- this.publicationCount = publicationCount;
- }
-
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index cba3a43808693c1ebe96e3858c2a5b76aa157f2a..6f4f9a1d17c8a19eb9d1a9963ea161389d02424a 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -62,7 +62,6 @@ import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@@ -130,7 +129,7 @@ public class ProjectRestImpl extends BaseRestImpl {
result.setVersion(model.getMapVersion());
result.setDescription(model.getNotes());
- Set<OverviewImage> set = new HashSet<OverviewImage>();
+ Set<OverviewImage> set = new HashSet<>();
set.addAll(model.getOverviewImages());
for (OverviewImage image : model.getOverviewImages()) {
for (OverviewLink ol : image.getLinks()) {
@@ -145,13 +144,6 @@ public class ProjectRestImpl extends BaseRestImpl {
logger.warn("Cannot determine top level image. Taking first one. " + model.getOverviewImages().get(0).getFilename());
result.setTopOverviewImage(factory.create(model.getOverviewImages().get(0)));
}
- result.setMap(new ModelMetaData(model));
-
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- result.setPublicationCount(publicationsRestImpl.getPublications(models).size());
-
}
return result;
@@ -313,8 +305,7 @@ public class ProjectRestImpl extends BaseRestImpl {
level(level - Configuration.MIN_ZOOM_LEVEL).//
nested(false).// automatically set nested view as invalid
scale(scale).//
- minColor(colorExtractor.getMinColor()).//
- maxColor(colorExtractor.getMaxColor()).//
+ colorExtractor(colorExtractor).//
sbgn(topModel.getProject().isSbgnFormat()).//
model(colorModel);
if (overlay != null) {
@@ -436,6 +427,8 @@ public class ProjectRestImpl extends BaseRestImpl {
}
result.put("reactionAnnotations", reactionAnnotations);
+
+ result.put("publications", publicationsRestImpl.getPublications(models).size());
return result;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index 702cb56cb24015b2109b31f7587346b44f66a22a..25c714b01695187487c30f571f98fa7d8dccb02f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -36,7 +36,6 @@ public class ChemicalRestImpl extends BaseRestImpl {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private Logger logger = Logger.getLogger(ChemicalRestImpl.class);
@Autowired
@@ -120,7 +119,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
this.modelService = modelService;
}
- private Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
+ protected Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
Map<String, Object> result = new HashMap<>();
String description = "Mesh term not available";
@@ -144,14 +143,18 @@ public class ChemicalRestImpl extends BaseRestImpl {
} else if (column.equals("references")) {
List<Map<String, Object>> references = new ArrayList<>();
references.add(createAnnotation(chemical.getChemicalId()));
- references.add(createAnnotation(chemical.getCasID()));
+ if (chemical.getCasID() != null) {
+ references.add(createAnnotation(chemical.getCasID()));
+ }
value = references;
} else if (column.equals("directevidencereferences")) {
value = createAnnotations(chemical.getDirectEvidencePublication());
} else if (column.equals("description")) {
value = description;
} else if (column.equals("directevidence")) {
- value = chemical.getDirectEvidence().getValue();
+ if (chemical.getDirectEvidence() != null) {
+ value = chemical.getDirectEvidence().getValue();
+ }
} else if (column.equals("synonyms")) {
value = synonyms;
} else if (column.equals("targets")) {
@@ -164,7 +167,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
return result;
}
- private Set<String> createChemicalColumnSet(String columns) {
+ protected Set<String> createChemicalColumnSet(String columns) {
Set<String> columnsSet = new HashSet<>();
if (columns.equals("")) {
columnsSet.add("name");
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index 85fed9a13c9f0af2de55ba2d27fbf0b93bcbbff6..a08a985d71237383216c776d64c2277356d19b05 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -22,7 +22,6 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.drug.IDrugService;
@@ -35,19 +34,16 @@ public class DrugRestImpl extends BaseRestImpl {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(DrugRestImpl.class);
+ private Logger logger = Logger.getLogger(DrugRestImpl.class);
@Autowired
- private IDrugService drugService;
+ private IDrugService drugService;
@Autowired
- private IModelService modelService;
+ private IModelService modelService;
@Autowired
- private IUserService userService;
-
- @Autowired
- private ElementMatcher elementMatcher;
+ private IUserService userService;
public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
AuthenticationToken authenticationToken = userService.getToken(token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
index 1d9f8fc7e6000f1e153f183877355f224b98fd99..3f0352abf05e0f668a86f494d30b1cd9b164e3a9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
@@ -33,13 +32,10 @@ public class MiRnaRestImpl extends BaseRestImpl {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(MiRnaRestImpl.class);
+ private Logger logger = Logger.getLogger(MiRnaRestImpl.class);
@Autowired
- private IMiRNAService miRnaService;
-
- @Autowired
- private ElementMatcher elementMatcher;
+ private IMiRNAService miRnaService;
public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
AuthenticationToken authenticationToken = getUserService().getToken(token);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
new file mode 100644
index 0000000000000000000000000000000000000000..1cecb23458d9dbb5021a4df738b7d44872f1474d
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -0,0 +1,44 @@
+package lcsb.mapviewer.api.projects.models;
+
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ModelController extends BaseController {
+ @Autowired
+ private ModelRestImpl modelController;
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<ModelMetaData> getModels(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return modelController.getModels(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Object getModel(//
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ if (modelId.equals("*")) {
+ return modelController.getModels(projectId, token);
+ } else {
+ return modelController.getModel(projectId, modelId, token);
+ }
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ModelMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
similarity index 94%
rename from rest-api/src/main/java/lcsb/mapviewer/api/projects/ModelMetaData.java
rename to rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
index 273364a57e42d047251b7e1cf358cce2bcb69a54..62181d0b379a22f618a5cb6fa1d51622a282704e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ModelMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.api.projects;
+package lcsb.mapviewer.api.projects.models;
import java.awt.geom.Point2D;
import java.io.Serializable;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..e2a747e9973f376d5fb3dd2c05c4f6796c3d3045
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.api.projects.models;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.view.AuthenticationToken;
+
+@Transactional(value = "txManager")
+public class ModelRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ModelRestImpl.class);
+
+ public List<ModelMetaData> getModels(String projectId, String token) throws SecurityException, ObjectNotFoundException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ List<ModelMetaData> result = createData(project, authenticationToken);
+ return result;
+ }
+
+ public ModelMetaData getModel(String projectId, String modelId, String token) throws SecurityException, ObjectNotFoundException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model submodel = model.getSubmodelById(modelId);
+ if (submodel == null) {
+ return null;
+ } else {
+ return new ModelMetaData(submodel);
+ }
+ }
+
+ private List<ModelMetaData> createData(Project project, AuthenticationToken token) {
+ List<ModelMetaData> result = new ArrayList<>();
+ Model model = getModelService().getLastModelByProjectId(project.getProjectId(), token);
+
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ for (Model model2 : models) {
+ result.add(new ModelMetaData(model2));
+ }
+ return result;
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index 4c2875005877e07e6f058fca0da1452b9260da88..ab3c736a4d03e7e1946654dd837e2382f238c9bc 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -19,8 +19,6 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ElementModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.model.map.species.field.Structure;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.services.SecurityException;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 1bab83b85dc597cfe316707de11b67229d6f8ed5..0d3e0349126edced91c82d2ad674c564cbd97505 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.api.projects.models.publications;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
@@ -33,7 +32,6 @@ import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
@@ -59,7 +57,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
@Autowired
private OverviewImageViewFactory factory;
- public SortedMap<MiriamData, List<BioEntity>> getPublications(List<Model> models) {
+ public SortedMap<MiriamData, List<BioEntity>> getPublications(Collection<Model> models) {
SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
for (Model modelData : models) {
for (Element element : modelData.getElements()) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index 0c2c7a6ea47a6108c58a00903ded58abedae174d..ec6bb96897cb4a0c4b6f3a8223ea59bc6be51813 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -47,11 +47,6 @@ public class OverlayRestImpl extends BaseRestImpl {
*/
private Logger logger = Logger.getLogger(OverlayRestImpl.class);
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
@Autowired
private ILayoutService layoutService;
@@ -60,31 +55,14 @@ public class OverlayRestImpl extends BaseRestImpl {
private LayoutDao layoutDao;
public List<LayoutView> getOverlayList(String token, String projectId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
return layoutService.getCustomLayouts(model, token);
}
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
/**
* @return the layoutService
* @see #layoutService
@@ -102,28 +80,11 @@ public class OverlayRestImpl extends BaseRestImpl {
this.layoutService = layoutService;
}
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
public List<Map<String, Object>> getOverlayElements(String token, String projectId, int overlayId, String columns) throws QueryException, SecurityException {
List<Map<String, Object>> result = new ArrayList<>();
- AuthenticationToken authenticationToken = userService.getToken(token);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -146,8 +107,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public LayoutView getOverlayById(String token, String projectId, String overlayId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -155,8 +116,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public FileEntry getOverlaySource(String token, String projectId, String overlayId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -175,8 +136,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public LayoutView updateOverlay(String token, String projectId, String overlayId, Map<String, Object> overlayData) throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -184,7 +145,7 @@ public class OverlayRestImpl extends BaseRestImpl {
throw new QueryException("overlay field cannot be undefined");
}
Project project = model.getProject();
- boolean isAdmin = userService.userHasPrivilege(authenticationToken, PrivilegeType.LAYOUT_MANAGEMENT, project);
+ boolean isAdmin = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.LAYOUT_MANAGEMENT, project);
try {
Integer id = Integer.valueOf(overlayId);
Layout layout = layoutService.getLayoutDataById(id, authenticationToken);
@@ -208,8 +169,8 @@ public class OverlayRestImpl extends BaseRestImpl {
}
public Map<String, Object> removeOverlay(String token, String projectId, String overlayId) throws QueryException, SecurityException, IOException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -249,12 +210,12 @@ public class OverlayRestImpl extends BaseRestImpl {
public LayoutView addOverlay(String token, String projectId, String name, String description, String content, String filename, String type)
throws SecurityException, QueryException, IOException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- User user = userService.getUserByToken(token);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ User user = getUserService().getUserByToken(token);
if (Configuration.ANONYMOUS_LOGIN.equals(user.getLogin())) {
throw new SecurityException("You have no privileges to add overlay");
}
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -284,9 +245,9 @@ public class OverlayRestImpl extends BaseRestImpl {
public Map<String, Object> getOverlayElement(String token, String projectId, Integer modelId, Integer overlayId, Integer elementId, String elementType,
String columns) throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = userService.getToken(token);
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model topModel = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (topModel == null) {
throw new QueryException("Project with given id doesn't exist");
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 1aef78c3c4651cfd214cb0854984783a3ef8f0ce..bcd07b094b7ae9854fe2952e8f656493de13458f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -76,6 +76,7 @@ public class UserRestImpl {
columnsSet.add("email");
columnsSet.add("minColor");
columnsSet.add("maxColor");
+ columnsSet.add("simpleColor");
columnsSet.add("removed");
columnsSet.add("privileges");
} else {
@@ -105,6 +106,8 @@ public class UserRestImpl {
value = user.getMinColor();
} else if (column.equals("maxcolor")) {
value = user.getMaxColor();
+ } else if (column.equals("simplecolor")) {
+ value = user.getSimpleColor();
} else if (column.equals("removed")) {
value = user.isRemoved();
} else if (column.equals("privileges") && admin) {
diff --git a/rest-api/src/main/resources/applicationContext-rest.xml b/rest-api/src/main/resources/applicationContext-rest.xml
index 5cbacb6fc6473c8ce69a2acb2117cc956ad83528..2642267ee9757e4925f78b5142c8022365264033 100644
--- a/rest-api/src/main/resources/applicationContext-rest.xml
+++ b/rest-api/src/main/resources/applicationContext-rest.xml
@@ -15,6 +15,7 @@
<bean id="CommentRestImpl" class="lcsb.mapviewer.api.projects.comments.CommentRestImpl"/>
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.projects.ProjectRestImpl"/>
+ <bean id="ModelRestImpl" class="lcsb.mapviewer.api.projects.models.ModelRestImpl"/>
<bean id="BioEntitiesRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.BioEntitiesRestImpl"/>
<bean id="ChemicalRestImpl" class="lcsb.mapviewer.api.projects.chemicals.ChemicalRestImpl"/>
<bean id="ElementsRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.elements.ElementsRestImpl"/>
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
index d79741c5e25c03a7d797206aead5653a624677be..60e3837712d839ffd77e188018a37d6f166f3601 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
@@ -4,13 +4,15 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.api.projects.chemicals.AllChemicalTests;
import lcsb.mapviewer.api.projects.drugs.AllDrugTests;
import lcsb.mapviewer.api.projects.mirnas.AllMiRnaTests;
import lcsb.mapviewer.api.projects.models.AllModelsTests;
import lcsb.mapviewer.api.projects.overlays.AllOverlaysTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllDrugTests.class, //
+@SuiteClasses({ AllChemicalTests.class, //
+ AllDrugTests.class, //
AllMiRnaTests.class, //
AllModelsTests.class, //
AllOverlaysTests.class, //
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java
index 521d3701fe25873c35726f782374abdef87d39f8..243de1dad24d1043b65385b0ad480c7f711c2be0 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java
@@ -9,7 +9,7 @@ import org.junit.Test;
import com.google.gson.Gson;
-import lcsb.mapviewer.api.projects.ModelMetaData;
+import lcsb.mapviewer.api.projects.models.ModelMetaData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/AllChemicalTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/AllChemicalTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..b673f23b80bc19b1cf4c22258ccf377958e36296
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/AllChemicalTests.java
@@ -0,0 +1,11 @@
+package lcsb.mapviewer.api.projects.chemicals;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ChemicalRestImplTest.class })
+public class AllChemicalTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..32b1acd9ede8099f67a72ad949d864f29c081051
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
@@ -0,0 +1,65 @@
+package lcsb.mapviewer.api.projects.chemicals;
+
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+
+import java.util.ArrayList;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.interfaces.IModelService;
+
+public class ChemicalRestImplTest extends RestTestFunctions {
+ Logger logger = Logger.getLogger(ChemicalRestImplTest.class);
+
+ @Autowired
+
+ private ChemicalRestImpl _drugRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPrepareChemical() throws Exception {
+ try {
+ Chemical chemical = new Chemical();
+ chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "D010300"));
+ Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ protected ChemicalRestImpl createMockChemicalRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _drugRestImpl.setModelService(mockModelService);
+ return _drugRestImpl;
+ }
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
index ecdad6a03327a32a4f42ada6da3b709d121edb99..880479f85b67aba56a6e8497d0967e9453089d1d 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
@@ -40,14 +40,14 @@ public class DrugRestImplTest extends RestTestFunctions {
@Test
@SuppressWarnings("unchecked")
- public void testGetModelAsImage() throws Exception {
+ public void testGetDrugsByQuery() throws Exception {
try {
DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/sample.xml");
Map<String, Object> result = drugRestImpl.getDrugsByQuery(token.getId(), "sample", "", "nadh").get(0);
List<Map<String, Object>> references = (List<Map<String, Object>>) result.get("references");
Map<String, Object> reference = references.get(0);
assertNotNull(reference.get("type"));
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
index 58bce555cf36a931dfc0b2cc6857edcb846f6004..3cb26a74c6f9c5eded78255a02e75de3bd9b137f 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
@@ -10,7 +10,8 @@ import lcsb.mapviewer.api.projects.models.publications.AllPublicationsTests;
@RunWith(Suite.class)
@SuiteClasses({ //
AllBioeEntitiesTests.class, //
- AllPublicationsTests.class//
+ AllPublicationsTests.class, //
+ ModelRestImplTest.class,//
})
public class AllModelsTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8340abe87ecc4061b61e2ab7a6dcd37e9a994217
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.api.projects.models;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+
+import java.util.List;
+import java.util.Map;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.interfaces.IModelService;
+
+public class ModelRestImplTest extends RestTestFunctions {
+
+ @Autowired
+ ModelRestImpl _projectRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testModels() throws Exception {
+ try {
+ ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
+ List<ModelMetaData> result = modelRest.getModels("sample", token.getId());
+ assertEquals(1, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private ModelRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _projectRestImpl.setModelService(mockModelService);
+ return _projectRestImpl;
+ }
+
+}
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 d1b2df719b2095c1424414e012dd19b1af3183d7..78513655c609304555e06f3ca6582b3cec52fca2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -935,7 +935,7 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
List<LightLayoutAliasView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -957,7 +957,7 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
List<LightLayoutReactionView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -980,7 +980,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
return command.getModifiedElements();
} catch (InvalidColorSchemaException e) {
throw new InvalidStateException(e);
@@ -1002,7 +1002,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
List<FullLayoutAliasView> result = new ArrayList<>();
@@ -1059,7 +1059,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
@@ -1085,7 +1085,7 @@ public class LayoutService implements ILayoutService {
Collection<ColorSchema> schemas;
schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
- ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
+ ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK, Color.BLACK));
FullLayoutReactionViewFactory factory = new FullLayoutReactionViewFactory();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index d202b0c4c8a7c2baada65e64b107a8b0c3a1150e..34186d37bba13fecb77bf1fad9c254e502f2796d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -28,10 +28,10 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Phenotype;
@@ -77,6 +77,12 @@ public class SearchService implements ISearchService {
*/
public static final String REACTION_SEARCH_PREFIX = "reaction";
+ /**
+ * Prefix used in search by name interface to limit results only to
+ * {@link Element}.
+ */
+ private static final String ELEMENT_SEARCH_PREFIX = "element";
+
/**
* Default class logger.
*/
@@ -240,6 +246,8 @@ public class SearchService implements ISearchService {
return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
} else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
result.add(fullAliasViewFactory.create(model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""))));
+ } else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
+ return getElementById(model, query.replaceFirst(ELEMENT_SEARCH_PREFIX, "").toLowerCase());
} else {
Set<Element> aliases = model.getElements();
@@ -309,14 +317,45 @@ public class SearchService implements ISearchService {
private List<IHeavyView> getReactionById(Model model, String reactionId) {
Set<Reaction> reactions = model.getReactions();
for (Reaction reaction : reactions) {
-
if (searchIndexer.getQueryStringForIndex(reaction.getIdReaction().toLowerCase(), new ArrayList<>()).equals(reactionId)) {
return reactionToResultList(reaction);
}
+ if (Integer.toString(reaction.getId()).equals(reactionId)) {
+ return reactionToResultList(reaction);
+ }
}
return new ArrayList<>();
}
+ /**
+ * Returns list with the element with a given id. If element with such id
+ * doesn't exist then empty list is returned.
+ *
+ * @param topModel
+ * where the search is performed
+ * @param elementId
+ * id of the element
+ * @return list that contains element with given id (or empty list if such
+ * element doesn't exist)
+ */
+ private List<IHeavyView> getElementById(Model topModel, String elementId) {
+ List<IHeavyView> result = new ArrayList<>();
+
+ Set<Model> models = new HashSet<>();
+ models.add(topModel);
+ models.addAll(topModel.getSubmodels());
+ for (Model model : models) {
+ for (Element element : model.getElements()) {
+ if (searchIndexer.getQueryStringForIndex(element.getElementId().toLowerCase(), new ArrayList<>()).equals(elementId)) {
+ result.add(fullAliasViewFactory.create(element));
+ } else if (Integer.toString(element.getId()).equals(elementId)) {
+ result.add(fullAliasViewFactory.create(element));
+ }
+ }
+ }
+ return result;
+ }
+
/**
* Transform {@link Reaction} into set of result entries.
*
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 60730c63a4088df7770e1854b34ba1e050322421..83dd4bfa7a342e6a5d14683ff31b33b3bd1b0f0c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -473,11 +473,13 @@ public class UserService implements IUserService {
public ColorExtractor getColorExtractorForUser(User loggedUser) {
Color colorMin = null;
Color colorMax = null;
+ Color colorSimple = null;
if (loggedUser != null) {
User dbUser = getUserById(loggedUser.getId());
if (dbUser != null) {
colorMin = dbUser.getMinColor();
colorMax = dbUser.getMaxColor();
+ colorSimple = dbUser.getSimpleColor();
}
}
ColorParser parser = new ColorParser();
@@ -488,7 +490,10 @@ public class UserService implements IUserService {
if (colorMax == null) {
colorMax = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.MAX_COLOR_VAL));
}
- return new ColorExtractor(colorMin, colorMax);
+ if (colorSimple == null) {
+ colorSimple = parser.parse(configurationService.getConfigurationValue(ConfigurationElementType.SIMPLE_COLOR_VAL));
+ }
+ return new ColorExtractor(colorMin, colorMax, colorSimple);
}
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
index c947104992856bb393f310779a596aae011ba27f..1e01f40e07ec338fd685ea16271578579d6fa1d2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -103,8 +103,17 @@ public class ElementMatcher {
return false;
case OTHER:
// in other case just compare names
- String name = target.getGenes().get(0).getResource();
- return element.getName().equalsIgnoreCase(name);
+ String targetName = null;
+ if (target.getGenes().size() > 0) {
+ targetName = target.getGenes().get(0).getResource();
+ }
+ if (targetName == null) {
+ targetName = target.getName();
+ }
+ if (targetName == null) {
+ return false;
+ }
+ return element.getName().equalsIgnoreCase(targetName);
default:
throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index b70b7bd0e6242fb11c95bfa3ffa91b5509224d1a..0a7a3244eacb3dc3dba1a2e3aa793323d4d9fc38 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -28,6 +28,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
/**
* Default class logger.
*/
+ @SuppressWarnings("unused")
private final Logger logger = Logger.getLogger(SearchResultFactory.class);
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java
new file mode 100644
index 0000000000000000000000000000000000000000..43bdc10b273b2dae5058ab2cf180b02bac634abf
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/DbSearchService.java
@@ -0,0 +1,48 @@
+package lcsb.mapviewer.services.search.db;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargettingStructure;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+@Transactional(value = "txManager")
+public abstract class DbSearchService {
+
+ /**
+ * Service accessing
+ * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ protected void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
+ Set<MiriamData> result = new HashSet<>();
+ result.addAll(targettingStructure.getSources());
+ for (Target target : targettingStructure.getTargets()) {
+ result.addAll(target.getGenes());
+ result.addAll(target.getReferences());
+
+ }
+
+ for (MiriamData miriamData : result) {
+ if (MiriamType.PUBMED.equals(miriamData.getDataType())) {
+ try {
+ pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
+ } catch (NumberFormatException | PubmedSearchException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
+
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
index 7ada8d540a60128a2b971d5fbdf54f7d30ac57ff..94eaaef9c453f396703f1b202b8d475d9a936906 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
@@ -17,12 +17,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargettingStructure;
import lcsb.mapviewer.annotation.services.ChemicalParser;
import lcsb.mapviewer.annotation.services.ChemicalSearchException;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -38,6 +34,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about chemicals.
@@ -46,7 +43,7 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
*
*/
@Transactional(value = "txManager")
-public class ChemicalService implements IChemicalService {
+public class ChemicalService extends DbSearchService implements IChemicalService {
/**
* Default class logger.
@@ -70,13 +67,6 @@ public class ChemicalService implements IChemicalService {
@Autowired
private HgncAnnotator hgncAnnotator;
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
/**
* Service that manages search history.
*/
@@ -323,25 +313,4 @@ public class ChemicalService implements IChemicalService {
}
}
- private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index e1bb55227d5eb21f88d83557c69df96d62a2e9e7..c220c2a4c102b82ea351dadb4c272f68aaad35e0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -13,12 +13,9 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargettingStructure;
import lcsb.mapviewer.annotation.services.ChEMBLParser;
import lcsb.mapviewer.annotation.services.DrugSearchException;
import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -33,6 +30,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about drugs.
@@ -41,7 +39,7 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
*
*/
@Transactional(value = "txManager")
-public class DrugService implements IDrugService {
+public class DrugService extends DbSearchService implements IDrugService {
/**
* Default class logger.
@@ -67,13 +65,6 @@ public class DrugService implements IDrugService {
@Autowired
private HgncAnnotator hgncAnnotator;
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
/**
* Service that manages search history.
*/
@@ -282,14 +273,14 @@ public class DrugService implements IDrugService {
}
}
try {
- List<Drug> drugs = drugBankParser.getDrugListByTargets(targetsMiriam);
+ List<Drug> drugs = drugBankParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
drugList.addAll(drugs);
} catch (DrugSearchException e) {
logger.error("Problem with accessing drugBank parser", e);
}
try {
- List<Drug> drugs = chEMBLParser.getDrugListByTargets(targetsMiriam);
+ List<Drug> drugs = chEMBLParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
drugList.addAll(drugs);
} catch (DrugSearchException e) {
logger.error("Problem with accessing chembl parser", e);
@@ -348,23 +339,6 @@ public class DrugService implements IDrugService {
this.searchHistoryService = searchHistoryService;
}
- /**
- * @return the pubmedParser
- * @see #pubmedParser
- */
- public PubmedParser getPubmedParser() {
- return pubmedParser;
- }
-
- /**
- * @param pubmedParser
- * the pubmedParser to set
- * @see #pubmedParser
- */
- public void setPubmedParser(PubmedParser pubmedParser) {
- this.pubmedParser = pubmedParser;
- }
-
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
logger.debug("Caching drug queries...");
@@ -386,9 +360,10 @@ public class DrugService implements IDrugService {
}
}
double counter = 0.0;
+ List<MiriamData> organisms = new ArrayList<>();
for (MiriamData md : targetMiriams) {
try {
- List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md);
+ List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md, organisms);
for (Drug chemical : chemicalList) {
cacheMiriamData(chemical);
}
@@ -396,7 +371,7 @@ public class DrugService implements IDrugService {
logger.error("Problem with accessing info about drugbank for target: " + md, e);
}
try {
- List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md);
+ List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md, organisms);
for (Drug chemical : chemicalList) {
cacheMiriamData(chemical);
}
@@ -409,26 +384,4 @@ public class DrugService implements IDrugService {
}
}
}
-
- private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
index 57ccbb24e684aa05fd347e39cc442cfdd3125d8a..136a1022424a2a323b18978ef40fa64aca9b8645 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
@@ -15,11 +15,8 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.MiRNA;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargettingStructure;
import lcsb.mapviewer.annotation.services.MiRNAParser;
import lcsb.mapviewer.annotation.services.MiRNASearchException;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
@@ -34,6 +31,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about che.
@@ -42,7 +40,7 @@ import lcsb.mapviewer.services.search.db.DbSearchCriteria;
*
*/
@Transactional(value = "txManager")
-public class MiRNAService implements IMiRNAService {
+public class MiRNAService extends DbSearchService implements IMiRNAService {
/**
* Default class logger.
@@ -68,13 +66,6 @@ public class MiRNAService implements IMiRNAService {
@Autowired
private ISearchHistoryService searchHistoryService;
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
/**
* Default constructor.
*/
@@ -243,25 +234,4 @@ public class MiRNAService implements IMiRNAService {
}
}
- private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
- Set<MiriamData> result = new HashSet<>();
- result.addAll(targettingStructure.getSources());
- for (Target target : targettingStructure.getTargets()) {
- result.addAll(target.getGenes());
- result.addAll(target.getReferences());
-
- }
-
- for (MiriamData miriamData : result) {
- if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
- try {
- pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
- } catch (NumberFormatException | PubmedSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- }
-
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
index e42bc74452ab802039cdd8f87ac09afeb0eff40f..c08811bee4ad4a6f7c1f75b4fd60143f0e862d03 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
@@ -5,6 +5,7 @@ import org.apache.log4j.Logger;
import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
import lcsb.mapviewer.model.map.species.Element;
@@ -18,18 +19,26 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaType;
*
*/
public class FullLayoutAliasViewFactory extends ElementViewFactory<Pair<Element, ColorSchema>, FullLayoutAliasView> {
+
+ /**
+ * Parser to map color into object that can be returned to client side.
+ */
+ private ColorParser parser = new ColorParser();
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(FullLayoutAliasViewFactory.class);
+ private static Logger logger = Logger.getLogger(FullLayoutAliasViewFactory.class);
@Override
public FullLayoutAliasView create(Pair<Element, ColorSchema> pair) {
ColorSchema schema = pair.getRight();
FullLayoutAliasView result = new FullLayoutAliasView(pair.getLeft());
- result.setColor(schema.getColor());
+ if (schema.getColor() != null) {
+ result.setColor(parser.colorToMap(schema.getColor()));
+ }
result.setValue(schema.getValue());
result.setDescription(schema.getDescription());
if (schema instanceof GeneVariationColorSchema) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
index bf8008175a72d11552548b7fc551cbeb968cf229..f4f8d5a612377b1428936b3d377afa5d1e692486 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.services.search.layout;
-import java.awt.Color;
+import java.util.Map;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementView;
@@ -18,17 +18,17 @@ public class LightLayoutAliasView extends ElementView {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Value used to highlight {@link Element} in a a layout.
*/
- private Double value;
+ private Double value;
/**
* Color used to highlight {@link Element} in a layout.
*/
- private Color color;
+ private Map<String, Object> color;
/**
* Default constructor.
@@ -68,7 +68,7 @@ public class LightLayoutAliasView extends ElementView {
* @return the color
* @see #color
*/
- public Color getColor() {
+ public Map<String, Object> getColor() {
return color;
}
@@ -77,7 +77,7 @@ public class LightLayoutAliasView extends ElementView {
* the color to set
* @see #color
*/
- public void setColor(Color color) {
+ public void setColor(Map<String, Object> color) {
this.color = color;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
index 0f37f3a0afe17a79edab2d9858bb2aed061e0d71..910a1b5a474907361138f8dbb12f91f18c58cc61 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
@@ -5,6 +5,7 @@ import org.apache.log4j.Logger;
import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementViewFactory;
@@ -16,16 +17,25 @@ import lcsb.mapviewer.services.search.ElementViewFactory;
*
*/
public class LightLayoutAliasViewFactory extends ElementViewFactory<Pair<Element, ColorSchema>, LightLayoutAliasView> {
+
+ /**
+ * Parser to map color into object that can be returned to client side.
+ */
+
+ private ColorParser parser = new ColorParser();
+
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LightLayoutAliasViewFactory.class);
+ private static Logger logger = Logger.getLogger(LightLayoutAliasViewFactory.class);
@Override
public LightLayoutAliasView create(Pair<Element, ColorSchema> pair) {
LightLayoutAliasView result = new LightLayoutAliasView(pair.getLeft());
- result.setColor(pair.getRight().getColor());
+ if (pair.getRight().getColor() != null) {
+ result.setColor(parser.colorToMap(pair.getRight().getColor()));
+ }
result.setValue(pair.getRight().getValue());
return result;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 94efeff004bd03caad4b272cf9f8d159c8d6bfa1..3d856d3868a883178a88bcc15e7f538993fa766c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -573,7 +573,7 @@ public class ColorSchemaReader {
String[] values = line.split("\t", -1);
ColorSchema schema = new GenericColorSchema();
processNameColumn(schema, values[0]);
- schema.setValue(1.0);
+ schema.setDescription("");
result.add(schema);
line = br.readLine();
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 3d409a1875ba3518299d2c78f88b95ec5cc1d51c..0d39e9cb6d0e88baaf86092b6775bf51f84a09f7 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -37,7 +37,7 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaType;
public class LayoutServiceTest2 {
Logger logger = Logger.getLogger(LayoutServiceTest2.class);
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@Before
public void setUp() throws Exception {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index c6d48d10ac8341433d4fd917f1f09ee5a60fcee7..8dc37c8a7c57e7defae75f518845ffa12ca8b0bf 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -31,6 +31,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
@@ -50,7 +51,6 @@ import lcsb.mapviewer.services.utils.SearchIndexer;
public class SearchServiceTest extends ServiceTestFunctions {
static Logger logger = Logger.getLogger(SearchServiceTest.class);
- private Model model = null;
SearchIndexer indexer = new SearchIndexer();
Map<Class<?>, String> speciesSearchPrefix = new HashMap<Class<?>, String>();
@@ -75,9 +75,10 @@ public class SearchServiceTest extends ServiceTestFunctions {
speciesSearchReversePrefix.put(prefix, clazz);
}
- protected void createFullModel() throws Exception {
- model = getModelForFile("testFiles/searchModel.xml", false);
+ protected Model createFullModel() throws Exception {
+ Model model = getModelForFile("testFiles/searchModel.xml", false);
model.setProject(new Project("unknown project"));
+ return model;
}
@After
@@ -87,7 +88,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByName() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
long count = searchHistoryDao.getCount();
SearchElementResult result = searchService.searchByQuery(model, "reaction:re21", 50, null, "127.0.0.1");
@@ -109,7 +110,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByName2() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, "BAD:BCL-2", 50, null, "127.0.0.1");
assertNotNull(result);
@@ -126,7 +127,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchById() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
model.getElements().iterator().next().addMiriamData(md);
SearchElementResult global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
@@ -138,10 +139,25 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testSearchByElementId() throws Exception {
+ try {
+ Model model = createFullModel();
+ Element element =model.getElements().iterator().next();
+ element.setId(907);
+ SearchElementResult global = searchService.searchByQuery(model, "element:907", 50, null, "127.0.0.1");
+ assertNotNull(global);
+ assertEquals(1, global.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testSearchByName4() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, "BC", 50, true, "127.0.0.1");
assertNotNull(result);
@@ -166,7 +182,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryName() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:re21", new HashSet<>()), 50, null, "127.0.0.1");
assertNotNull(result);
@@ -185,7 +201,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryReactionId() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
model.getReactions().iterator().next().setIdReaction("R_x1");
SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:r_x1", new HashSet<>()), 50, null, "127.0.0.1");
@@ -199,10 +215,30 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testQueryReactionId2() throws Exception {
+ try {
+ Model model = createFullModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ reaction.setId(154);
+ reaction.setIdReaction("test-name");
+ SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:154", new HashSet<>()), 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ FullReactionView resultReaction = (FullReactionView) result.get(0);
+ logger.debug(resultReaction.getName());
+ assertTrue(resultReaction.getName().contains("test-name"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testQueryName2() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
model.getModelData().setId(-13);
SearchElementResult result = searchService
.searchByQuery(model, indexer.getQueryStringForIndex("BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
@@ -219,7 +255,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryName3() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService.searchByQuery(model, "fdhgjkhdsfsdhfgfhsd", 50, null, "127.0.0.1");
assertNotNull(result);
@@ -233,7 +269,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testQueryName4() throws Exception {
try {
- createFullModel();
+ Model model = createFullModel();
SearchElementResult result = searchService
.searchByQuery(model, indexer.getQueryStringForIndex("protein:BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
assertNotNull(result);
@@ -249,7 +285,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchClosest() throws Exception {
try {
- model = getModelForFile("testFiles/graph_path_example3.xml", true);
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(5, elements.size());
@@ -278,7 +314,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchClosest2() throws Exception {
try {
- model = new ModelFullIndexed(null);
+ Model model = new ModelFullIndexed(null);
GenericProtein protein1 = new GenericProtein("s1");
protein1.setWidth(20);
protein1.setHeight(20);
@@ -317,7 +353,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Test
public void testSearchClosestWithEmptyModel() throws Exception {
try {
- model = new ModelFullIndexed(null);
+ Model model = new ModelFullIndexed(null);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(0, elements.size());
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
index 0073cd477c59c7639df3b1bd57795fbf69a7b87d..512a3b462cb76482a560273f03114acb946038b1 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
@@ -13,7 +13,8 @@ import lcsb.mapviewer.services.search.layout.AllSearchLayoutTests;
@SuiteClasses({ AllCommentTests.class, //
AllSearchDbTests.class, //
AllSearchDataTests.class, //
- AllSearchLayoutTests.class,//
+ AllSearchLayoutTests.class, //
+ ElementMatcherTest.class, //
})
public class AllSearchTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
similarity index 66%
rename from service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
rename to service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
index 7a310be346eede812e93543470d29662e40af3fc..c34aa859e2cda767baf89001ebd4062493888e17 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/ElementMatcherTest.java
@@ -1,60 +1,68 @@
-package lcsb.mapviewer.services.search;
-
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.comment.FullCommentViewFactory;
-import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
-
-public class SearchResultFactoryTest extends ServiceTestFunctions {
-
- Logger logger = Logger.getLogger(SearchResultFactoryTest.class);
-
- @Autowired
- FullCommentViewFactory factory;
-
- @Autowired
- IChemicalService chemicalService;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testElementMatch() {
- String geneName = "GDNF";
- Chemical view = chemicalService.getByName("Amphetamine", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
- Target target = null;
- for (Target t : view.getInferenceNetwork()) {
- for (MiriamData row : t.getGenes()) {
- if (row.getResource().equals(geneName)) {
- target = t;
- }
- }
- }
-
- Element element = new Rna("id");
- element.setName(geneName);
-
- assertTrue(factory.elementMatch(target, element));
-
- }
-
-}
+package lcsb.mapviewer.services.search;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+
+public class ElementMatcherTest extends ServiceTestFunctions {
+
+ @Autowired
+ ElementMatcher elementMatcher;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testMatchOther() {
+ Target target = new Target();
+
+ target.setType(TargetType.OTHER);
+ assertFalse(elementMatcher.elementMatch(target, new GenericProtein("s1")));
+ }
+
+ @Test
+ public void testElementMatch() {
+ String geneName = "GDNF";
+ Chemical view = chemicalService.getByName("Amphetamine", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+ Target target = null;
+ for (Target t : view.getInferenceNetwork()) {
+ for (MiriamData row : t.getGenes()) {
+ if (row.getResource().equals(geneName)) {
+ target = t;
+ }
+ }
+ }
+
+ Element element = new Rna("id");
+ element.setName(geneName);
+
+ assertTrue(elementMatcher.elementMatch(target, element));
+
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 38c9407b576bc47ea3f6eb74f173dff5c0cee8e3..4553b58724e916c312df2e16878c6d6076091161 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -224,7 +224,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
@Test
public void testColoring3() throws Exception {
try {
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
Model model = getModelForFile("testFiles/coloring/protein_to_color.xml", false);
diff --git a/web/src/main/webapp/index.xhtml b/web/src/main/webapp/index.xhtml
index f950f192d10f51a8dfaa31c11052bdc16080fdc7..086a2b1b27aeeeda422c626983d0a9a2d79269c6 100644
--- a/web/src/main/webapp/index.xhtml
+++ b/web/src/main/webapp/index.xhtml
@@ -47,10 +47,10 @@ function initMap(){
</script>
</h:head>
<h:body onload="initMap();" >
+<h:outputStylesheet library="css" name="bootstrap.min.css"/>
<h:outputStylesheet library="css" name="style.css"/>
<h:outputStylesheet library="css" name="minerva.css" />
<h:outputStylesheet library="css" name="pileup.css"/>
-<h:outputStylesheet library="css" name="bootstrap.min.css"/>
<h:outputScript library="primefaces" name="jquery/jquery.js" target="head" />
<div id="minervaAppDiv" style="height: 100%;width: 100%;margin: 0;"/>
diff --git a/web/src/main/webapp/resources/css/search.css b/web/src/main/webapp/resources/css/search.css
index 5f9eae51172c413f0011fdbbf61bd1d15e2b77e7..b96ebd2589bd2cf77a53d8730adfb687c1e484dc 100644
--- a/web/src/main/webapp/resources/css/search.css
+++ b/web/src/main/webapp/resources/css/search.css
@@ -52,18 +52,3 @@ a.searchElementSubmodelLink {
background: #ffffff;
}
-.searchDescriptionLabel {
- font-weight: 900;
- background: #ffffff;
- line-height: 24px;
-}
-
-.annotationRowOdd {
- padding: 5px;
- background-color: #EAEAEA;
-}
-
-.annotationRowEven {
- padding: 5px;
- background-color: #ffffff;
-}
\ No newline at end of file
diff --git a/web/src/main/webapp/resources/css/style.css b/web/src/main/webapp/resources/css/style.css
index a47422dfd5be6de7fc1d75ddd13c0843f2a0f068..5b9d8758dc9ac33f1871c5ec80a41a4a62208dcd 100644
--- a/web/src/main/webapp/resources/css/style.css
+++ b/web/src/main/webapp/resources/css/style.css
@@ -1016,14 +1016,7 @@ ui-overlay-visible *{visibility:visible !important;}
.ui-wizard-nav-next{float:right;}
.ui-wizard-step-title{font-size:18px;margin:0 3px 0 0;padding:0.4em;float:left;}
-.overview_button {color:#FFFFFF; height:36px; line-height:35px; padding:0 18px; margin:0; border:none; background-color:#017DA7; font-size:13px; font-weight:900; border-right:1px solid #9DE1F8; cursor:pointer; transition: background-color 0.4s ease-in-out 0s; }
-.overview_button:hover {background-color:#01536D; transition: background-color 0.4s ease-in-out 0s; }
-
.rightHeaderMenu{height:36px; line-height:35px; font-size:13px; font-weight:900; color:#ffffff; display:inline; width:auto; float:right}
-.div4checkboxes {height:36px; vertical-align:top; font-size:13px; font-weight:900; color:#ffffff; display:inline; width:auto; float:left; text-align:left; padding:0 0 0 15px; margin:0;}
-.div4checkboxes label {padding:0 15px 0 5px; font-size:11px; line-height:35px; display:inline; float:left;}
-.div4checkboxes input {margin-top:12px; display:inline; float:left;}
-
.ui-galleria-filmstrip {background-color:#21BDF1; padding:2px; height:68px; margin-top:0;}
.ui-galleria-frame {border:1px solid #cccccc; height:34px !important;}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
index a75abab727b5737db2148f8b83116b39767a62a9..de78f41fcc601f02c197278c77d4208869803382 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/ConfigurationBeanTest.java
@@ -1,19 +1,6 @@
package lcsb.mapviewer.bean;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.view.ConfigurationView;
-import lcsb.mapviewer.services.view.ConfigurationViewFactory;
-import lcsb.mapviewer.services.view.ProjectView;
import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
@@ -21,15 +8,21 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.view.ConfigurationViewFactory;
+
public class ConfigurationBeanTest extends WebTestFunctions {
- ConfigurationBean cBean;
- UserBean uBean;
- String oldValue;
- User user2;
+ ConfigurationBean cBean;
+ UserBean uBean;
+ String oldValue;
+ User user2;
@Autowired
- ConfigurationViewFactory configurationViewFactory;
+ ConfigurationViewFactory configurationViewFactory;
@Before
public void setUp() throws Exception {
@@ -41,6 +34,7 @@ public class ConfigurationBeanTest extends WebTestFunctions {
user2 = new User();
userService.addUser(user2);
userService.setUserPrivilege(user2, PrivilegeType.CONFIGURATION_MANAGE);
+ userService.setUserPrivilege(user2, PrivilegeType.ADD_MAP);
uBean.setLoggedUser(user2);
oldValue = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
@@ -54,35 +48,6 @@ public class ConfigurationBeanTest extends WebTestFunctions {
configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_MAP, oldValue);
}
- @Test
- public void test() throws Exception {
- try {
- cBean.refreshValues(null);
-
- assertTrue(cBean.getValues().size() > 0);
- List<ConfigurationView> list = new ArrayList<ConfigurationView>();
- ConfigurationView element = configurationViewFactory.create(configurationDao.getByType(ConfigurationElementType.DEFAULT_MAP));
- element.setValue("sdfsa");
- list.add(element);
-
- // rollback should appear
- cBean.setValues(list);
- assertTrue(cBean.getValues().size() != 1);
-
- for (ProjectView row : projectService.getAllProjectViews()) {
- if (row.getProjectId() == null)
- continue;
- element.setValue(row.getProjectId());
- cBean.setValues(list);
- assertEquals(cBean.getValues(), list);
- cBean.setValues(new ArrayList<ConfigurationView>());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
/**
* Checks if bean implements {@link Serializable} properly.
*/