diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4c8e77f73dc9ab17d7d6cec19defa40c7f5d9f30
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,12 @@
+image: node
+
+before_script:
+ - cd frontend-js
+ - npm install
+ - cd ..
+
+test_frontend:
+ script:
+ - cd frontend-js
+ - npm test
+
\ No newline at end of file
diff --git a/CHANGELOG b/CHANGELOG
index c2676d95aba4ed7e0ebf37528b679ace16e4272e..1eb8ddc1b403c90693a938fee296419777858e4b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,5 +1,26 @@
+minerva (11.0.1) stable; urgency=medium
+ * Bug fix: logout caused issues with session data
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
+
minerva (11.0.0) stable; urgency=medium
+ * Bug fix: security issue - access to specific map can be restricted
+ by the userlogin
+ * Bug fix: sbgn import
+ * Bug fix: mesh connector
+ * Rest API (documentation can be found here:
+ https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
+ * Selecting an element on the map shows info about it in the bottom left
+ corner (when Search tab is not open)
+ * Upload of data overlays allows to upload just names of the proteins
+ (or other elements), it can be done via file or just by typing in the
+ proper text box
+ * Layout changes: the main one is that there are only 3 tab panels
+ (search, overlay, info), so it should be easier to navigate
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
+
minerva (10.0.5) stable; urgency=medium
* Bug fix: interacting drugs can be found for RNAs
diff --git a/README.md b/README.md
index c8bb6d65f4fc5cbd20d1234135c1e1d56efa5339..1c4a3a4035e872ea0c8f7505b3bbc12d039678ff 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+[](https://git-r3lab.uni.lu/piotr.gawron/minerva/commits/207-continous-integration-tests)
+
# Rest API (version 11)
## Introduction
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 dde647a3bf294e8e2aaeeb1e3744ae451ee458c8..6703789f93909815b9ead7e506c659265d2b3e7e 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 annotatior.
*/
- 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/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index b68e455da37eb7e0b00243a6afc9858cfb3ea534..98ad19ad4dc01856566b7fefaa0ad30befe659ba 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());
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/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index 13aac7e4274322704c0f9a06b4f4c245a59a844d..af923b647b8791a013b4a3e7c532d40c9e38c870 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
@@ -1,9 +1,17 @@
package lcsb.mapviewer.converter.graphics;
import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
import org.junit.After;
import org.junit.Before;
+import org.junit.Ignore;
import org.junit.Test;
import lcsb.mapviewer.commands.ColorExtractor;
@@ -37,4 +45,42 @@ public class ConverterTest {
}
}
+ @Test
+ @Ignore("it's just code for generating scale")
+ public void testX() throws IOException {
+ BufferedImage tmpBI = new BufferedImage(900, 100, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D tmpGraphics = tmpBI.createGraphics();
+ int startX = 10;
+ int startY = 15;
+ int stepSize = 40;
+ int height = 25;
+ tmpGraphics.setColor(Color.BLACK);
+ for (int i = 0; i < 21; i++) {
+ tmpGraphics.drawLine(startX + i * stepSize, height+startY, startX + i * stepSize, height*2);
+ String str = ""+((double)(i-10))/((double)(10));
+ tmpGraphics.drawString(str, startX + i * stepSize, height*2+startY);
+ }
+ for (int i = 0; i < 10 * stepSize; i++) {
+ double ratio = ((double) i) / ((double) (10 * stepSize));
+ tmpGraphics.setBackground(getColor(ratio, Color.BLUE, Color.WHITE));
+ tmpGraphics.setColor(getColor(ratio, Color.BLUE, Color.WHITE));
+ tmpGraphics.drawRect(startX + i, startY , 1, height);
+ }
+ for (int i = 0; i < 10 * stepSize; i++) {
+ double ratio = ((double) i) / ((double) (10 * stepSize));
+ tmpGraphics.setBackground(getColor(ratio, Color.WHITE, Color.RED));
+ tmpGraphics.setColor(getColor(ratio, Color.WHITE, Color.RED));
+ tmpGraphics.drawRect(10 * stepSize + startX + i, startY , 1, height);
+ }
+ ImageIO.write(tmpBI, "PNG", new File("tmp.png"));
+ Desktop.getDesktop().open(new File("tmp.png"));
+ }
+
+ private Color getColor(double d, Color startColor, Color endColor) {
+
+ return new Color((int) (startColor.getRed() + d * (endColor.getRed() - startColor.getRed())), //
+ (int) (startColor.getGreen() + d * (endColor.getGreen() - startColor.getGreen())), //
+ (int) (startColor.getBlue() + d * (endColor.getBlue() - startColor.getBlue())));
+ }
+
}
diff --git a/debian/create-debian-pkg.sh b/debian/create-debian-pkg.sh
index f390d7a4080cc8f5a1a37433c3bbfd97d6f5a930..1a6936e6fc9fa7c2cd17bd88b313eb2a8acc7a19 100755
--- a/debian/create-debian-pkg.sh
+++ b/debian/create-debian-pkg.sh
@@ -49,6 +49,8 @@ gzip $SRC_DIR/minerva.txt
#copy configuration of logrotate
cp debian/logrotate/* $SRC_DIR/
+cp debian/scripts/common.sh $SRC_DIR/
+
#copy changelog file
cp CHANGELOG $ROOT_DIR/debian/template/changelog
@@ -150,22 +152,17 @@ find -name '*.ex' ! -name 'minerva*' -type f -exec rm -f {} +
#our pre/post inst/rm scripts use __CURRENT_VERSION__ as a version of currently
#installed package
-sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/preinst
-sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/postinst
-sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/prerm
-sed -i "s/__CURRENT_VERSION__/$current_version/g" debian/postrm
-
-sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/preinst
-sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/postinst
-sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/prerm
-sed -i "s/__LOG_FILE__/$LOG_FILE/g" debian/postrm
+sed -i "s/__CURRENT_VERSION__/$current_version/g" common.sh
+sed -i "s/__LOG_FILE__/$LOG_FILE/g" common.sh
#__DB_SCRIPT_DIR__ in our scripts points to place where db schema files are placed
#in the filesystem where package is installed
-sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/postinst
-sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/postrm
-sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/prerm
-sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" debian/preinst
+sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" common.sh
+
+sed -i -e "1r common.sh" debian/postinst
+sed -i -e "1r common.sh" debian/postrm
+sed -i -e "1r common.sh" debian/preinst
+sed -i -e "1r common.sh" debian/prerm
#put scripts into $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
#escaped
diff --git a/debian/scripts/common.sh b/debian/scripts/common.sh
new file mode 100644
index 0000000000000000000000000000000000000000..246724cb9444cdf4d2c503fe804ab3d973ffa338
--- /dev/null
+++ b/debian/scripts/common.sh
@@ -0,0 +1,29 @@
+#file with common script functions for postrm/prerm/postinst/preinst
+log(){
+ echo "[" $CURRENT_VERSION "]" "$@" >>__LOG_FILE__
+}
+LOG_FILE="__LOG_FILE__"
+
+DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
+
+#new (current) version of the package
+CURRENT_VERSION="__CURRENT_VERSION__"
+#if we update package then this will be the old version of the package
+OLD_VERSION=$2
+
+if [ "$OLD_VERSION" = "$CURRENT_VERSION" ]
+then
+ OLD_VERSION="";
+fi
+
+TOMCAT_PACKAGE="";
+TOMCAT7_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat7|grep "install ok installed")
+TOMCAT8_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat8|grep "install ok installed")
+if [ "$TOMCAT7_OK" != "" ];
+then
+ TOMCAT_PACKAGE='tomcat7'
+fi
+if [ "$TOMCAT8_OK" != "" ];
+then
+ TOMCAT_PACKAGE='tomcat8'
+fi
diff --git a/debian/template/control b/debian/template/control
index 25913b4c153d4c4f53324c1e96d205742ce30b35..dcb5946ab20574544cfcc59508f78714bc39af25 100644
--- a/debian/template/control
+++ b/debian/template/control
@@ -13,4 +13,4 @@ Description: Standalone web application for visualization, exploration and
Tomcat server later to change the address.
Section: science
Homepage: http://r3lab.uni.lu/web/minerva-website/
-Depends: ${misc:Depends}, tomcat7, oracle-java8-set-default, postgresql (>=9.3)
+Depends: ${misc:Depends}, tomcat7 | tomcat8, oracle-java8-set-default, postgresql (>=9.3)
diff --git a/debian/template/install b/debian/template/install
index 493361aaa4fa86ab02bede0f7ff7a1f42c031491..7e81d5fb433700abf97710e8570f13708aa0b5ef 100644
--- a/debian/template/install
+++ b/debian/template/install
@@ -1 +1 @@
-minerva.war /var/lib/tomcat7/webapps
+minerva.war /usr/share/minerva/
diff --git a/debian/template/postinst b/debian/template/postinst
index a1b144da74bc63a39bcf6be638790e68c0688b04..44228b77f9db6a5d9d50ee43d4917a886fe73f9e 100644
--- a/debian/template/postinst
+++ b/debian/template/postinst
@@ -13,28 +13,12 @@
# <conflicting-package> <version>
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
-log(){
- echo "$@" >>__LOG_FILE__
-}
log "Running postinst" $1 $2;
+invoke-rc.d $TOMCAT_PACKAGE status >> $LOG_FILE
# we execute it here because if some packages are missing then dpkg will return non-zero exit code
set -e
-
-#new (current) version of the package
-CURRENT_VERSION="__CURRENT_VERSION__"
-#if we update package then this will be the old version of the package
-OLD_VERSION=$2
-
-DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
-
-if [ "$OLD_VERSION" = "$CURRENT_VERSION" ]
-then
- OLD_VERSION="";
-fi
-
-
case "$1" in
configure)
invoke-rc.d postgresql start
@@ -42,9 +26,9 @@ case "$1" in
#if we install
if [ "$OLD_VERSION" = "" ]
then
- su - postgres -c "createuser -d -r -s map_viewer" >>__LOG_FILE__ 2>>__LOG_FILE__
- su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql" >>__LOG_FILE__ 2>>__LOG_FILE__
- su - postgres -c "createdb -O map_viewer map_viewer" >>__LOG_FILE__ 2>>__LOG_FILE__
+ su - postgres -c "createuser -d -r -s map_viewer" >>$LOG_FILE 2>>$LOG_FILE
+ su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql" >>$LOG_FILE 2>>$LOG_FILE
+ su - postgres -c "createdb -O map_viewer map_viewer" >>$LOG_FILE 2>>$LOG_FILE
hba_conf=`su - postgres -c "psql -t -P format=unaligned -c 'show hba_file';"`;
cp $hba_conf $hba_conf".bac"
@@ -53,13 +37,13 @@ case "$1" in
invoke-rc.d postgresql restart
#install base version of the framework
- su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0.sql" >>__LOG_FILE__ 2>>__LOG_FILE__
+ su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0.sql" >>$LOG_FILE 2>>$LOG_FILE
#install patch to current version
- su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0_to_$CURRENT_VERSION\".sql\"" >>__LOG_FILE__ 2>>__LOG_FILE__
+ su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_0_to_$CURRENT_VERSION\".sql\"" >>$LOG_FILE 2>>$LOG_FILE
else
#if we update the package
- su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_$OLD_VERSION\"_to_\"$CURRENT_VERSION\".sql\"" >>__LOG_FILE__ 2>>__LOG_FILE__
+ su - postgres -c "psql map_viewer -f $DB_SCRIPT_DIR/db_$OLD_VERSION\"_to_\"$CURRENT_VERSION\".sql\"" >>$LOG_FILE 2>>$LOG_FILE
fi
#print a disclaimer
@@ -78,7 +62,10 @@ case "$1" in
#we have to restart tomcat, because application was started on the old database and it might crash during deplyment
#for instance in the new war file there was init script that uses some new database features, but they are not
#availble when new war is deployed from debian package, so tomcat will catch SQL exception and stop deployment
- invoke-rc.d tomcat7 restart
+ invoke-rc.d $TOMCAT_PACKAGE stop || true
+ rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
+ ln -s /usr/share/minerva/minerva.war /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
+ invoke-rc.d $TOMCAT_PACKAGE start
;;
*)
echo "postinst called with unknown argument \`$1'" >&2
diff --git a/debian/template/postrm b/debian/template/postrm
index 1bbb913d1ea531617049d130f6a4fd0d442be495..89144fb629ef34fd3761bc2c749f6cebfcfd4840 100644
--- a/debian/template/postrm
+++ b/debian/template/postrm
@@ -7,9 +7,6 @@
# * <old-postrm> `upgrade' <new-version>
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
-log(){
- echo "$@" >>__LOG_FILE__
-}
log "Running postrm" $1 $2;
@@ -27,13 +24,15 @@ set -e
case "$1" in
upgrade)
- rm -rf /var/lib/tomcat7/webapps/minerva
- invoke-rc.d tomcat7 start || true
- invoke-rc.d postgresql start || true
+ rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
+ rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
+# invoke-rc.d $TOMCAT_PACKAGE start || true
+# invoke-rc.d postgresql start || true
;;
remove)
- rm -rf /var/lib/tomcat7/webapps/minerva
- invoke-rc.d tomcat7 start || true
+ rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
+ rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
+ invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ]
then
log "No postgresql package found.";
@@ -44,7 +43,7 @@ case "$1" in
fi
;;
abort-install)
- invoke-rc.d tomcat7 start || true
+ invoke-rc.d $TOMCAT_PACKAGE start || true
if [ "" = "$POSTGRES_OK" ];
then
diff --git a/debian/template/preinst b/debian/template/preinst
index 1abc655eb13bdd0e7687c11f932d13629824dd1d..c6ad957eb6803a810a043143bf5845e16a3017ef 100644
--- a/debian/template/preinst
+++ b/debian/template/preinst
@@ -9,11 +9,6 @@
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
-
-log(){
- echo "$@" >>__LOG_FILE__
-}
-
log "Running preinst" $1 $2;
# we execute it here because if some packages are missing then dpkg will return non-zero exit code
@@ -29,11 +24,11 @@ ln -s $path $DEFAULT_JAVA_SYMLINK
case "$1" in
install|upgrade)
- invoke-rc.d tomcat7 stop || true
+ invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
;;
abort-upgrade)
- invoke-rc.d tomcat7 stop || true
+ invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
;;
*)
diff --git a/debian/template/prerm b/debian/template/prerm
index d6c80c445fb07e3c6621618992daf9ed789f71b0..c43b60f8fa2c3f996db03de69cc8b7e261d9220e 100644
--- a/debian/template/prerm
+++ b/debian/template/prerm
@@ -8,14 +8,9 @@ set -e
# * <new-preinst> `upgrade' <old-version>
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
-log(){
- echo "$@" >>__LOG_FILE__
-}
log "Running preinst" $1 $2;
-DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
-
# we execute it here because if some packages are missing then dpkg will return non-zero exit code
set -e
@@ -30,11 +25,11 @@ su - postgres -c "pg_dump map_viewer" | gzip > "$DUMP_FILE".gz
case "$1" in
upgrade)
- invoke-rc.d tomcat7 stop || true
+ invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
;;
remove)
- invoke-rc.d tomcat7 stop || true
+ invoke-rc.d $TOMCAT_PACKAGE stop || true
invoke-rc.d postgresql stop || true
;;
*)
diff --git a/frontend-js/.gitignore b/frontend-js/.gitignore
index 23ccee19c2ced758953730bdbcbebf2b33922f62..6e21c03544a53f12f08700ccbb114dfbebe1e590 100644
--- a/frontend-js/.gitignore
+++ b/frontend-js/.gitignore
@@ -1,3 +1,4 @@
+.idea/workspace.xml
/dist/
/coverage/
/node_modules/
diff --git a/frontend-js/.idea/dictionaries/piotr_gawron.xml b/frontend-js/.idea/dictionaries/piotr_gawron.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6a8c909a47f60a556bc261805af778533e72b7eb
--- /dev/null
+++ b/frontend-js/.idea/dictionaries/piotr_gawron.xml
@@ -0,0 +1,7 @@
+<component name="ProjectDictionaryState">
+ <dictionary name="piotr.gawron">
+ <words>
+ <w>mailto</w>
+ </words>
+ </dictionary>
+</component>
\ No newline at end of file
diff --git a/frontend-js/.idea/frontend-js.iml b/frontend-js/.idea/frontend-js.iml
new file mode 100644
index 0000000000000000000000000000000000000000..69ef67a424b4d72230aac1a2e4ddc77c7a75b52b
--- /dev/null
+++ b/frontend-js/.idea/frontend-js.iml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="WEB_MODULE" version="4">
+ <component name="NewModuleRootManager">
+ <content url="file://$MODULE_DIR$">
+ <excludeFolder url="file://$MODULE_DIR$/.tmp" />
+ <excludeFolder url="file://$MODULE_DIR$/dist" />
+ <excludeFolder url="file://$MODULE_DIR$/temp" />
+ <excludeFolder url="file://$MODULE_DIR$/tmp" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/frontend-js/.idea/modules.xml b/frontend-js/.idea/modules.xml
new file mode 100644
index 0000000000000000000000000000000000000000..45e3bd378c0fc59f695ea33bf88ea0ebcc9a62e4
--- /dev/null
+++ b/frontend-js/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectModuleManager">
+ <modules>
+ <module fileurl="file://$PROJECT_DIR$/.idea/frontend-js.iml" filepath="$PROJECT_DIR$/.idea/frontend-js.iml" />
+ </modules>
+ </component>
+</project>
\ No newline at end of file
diff --git a/frontend-js/.idea/preferred-vcs.xml b/frontend-js/.idea/preferred-vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..848cfc44550cbfba31b047a54bb77ecd25feb0c7
--- /dev/null
+++ b/frontend-js/.idea/preferred-vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="PreferredVcsStorage">
+ <preferredVcsName>ApexVCS</preferredVcsName>
+ </component>
+</project>
\ No newline at end of file
diff --git a/frontend-js/.idea/vcs.xml b/frontend-js/.idea/vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6c0b8635858dc7ad44b93df54b762707ce49eefc
--- /dev/null
+++ b/frontend-js/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="$PROJECT_DIR$/.." vcs="Git" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/frontend-js/package.json b/frontend-js/package.json
index 5fb54350658b7055fa7bba9c60112f64877eeed0..a421f03d02033e2d2348c13b8cb5eb863099b9b1 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -38,9 +38,11 @@
"dependencies": {
"dual-listbox": "^1.0.7",
"file-saver": "^1.3.3",
+ "del": "^3.0.0",
"http-status-codes": "^1.1.6",
"js-cookie": "^2.1.3",
"log4js": "0.6.38",
+ "mkdirp": "^0.5.1",
"pileup": "^0.6.8",
"request": "^2.79.0"
}
diff --git a/frontend-js/scripts/clean.js b/frontend-js/scripts/clean.js
new file mode 100644
index 0000000000000000000000000000000000000000..1822779c31f651f8caa6538c5138f32fd1f666cc
--- /dev/null
+++ b/frontend-js/scripts/clean.js
@@ -0,0 +1,15 @@
+var del = require('del');
+var mkdirp = require('mkdirp');
+
+
+var exec = require('child_process').exec;
+function puts(error, stdout, stderr) { console.log(stdout) }
+
+
+var os = require('os');
+//control OS
+//then run command depengin on the OS
+
+del(["dist/"]).then(function(){
+ return mkdirp("dist");
+});
diff --git a/frontend-js/src/main/js/ConfigurationType.js b/frontend-js/src/main/js/ConfigurationType.js
index aa792f821a083b1e4dfbb66bbb720ca43a89ff2f..ca7078fe5cc21ffc87eaba1dd3516153ea8dd8b7 100644
--- a/frontend-js/src/main/js/ConfigurationType.js
+++ b/frontend-js/src/main/js/ConfigurationType.js
@@ -1,16 +1,17 @@
"use strict";
var ConfigurationType = {
- DEFAULT_MAP : "DEFAULT_MAP",
- GOOGLE_ANALYTICS_IDENTIFIER : "GOOGLE_ANALYTICS_IDENTIFIER",
- LOGO_IMG : "LOGO_IMG",
- LOGO_LINK : "LOGO_LINK",
- 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",
+ DEFAULT_MAP: "DEFAULT_MAP",
+ GOOGLE_ANALYTICS_IDENTIFIER: "GOOGLE_ANALYTICS_IDENTIFIER",
+ LOGO_IMG: "LOGO_IMG",
+ LOGO_LINK: "LOGO_LINK",
+ LEGEND_FILES: "LEGEND_FILES",
+ MIN_COLOR_VAL: "MIN_COLOR_VAL",
+ MAX_COLOR_VAL: "MAX_COLOR_VAL",
+ REQUEST_ACCOUNT_EMAIL: "REQUEST_ACCOUNT_EMAIL",
+ SIMPLE_COLOR_VAL: "SIMPLE_COLOR_VAL",
+ SEARCH_DISTANCE: "SEARCH_DISTANCE",
+ USER_MANUAL_FILE: "USER_MANUAL_FILE",
};
module.exports = ConfigurationType;
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index 1cc63b91534a7f15b475de1e1914287bd1333bb9..f377b8ab177acafc302e15041874d6fd2ad2ba42 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -5,6 +5,7 @@ var logger = require('./logger');
var Functions = require('./Functions');
var SecurityError = require('./SecurityError');
var GuiMessageError = require('./gui/GuiMessageError');
+var NetworkError = require('./NetworkError');
/**
* This static global object contains set of functions that returns/set data in
@@ -26,11 +27,11 @@ GuiConnector.yPos = 0;
* List of GET params passed via url.
*/
-GuiConnector.init = function() {
+GuiConnector.init = function () {
var self = this;
if (!String.prototype.endsWith) {
- String.prototype.endsWith = function(pattern) {
+ String.prototype.endsWith = function (pattern) {
var d = this.length - pattern.length;
return d >= 0 && this.lastIndexOf(pattern) === d;
};
@@ -41,7 +42,7 @@ GuiConnector.init = function() {
alert("This webpage works well with Chrome, Firefox and Safari.");
}
// bootstrap tab initialization
- $("ul.nav-tabs a").click(function(e) {
+ $("ul.nav-tabs a").click(function (e) {
e.preventDefault();
$(this).tab('show');
});
@@ -49,16 +50,17 @@ GuiConnector.init = function() {
self.getParams = [];
// find GuiConnector.getParams
- window.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function() {
+ window.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function () {
function decode(s) {
return decodeURIComponent(s.split("+").join(" "));
}
+
GuiConnector.getParams[decode(arguments[1])] = decode(arguments[2]);
});
// forser browser to update mouse coordinates whenever mouse move
- jQuery(document).ready(function() {
- $(document).mousemove(function(e) {
+ jQuery(document).ready(function () {
+ $(document).mousemove(function (e) {
GuiConnector.updateMouseCoordinates(e.pageX, e.pageY);
});
});
@@ -70,7 +72,7 @@ GuiConnector.init = function() {
self.addWindowResizeEvent(window.onresize);
}
- window.onresize = function() {
+ window.onresize = function () {
for (var i = 0; i < self._windowResizeEvents.length; i++) {
self._windowResizeEvents[i]();
}
@@ -78,18 +80,18 @@ GuiConnector.init = function() {
}
};
-GuiConnector.addWindowResizeEvent = function(handler) {
+GuiConnector.addWindowResizeEvent = function (handler) {
this._windowResizeEvents.push(handler);
};
/**
* Returns name of the file with LCSB logo.
- *
+ *
* @param bigLogo
* {@link Boolean} value determining if we want to have big logo or
* small one
*/
-GuiConnector.getLcsbLogoImg = function(bigLogo) {
+GuiConnector.getLcsbLogoImg = function (bigLogo) {
if (bigLogo) {
return 'lcsb_logo_mid.png';
} else {
@@ -101,26 +103,26 @@ GuiConnector.getLcsbLogoImg = function(bigLogo) {
* Returns name of the file with image that should be presented when we are
* wainting for data to be loaded.
*/
-GuiConnector.getLoadingImg = function() {
+GuiConnector.getLoadingImg = function () {
return "icons/ajax-loader.gif";
};
/**
* Returns home directory for images in the application.
*/
-GuiConnector.getImgPrefix = function() {
+GuiConnector.getImgPrefix = function () {
return "resources/images/";
};
/**
* Updates coordinates of the mouse in the browser.
*/
-GuiConnector.updateMouseCoordinates = function(x, y) {
+GuiConnector.updateMouseCoordinates = function (x, y) {
this.xPos = x;
this.yPos = y;
};
-GuiConnector.showProcessing = function(messageText) {
+GuiConnector.showProcessing = function (messageText) {
var self = GuiConnector;
if (self._processingDialog === undefined) {
self._processingDialog = document.createElement("div");
@@ -139,8 +141,8 @@ GuiConnector.showProcessing = function(messageText) {
messageText = "PROCESSING";
}
var messageImg = Functions.createElement({
- type : "img",
- src : 'resources/images/icons/ajax-loader.gif',
+ type: "img",
+ src: 'resources/images/icons/ajax-loader.gif',
});
self._processingDialogContent.innerHTML = "";
self._processingDialogContent.style.textAlign = "center";
@@ -151,12 +153,12 @@ GuiConnector.showProcessing = function(messageText) {
$(self._processingDialog).dialog("open");
};
-GuiConnector.hideProcessing = function() {
+GuiConnector.hideProcessing = function () {
var self = GuiConnector;
$(self._processingDialog).dialog("close");
};
-GuiConnector.alert = function(error) {
+GuiConnector.alert = function (error) {
var self = GuiConnector;
logger.error(error);
if (self._errorDialog === undefined) {
@@ -165,20 +167,22 @@ GuiConnector.alert = function(error) {
self._errorDialog.appendChild(self._errorDialogContent);
document.body.appendChild(self._errorDialog);
$(self._errorDialog).dialog({
- classes : {
- "ui-dialog" : "ui-state-error"
+ classes: {
+ "ui-dialog": "ui-state-error"
},
- modal : true,
- title : "ERROR"
+ modal: true,
+ title: "ERROR"
}).siblings('.ui-dialog-titlebar').css("background", "red");
}
var message = error;
if (message instanceof SecurityError) {
- message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resuorce</p>";
+ message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resource</p>";
+ } else if (message instanceof NetworkError && (error.message === "XHR error" || error.message === "Failed to fetch")) {
+ message = "File to big.<br>Please reduce file size or contact administrators.";
} else if (message instanceof GuiMessageError) {
- message = error.message;
+ message = error.message;
} else if (message instanceof Error) {
- message = "Unexpected error occured:<p>" + error.message + "</p>";
+ message = "Unexpected error occurred:<p>" + error.message + "</p>";
}
self._errorDialogContent.innerHTML = message;
$(self._errorDialog).dialog("open");
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 9b45634d588b0fe75d92495999b9f4a9535f4aba..535e6776cdfcd8bd004021fa94a09653dbe939cc 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -83,7 +83,7 @@ ServerConnector.returnUserOrSystemColor = function(userColor, systemPromisedColo
});
};
-ServerConnector.getSimpleOverlayColorInt = function() {
+ServerConnector.getSimpleOverlayColorInt = function () {
var self = this;
return self.getLoggedUser().then(function(user) {
var userColor = user.getSimpleColor();
@@ -91,7 +91,7 @@ ServerConnector.getSimpleOverlayColorInt = function() {
});
};
-ServerConnector.getMaxOverlayColorInt = function() {
+ServerConnector.getMaxOverlayColorInt = function () {
var self = this;
return self.getLoggedUser().then(function(user) {
var userColor = user.getMaxColor();
@@ -127,11 +127,11 @@ ServerConnector.sendRequest = function(params) {
}).then(function(result) {
content = result;
return self.callListeners("onDataLoadStop", description);
- }, function(error) {
- return self.callListeners("onDataLoadStop", description).then(function() {
+ }, function (error) {
+ return self.callListeners("onDataLoadStop", description).then(function () {
return Promise.reject(error);
});
- }).then(function() {
+ }).then(function () {
return content;
});
@@ -141,7 +141,10 @@ ServerConnector._sendRequest = function(params) {
return new Promise(function(resolve, reject) {
request(params, function(error, response, body) {
if (error) {
- reject(error);
+ reject(new NetworkError(error.message, {
+ content: body,
+ url: url
+ }));
} else if (response.statusCode !== 200) {
reject(new NetworkError(params.url + " rejected with status code: " + response.statusCode, {
content : body,
@@ -187,17 +190,15 @@ ServerConnector.sendPatchRequest = function(url, json) {
ServerConnector.getToken = function() {
var self = this;
-
+ var login = self.getSessionData(null).getLogin()
var token = self.getSessionData(null).getToken();
- if (token === undefined) {
+ if (token === undefined || login === undefined) {
return self.login();
} else {
// if the project is not initialized then check if we can download data
// using current token
if (self.getSessionData().getProject() === null) {
- return self.getConfiguration({
- token : token
- }).then(function() {
+ return self.getConfiguration().then(function () {
return token;
// if there was an error accessing configuration it means our token is
// invalid
@@ -210,11 +211,11 @@ ServerConnector.getToken = function() {
}
};
-ServerConnector.getApiBaseUrl = function() {
+ServerConnector.getApiBaseUrl = function () {
return this.getServerBaseUrl() + "/api/";
};
-ServerConnector.getServerBaseUrl = function() {
+ServerConnector.getServerBaseUrl = function () {
if (this._serverBaseUrl === undefined) {
var url = "" + window.location.href;
if (!url.endsWith("/")) {
@@ -225,7 +226,7 @@ ServerConnector.getServerBaseUrl = function() {
return this._serverBaseUrl;
};
-ServerConnector.createGetParams = function(params, prefix) {
+ServerConnector.createGetParams = function (params, prefix) {
var sorted = [], key;
for (key in params) {
@@ -261,7 +262,7 @@ ServerConnector.createGetParams = function(params, prefix) {
return result;
};
-ServerConnector.getApiUrl = function(paramObj) {
+ServerConnector.getApiUrl = function (paramObj) {
var type = paramObj.type;
var method = paramObj.method;
var params = this.createGetParams(paramObj.params);
@@ -279,7 +280,7 @@ ServerConnector.getApiUrl = function(paramObj) {
return result;
};
-ServerConnector.getProjectsUrl = function(queryParams, filterParams) {
+ServerConnector.getProjectsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
type : "projects/",
params : filterParams,
@@ -294,67 +295,73 @@ ServerConnector.getProjectUrl = function(queryParams, filterParams) {
});
};
-ServerConnector.getProjectStatisticsUrl = function(queryParams, filterParams) {
+ServerConnector.getProjectStatisticsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url : this.getProjectUrl(queryParams) + "statistics/",
params : filterParams,
});
};
-ServerConnector.getPublicationsUrl = function(queryParams, filterParams) {
+ServerConnector.getPublicationsUrl = function (queryParams, filterParams) {
filterParams.start = filterParams.start || 0;
filterParams.length = filterParams.length || 10;
return this.getApiUrl({
- url : this.getModelsUrl(queryParams) + "publications/",
- params : filterParams,
+ url: this.getModelsUrl(queryParams) + "publications/",
+ params: filterParams,
});
};
-ServerConnector.getReferenceGenomeUrl = function(queryParams, filterParams) {
+ServerConnector.getReferenceGenomeUrl = function (queryParams, filterParams) {
var version = this.getIdOrAsterisk(queryParams.version);
return this.getApiUrl({
- type : "genomics/taxonomies/" + queryParams.organism + "/genomeTypes/" + queryParams.type + "/versions/" + version
- + "/",
- params : filterParams
+ type: "genomics/taxonomies/" + queryParams.organism + "/genomeTypes/" + queryParams.type + "/versions/" + version
+ + "/",
+ params: filterParams
});
};
-ServerConnector.loginUrl = function() {
+ServerConnector.loginUrl = function () {
return this.getApiUrl({
- type : "/doLogin",
+ type: "/doLogin",
});
};
-ServerConnector.getSuggestedQueryListUrl = function(queryParams, filterParams) {
+ServerConnector.logoutUrl = function () {
return this.getApiUrl({
- url : this.getBioEntitiesUrl(queryParams) + "suggestedQueryList/",
- params : filterParams,
+ type: "/doLogout",
+ });
+};
+
+ServerConnector.getSuggestedQueryListUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ url: this.getBioEntitiesUrl(queryParams) + "suggestedQueryList/",
+ params: filterParams,
});
};
-ServerConnector.addCommentUrl = function(queryParams) {
+ServerConnector.addCommentUrl = function (queryParams) {
return this.getApiUrl({
- url : this.getCommentsUrl(queryParams)
+ url: this.getCommentsUrl(queryParams)
});
};
-ServerConnector.addOverlayUrl = function(queryParams) {
+ServerConnector.addOverlayUrl = function (queryParams) {
return this.getApiUrl({
- url : this.getOverlaysUrl(queryParams)
+ url: this.getOverlaysUrl(queryParams)
});
};
-ServerConnector.updateOverlayUrl = function(queryParams) {
+ServerConnector.updateOverlayUrl = function (queryParams) {
return this.getApiUrl({
- url : this.getOverlayByIdUrl(queryParams)
+ url: this.getOverlayByIdUrl(queryParams)
});
};
-ServerConnector.deleteOverlayUrl = function(queryParams) {
+ServerConnector.deleteOverlayUrl = function (queryParams) {
return this.getApiUrl({
- url : this.getOverlayByIdUrl(queryParams),
+ url: this.getOverlayByIdUrl(queryParams),
});
};
@@ -371,7 +378,7 @@ ServerConnector.getOverlaysUrl = function(queryParams, filterParams) {
});
};
-ServerConnector.getCommentsUrl = function(queryParams, filterParams) {
+ServerConnector.getCommentsUrl = function (queryParams, filterParams) {
var modelId = this.getIdOrAsterisk(queryParams.modelId);
var url = this.getProjectUrl(queryParams) + "comments/models/" + modelId + "/";
if (queryParams.elementType !== undefined) {
@@ -386,41 +393,41 @@ ServerConnector.getCommentsUrl = function(queryParams, filterParams) {
}
}
return this.getApiUrl({
- url : url,
- params : filterParams,
+ url: url,
+ params: filterParams,
});
};
-ServerConnector.getOverlayByIdUrl = function(queryParams, filterParams) {
+ServerConnector.getOverlayByIdUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getOverlaysUrl(queryParams) + queryParams.overlayId + "/",
- params : filterParams,
+ url: this.getOverlaysUrl(queryParams) + queryParams.overlayId + "/",
+ params: filterParams,
});
};
-ServerConnector.getOverlayElementsUrl = function(queryParams, filterParams) {
+ServerConnector.getOverlayElementsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getModelsUrl(queryParams) + "bioEntities/",
- params : filterParams,
+ url: this.getModelsUrl(queryParams) + "bioEntities/",
+ params: filterParams,
});
};
-ServerConnector.getFullOverlayElementUrl = function(queryParams, filterParams) {
+ServerConnector.getFullOverlayElementUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getAliasesUrl(queryParams) + queryParams.id + "/",
- params : filterParams,
+ url: this.getAliasesUrl(queryParams) + queryParams.id + "/",
+ params: filterParams,
});
};
-ServerConnector.idsToString = function(ids) {
+ServerConnector.idsToString = function (ids) {
var result = "";
if (ids !== undefined) {
- ids.sort(function(a, b) {
+ ids.sort(function (a, b) {
return a - b;
});
for (var i = 0; i < ids.length; i++) {
@@ -436,7 +443,7 @@ ServerConnector.idsToString = function(ids) {
return result;
};
-ServerConnector.pointToString = function(point) {
+ServerConnector.pointToString = function (point) {
return point.x.toFixed(2) + "," + point.y.toFixed(2);
};
@@ -449,17 +456,17 @@ ServerConnector.getModelsUrl = function(queryParams) {
}
return this.getApiUrl({
- url : url + "models/" + modelId + "/",
+ url: url + "models/" + modelId + "/",
});
};
-ServerConnector.getBioEntitiesUrl = function(queryParams) {
+ServerConnector.getBioEntitiesUrl = function (queryParams) {
return this.getApiUrl({
- url : this.getModelsUrl(queryParams) + "bioEntities/",
+ url: this.getModelsUrl(queryParams) + "bioEntities/",
});
};
-ServerConnector.getIdOrAsterisk = function(id) {
+ServerConnector.getIdOrAsterisk = function (id) {
if (id === undefined || id === "" || id === null) {
return "*";
} else {
@@ -467,81 +474,81 @@ ServerConnector.getIdOrAsterisk = function(id) {
}
};
-ServerConnector.getReactionsUrl = function(queryParams, filterParams) {
+ServerConnector.getReactionsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getBioEntitiesUrl(queryParams) + "reactions/",
- params : filterParams,
+ url: this.getBioEntitiesUrl(queryParams) + "reactions/",
+ params: filterParams,
});
};
-ServerConnector.getAliasesUrl = function(queryParams, filterParams) {
+ServerConnector.getAliasesUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getBioEntitiesUrl(queryParams) + "elements/",
- params : filterParams,
+ url: this.getBioEntitiesUrl(queryParams) + "elements/",
+ params: filterParams,
});
};
-ServerConnector.getConfigurationUrl = function(queryParams, filterParams) {
+ServerConnector.getConfigurationUrl = function (queryParams, filterParams) {
var result = this.getApiUrl({
- type : "configuration/",
- params : filterParams
+ type: "configuration/",
+ params: filterParams
});
return result;
};
-ServerConnector.getSearchUrl = function(queryParams, filterParams) {
+ServerConnector.getSearchUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getModelsUrl(queryParams) + "bioEntities:search",
- params : filterParams,
+ url: this.getModelsUrl(queryParams) + "bioEntities:search",
+ params: filterParams,
});
};
-ServerConnector.getSearchDrugsUrl = function(queryParams, filterParams) {
+ServerConnector.getSearchDrugsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url : this.getProjectUrl(queryParams) + "drugs:search",
params : filterParams,
});
};
-ServerConnector.getSearchMiRnasUrl = function(queryParams, filterParams) {
+ServerConnector.getSearchMiRnasUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url : this.getProjectUrl(queryParams) + "miRnas:search",
params : filterParams,
});
};
-ServerConnector.getSearchChemicalsUrl = function(queryParams, filterParams) {
+ServerConnector.getSearchChemicalsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url : this.getProjectUrl(queryParams) + "chemicals:search",
params : filterParams,
});
};
-ServerConnector.getOverlaySourceUrl = function(queryParams, filterParams) {
+ServerConnector.getOverlaySourceUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- url : this.getOverlaysUrl(queryParams) + queryParams.overlayId + ":downloadSource",
- params : filterParams
+ url: this.getOverlaysUrl(queryParams) + queryParams.overlayId + ":downloadSource",
+ params: filterParams
});
};
-ServerConnector.getImageUrl = function(queryParams, filterParams) {
+ServerConnector.getImageUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url : this.getProjectUrl(queryParams) + "models/" + queryParams.modelId + ":downloadImage",
params : filterParams,
});
};
-ServerConnector.getModelPartUrl = function(queryParams, filterParams) {
+ServerConnector.getModelPartUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url : this.getProjectUrl(queryParams) + "models/" + queryParams.modelId + ":downloadModel",
params : filterParams,
});
};
-ServerConnector.getProjectSourceUrl = function(queryParams, filterParams) {
+ServerConnector.getProjectSourceUrl = function (queryParams, filterParams) {
return this.getApiUrl({
- type : "projects/" + queryParams.projectId + ":downloadSource",
- params : filterParams
+ type: "projects/" + queryParams.projectId + ":downloadSource",
+ params: filterParams
});
};
@@ -566,10 +573,7 @@ ServerConnector.getUpdateUserPrivilegesUrl = function(queryParams, filterParams)
});
};
-ServerConnector.getConfiguration = function(params) {
- if (params === undefined) {
- params = {};
- }
+ServerConnector.getConfiguration = function () {
var self = this;
if (this._configuration === undefined) {
return self.sendGetRequest(self.getConfigurationUrl()).then(function(content) {
@@ -581,14 +585,17 @@ ServerConnector.getConfiguration = function(params) {
}
};
-ServerConnector.getConfigurationParam = function(paramId) {
+ServerConnector.getConfigurationParam = function (paramId) {
+ if (paramId === undefined) {
+ return Promise.reject(new Error("Unknown param type"));
+ }
var self = this;
- return self.getConfiguration().then(function(configuration) {
+ return self.getConfiguration().then(function (configuration) {
return configuration.getOption(paramId);
});
};
-ServerConnector.getModels = function(projectId) {
+ServerConnector.getModels = function (projectId) {
var queryParams = {};
var filterParams = {};
var self = this;
@@ -610,7 +617,7 @@ ServerConnector.getProject = function(projectId) {
var filterParams = {};
var project;
var self = this;
- return self.getProjectId(projectId).then(function(result) {
+ return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getProjectUrl(queryParams, filterParams));
}).then(function(content) {
@@ -634,15 +641,15 @@ ServerConnector.getProject = function(projectId) {
}).then(function(overlays) {
project.getModel().addLayouts(overlays);
return project;
- }).then(null, function(error) {
+ }).then(null, function (error) {
if ((error instanceof NetworkError)) {
switch (error.statusCode) {
- case HttpStatus.NOT_FOUND:
- return null;
- case HttpStatus.FORBIDDEN:
- return Promise.reject(new SecurityError("Access denied."));
- default:
- return Promise.reject(error);
+ case HttpStatus.NOT_FOUND:
+ return null;
+ case HttpStatus.FORBIDDEN:
+ return Promise.reject(new SecurityError("Access denied."));
+ default:
+ return Promise.reject(error);
}
} else {
return Promise.reject(error);
@@ -731,22 +738,22 @@ ServerConnector.getProjectStatistics = function(projectId) {
});
};
-ServerConnector.getLoggedUser = function() {
+ServerConnector.getLoggedUser = function () {
var self = this;
if (self._loggedUser !== undefined) {
return Promise.resolve(self._loggedUser);
} else {
- return self.getUser(self.getSessionData().getLogin()).then(function(user) {
+ return self.getUser(self.getSessionData().getLogin()).then(function (user) {
self._loggedUser = user;
return self._loggedUser;
});
}
};
-ServerConnector.getUser = function(login) {
+ServerConnector.getUser = function (login) {
var self = this;
var queryParams = {
- login : login,
+ login: login,
};
var filterParams = {};
@@ -862,17 +869,17 @@ ServerConnector.getOverlayElements = function(overlayId, projectId) {
});
};
-ServerConnector.getFullOverlayElement = function(params) {
+ServerConnector.getFullOverlayElement = function (params) {
var self = this;
var queryParams = {
- overlayId : params.overlay.getId(),
- modelId : params.element.getModelId(),
- id : params.element.getId(),
+ overlayId: params.overlay.getId(),
+ modelId: params.element.getModelId(),
+ id: params.element.getId(),
};
var filterParams = {};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getFullOverlayElementUrl(queryParams, filterParams));
}).then(function(content) {
@@ -889,7 +896,7 @@ ServerConnector.getFullOverlayElement = function(params) {
});
};
-ServerConnector.getProjectId = function(projectId) {
+ServerConnector.getProjectId = function (projectId) {
var self = this;
if (projectId !== undefined && projectId !== null && projectId !== "") {
return Promise.resolve(projectId);
@@ -900,25 +907,25 @@ ServerConnector.getProjectId = function(projectId) {
}
};
-ServerConnector.getLogoImg = function() {
+ServerConnector.getLogoImg = function () {
return this.getConfigurationParam(ConfigurationType.LOGO_IMG);
};
-ServerConnector.getLogoLink = function() {
+ServerConnector.getLogoLink = function () {
return this.getConfigurationParam(ConfigurationType.LOGO_LINK);
};
-ServerConnector.getMaxSearchDistance = function() {
+ServerConnector.getMaxSearchDistance = function () {
return this.getConfigurationParam(ConfigurationType.SEARCH_DISTANCE);
};
-ServerConnector.getOverlayById = function(overlayId, projectId) {
+ServerConnector.getOverlayById = function (overlayId, projectId) {
var self = this;
var queryParams = {
- overlayId : overlayId
+ overlayId: overlayId
};
var filterParams = {};
- return self.getProjectId(projectId).then(function(data) {
+ return self.getProjectId(projectId).then(function (data) {
queryParams.projectId = data;
return self.sendGetRequest(self.getOverlayByIdUrl(queryParams, filterParams));
}).then(function(content) {
@@ -926,7 +933,7 @@ ServerConnector.getOverlayById = function(overlayId, projectId) {
});
};
-ServerConnector.getReactions = function(params) {
+ServerConnector.getReactions = function (params) {
var self = this;
var queryParams = {};
if (params.ids === undefined) {
@@ -936,9 +943,9 @@ ServerConnector.getReactions = function(params) {
params.participantId = [];
}
var filterParams = {
- id : params.ids,
- columns : params.columns,
- participantId : params.participantId,
+ id: params.ids,
+ columns: params.columns,
+ participantId: params.participantId,
};
return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
@@ -1025,7 +1032,7 @@ ServerConnector.getComments = function(params) {
});
};
-ServerConnector.getSessionData = function(project) {
+ServerConnector.getSessionData = function (project) {
if (this._sessionData === undefined) {
this._sessionData = new SessionData(project);
}
@@ -1035,16 +1042,16 @@ ServerConnector.getSessionData = function(project) {
return this._sessionData;
};
-ServerConnector.getClosestElementsByCoordinates = function(params) {
+ServerConnector.getClosestElementsByCoordinates = function (params) {
var self = this;
var queryParams = {
- modelId : params.modelId
+ modelId: params.modelId
};
var filterParams = {
- coordinates : params.coordinates,
- count : params.count,
+ coordinates: params.coordinates,
+ count: params.count,
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1057,20 +1064,20 @@ ServerConnector.getClosestElementsByCoordinates = function(params) {
});
};
-ServerConnector.login = function(login, password) {
+ServerConnector.login = function (login, password) {
var self = this;
var params = {};
- if (login !== undefined) {
+ if (login !== undefined && login !== "") {
params.login = login;
params.password = password;
} else {
params.login = "anonymous";
}
self.getSessionData().setToken("");
- return self.sendPostRequest(self.loginUrl(), params).then(function() {
+ return self.sendPostRequest(self.loginUrl(), params).then(function () {
self.getSessionData().setLogin(params.login);
return Promise.resolve(self.getSessionData().getToken());
- }, function(error) {
+ }, function (error) {
if (error instanceof NetworkError && error.statusCode === HttpStatus.FORBIDDEN) {
throw new InvalidCredentialsError("Invalid credentials");
} else {
@@ -1079,24 +1086,24 @@ ServerConnector.login = function(login, password) {
});
};
-ServerConnector.logout = function() {
+ServerConnector.logout = function () {
var self = this;
self.getSessionData().setToken(undefined);
self.getSessionData().setLogin(undefined);
- return Promise.resolve();
+ return self.sendGetRequest(self.logoutUrl());
};
-ServerConnector.getElementsByQuery = function(params) {
+ServerConnector.getElementsByQuery = function (params) {
var self = this;
var queryParams = {
- modelId : params.modelId
+ modelId: params.modelId
};
var filterParams = {
- query : params.query,
- perfectMatch : params.perfectMatch,
+ query: params.query,
+ perfectMatch: params.perfectMatch,
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1109,13 +1116,13 @@ ServerConnector.getElementsByQuery = function(params) {
});
};
-ServerConnector.getDrugsByQuery = function(params) {
+ServerConnector.getDrugsByQuery = function (params) {
var self = this;
var queryParams = {};
var filterParams = {
- query : params.query
+ query: params.query
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchDrugsUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1147,13 +1154,13 @@ ServerConnector.getMiRnasByQuery = function(params) {
});
};
-ServerConnector.getChemicalsByQuery = function(params) {
+ServerConnector.getChemicalsByQuery = function (params) {
var self = this;
var queryParams = {};
var filterParams = {
- query : params.query
+ query: params.query
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchChemicalsUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1166,93 +1173,93 @@ ServerConnector.getChemicalsByQuery = function(params) {
});
};
-ServerConnector.getOverlaySourceDownloadUrl = function(params) {
+ServerConnector.getOverlaySourceDownloadUrl = function (params) {
var self = this;
var queryParams = {
- overlayId : params.overlayId
+ overlayId: params.overlayId
};
var filterParams = {};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.getOverlaySourceUrl(queryParams, filterParams);
});
};
-ServerConnector.getImageDownloadUrl = function(params) {
+ServerConnector.getImageDownloadUrl = function (params) {
var self = this;
var queryParams = {
- projectId : params.projectId,
- modelId : params.modelId,
+ projectId: params.projectId,
+ modelId: params.modelId,
};
var filterParams = {
- token : params.token,
- polygonString : params.polygonString,
- handlerClass : params.handlerClass,
- backgroundOverlayId : params.backgroundOverlayId,
- zoomLevel : params.zoomLevel,
- overlayIds : this.idsToString(params.overlayIds),
+ token: params.token,
+ polygonString: params.polygonString,
+ handlerClass: params.handlerClass,
+ backgroundOverlayId: params.backgroundOverlayId,
+ zoomLevel: params.zoomLevel,
+ overlayIds: this.idsToString(params.overlayIds),
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.getImageUrl(queryParams, filterParams);
});
};
-ServerConnector.getModelDownloadUrl = function(params) {
+ServerConnector.getModelDownloadUrl = function (params) {
var self = this;
var queryParams = {
- projectId : params.projectId,
- modelId : params.modelId,
+ projectId: params.projectId,
+ modelId: params.modelId,
};
var filterParams = {
- token : params.token,
- polygonString : params.polygonString,
- handlerClass : params.handlerClass,
- backgroundOverlayId : params.backgroundOverlayId,
- zoomLevel : params.zoomLevel,
- overlayIds : this.idsToString(params.overlayIds),
+ token: params.token,
+ polygonString: params.polygonString,
+ handlerClass: params.handlerClass,
+ backgroundOverlayId: params.backgroundOverlayId,
+ zoomLevel: params.zoomLevel,
+ overlayIds: this.idsToString(params.overlayIds),
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.getModelPartUrl(queryParams, filterParams);
});
};
-ServerConnector.getImageConverters = function() {
+ServerConnector.getImageConverters = function () {
var self = this;
- return self.getConfiguration().then(function(configuration) {
+ return self.getConfiguration().then(function (configuration) {
return configuration.getImageConverters();
});
};
-ServerConnector.getModelConverters = function() {
+ServerConnector.getModelConverters = function () {
var self = this;
- return self.getConfiguration().then(function(configuration) {
+ return self.getConfiguration().then(function (configuration) {
return configuration.getModelConverters();
});
};
-ServerConnector.getProjectSourceDownloadUrl = function(params) {
+ServerConnector.getProjectSourceDownloadUrl = function (params) {
if (params === undefined) {
params = {};
}
var queryParams = {};
var filterParams = {};
var self = this;
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.getProjectSourceUrl(queryParams, filterParams);
});
};
-ServerConnector.getDrugNamesByTarget = function(params) {
+ServerConnector.getDrugNamesByTarget = function (params) {
var self = this;
var queryParams = {};
var filterParams = {
- columns : [ "name" ],
- target : params.target.getType() + ":" + params.target.getId()
+ columns: ["name"],
+ target: params.target.getType() + ":" + params.target.getId()
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchDrugsUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1265,14 +1272,14 @@ ServerConnector.getDrugNamesByTarget = function(params) {
});
};
-ServerConnector.getMiRnaNamesByTarget = function(params) {
+ServerConnector.getMiRnaNamesByTarget = function (params) {
var self = this;
var queryParams = {};
var filterParams = {
- columns : [ "name" ],
- target : params.target.getType() + ":" + params.target.getId()
+ columns: ["name"],
+ target: params.target.getType() + ":" + params.target.getId()
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchMiRnasUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1285,14 +1292,14 @@ ServerConnector.getMiRnaNamesByTarget = function(params) {
});
};
-ServerConnector.getChemicalNamesByTarget = function(params) {
+ServerConnector.getChemicalNamesByTarget = function (params) {
var self = this;
var queryParams = {};
var filterParams = {
- columns : [ "name" ],
- target : params.target.getType() + ":" + params.target.getId()
+ columns: ["name"],
+ target: params.target.getType() + ":" + params.target.getId()
};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchChemicalsUrl(queryParams, filterParams));
}).then(function(content) {
@@ -1305,13 +1312,13 @@ ServerConnector.getChemicalNamesByTarget = function(params) {
});
};
-ServerConnector.addComment = function(params) {
+ServerConnector.addComment = function (params) {
var self = this;
var queryParams = {
- elementId : params.elementId,
- elementType : params.elementType,
- coordinates : self.pointToString(params.coordinates),
- modelId : params.modelId,
+ elementId: params.elementId,
+ elementType: params.elementType,
+ coordinates: self.pointToString(params.coordinates),
+ modelId: params.modelId,
};
var filterParams = params;
delete filterParams.elementId;
@@ -1322,10 +1329,10 @@ ServerConnector.addComment = function(params) {
filterParams.coordinates = self.pointToString(params.coordinates);
}
delete filterParams.modelId;
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendPostRequest(self.addCommentUrl(queryParams), filterParams);
- }).then(function(content) {
+ }).then(function (content) {
var response = JSON.parse(content);
return new Comment(response);
});
@@ -1368,13 +1375,13 @@ ServerConnector.updateOverlay = function(overlay) {
return self.sendPatchRequest(self.updateOverlayUrl(queryParams), filterParams);
};
-ServerConnector.removeOverlay = function(params) {
+ServerConnector.removeOverlay = function (params) {
var self = this;
var queryParams = {
- overlayId : params.overlayId
+ overlayId: params.overlayId
};
var filterParams = {};
- return self.getProjectId(params.projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
return self.sendDeleteRequest(self.deleteOverlayUrl(queryParams), filterParams);
});
@@ -1394,24 +1401,24 @@ ServerConnector.removeComment = function(params) {
ServerConnector.getSuggestedQueryList = function(projectId) {
var self = this;
- return self.getProjectId(projectId).then(function(result) {
+ return self.getProjectId(projectId).then(function (result) {
projectId = result;
return self.sendGetRequest(self.getSuggestedQueryListUrl({
projectId : projectId
}));
- }).then(function(content) {
+ }).then(function (content) {
return JSON.parse(content);
});
};
-ServerConnector.getOverlayTypes = function() {
+ServerConnector.getOverlayTypes = function () {
var self = this;
- return self.getConfiguration().then(function(configuration) {
+ return self.getConfiguration().then(function (configuration) {
return configuration.getOverlayTypes();
});
};
-ServerConnector.getPublications = function(params) {
+ServerConnector.getPublications = function (params) {
var self = this;
if (params === undefined) {
params = {};
@@ -1419,11 +1426,11 @@ ServerConnector.getPublications = function(params) {
var queryParams = {};
var filterParams = {
- start : params.start,
- length : params.length,
- sortColumn : params.sortColumn,
- sortOrder : params.sortOrder,
- search : params.search,
+ start: params.start,
+ length: params.length,
+ sortColumn: params.sortColumn,
+ sortOrder: params.sortOrder,
+ search: params.search,
};
return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index 2f259e4b172013e5205b07556512c97433162376..ece24447a4ee238c8c4852710187eff1be2fe0d9 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -8,7 +8,7 @@ var GuiUtils = require('./leftPanel/GuiUtils');
var LayoutData = require('../map/data/LayoutData');
var NetworkError = require('../NetworkError');
-var Functions = require('../functions');
+var Functions = require('../Functions');
var logger = require('../logger');
var HttpStatus = require('http-status-codes');
@@ -89,10 +89,13 @@ AddOverlayDialog.prototype.processFile = function(file) {
nameInput.value = data.name;
} else {
var filename = $("[name='overlay-file']", self.getElement())[0].value;
- if (filename.indexOf(".") > 0) {
- filename.substr(0, filename.indexOf(".") - 1);
- }
- nameInput.value = filename;
+ if (filename.indexOf(".") > 0) {
+ filename = filename.substr(0, filename.indexOf("."));
+ }
+ if (filename.lastIndexOf("\\") >= 0) {
+ filename = filename.substr(filename.lastIndexOf("\\") + 1);
+ }
+ nameInput.value = filename;
}
if (data.description !== undefined) {
descriptionInput.value = data.description;
@@ -173,6 +176,8 @@ AddOverlayDialog.prototype.open = function() {
var fileContent = self.getFileContent();
if (fileContent === null) {
GuiConnector.alert("Neither file was selected nor data was entered");
+ } else if (fileContent.length > 1024 * 256) {
+ GuiConnector.alert("File to big.<br>Please reduce file size or contact administrators.");
} else {
return self.addOverlay().then(function(result) {
$(dialog).dialog("close");
diff --git a/frontend-js/src/main/js/gui/CommentDialog.js b/frontend-js/src/main/js/gui/CommentDialog.js
index 5f4fe6f82785119e6837b89fb0ab56484c6ed9d8..1974a065715d6907b2c1b95be4a7f86a3ba1d375 100644
--- a/frontend-js/src/main/js/gui/CommentDialog.js
+++ b/frontend-js/src/main/js/gui/CommentDialog.js
@@ -85,6 +85,8 @@ CommentDialog.prototype._createGui = function() {
pinnedLabel.innerHTML = "Pinned";
var pinnedCheckbox = document.createElement('input');
pinnedCheckbox.type = "checkbox";
+ pinnedCheckbox.checked = "checked";
+
table.appendChild(createRow([ pinnedLabel, pinnedCheckbox ]));
this.setPinnedCheckbox(pinnedCheckbox);
diff --git a/frontend-js/src/main/js/gui/LoginDialog.js b/frontend-js/src/main/js/gui/LoginDialog.js
index 51c4bbae09c35840b14954df1dbae5ea56eba717..3df04cffff422f59c05771a8e0424f6c88160096 100644
--- a/frontend-js/src/main/js/gui/LoginDialog.js
+++ b/frontend-js/src/main/js/gui/LoginDialog.js
@@ -6,8 +6,9 @@ var AbstractGuiElement = require('./AbstractGuiElement');
var GuiConnector = require('../GuiConnector');
var InvalidCredentialsError = require('../InvalidCredentialsError');
var PanelControlElementType = require('./PanelControlElementType');
+var ConfigurationType = require("../ConfigurationType");
-var Functions = require('../functions');
+var Functions = require('../Functions');
var logger = require('../logger');
function LoginDialog(params) {
@@ -15,18 +16,18 @@ function LoginDialog(params) {
var self = this;
self._createLoginTab();
$(self.getElement()).dialog({
- autoOpen : false,
- resizable : false,
+ autoOpen: false,
+ resizable: false,
});
var loginButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON);
- loginButton.onclick = function() {
+ loginButton.onclick = function () {
var login = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT).value;
var password = self.getControlElement(PanelControlElementType.USER_TAB_PASSOWRD_INPUT_TEXT).value;
- return ServerConnector.login(login, password).then(function() {
+ return ServerConnector.login(login, password).then(function () {
window.location.reload(false);
- }).then(null, function(error) {
+ }).then(null, function (error) {
if (error instanceof InvalidCredentialsError) {
GuiConnector.alert("invalid credentials");
} else {
@@ -40,16 +41,16 @@ function LoginDialog(params) {
LoginDialog.prototype = Object.create(AbstractGuiElement.prototype);
LoginDialog.prototype.constructor = LoginDialog;
-LoginDialog.prototype.createTableRow = function(elements) {
+LoginDialog.prototype.createTableRow = function (elements) {
var row = Functions.createElement({
- type : "div",
- style : "display: table-row;"
+ type: "div",
+ style: "display: table-row;"
});
for (var i = 0; i < elements.length; i++) {
var cell = Functions.createElement({
- type : "div",
- style : "display: table-cell;"
+ type: "div",
+ style: "display: table-cell;"
});
cell.appendChild(elements[i]);
row.appendChild(cell);
@@ -57,65 +58,81 @@ LoginDialog.prototype.createTableRow = function(elements) {
return row;
};
-LoginDialog.prototype._createLoginTab = function() {
+LoginDialog.prototype._createLoginTab = function () {
var self = this;
var authorizationFormTab = Functions.createElement({
- type : "div",
- style : "width:100%;display: table;border-spacing: 10px;"
+ type: "div",
+ style: "width:100%;display: table;border-spacing: 10px;"
});
this.getElement().appendChild(authorizationFormTab);
var loginLabel = Functions.createElement({
- type : "div",
- content : "LOGIN:"
+ type: "div",
+ content: "LOGIN:"
});
var loginInput = Functions.createElement({
- type : "input",
- inputType : "text",
- style : "width:100%",
- name : "loginText"
+ type: "input",
+ inputType: "text",
+ style: "width:100%",
+ name: "loginText"
});
this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT, loginInput);
- authorizationFormTab.appendChild(self.createTableRow([ loginLabel, loginInput ]));
+ authorizationFormTab.appendChild(self.createTableRow([loginLabel, loginInput]));
var passwordLabel = Functions.createElement({
- type : "div",
- content : "PASSWORD:"
+ type: "div",
+ content: "PASSWORD:"
});
var passwordInput = Functions.createElement({
- type : "input",
- inputType : "password",
- style : "width:100%",
- name : "passwordText"
+ type: "input",
+ inputType: "password",
+ style: "width:100%",
+ name: "passwordText"
});
this.setControlElement(PanelControlElementType.USER_TAB_PASSOWRD_INPUT_TEXT, passwordInput);
- authorizationFormTab.appendChild(self.createTableRow([ passwordLabel, passwordInput ]));
+ authorizationFormTab.appendChild(self.createTableRow([passwordLabel, passwordInput]));
var centerTag = Functions.createElement({
- type : "center"
+ type: "center"
});
this.getElement().appendChild(centerTag);
var loginButton = Functions.createElement({
- type : "button",
- name : "loginButton",
- content : "LOGIN"
+ type: "button",
+ name: "loginButton",
+ content: "LOGIN"
});
centerTag.appendChild(loginButton);
this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON, loginButton);
+ this.getElement().appendChild(Functions.createElement({type: "br"}));
+ this.getElement().appendChild(Functions.createElement({
+ type: "a",
+ name: "requestAccount",
+ content: "Request an account",
+ href: "#",
+ }));
+
+};
+
+LoginDialog.prototype.init = function () {
+ var self = this;
+ return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (value) {
+ var link = $("[name=requestAccount]", self.getElement());
+ link.attr("href", "mailto:" + value + "?subject=MINERVA account request");
+ });
};
-LoginDialog.prototype.open = function() {
+LoginDialog.prototype.open = function () {
var self = this;
$(self.getElement()).dialog('option', 'title', 'AUTHORIZATION FORM');
$(self.getElement()).dialog("open");
};
-LoginDialog.prototype.destroy = function() {
+LoginDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
diff --git a/frontend-js/src/main/js/gui/OverviewDialog.js b/frontend-js/src/main/js/gui/OverviewDialog.js
index 9f59235c22a74cf2ea1719175d72e3ed6971d5e9..7237b783f1ba296c4c56dd13fc759c2625fc5f07 100644
--- a/frontend-js/src/main/js/gui/OverviewDialog.js
+++ b/frontend-js/src/main/js/gui/OverviewDialog.js
@@ -5,7 +5,7 @@
var AbstractGuiElement = require('./AbstractGuiElement');
var GuiConnector = require('../GuiConnector');
-var functions = require('../functions');
+var functions = require('../Functions');
var logger = require('../logger');
function OverviewDialog(params) {
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index b795684725a8951e126d858514bf8b33bf4f6ec3..8abb8cd323817b0f3c44f084a043d50cf3fe16d0 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -6,7 +6,7 @@ var Promise = require("bluebird");
var AbstractGuiElement = require('../AbstractGuiElement');
var GuiConnector = require('../../GuiConnector');
-var Functions = require('../../functions');
+var Functions = require('../../Functions');
var logger = require('../../logger');
var guiUtils = new (require('../leftPanel/GuiUtils'))();
diff --git a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
index c61b199cb6c02037f970090dfb453315674d092b..702f7966703c8d059dcccdb674a105b29b56ef46 100644
--- a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
@@ -8,7 +8,7 @@ var AddOverlayDialog = require('../AddOverlayDialog');
var Annotation = require('../../map/data/Annotation');
var GuiConnector = require('../../GuiConnector');
-var Functions = require('../../functions');
+var Functions = require('../../Functions');
var logger = require('../../logger');
var guiUtils = new (require('../leftPanel/GuiUtils'))();
diff --git a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
index cf773acd3bffa346f359b3b7b75b89102a20e36d..b927d2f85c6f1c5f9d805c9c5a3be02ef977161e 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
@@ -11,22 +11,25 @@ var PanelControlElementType = require('../PanelControlElementType');
function ChemicalPanel(params) {
params.panelName = "chemical";
params.helpTip = '<p>source: Comparative Toxicogenomics Database <a target="_ctd" href="http://ctdbase.org/">ctdbase.org</a></p>'
- + '<p>use only the full name of chemicals according to <a target="_ctd_chemicals" href="http://ctdbase.org/voc.go?type=chem"> ctdbase/chem</a> for search</p>'
- + '<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';
+ + '<p>only 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>use only the full name of chemicals according to <a target="_ctd_chemicals" href="http://ctdbase.org/voc.go?type=chem"> ctdbase/chem</a> for search</p>'
+ + 'if the chemical name includes comma(s), place a semicolon behind the name to avoid a segmentation of the name</p>'
+ + '<p>separate multiple search by semicolon';
params.placeholder = "full chemical name (CTD)";
+
AbstractDbPanel.call(this, params);
if (this.getMap().getProject().getDisease() === undefined) {
this.disablePanel("DISEASE NOT DEFINED FOR PROJECT. PLEASE, DEFINE IT IN THE ADMIN SECTION.");
}
}
+
ChemicalPanel.prototype = Object.create(AbstractDbPanel.prototype);
ChemicalPanel.prototype.constructor = ChemicalPanel;
-ChemicalPanel.prototype.createPreamble = function(chemical) {
+ChemicalPanel.prototype.createPreamble = function (chemical) {
var self = this;
var guiUtils = self.getGuiUtils();
var result = document.createElement("div");
@@ -37,8 +40,7 @@ ChemicalPanel.prototype.createPreamble = function(chemical) {
result.appendChild(guiUtils.createParamLine("Description: ", chemical.getDescription()));
result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", chemical.getSynonyms()));
result.appendChild(guiUtils.createParamLine("Direct Evidence: ", chemical.getDirectEvidence()));
- result.appendChild(guiUtils
- .createAnnotations("Directe Evidence Publications: ", chemical.getDirectEvidenceReferences()));
+ result.appendChild(guiUtils.createAnnotations("Direct Evidence Publications: ", chemical.getDirectEvidenceReferences()));
result.appendChild(guiUtils.createAnnotations("Sources: ", chemical.getReferences()));
result.appendChild(guiUtils.createNewLine());
}
@@ -46,18 +48,18 @@ ChemicalPanel.prototype.createPreamble = function(chemical) {
return result;
};
-ChemicalPanel.prototype.createTableElement = function(target, icon) {
+ChemicalPanel.prototype.createTableElement = function (target, icon) {
return this.createTargetRow(target, icon);
};
-ChemicalPanel.prototype.searchByQuery = function() {
+ChemicalPanel.prototype.searchByQuery = function () {
var self = this;
var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
return self.getOverlayDb().searchByQuery(query);
};
-ChemicalPanel.prototype.init = function() {
+ChemicalPanel.prototype.init = function () {
var query = ServerConnector.getSessionData().getChemicalQuery();
if (query !== undefined) {
return this.getOverlayDb().searchByEncodedQuery(query);
diff --git a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
index fe553ab1f70c2fad8f51b4989e9e637f37b62b97..a8ae7a7e411f49c94e0851a80e900bb60f441590 100644
--- a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
@@ -151,6 +151,7 @@ LeftPanel.prototype.init = function() {
resolve();
});
promises.push(initEvents);
+ promises.push(self.getLoginDialog().init());
return Promise.all(promises);
};
@@ -185,7 +186,8 @@ LeftPanel.prototype.showElementDetails = function(element) {
if (element !== undefined && (openTabName.indexOf("SEARCH") === -1 || searchTabName !== "GENERIC")) {
var model = self.getMap().getSubmapById(element.getModelId()).getModel();
return model.getByIdentifiedElement(element, true).then(function(bioEntity) {
- div.innerHTML = self.prepareElementDetailsContent(bioEntity).innerHTML;
+ div.innerHTML ="";
+ div.appendChild(self.prepareElementDetailsContent(bioEntity));
$(div).dialog("open");
$(div).dialog("option", "title", self.getElementTitle(bioEntity));
$(div).scrollTop(0);
diff --git a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
index 4cc29424ce41f56ce2d4e8af922f71db85bb63e3..f3ea0d84c5c4e6ddddbc5a6382e0463a2d72754e 100644
--- a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
@@ -27,7 +27,7 @@ MiRnaPanel.prototype.createPreamble = function(miRna) {
result.appendChild(guiUtils.createLabel("NOT FOUND"));
} else {
var line = document.createElement("div");
- line.appendChild(guiUtils.createLabel("μRna: "));
+ line.appendChild(guiUtils.createLabel("MiRNA: "));
line.appendChild(guiUtils.createLink("http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" + miRna.getName(), miRna
.getName()));
line.appendChild(guiUtils.createNewLine());
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index f4c13ff1493d3f8bb8b227c609d95552cd32779a..684096e62fc6bda430bb87acd7d744ec92349cbd 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -14,8 +14,8 @@ function OverlayPanel(params) {
params.panelName = "overlays";
params.scrollable = true;
params.helpTip = "<p>Overlays tab allows to display or generate custom coloring of elements and interactions in the map.</p>"
- + "<p>General overlays are overlays accessible for every user viewing the content.</p>"
- + "<p>Custom overlays are user-provided overlays, this menu becomes available upon login (see below).</p>";
+ + "<p>General overlays are overlays accessible for every user viewing the content.</p>"
+ + "<p>Custom overlays are user-provided overlays, this menu becomes available upon login (see below).</p>";
Panel.call(this, params);
var self = this;
@@ -24,7 +24,7 @@ function OverlayPanel(params) {
var addButton = this.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
- addButton.onclick = function() {
+ addButton.onclick = function () {
self.openAddOverlayDialog();
};
@@ -36,70 +36,70 @@ function OverlayPanel(params) {
OverlayPanel.prototype = Object.create(Panel.prototype);
OverlayPanel.prototype.constructor = OverlayPanel;
-OverlayPanel.prototype._createOverlayPanelGui = function() {
+OverlayPanel.prototype._createOverlayPanelGui = function () {
var generalOverlaysDiv = Functions.createElement({
- type : "div",
- name : "generalOverlays",
- className : "searchPanel"
+ type: "div",
+ name: "generalOverlays",
+ className: "searchPanel"
});
this.getElement().appendChild(generalOverlaysDiv);
this.setControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_DIV, generalOverlaysDiv);
var generalOverlaysTitle = Functions.createElement({
- type : "h5",
- content : "GENERAL OVERLAYS:"
+ type: "h5",
+ content: "GENERAL OVERLAYS:"
});
generalOverlaysDiv.appendChild(generalOverlaysTitle);
var generalOverlaysTableDiv = Functions.createElement({
- type : "table",
- name : "generalOverlaysTab",
- className : "table table-bordered",
- style : "width:100%"
+ type: "table",
+ name: "generalOverlaysTab",
+ className: "table table-bordered",
+ style: "width:100%"
});
generalOverlaysDiv.appendChild(generalOverlaysTableDiv);
this.setControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE, generalOverlaysTableDiv);
var customOverlaysDiv = Functions.createElement({
- type : "div",
- name : "customOverlays",
- className : "searchPanel"
+ type: "div",
+ name: "customOverlays",
+ className: "searchPanel"
});
this.getElement().appendChild(customOverlaysDiv);
this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_DIV, customOverlaysDiv);
var customOverlaysTitle = Functions.createElement({
- type : "h5",
- name : "customOverlaysTitle",
- content : "USER-PROVIDED OVERLAYS:"
+ type: "h5",
+ name: "customOverlaysTitle",
+ content: "USER-PROVIDED OVERLAYS:"
});
customOverlaysDiv.appendChild(customOverlaysTitle);
this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE, customOverlaysTitle);
var customOverlaysTableDiv = Functions.createElement({
- type : "table",
- name : "customOverlaysTab",
- className : "table table-bordered",
- style : "width:100%"
+ type: "table",
+ name: "customOverlaysTab",
+ className: "table table-bordered",
+ style: "width:100%"
});
customOverlaysDiv.appendChild(customOverlaysTableDiv);
this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE, customOverlaysTableDiv);
var centerTag = Functions.createElement({
- type : "center"
+ type: "center"
});
customOverlaysDiv.appendChild(centerTag);
var addOverlayButton = Functions.createElement({
- type : "button",
- name : "addOverlay",
- content : "Add overlay"
+ type: "button",
+ name: "addOverlay",
+ content: "Add overlay"
});
centerTag.appendChild(addOverlayButton);
this.setControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON, addOverlayButton);
};
-OverlayPanel.prototype.clear = function() {
+OverlayPanel.prototype.clear = function () {
var table = this.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
while (table.firstChild) {
table.removeChild(table.firstChild);
@@ -112,7 +112,7 @@ OverlayPanel.prototype.clear = function() {
};
-OverlayPanel.prototype.createTableHeader = function(edit) {
+OverlayPanel.prototype.createTableHeader = function (edit) {
var result = document.createElement("thead");
var row = document.createElement("tr");
@@ -139,7 +139,7 @@ OverlayPanel.prototype.createTableHeader = function(edit) {
return result;
};
-OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
+OverlayPanel.prototype.createOverlayRow = function (overlay, checked) {
var self = this;
var guiUtils = self.getGuiUtils();
var result = document.createElement("tr");
@@ -157,7 +157,7 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
var checkbox = document.createElement("input");
checkbox.type = "checkbox";
checkbox.checked = checked;
- checkbox.onclick = function() {
+ checkbox.onclick = function () {
if (this.checked) {
return self.getMap().openDataOverlay(overlay.getId()).then(null, GuiConnector.alert);
} else {
@@ -169,7 +169,7 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
var img = guiUtils.createIcon("icons/search.png");
var link = document.createElement("a");
link.href = "#";
- link.onclick = function() {
+ link.onclick = function () {
self.getMap().openDataOverlay(overlay.getId());
$(result).addClass('active').siblings().removeClass('active');
};
@@ -182,10 +182,10 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
if (overlay.getInputDataAvailable()) {
var button = document.createElement("button");
button.setAttribute("name", "download-overlay-" + overlay.getId());
- button.onclick = function() {
+ button.onclick = function () {
return ServerConnector.getOverlaySourceDownloadUrl({
- overlayId : overlay.getId()
- }).then(function(url) {
+ overlayId: overlay.getId()
+ }).then(function (url) {
return self.downloadFile(url);
}).then(null, GuiConnector.alert);
};
@@ -199,7 +199,7 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
var editTd = document.createElement("td");
var editButton = document.createElement("button");
editButton.setAttribute("name", "editButton");
- editButton.onclick = function() {
+ editButton.onclick = function () {
self.openEditOverlayDialog(overlay);
};
editButton.innerHTML = "<span class='ui-icon ui-icon-document'></span>";
@@ -210,72 +210,72 @@ OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
return result;
};
-OverlayPanel.prototype.openEditOverlayDialog = function(overlay) {
+OverlayPanel.prototype.openEditOverlayDialog = function (overlay) {
var self = this;
var guiUtils = self.getGuiUtils();
var content = document.createElement("fieldset");
var nameInput = guiUtils.createInputText(overlay.getName());
- var row = guiUtils.createTableRow([ guiUtils.createLabel("Name: "), nameInput ]);
+ var row = guiUtils.createTableRow([guiUtils.createLabel("Name: "), nameInput]);
content.appendChild(row);
var descriptionInput = guiUtils.createTextArea(overlay.getDescription());
- row = guiUtils.createTableRow([ guiUtils.createLabel("Description: "), descriptionInput ]);
+ row = guiUtils.createTableRow([guiUtils.createLabel("Description: "), descriptionInput]);
content.appendChild(row);
- var buttons = [ {
- text : "SAVE",
- click : function() {
+ var buttons = [{
+ text: "SAVE",
+ click: function () {
var windowSelf = this;
overlay.setName(nameInput.value);
overlay.setDescription(descriptionInput.value);
return ServerConnector.updateOverlay(overlay).then(function() {
return self.refresh();
- }).then(function() {
+ }).then(function () {
$(windowSelf).dialog("close");
}).then(null, GuiConnector.alert);
}
}, {
- text : "REMOVE",
- click : function() {
+ text: "REMOVE",
+ click: function () {
self.getMap().removeSelectedLayout(overlay.getId());
var windowSelf = this;
return ServerConnector.removeOverlay({
- overlayId : overlay.getId()
- }).then(function() {
+ overlayId: overlay.getId()
+ }).then(function () {
return self.refresh();
- }).then(function() {
+ }).then(function () {
$(windowSelf).dialog("close");
}).then(null, GuiConnector.alert);
}
}, {
- text : "CANCEL",
- click : function() {
+ text: "CANCEL",
+ click: function () {
$(this).dialog("close");
}
- } ];
+ }];
self.openDialog(content, {
- id : overlay.getId(),
- buttons : buttons,
- title : "Data overlay: " + overlay.getName(),
- className : "minerva-overlay-dialog",
+ id: overlay.getId(),
+ buttons: buttons,
+ title: "Data overlay: " + overlay.getName(),
+ className: "minerva-overlay-dialog",
});
};
-OverlayPanel.prototype.refresh = function() {
+OverlayPanel.prototype.refresh = function () {
var self = this;
var user = null;
var overlayTypes = [];
var selectedOverlay = [];
- return ServerConnector.getOverlayTypes().then(function(types) {
+ return ServerConnector.getOverlayTypes().then(function (types) {
overlayTypes = types;
return ServerConnector.getLoggedUser();
- }).then(function(loggedUser) {
+ }).then(function (loggedUser) {
user = loggedUser;
return self.getMap().getVisibleDataOverlays();
- }).then(function(visibleDataOverlays) {
+ }).then(function (visibleDataOverlays) {
for (var j = 0; j < visibleDataOverlays.length; j++) {
selectedOverlay[visibleDataOverlays[j].getId()] = true;
}
@@ -285,15 +285,15 @@ OverlayPanel.prototype.refresh = function() {
creator : user.getLogin(),
});
}).then(
- function(customOverlays) {
+ 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++) {
@@ -303,56 +303,55 @@ OverlayPanel.prototype.refresh = function() {
}
}
- 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");
+ 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<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));
+
+ body = document.createElement("tbody");
table.appendChild(body);
- for (i = 0; i < generalOverlays.length; i++) {
- overlay = generalOverlays[i];
+ for (i = 0; i < customOverlays.length; i++) {
+ overlay = customOverlays[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<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));
-
- 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) {
+OverlayPanel.prototype.setCustomOverlaysMessage = function (customOverlaysMessage) {
this._customOverlaysMessage = customOverlaysMessage;
};
-OverlayPanel.prototype.getCustomOverlaysMessage = function() {
+OverlayPanel.prototype.getCustomOverlaysMessage = function () {
return this._customOverlaysMessage;
};
-
-OverlayPanel.prototype.openAddOverlayDialog = function() {
+OverlayPanel.prototype.openAddOverlayDialog = function () {
var self = this;
var addOverlayDialog = new AddOverlayDialog({
project : self.getProject(),
@@ -368,7 +367,7 @@ OverlayPanel.prototype.openAddOverlayDialog = function() {
});
};
-OverlayPanel.prototype.init = function() {
+OverlayPanel.prototype.init = function () {
return this.refresh();
};
module.exports = OverlayPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
index c4d3efe8417d17024b75cb34111bce27e98603bc..7de49eae84b03d2ac4391f7ee4a182a65f47880d 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
@@ -21,8 +21,8 @@ function ProjectInfoPanel(params) {
self._createUserDataTab();
var logoutButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON);
- logoutButton.onclick = function() {
- return ServerConnector.logout().then(function() {
+ logoutButton.onclick = function () {
+ return ServerConnector.logout().then(function () {
window.location.reload(false);
}).then(null, GuiConnector.alert);
};
@@ -32,292 +32,293 @@ function ProjectInfoPanel(params) {
ProjectInfoPanel.prototype = Object.create(Panel.prototype);
ProjectInfoPanel.prototype.constructor = ProjectInfoPanel;
-ProjectInfoPanel.prototype._createInfoPanelGui = function() {
+ProjectInfoPanel.prototype._createInfoPanelGui = function () {
var self = this;
var guiUtils = self.getGuiUtils();
var projectId = self.getMap().getProject().getProjectId();
var infoDiv = Functions.createElement({
- type : "div",
- name : "infoDiv",
- className : "searchPanel"
+ type: "div",
+ name: "infoDiv",
+ className: "searchPanel"
});
this.getElement().appendChild(infoDiv);
this.setControlElement(PanelControlElementType.INFO_DIV, infoDiv);
var infoTitle = Functions.createElement({
- type : "h4",
- content : "PROJECT INFO:"
+ type: "h4",
+ content: "PROJECT INFO:"
});
infoDiv.appendChild(infoTitle);
var dataTab = Functions.createElement({
- type : "div",
- style : "width:100%;display: table;border-spacing: 10px;"
+ type: "div",
+ style: "width:100%;display: table;border-spacing: 10px;"
});
infoDiv.appendChild(dataTab);
var projectNameLabel = Functions.createElement({
- type : "div",
- content : "Name:"
+ type: "div",
+ content: "Name:"
});
var projectNameText = Functions.createElement({
- type : "div",
- style : "width:100%",
- name : "projectNameText"
+ type: "div",
+ style: "width:100%",
+ name: "projectNameText"
});
this.setControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT, projectNameText);
- dataTab.appendChild(guiUtils.createTableRow([ projectNameLabel, projectNameText ]));
+ dataTab.appendChild(guiUtils.createTableRow([projectNameLabel, projectNameText]));
var projectVersionLabel = Functions.createElement({
- type : "div",
- content : "Version:"
+ type: "div",
+ content: "Version:"
});
var projectVersionText = Functions.createElement({
- type : "div",
- style : "width:100%",
- name : "projectVersionText"
+ type: "div",
+ style: "width:100%",
+ name: "projectVersionText"
});
this.setControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT, projectVersionText);
- dataTab.appendChild(guiUtils.createTableRow([ projectVersionLabel, projectVersionText ]));
+ dataTab.appendChild(guiUtils.createTableRow([projectVersionLabel, projectVersionText]));
infoTitle = Functions.createElement({
- type : "h4",
- content : "Data:"
+ type: "h4",
+ content: "Data:"
});
infoDiv.appendChild(infoTitle);
var dialogDiv = Functions.createElement({
- type : "div",
+ type: "div",
});
this.publicationListDialog = new PublicationListDialog({
- customMap : self.getMap(),
- element : dialogDiv,
+ customMap: self.getMap(),
+ element: dialogDiv,
});
dataTab = Functions.createElement({
- type : "ul",
+ type: "ul",
});
infoDiv.appendChild(dataTab);
var projectPublicationsText = Functions.createElement({
- type : "span",
- name : "projectPublicationsText",
- style : "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
+ type: "span",
+ name: "projectPublicationsText",
+ style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
});
this.setControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT, projectPublicationsText);
var projectPublicationsButton = Functions.createElement({
- type : "a",
- name : "projectPublicationsButton",
+ type: "a",
+ name: "projectPublicationsButton",
});
projectPublicationsButton.appendChild(Functions.createElement({
- type : "span",
- content : "<i class='fa fa-list'> ",
+ type: "span",
+ content: "<i class='fa fa-list'> ",
}));
projectPublicationsButton.appendChild(projectPublicationsText);
projectPublicationsButton.appendChild(Functions.createElement({
- type : "span",
- style : "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
- content : " publication(s)",
+ type: "span",
+ style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
+ content: " publication(s)",
}));
this.setControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON, projectPublicationsButton);
var liElement = Functions.createElement({
- type : "li",
- style : "line-height: 30px;",
+ type: "li",
+ style: "line-height: 30px;",
});
liElement.appendChild(projectPublicationsButton);
dataTab.appendChild(liElement);
var projectOriginalFileButton = Functions.createElement({
- type : "a",
- name : "projectOriginalFileButton",
- href : "#",
- content : "<i class='fa fa-files-o'> source file",
+ type: "a",
+ name: "projectOriginalFileButton",
+ href: "#",
+ content: "<i class='fa fa-files-o'> source file",
});
this.setControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON, projectOriginalFileButton);
liElement = Functions.createElement({
- type : "li",
- style : "line-height: 30px",
+ type: "li",
+ style: "line-height: 30px",
});
liElement.appendChild(projectOriginalFileButton);
dataTab.appendChild(liElement);
var exportButton = Functions.createElement({
- type : "a",
- href : ServerConnector.getServerBaseUrl() + "/export.xhtml?id=" + projectId,
- content : '<i class="fa fa-mail-forward"> EXPORT',
+ type: "a",
+ href: ServerConnector.getServerBaseUrl() + "/export.xhtml?id=" + projectId,
+ content: '<i class="fa fa-mail-forward"> EXPORT',
});
liElement = Functions.createElement({
- type : "li",
- style : "line-height: 30px",
+ type: "li",
+ style: "line-height: 30px",
});
liElement.appendChild(exportButton);
dataTab.appendChild(liElement);
var manualButton = Functions.createElement({
- type : "a",
- name : "manualLink",
- content : '<i class="fa fa-file"> MANUAL',
+ type: "a",
+ name: "manualLink",
+ content: '<i class="fa fa-file"> MANUAL',
});
manualButton.href = "#";
- manualButton.onclick = function() {
- return ServerConnector.getConfigurationParam(ConfigurationType.USER_MANUAL_FILE).then(function(manualFileUrl) {
+ manualButton.onclick = function () {
+ return ServerConnector.getConfigurationParam(ConfigurationType.USER_MANUAL_FILE).then(function (manualFileUrl) {
var win = window.open(manualFileUrl, '_user_manual_');
win.focus();
});
};
liElement = Functions.createElement({
- type : "li",
- style : "line-height: 30px",
+ type: "li",
+ style: "line-height: 30px",
});
liElement.appendChild(manualButton);
dataTab.appendChild(liElement);
};
-ProjectInfoPanel.prototype._createInfoPanelLogic = function() {
+ProjectInfoPanel.prototype._createInfoPanelLogic = function () {
var self = this;
var downloadSourceButton = self.getControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON);
var showPublicationsButton = self.getControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON);
- downloadSourceButton.onclick = function() {
+ downloadSourceButton.onclick = function () {
return self.downloadSourceFile();
};
- showPublicationsButton.onclick = function() {
+ showPublicationsButton.onclick = function () {
return self.showPublicationListDialog();
};
};
-ProjectInfoPanel.prototype.downloadSourceFile = function() {
+ProjectInfoPanel.prototype.downloadSourceFile = function () {
var self = this;
- return ServerConnector.getProjectSourceDownloadUrl().then(function(url) {
+ return ServerConnector.getProjectSourceDownloadUrl().then(function (url) {
return self.downloadFile(url);
}).then(null, GuiConnector.alert);
};
-ProjectInfoPanel.prototype.showPublicationListDialog = function() {
+ProjectInfoPanel.prototype.showPublicationListDialog = function () {
return this.publicationListDialog.show();
};
-ProjectInfoPanel.prototype.refresh = function() {
+ProjectInfoPanel.prototype.refresh = function () {
var self = this;
var projectNameText = self.getControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT);
var projectVersionText = self.getControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT);
var projectPublicationsText = self.getControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT);
- return ServerConnector.getProject().then(function(project) {
+ return ServerConnector.getProject().then(function (project) {
projectNameText.innerHTML = project.getName();
projectVersionText.innerHTML = project.getVersion();
return ServerConnector.getProjectStatistics();
- }).then(function(statistics) {
+ }).then(function (statistics) {
projectPublicationsText.innerHTML = statistics.getPublicationCount();
return ServerConnector.getLoggedUser();
- }).then(function(user) {
+ }).then(function (user) {
self.showUserProfilePage(user);
});
};
-ProjectInfoPanel.prototype._createUserDataTab = function() {
+ProjectInfoPanel.prototype._createUserDataTab = function () {
var self = this;
var guiUtils = self.getGuiUtils();
var userDataDiv = Functions.createElement({
- type : "div",
- name : "userDataTab",
- className : "searchPanel",
- style : "display:none"
+ type: "div",
+ name: "userDataTab",
+ className: "searchPanel",
+ style: "display:none"
});
this.getElement().appendChild(userDataDiv);
this.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
var userDataTitle = Functions.createElement({
- type : "h3",
- content : '<img src="./resources/images/profile.png" border="0" align="left"/><br/>User data<br/>'
+ type: "h3",
+ content: '<img src="./resources/images/profile.png" border="0" align="left"/><br/>User data<br/>'
});
userDataDiv.appendChild(userDataTitle);
var userDataFormTab = Functions.createElement({
- type : "div",
- style : "width:100%;display: table;border-spacing: 10px;"
+ type: "div",
+ style: "width:100%;display: table;border-spacing: 10px;"
});
userDataDiv.appendChild(userDataFormTab);
var loginLabel = Functions.createElement({
- type : "span",
- content : "LOGIN:",
- style : "color:#999999"
+ type: "span",
+ content: "LOGIN:",
+ style: "color:#999999"
});
var loginText = Functions.createElement({
- type : "span",
- name : "loginValue"
+ type: "span",
+ name: "loginValue"
});
this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_TEXT, loginText);
- userDataDiv.appendChild(guiUtils.createTableRow([ loginLabel, loginText ]));
+ userDataDiv.appendChild(guiUtils.createTableRow([loginLabel, loginText]));
var nameLabel = Functions.createElement({
- type : "span",
- content : "NAME:",
- style : "color:#999999"
+ type: "span",
+ content: "NAME:",
+ style: "color:#999999"
});
var nameText = Functions.createElement({
- type : "span",
- name : "nameValue"
+ type: "span",
+ name: "nameValue"
});
this.setControlElement(PanelControlElementType.USER_TAB_NAME_TEXT, nameText);
- userDataDiv.appendChild(guiUtils.createTableRow([ nameLabel, nameText ]));
+ userDataDiv.appendChild(guiUtils.createTableRow([nameLabel, nameText]));
var surnameLabel = Functions.createElement({
- type : "span",
- content : "SURNAME:",
- style : "color:#999999"
+ type: "span",
+ content: "SURNAME:",
+ style: "color:#999999"
});
var surnameText = Functions.createElement({
- type : "span",
- name : "surnameValue"
+ type: "span",
+ name: "surnameValue"
});
this.setControlElement(PanelControlElementType.USER_TAB_SURNAME_TEXT, surnameText);
- userDataDiv.appendChild(guiUtils.createTableRow([ surnameLabel, surnameText ]));
+ userDataDiv.appendChild(guiUtils.createTableRow([surnameLabel, surnameText]));
var emailLabel = Functions.createElement({
- type : "span",
- content : "EMAIL:",
- style : "color:#999999"
+ type: "span",
+ content: "EMAIL:",
+ style: "color:#999999"
});
var emailText = Functions.createElement({
- type : "span",
- name : "emailValue"
+ type: "span",
+ name: "emailValue"
});
self.setControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT, emailText);
- userDataDiv.appendChild(guiUtils.createTableRow([ emailLabel, emailText ]));
+ userDataDiv.appendChild(guiUtils.createTableRow([emailLabel, emailText]));
var centerTag = Functions.createElement({
- type : "center"
+ type: "center"
});
userDataDiv.appendChild(centerTag);
var logoutButton = Functions.createElement({
- type : "button",
- name : "logoutButton",
- content : "LOGOUT"
+ type: "button",
+ name: "logoutButton",
+ content: "LOGOUT"
});
centerTag.appendChild(logoutButton);
self.setControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON, logoutButton);
self.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
var loginTabDiv = Functions.createElement({
- type : "div",
- name : "userLoginTab",
- 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/>' + '<center><button>LOGIN</button></center>',
- });
- $(loginTabDiv).find("button")[0].onclick = function() {
+ type: "div",
+ name: "userLoginTab",
+ 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/>' + '<center><button>LOGIN</button></center>' +
+ '<br/><a hreg="#" name="requestAccount">Request an account</a>',
+ });
+ $(loginTabDiv).find("button")[0].onclick = function () {
return self.getParent().getLoginDialog().open();
};
@@ -326,7 +327,7 @@ ProjectInfoPanel.prototype._createUserDataTab = function() {
};
-ProjectInfoPanel.prototype.showUserProfilePage = function(user) {
+ProjectInfoPanel.prototype.showUserProfilePage = function (user) {
var self = this;
var userDataTabDiv = self.getControlElement(PanelControlElementType.USER_TAB_USER_DIV);
@@ -351,8 +352,13 @@ ProjectInfoPanel.prototype.showUserProfilePage = function(user) {
}
};
-ProjectInfoPanel.prototype.init = function() {
- return this.refresh();
+ProjectInfoPanel.prototype.init = function () {
+ var self = this;
+ return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (value) {
+ var link = $("[name=requestAccount]", self.getElement());
+ link.attr("href", "mailto:" + value + "?subject=MINERVA account request");
+ return self.refresh();
+ });
};
module.exports = ProjectInfoPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
index 39df083d6cec0f4c00860e99358aca836b67c591..eb5ec1203e3a5530fead452e39fc54fbc0b0b6a7 100644
--- a/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
+++ b/frontend-js/src/main/js/gui/leftPanel/PublicationListDialog.js
@@ -9,7 +9,7 @@ var Alias = require('../../map/data/Alias');
var IdentifiedElement = require('../../map/data/IdentifiedElement');
var Reaction = require('../../map/data/Reaction');
-var Functions = require('../../functions');
+var Functions = require('../../Functions');
var logger = require('../../logger');
function PublicationListDialog(params) {
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index e6129ba9d240428750c9fdb13af7ef9a918c6d6f..06bccc48ba2d14113796d306a09dae71c9f2038b 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -78,9 +78,9 @@ AbstractCustomMap.prototype.constructor = AbstractCustomMap;
/**
* Assigns layouts with images to the google map (which set of images should be
* used by google maps api for which layout).
- *
+ *
*/
-AbstractCustomMap.prototype.setupLayouts = function() {
+AbstractCustomMap.prototype.setupLayouts = function () {
for (var i = 0; i < this.getLayouts().length; i++) {
var layout = this.getLayouts()[i];
var typeOptions = this.createTypeOptions(layout);
@@ -92,9 +92,9 @@ AbstractCustomMap.prototype.setupLayouts = function() {
/**
* Creates general google maps options used in this map.
- *
+ *
*/
-AbstractCustomMap.prototype.creatMapOptions = function() {
+AbstractCustomMap.prototype.creatMapOptions = function () {
var self = this;
var centerPoint = this.getModel().getCenterLatLng();
@@ -106,19 +106,19 @@ AbstractCustomMap.prototype.creatMapOptions = function() {
}
var result = {
- center : centerPoint,
- rotateControl : true,
- panControl : true,
- mapTypeControl : false,
- zoom : this.getMinZoom(),
- streetViewControl : false,
-
- panControlOptions : {
- position : google.maps.ControlPosition.LEFT_TOP
+ center: centerPoint,
+ rotateControl: true,
+ panControl: true,
+ mapTypeControl: false,
+ zoom: this.getMinZoom(),
+ streetViewControl: false,
+
+ panControlOptions: {
+ position: google.maps.ControlPosition.LEFT_TOP
},
- zoomControlOptions : {
- style : google.maps.ZoomControlStyle.LARGE,
- position : google.maps.ControlPosition.LEFT_TOP
+ zoomControlOptions: {
+ style: google.maps.ZoomControlStyle.LARGE,
+ position: google.maps.ControlPosition.LEFT_TOP
}
};
@@ -127,16 +127,16 @@ AbstractCustomMap.prototype.creatMapOptions = function() {
/**
* Create google maps configuration options object for a specific layout.
- *
+ *
* @param param
* object with information about layout
*/
-AbstractCustomMap.prototype.createTypeOptions = function(param) {
+AbstractCustomMap.prototype.createTypeOptions = function (param) {
var self = this;
var result = {
// this is a function that will retrieve valid url to png images for
// tiles on different zoom levels
- getTileUrl : function(coord, zoom) {
+ getTileUrl: function (coord, zoom) {
// we have 1 tile on self.getConfiguration().MIN_ZOOM and
// therefore must limit tails according to this
/* jshint bitwise: false */
@@ -147,28 +147,28 @@ AbstractCustomMap.prototype.createTypeOptions = function(param) {
var addr = "../map_images/" + param.getDirectory() + "/" + zoom + "/" + coord.x + "/" + coord.y + ".PNG";
return addr;
},
- tileSize : new google.maps.Size(this.getTileSize(), this.getTileSize()),
- maxZoom : this.getMaxZoom(),
- minZoom : this.getMinZoom(),
- radius : 360,
- name : param.name
+ tileSize: new google.maps.Size(this.getTileSize(), this.getTileSize()),
+ maxZoom: this.getMaxZoom(),
+ minZoom: this.getMinZoom(),
+ radius: 360,
+ name: param.name
};
return result;
};
/**
* Sets maximum zoom level on google map.
- *
+ *
*/
-AbstractCustomMap.prototype.setMaxZoomLevel = function() {
+AbstractCustomMap.prototype.setMaxZoomLevel = function () {
this.getGoogleMap().setZoom(this.getMaxZoom());
};
/**
* Returns mouse coordinate on the map in lat,lng system.
- *
+ *
*/
-AbstractCustomMap.prototype.getMouseLatLng = function() {
+AbstractCustomMap.prototype.getMouseLatLng = function () {
// this method is tricky, the main problem is how to map mouse coordinate to
// google map
// to do that we need a point of reference in both systems (x,y and lat,lng)
@@ -189,19 +189,19 @@ AbstractCustomMap.prototype.getMouseLatLng = function() {
}
var offset = {
- x : lx,
- y : ly
+ x: lx,
+ y: ly
};
var center = {
- x : self.getGoogleMap().getDiv().offsetWidth / 2,
- y : self.getGoogleMap().getDiv().offsetHeight / 2
+ x: self.getGoogleMap().getDiv().offsetWidth / 2,
+ y: self.getGoogleMap().getDiv().offsetHeight / 2
};
// and now find how far from center point we are (in pixels)
var relativeDist = {
- x : (GuiConnector.xPos - offset.x - center.x),
- y : (GuiConnector.yPos - offset.y - center.y)
+ x: (GuiConnector.xPos - offset.x - center.x),
+ y: (GuiConnector.yPos - offset.y - center.y)
};
// transform pixels into x,y distance
@@ -219,14 +219,14 @@ AbstractCustomMap.prototype.getMouseLatLng = function() {
/**
* Transform distance (coordinates) in pixels into x,y distance on the map.
- *
+ *
* @param pixels
* x,y distance in pixels
* @param zoomLevel
* at which zoom level this pixels where mesaured
- *
+ *
*/
-AbstractCustomMap.prototype.fromPixelsToPoint = function(pixels, zoomLevel) {
+AbstractCustomMap.prototype.fromPixelsToPoint = function (pixels, zoomLevel) {
var zoomScale = this.getPictureSize() / (Math.pow(2, zoomLevel - this.getMinZoom()) * this.getTileSize());
var pointx = pixels.x * zoomScale;
var pointy = pixels.y * zoomScale;
@@ -236,13 +236,13 @@ AbstractCustomMap.prototype.fromPixelsToPoint = function(pixels, zoomLevel) {
/**
* Transforms coordinates on the map from google.maps.LatLng to
* google.maps.Point
- *
+ *
* @param latlng
* cooordinates in x,y format
* @param coordinates
* in lat,lng format
*/
-AbstractCustomMap.prototype.fromLatLngToPoint = function(latLng) {
+AbstractCustomMap.prototype.fromLatLngToPoint = function (latLng) {
var me = this;
var point = new google.maps.Point(0, 0);
var origin = me.pixelOrigin_;
@@ -264,12 +264,12 @@ AbstractCustomMap.prototype.fromLatLngToPoint = function(latLng) {
/**
* Transforms coordinates on the map from google.maps.Point to
* google.maps.LatLng
- *
+ *
* @param point
* coordinates in standard x,y format
* @return cooordinates in lat,lng format
*/
-AbstractCustomMap.prototype.fromPointToLatLng = function(point) {
+AbstractCustomMap.prototype.fromPointToLatLng = function (point) {
var me = this;
// rescale the point (all computations are done assuming that we work on
@@ -285,26 +285,26 @@ AbstractCustomMap.prototype.fromPointToLatLng = function(point) {
/**
* Transforms google.maps.LatLng to tile coordinate (for instance on which tile
* mouse clicked).
- *
- *
+ *
+ *
* @param latlng
* coordinates in latlng format
* @param z
* zoom level at which we want to find coordinates of tile
* @return cooordinates of a tile
*/
-AbstractCustomMap.prototype.latLngToTile = function(latLng, z) {
+AbstractCustomMap.prototype.latLngToTile = function (latLng, z) {
var worldCoordinate = this.fromLatLngToPoint(latLng);
var pixelCoordinate = new google.maps.Point(worldCoordinate.x * Math.pow(2, z), worldCoordinate.y * Math.pow(2, z));
var tileCoordinate = new google.maps.Point(Math.floor(pixelCoordinate.x / this.getTileSize()), Math
- .floor(pixelCoordinate.y / this.getTileSize()));
+ .floor(pixelCoordinate.y / this.getTileSize()));
return tileCoordinate;
};
/**
* Register events responsible for click events
*/
-AbstractCustomMap.prototype.registerMapClickEvents = function() {
+AbstractCustomMap.prototype.registerMapClickEvents = function () {
// find top map (CustomMap)
//
@@ -313,30 +313,30 @@ AbstractCustomMap.prototype.registerMapClickEvents = function() {
var self = this;
// search event
- google.maps.event.addListener(this.getGoogleMap(), 'click', function(mouseEvent) {
+ google.maps.event.addListener(this.getGoogleMap(), 'click', function (mouseEvent) {
var point = self.fromLatLngToPoint(mouseEvent.latLng);
var searchDb = customMap.getOverlayByName('search');
return searchDb.searchByCoordinates({
- modelId : self.getModel().getId(),
- coordinates : point,
- zoom : self.getGoogleMap().getZoom()
+ modelId: self.getModel().getId(),
+ coordinates: point,
+ zoom: self.getGoogleMap().getZoom()
}).then(null, GuiConnector.alert);
});
// select last clicked map
- google.maps.event.addListener(this.getGoogleMap(), 'click', function(mouseEvent) {
+ google.maps.event.addListener(this.getGoogleMap(), 'click', function (mouseEvent) {
customMap.setActiveSubmapId(self.getId());
customMap.setActiveSubmapClickCoordinates(self.fromLatLngToPoint(mouseEvent.latLng));
});
// select last clicked map
- google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function(mouseEvent) {
+ google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function (mouseEvent) {
customMap.setActiveSubmapId(self.getId());
customMap.setActiveSubmapClickCoordinates(self.fromLatLngToPoint(mouseEvent.latLng));
});
// prepare for image export
- google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function() {
+ google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function () {
var bounds = self.getGoogleMap().getBounds();
var polygon = "";
@@ -363,7 +363,7 @@ AbstractCustomMap.prototype.registerMapClickEvents = function() {
});
// context menu event
- google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function() {
+ google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function () {
self.getTopMap().getContextMenu().open(GuiConnector.xPos, GuiConnector.yPos);
});
};
@@ -371,9 +371,9 @@ AbstractCustomMap.prototype.registerMapClickEvents = function() {
/**
* It toggle drawing manager used on the map: if it's on then it will turn it
* off, if it's off it will turn it on
- *
+ *
*/
-AbstractCustomMap.prototype._turnOnOffDrawing = function() {
+AbstractCustomMap.prototype._turnOnOffDrawing = function () {
if (this.isDrawingOn()) {
this.turnOffDrawing();
} else {
@@ -383,16 +383,16 @@ AbstractCustomMap.prototype._turnOnOffDrawing = function() {
/**
* Checks if the drawing manager for the map is on.
- *
+ *
*/
-AbstractCustomMap.prototype.isDrawingOn = function() {
+AbstractCustomMap.prototype.isDrawingOn = function () {
return this._drawingManager !== null;
};
/**
* Turns on drawing manager on the map.
*/
-AbstractCustomMap.prototype.turnOnDrawing = function() {
+AbstractCustomMap.prototype.turnOnDrawing = function () {
if (this.isDrawingOn()) {
logger.warn("Trying to turn on drawing manager, but it is already available.");
return;
@@ -400,28 +400,28 @@ AbstractCustomMap.prototype.turnOnDrawing = function() {
var customMap = this.getTopMap();
var self = this;
this._drawingManager = new google.maps.drawing.DrawingManager({
- drawingMode : google.maps.drawing.OverlayType.MARKER,
- drawingControl : true,
- drawingControlOptions : {
- position : google.maps.ControlPosition.TOP_CENTER,
- drawingModes : [ google.maps.drawing.OverlayType.POLYGON, ]
+ drawingMode: google.maps.drawing.OverlayType.MARKER,
+ drawingControl: true,
+ drawingControlOptions: {
+ position: google.maps.ControlPosition.TOP_CENTER,
+ drawingModes: [google.maps.drawing.OverlayType.POLYGON,]
},
- markerOptions : {
- icon : 'images/beachflag.png'
+ markerOptions: {
+ icon: 'images/beachflag.png'
},
- circleOptions : {
- fillColor : '#ffff00',
- fillOpacity : 1,
- strokeWeight : 5,
- clickable : false,
- editable : true,
- zIndex : 1
+ circleOptions: {
+ fillColor: '#ffff00',
+ fillOpacity: 1,
+ strokeWeight: 5,
+ clickable: false,
+ editable: true,
+ zIndex: 1
}
});
this._drawingManager.setMap(this.getGoogleMap());
this._drawingManager.setDrawingMode(google.maps.drawing.OverlayType.POLYGON);
- google.maps.event.addListener(this._drawingManager, 'overlaycomplete', function(e) {
+ google.maps.event.addListener(this._drawingManager, 'overlaycomplete', function (e) {
if (e.type !== google.maps.drawing.OverlayType.MARKER) {
// Switch back to non-drawing mode after drawing a shape.
self._drawingManager.setDrawingMode(null);
@@ -430,7 +430,7 @@ AbstractCustomMap.prototype.turnOnDrawing = function() {
// user mouses down on it.
var newShape = e.overlay;
newShape.type = e.type;
- google.maps.event.addListener(newShape, 'rightclick', function(e) {
+ google.maps.event.addListener(newShape, 'rightclick', function (e) {
// select map that was clicked
customMap.setActiveSubmapId(self.getId());
@@ -448,25 +448,25 @@ AbstractCustomMap.prototype.turnOnDrawing = function() {
/**
* Sets selectedArea on this map.
- *
+ *
*/
-AbstractCustomMap.prototype.setSelectedArea = function(area) {
+AbstractCustomMap.prototype.setSelectedArea = function (area) {
this._selectedArea = area;
};
/**
* Returns selectedArea on this map.
- *
+ *
*/
-AbstractCustomMap.prototype.getSelectedArea = function() {
+AbstractCustomMap.prototype.getSelectedArea = function () {
return this._selectedArea;
};
/**
* Transforms google.maps.Polygon into string with coordinates.
- *
+ *
*/
-AbstractCustomMap.prototype.areaToString = function(area) {
+AbstractCustomMap.prototype.areaToString = function (area) {
var len = area.getPath().length;
var path = area.getPath();
var res = "";
@@ -480,7 +480,7 @@ AbstractCustomMap.prototype.areaToString = function(area) {
/**
* Removes selected area (polygon) from the map.
*/
-AbstractCustomMap.prototype._removeSelection = function() {
+AbstractCustomMap.prototype._removeSelection = function () {
if (this._selectedArea) {
this._selectedArea.setMap(null);
this._selectedArea = null;
@@ -492,7 +492,7 @@ AbstractCustomMap.prototype._removeSelection = function() {
/**
* Turns off drawing manager on the map.
*/
-AbstractCustomMap.prototype.turnOffDrawing = function() {
+AbstractCustomMap.prototype.turnOffDrawing = function () {
if (this.isDrawingOn()) {
this._drawingManager.setMap(null);
this._drawingManager = null;
@@ -505,10 +505,10 @@ AbstractCustomMap.prototype.turnOffDrawing = function() {
* Returns top map. TODO implementation of this function should be probably
* moved to Submap and CustomMap classes and here only abstract function
* definition
- *
+ *
* @returns {CustomMap}
*/
-AbstractCustomMap.prototype.getTopMap = function() {
+AbstractCustomMap.prototype.getTopMap = function () {
logger.fatal("Not implemented");
};
@@ -518,7 +518,7 @@ AbstractCustomMap.prototype.getTopMap = function() {
* visualized at the same time then index contains information where this new
* layout is placed in the list (starting from 0) and length contains
* information how many layouts we visualize in total.
- *
+ *
* @param layoutId
* identifier of a layout
* @param index
@@ -528,9 +528,9 @@ AbstractCustomMap.prototype.getTopMap = function() {
* @param length
* number of layouts that are currently visualized
*/
-AbstractCustomMap.prototype._resizeSelectedLayout = function(layoutId, index, length) {
+AbstractCustomMap.prototype._resizeSelectedLayout = function (layoutId, index, length) {
var self = this;
- return new Promise(function(resolve) {
+ return new Promise(function (resolve) {
// if map is not initialized then don't perform this operation
if (!self.initialized) {
logger.debug("Model " + self.getId() + " not initialized");
@@ -554,7 +554,7 @@ AbstractCustomMap.prototype._resizeSelectedLayout = function(layoutId, index, le
* the same time then index contains information where this new layout is placed
* in the list (starting from 0) and length contains information how many
* layouts we visualize in total.
- *
+ *
* @param layoutId
* identifier of a layout
* @param index
@@ -564,10 +564,10 @@ AbstractCustomMap.prototype._resizeSelectedLayout = function(layoutId, index, le
* @param length
* number of layouts that are currently visualized
*/
-AbstractCustomMap.prototype._showSelectedLayout = function(layoutId, index, length) {
+AbstractCustomMap.prototype._showSelectedLayout = function (layoutId, index, length) {
var self = this;
// if map is not initialized then don't perform this operation
- return new Promise(function(resolve, reject) {
+ return new Promise(function (resolve, reject) {
if (!self.initialized) {
logger.debug("Model " + self.getId() + " not initialized");
resolve();
@@ -586,49 +586,64 @@ AbstractCustomMap.prototype._showSelectedLayout = function(layoutId, index, leng
var layoutAliases;
var layoutReactions;
- return self.getTopMap().getModel().getLayoutDataById(layoutId).then(function(layout) {
+ return self.getTopMap().getModel().getLayoutDataById(layoutId).then(function (layout) {
layoutAliases = layout.getAliases();
layoutReactions = layout.getReactions();
- return Promise.each(layoutAliases, function(layoutAlias) {
+ var identifiedElements = [];
+ var i;
+ for (i = 0; i < layoutAliases.length; i++) {
+ if (layoutAliases[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(layoutAliases[i]));
+ }
+ }
+ var reactionIds = [];
+ for (i = 0; i < layoutReactions.length; i++) {
+ if (layoutReactions[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(layoutReactions[i]));
+ }
+ }
+ return self.getModel().getByIdentifiedElements(identifiedElements, false);
+ }).then(function () {
+ return Promise.each(layoutAliases, function (layoutAlias) {
if (layoutAlias.getModelId() === self.getId()) {
var surface;
var element;
- return self.getModel().getAliasById(layoutAlias.getId()).then(function(aliasData) {
+ return self.getModel().getAliasById(layoutAlias.getId()).then(function (aliasData) {
element = new IdentifiedElement(aliasData);
return AliasSurface.create({
- overlayAlias : layoutAlias,
- alias : aliasData,
- map : self,
- startX : startX,
- endX : endX,
- onClick : [ function() {
+ overlayAlias: layoutAlias,
+ alias: aliasData,
+ map: self,
+ startX: startX,
+ endX: endX,
+ onClick: [function () {
return self._openInfoWindowForAlias(aliasData, surface.getGoogleMarker());
- }, function() {
+ }, function () {
return self.getTopMap().callListeners("onBioEntityClick", element);
- } ]
+ }]
});
- }).then(function(result) {
+ }).then(function (result) {
surface = result;
self.selectedLayoutOverlays[layoutId].push(surface);
});
}
});
- }).then(function() {
- return Promise.each(layoutReactions, function(layoutReaction) {
+ }).then(function () {
+ return Promise.each(layoutReactions, function (layoutReaction) {
if (layoutReaction.getModelId() === self.getId()) {
- return self.getModel().getReactionById(layoutReaction.getId()).then(function(reactionData) {
+ return self.getModel().getReactionById(layoutReaction.getId()).then(function (reactionData) {
var element = new IdentifiedElement(reactionData);
var surface = new ReactionSurface({
- layoutReaction : layoutReaction,
- reaction : reactionData,
- map : self,
- onClick : [ function() {
+ layoutReaction: layoutReaction,
+ reaction: reactionData,
+ map: self,
+ onClick: [function () {
return self._openInfoWindowForReaction(reactionData, surface.getGoogleMarker());
- }, function() {
+ }, function () {
return self.getTopMap().callListeners("onBioEntityClick", element);
- } ],
- customized : (length === 1)
+ }],
+ customized: (length === 1)
});
self.selectedLayoutOverlays[layoutId].push(surface);
@@ -636,7 +651,7 @@ AbstractCustomMap.prototype._showSelectedLayout = function(layoutId, index, leng
});
}
});
- }).then(function() {
+ }).then(function () {
resolve();
}).then(null, reject);
});
@@ -644,11 +659,11 @@ AbstractCustomMap.prototype._showSelectedLayout = function(layoutId, index, leng
/**
* Hides all elements from layout.
- *
+ *
* @param layoutId
* identifier of a layout
*/
-AbstractCustomMap.prototype._hideSelectedLayout = function(layoutId) {
+AbstractCustomMap.prototype._hideSelectedLayout = function (layoutId) {
// if map is not initialized then don't perform this operation
if (!this.initialized) {
logger.debug("Model " + this.getId() + " not initialized");
@@ -662,11 +677,11 @@ AbstractCustomMap.prototype._hideSelectedLayout = function(layoutId) {
/**
* Opens {@link AliasInfoWindow} for given alias.
- *
+ *
* @param aliasId
* identifier of the alias
*/
-AbstractCustomMap.prototype._openInfoWindowForAlias = function(alias, googleMarker) {
+AbstractCustomMap.prototype._openInfoWindowForAlias = function (alias, googleMarker) {
var self = this;
var infoWindow = this.getAliasInfoWindowById(alias.getId());
@@ -679,9 +694,9 @@ AbstractCustomMap.prototype._openInfoWindowForAlias = function(alias, googleMark
return Promise.resolve(infoWindow);
} else {
self._aliasInfoWindow[alias.getId()] = new AliasInfoWindow({
- alias : alias,
- map : self,
- marker : googleMarker,
+ alias: alias,
+ map: self,
+ marker: googleMarker,
});
return self._aliasInfoWindow[alias.getId()].init();
}
@@ -690,15 +705,15 @@ AbstractCustomMap.prototype._openInfoWindowForAlias = function(alias, googleMark
/**
* Returns promise of a list of {@link LayoutAlias} information for a given
* {@link Alias} in all currently visualized layouts.
- *
+ *
* @param aliasId
* identifier of the {@link Alias}
* @returns promise of an {Array} with list of {@link LayoutAlias} information
* for a given {@link Alias} in all currently visualized layouts
*/
-AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function(aliasId) {
+AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function (aliasId) {
var self = this;
- return self.getTopMap().getVisibleDataOverlays().then(function(visibleDataOverlays) {
+ return self.getTopMap().getVisibleDataOverlays().then(function (visibleDataOverlays) {
var result = [];
for (var i = 0; i < visibleDataOverlays.length; i++) {
var layout = visibleDataOverlays[i];
@@ -711,16 +726,16 @@ AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function(aliasId) {
/**
* Refresh content of all {@link AliasInfoWindow} in this map.
*/
-AbstractCustomMap.prototype._refreshInfoWindows = function() {
+AbstractCustomMap.prototype._refreshInfoWindows = function () {
var promises = [];
- for ( var key in this._pointInfoWindow) {
+ for (var key in this._pointInfoWindow) {
if (this._pointInfoWindow.hasOwnProperty(key)) {
if (this._pointInfoWindow[key].isOpened()) {
promises.push(this._pointInfoWindow[key].update());
}
}
}
- for ( var aliasKey in this._aliasInfoWindow) {
+ for (var aliasKey in this._aliasInfoWindow) {
if (this._aliasInfoWindow.hasOwnProperty(aliasKey)) {
if (this._aliasInfoWindow[aliasKey].isOpened()) {
promises.push(this._aliasInfoWindow[aliasKey].update());
@@ -733,11 +748,11 @@ AbstractCustomMap.prototype._refreshInfoWindows = function() {
/**
* Opens {@link ReactionInfoWindow} for given reaction identifier.
- *
+ *
* @param reactionId
* reaction identifier
*/
-AbstractCustomMap.prototype._openInfoWindowForReaction = function(reaction, googleMarker) {
+AbstractCustomMap.prototype._openInfoWindowForReaction = function (reaction, googleMarker) {
var infoWindow = this.getReactionInfoWindowById(reaction.getId());
var self = this;
if (infoWindow !== null && infoWindow !== undefined) {
@@ -748,21 +763,21 @@ AbstractCustomMap.prototype._openInfoWindowForReaction = function(reaction, goog
}
return Promise.resolve(infoWindow);
} else {
- return self.getModel().getReactionById(reaction.getId()).then(function(reaction) {
+ return self.getModel().getReactionById(reaction.getId()).then(function (reaction) {
infoWindow = new ReactionInfoWindow({
- reaction : reaction,
- map : self,
- marker : googleMarker,
+ reaction: reaction,
+ map: self,
+ marker: googleMarker,
});
self._reactionInfoWindow[reaction.getId()] = infoWindow;
return infoWindow.init();
- }).then(function() {
+ }).then(function () {
return infoWindow;
});
}
};
-AbstractCustomMap.prototype._openInfoWindowForPoint = function(pointData, googleMarker) {
+AbstractCustomMap.prototype._openInfoWindowForPoint = function (pointData, googleMarker) {
var self = this;
var infoWindow = this.getPointInfoWindowById(pointData.getId());
@@ -774,9 +789,9 @@ AbstractCustomMap.prototype._openInfoWindowForPoint = function(pointData, google
}
} else {
infoWindow = new PointInfoWindow({
- point : pointData,
- map : self,
- marker : googleMarker,
+ point: pointData,
+ map: self,
+ marker: googleMarker,
});
this._pointInfoWindow[pointData.getId()] = infoWindow;
}
@@ -785,11 +800,11 @@ AbstractCustomMap.prototype._openInfoWindowForPoint = function(pointData, google
/**
* Opens {@link AbstractInfoWindow} for a marker.
- *
+ *
* @param marker
* marker for which we are opening window
*/
-AbstractCustomMap.prototype.returnInfoWindowForIdentifiedElement = function(element) {
+AbstractCustomMap.prototype.returnInfoWindowForIdentifiedElement = function (element) {
var markerId = element.getId();
if (element.getType() === "ALIAS") {
return this.getAliasInfoWindowById(markerId);
@@ -804,30 +819,30 @@ AbstractCustomMap.prototype.returnInfoWindowForIdentifiedElement = function(elem
/**
* Returns identifier.
- *
+ *
* @returns identifier
*/
-AbstractCustomMap.prototype.getId = function() {
+AbstractCustomMap.prototype.getId = function () {
return this.getModel().getId();
};
-AbstractCustomMap.prototype.getConfiguration = function() {
+AbstractCustomMap.prototype.getConfiguration = function () {
return this._configuration;
};
-AbstractCustomMap.prototype.setConfiguration = function(configuration) {
+AbstractCustomMap.prototype.setConfiguration = function (configuration) {
this._configuration = configuration;
};
-AbstractCustomMap.prototype._createMapChangedCallbacks = function() {
+AbstractCustomMap.prototype._createMapChangedCallbacks = function () {
var self = this;
var sessionData = ServerConnector.getSessionData(self.getTopMap().getProject());
// listener for changing zoom level
- google.maps.event.addListener(this.getGoogleMap(), 'zoom_changed', function() {
+ google.maps.event.addListener(this.getGoogleMap(), 'zoom_changed', function () {
sessionData.setZoomLevel(self.getModel(), self.getGoogleMap().getZoom());
});
// listener for changing location of the map (moving left/reght/top/bottom
- google.maps.event.addListener(this.getGoogleMap(), 'center_changed', function() {
+ google.maps.event.addListener(this.getGoogleMap(), 'center_changed', function () {
var coord = self.getGoogleMap().getCenter();
var point = self.fromLatLngToPoint(coord);
sessionData.setCenter(self.getModel(), point);
@@ -836,62 +851,62 @@ AbstractCustomMap.prototype._createMapChangedCallbacks = function() {
/**
* Returns {@link ReactionInfoWindow} for given reaction identifier
- *
+ *
* @param reactionId
* reaction identifier
* @returns {@link ReactionInfoWindow} for given reaction identifier
*/
-AbstractCustomMap.prototype.getReactionInfoWindowById = function(reactionId) {
+AbstractCustomMap.prototype.getReactionInfoWindowById = function (reactionId) {
return this._reactionInfoWindow[reactionId];
};
/**
* Returns {@link AliasInfoWindow} for given alias identifier
- *
+ *
* @param aliasId
* alias identifier
* @returns {@link AliasInfoWindow} for given alias identifier
*/
-AbstractCustomMap.prototype.getAliasInfoWindowById = function(aliasId) {
+AbstractCustomMap.prototype.getAliasInfoWindowById = function (aliasId) {
return this._aliasInfoWindow[aliasId];
};
/**
* Returns {@link PointInfoWindow} for given point identifier
- *
+ *
* @param pointId
* point identifier
* @returns {@link PointInfoWindow} for given point identifier
*/
-AbstractCustomMap.prototype.getPointInfoWindowById = function(pointId) {
+AbstractCustomMap.prototype.getPointInfoWindowById = function (pointId) {
return this._pointInfoWindow[pointId];
};
-AbstractCustomMap.prototype.getModel = function() {
+AbstractCustomMap.prototype.getModel = function () {
return this._model;
};
-AbstractCustomMap.prototype.setModel = function(model) {
+AbstractCustomMap.prototype.setModel = function (model) {
this._model = model;
};
-AbstractCustomMap.prototype.getTileSize = function() {
+AbstractCustomMap.prototype.getTileSize = function () {
return this.getModel().getTileSize();
};
-AbstractCustomMap.prototype.getMinZoom = function() {
+AbstractCustomMap.prototype.getMinZoom = function () {
return this.getModel().getMinZoom();
};
-AbstractCustomMap.prototype.getMaxZoom = function() {
+AbstractCustomMap.prototype.getMaxZoom = function () {
return this.getModel().getMaxZoom();
};
-AbstractCustomMap.prototype.getLayouts = function() {
+AbstractCustomMap.prototype.getLayouts = function () {
return this.getModel().getLayouts();
};
-AbstractCustomMap.prototype.getPictureSize = function() {
+AbstractCustomMap.prototype.getPictureSize = function () {
return this.getModel().getPictureSize();
};
@@ -899,45 +914,45 @@ AbstractCustomMap.prototype.getPictureSize = function() {
* Returns array containining elements that are presented on a specific layout
* (set of google map objects representing lines/areas that are associated with
* layout).
- *
+ *
* @returns {Array} containining elements that are presented on a specific
* layout (set of google map objects representing lines/areas that are
* associated with layout).
*/
-AbstractCustomMap.prototype.getSelectedLayoutOverlays = function() {
+AbstractCustomMap.prototype.getSelectedLayoutOverlays = function () {
return this.selectedLayoutOverlays;
};
/**
* Returns google.maps.map object used to representing data.
- *
+ *
* @returns google.maps.map object used to representing data
*/
-AbstractCustomMap.prototype.getGoogleMap = function() {
+AbstractCustomMap.prototype.getGoogleMap = function () {
return this._map;
};
/**
* Sets google.maps.map object used to representing data.
- *
+ *
*/
-AbstractCustomMap.prototype.setGoogleMap = function(gmap) {
+AbstractCustomMap.prototype.setGoogleMap = function (gmap) {
this._map = gmap;
};
-AbstractCustomMap.prototype.isMarkerOptimization = function() {
+AbstractCustomMap.prototype.isMarkerOptimization = function () {
return this._markerOptimization;
};
-AbstractCustomMap.prototype.isBigLogo = function() {
+AbstractCustomMap.prototype.isBigLogo = function () {
return this._bigLogo;
};
-AbstractCustomMap.prototype.isCustomTouchInterface = function() {
+AbstractCustomMap.prototype.isCustomTouchInterface = function () {
return this._customTouchInterface;
};
-AbstractCustomMap.prototype.setDebug = function(debug) {
+AbstractCustomMap.prototype.setDebug = function (debug) {
if (debug !== undefined) {
if (typeof debug !== "boolean") {
logger.warn("param must be boolean");
@@ -946,32 +961,32 @@ AbstractCustomMap.prototype.setDebug = function(debug) {
}
};
-AbstractCustomMap.prototype.isDebug = function() {
+AbstractCustomMap.prototype.isDebug = function () {
return this._debug === true;
};
-AbstractCustomMap.prototype.getTopLeftLatLng = function() {
+AbstractCustomMap.prototype.getTopLeftLatLng = function () {
return this.getModel().getTopLeftLatLng();
};
-AbstractCustomMap.prototype.getBottomRightLatLng = function() {
+AbstractCustomMap.prototype.getBottomRightLatLng = function () {
return this.getModel().getBottomRightLatLng();
};
-AbstractCustomMap.prototype.getElement = function() {
+AbstractCustomMap.prototype.getElement = function () {
return this._element;
};
-AbstractCustomMap.prototype.setElement = function(element) {
+AbstractCustomMap.prototype.setElement = function (element) {
this._element = element;
};
/**
* Sets center point for google maps.
- *
+ *
* @param coordinates
* new center point on map
*/
-AbstractCustomMap.prototype.setCenter = function(coordinates) {
+AbstractCustomMap.prototype.setCenter = function (coordinates) {
if (coordinates instanceof google.maps.Point) {
coordinates = this.fromPointToLatLng(coordinates);
}
@@ -985,13 +1000,13 @@ AbstractCustomMap.prototype.setCenter = function(coordinates) {
/**
* Sets zoom level for google maps.
- *
+ *
* @param mapIdentifier
* id of the model for which we change zoom level
* @param zoom
* new zoom level on map
*/
-AbstractCustomMap.prototype.setZoom = function(zoom) {
+AbstractCustomMap.prototype.setZoom = function (zoom) {
if (this.initialized) {
return Promise.resolve(this.getGoogleMap().setZoom(zoom));
} else {
@@ -1000,7 +1015,7 @@ AbstractCustomMap.prototype.setZoom = function(zoom) {
}
};
-AbstractCustomMap.prototype.fitBounds = function(markers) {
+AbstractCustomMap.prototype.fitBounds = function (markers) {
var self = this;
var map = self.getGoogleMap();
if (map !== undefined) {
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 0ad9cc8620eaeeb7886d310f8cc178f3ceb9571d..9d55d00fe139b738143d44e2d285dce0ffa644cc 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -28,7 +28,7 @@ var TouchMap = require('./TouchMap');
/**
* Default constructor.
- *
+ *
* @param options
* CustomMapOptions object representing all parameters needed for map
* creation
@@ -75,12 +75,12 @@ CustomMap.prototype.constructor = CustomMap;
/**
* This code must be run after the object is created. It requires to download
* some data via promises.
- *
+ *
* @return promise with empty result
*/
-CustomMap.prototype.init = function() {
+CustomMap.prototype.init = function () {
var self = this;
- return ServerConnector.getLogoImg().then(function(url) {
+ return ServerConnector.getLogoImg().then(function (url) {
var logo2 = self.getControl(ControlType.LOGO_2_IMG);
if (!/^(f|ht)tps?:\/\//i.test(url)) {
url = GuiConnector.getImgPrefix() + url;
@@ -92,7 +92,7 @@ CustomMap.prototype.init = function() {
/**
* Create submaps.
*/
-CustomMap.prototype.createSubmaps = function() {
+CustomMap.prototype.createSubmaps = function () {
this.submaps = [];
for (var i = 0; i < this.getModel().getSubmodels().length; i++) {
this.submaps.push(new Submap(this, this.getModel().getSubmodels()[i]));
@@ -102,7 +102,7 @@ CustomMap.prototype.createSubmaps = function() {
/**
* Creates logo and put it on the google map.
*/
-CustomMap.prototype.createLogo = function() {
+CustomMap.prototype.createLogo = function () {
var logoControlDiv2 = document.createElement('DIV');
var logo2 = document.createElement('IMG');
logo2.style.cursor = 'pointer';
@@ -111,8 +111,8 @@ CustomMap.prototype.createLogo = function() {
this.addControl(logo2);
logoControlDiv2.appendChild(logo2);
- google.maps.event.addDomListener(logo2, 'click', function() {
- return ServerConnector.getLogoLink().then(function(url) {
+ google.maps.event.addDomListener(logo2, 'click', function () {
+ return ServerConnector.getLogoLink().then(function (url) {
var win = window.open(url, '_blank');
win.focus();
});
@@ -130,7 +130,7 @@ CustomMap.prototype.createLogo = function() {
this.addControl(logo);
logoControlDiv.appendChild(logo);
- google.maps.event.addDomListener(logo, 'click', function() {
+ google.maps.event.addDomListener(logo, 'click', function () {
var win = window.open('http://wwwen.uni.lu/lcsb/', '_blank');
win.focus();
});
@@ -142,9 +142,9 @@ CustomMap.prototype.createLogo = function() {
/**
* Clear all AbstractDbOverlay.
*/
-CustomMap.prototype.clearDbOverlays = function() {
+CustomMap.prototype.clearDbOverlays = function () {
var promises = [];
- for ( var overlayName in this.overlayCollections) {
+ for (var overlayName in this.overlayCollections) {
if (this.overlayCollections.hasOwnProperty(overlayName)) {
var collection = this.overlayCollections[overlayName];
promises.push(collection.clear());
@@ -155,11 +155,11 @@ CustomMap.prototype.clearDbOverlays = function() {
/**
* Open data overlay given in the parameter.
- *
+ *
* @param param
* identifier or LayoutData identifing data overlay to open
*/
-CustomMap.prototype.openDataOverlay = function(param) {
+CustomMap.prototype.openDataOverlay = function (param) {
logger.debug("Opening data overlay: " + param);
var self = this;
@@ -186,14 +186,14 @@ CustomMap.prototype.openDataOverlay = function(param) {
if (index === null) {
throw new SecurityError("You have no privileges for selected overlay");
} else {
- return overlayToOpen.init().then(function() {
+ return overlayToOpen.init().then(function () {
if (overlayToOpen.getInputDataAvailable()) {
if (self._selectedOverlays[identifier] === true) {
logger.warn("Overlay " + identifier + " already selected");
return Promise.resolve();
} else {
self._selectedOverlays[identifier] = true;
- return self.getVisibleDataOverlays().then(function(visibleDataOverlays) {
+ return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
var ids = [];
for (var i = 0; i < visibleDataOverlays.length; i++) {
ids.push(visibleDataOverlays[i].getId());
@@ -220,7 +220,7 @@ CustomMap.prototype.openDataOverlay = function(param) {
/**
* Returns data overlay that is used as a background.
*/
-CustomMap.prototype.getBackgroundDataOverlay = function() {
+CustomMap.prototype.getBackgroundDataOverlay = function () {
var identifier = parseInt(this.getGoogleMap().getMapTypeId());
for (var i = 0; i < this.getLayouts().length; i++) {
var layout = this.getLayouts()[i];
@@ -233,54 +233,54 @@ CustomMap.prototype.getBackgroundDataOverlay = function() {
/**
* Register AbstractDbOverlay in the map.
- *
+ *
* @param dbOverlay
* database overlay to be connected to the map
*/
-CustomMap.prototype.registerDbOverlay = function(dbOverlay) {
+CustomMap.prototype.registerDbOverlay = function (dbOverlay) {
var self = this;
this.overlayCollections[dbOverlay.getName()] = dbOverlay;
dbOverlay.markers = {
- ALIAS : [],
- REACTION : [],
- POINT : []
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
};
dbOverlay.mapOverlays = {
- ALIAS : [],
- REACTION : [],
- POINT : []
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
};
if (dbOverlay.getName() === "search" || dbOverlay.getName() === "user") {
- dbOverlay.addListener("onSearch", function(e) {
+ dbOverlay.addListener("onSearch", function (e) {
return self.renderOverlayCollection({
- overlayCollection : dbOverlay,
- fitBounds : e.arg.fitBounds
+ overlayCollection: dbOverlay,
+ fitBounds: e.arg.fitBounds
});
});
}
if (dbOverlay.getName() === "drug" || dbOverlay.getName() === "chemical" || dbOverlay.getName() === "mirna") {
- dbOverlay.addListener("onSearch", function(e) {
+ dbOverlay.addListener("onSearch", function (e) {
return self.renderOverlayCollection({
- overlayCollection : dbOverlay,
- fitBounds : e.arg.fitBounds
+ overlayCollection: dbOverlay,
+ fitBounds: e.arg.fitBounds
});
});
- dbOverlay.addListener("onTargetVisibilityChange", function() {
+ dbOverlay.addListener("onTargetVisibilityChange", function () {
return self.renderOverlayCollection({
- overlayCollection : dbOverlay,
- fitBounds : false
+ overlayCollection: dbOverlay,
+ fitBounds: false
});
});
}
if (dbOverlay.getName() === "comment") {
- var listener = function() {
+ var listener = function () {
return self.renderOverlayCollection({
- overlayCollection : dbOverlay,
- fitBounds : false
+ overlayCollection: dbOverlay,
+ fitBounds: false
});
};
dbOverlay.addListener("onRefresh", listener);
@@ -291,10 +291,10 @@ CustomMap.prototype.registerDbOverlay = function(dbOverlay) {
/**
* Refresh comment list.
- *
+ *
* @return promise that is resolved when comment list is refreshed
*/
-CustomMap.prototype.refreshComments = function() {
+CustomMap.prototype.refreshComments = function () {
var self = this;
var commentDbOverlay = self.getOverlayByName("comment");
@@ -311,7 +311,7 @@ CustomMap.prototype.refreshComments = function() {
/**
* Turns on/off drawing module on google maps.
*/
-CustomMap.prototype.turnOnOffDrawing = function() {
+CustomMap.prototype.turnOnOffDrawing = function () {
var model = this.getSubmapById(this.getActiveSubmapId());
if (model !== undefined) {
model._turnOnOffDrawing();
@@ -320,24 +320,24 @@ CustomMap.prototype.turnOnOffDrawing = function() {
}
};
-CustomMap.prototype.refreshMarkers = function() {
+CustomMap.prototype.refreshMarkers = function (force) {
logger.debug("Refresh Markers: ");
- for ( var overlayName in this.overlayCollections) {
+ for (var overlayName in this.overlayCollections) {
if (this.overlayCollections.hasOwnProperty(overlayName)) {
var collection = this.overlayCollections[overlayName];
- this.refreshOverlayMarkers(collection);
+ this.refreshOverlayMarkers(collection, force);
}
}
};
-CustomMap.prototype.refreshOverlayMarkers = function(overlay) {
+CustomMap.prototype.refreshOverlayMarkers = function (overlay, force) {
logger.debug("Refresh overlay: " + overlay.name);
- if (!this.isMarkerOptimization()) {
- for ( var markerType in overlay.markers) {
+ if (!this.isMarkerOptimization() || force) {
+ for (var markerType in overlay.markers) {
if (overlay.markers.hasOwnProperty(markerType)) {
var markers = overlay.markers[markerType];
- for ( var key in markers) {
+ for (var key in markers) {
if (markers.hasOwnProperty(key)) {
var marker = markers[key];
marker.hide();
@@ -352,11 +352,11 @@ CustomMap.prototype.refreshOverlayMarkers = function(overlay) {
/**
* Returns HTML div that is attached to jQuery dialog that should be used for
* opening submap.
- *
+ *
* @param id
* identifier of the submap
*/
-CustomMap.prototype.getSubmapDialogDiv = function(id) {
+CustomMap.prototype.getSubmapDialogDiv = function (id) {
var dialogDiv = this._dialogs[id];
if (dialogDiv === undefined) {
@@ -366,7 +366,7 @@ CustomMap.prototype.getSubmapDialogDiv = function(id) {
this._dialogs[id] = dialogDiv;
$(dialogDiv).dialog({
- autoOpen : false
+ autoOpen: false
});
}
return dialogDiv;
@@ -375,7 +375,7 @@ CustomMap.prototype.getSubmapDialogDiv = function(id) {
/**
* Opens a dialog with a submodel.
*/
-CustomMap.prototype.openSubmap = function(id) {
+CustomMap.prototype.openSubmap = function (id) {
var self = this;
var submap = self.getSubmapById(id);
if (submap === null) {
@@ -388,12 +388,12 @@ CustomMap.prototype.openSubmap = function(id) {
submap.open(dialogDiv);
// we have to perform it on top map, because on submaps id is different
- return this.openDataOverlay(self.getGoogleMap().getMapTypeId()).then(function() {
+ return this.openDataOverlay(self.getGoogleMap().getMapTypeId()).then(function () {
// now we have to visualize layouts
var layouts = [];
// get list of layouts
- for ( var key in self._selectedOverlays) {
+ for (var key in self._selectedOverlays) {
if (self._selectedOverlays.hasOwnProperty(key) && self._selectedOverlays[key] === true) {
layouts.push(key);
}
@@ -405,14 +405,14 @@ CustomMap.prototype.openSubmap = function(id) {
submap._showSelectedLayout(layoutId, i, layouts.length);
}
if (!wasInitialized) {
- return self.refreshMarkers();
+ return self.refreshMarkers(true);
}
});
}
};
-CustomMap.prototype.customizeGoogleMapView = function(div) {
+CustomMap.prototype.customizeGoogleMapView = function (div) {
var mapOptions = this.creatMapOptions();
this.setGoogleMap(new google.maps.Map(div, mapOptions));
this.setupLayouts();
@@ -440,7 +440,7 @@ CustomMap.prototype.customizeGoogleMapView = function(div) {
* Creates listeners for google.maps.Map object that will actualize the data in
* user session.
*/
-CustomMap.prototype.createMapChangedCallbacks = function() {
+CustomMap.prototype.createMapChangedCallbacks = function () {
this._createMapChangedCallbacks();
var self = this;
var sessionData = ServerConnector.getSessionData(self.getProject());
@@ -455,7 +455,7 @@ CustomMap.prototype.createMapChangedCallbacks = function() {
}
// listener for changing type of layout
- google.maps.event.addListener(self.getGoogleMap(), 'maptypeid_changed', function() {
+ google.maps.event.addListener(self.getGoogleMap(), 'maptypeid_changed', function () {
sessionData.setSelectedBackgroundOverlay(self.getGoogleMap().getMapTypeId());
});
@@ -477,12 +477,12 @@ CustomMap.prototype.createMapChangedCallbacks = function() {
/**
* Returns submap (or this map) by id.
- *
+ *
* @param identifier
* identifier of the submap
* @returns submap (or this map) with given identfier of the model
*/
-CustomMap.prototype.getSubmapById = function(identifier) {
+CustomMap.prototype.getSubmapById = function (identifier) {
identifier = parseInt(identifier);
if (this.getId() === identifier) {
return this;
@@ -496,7 +496,7 @@ CustomMap.prototype.getSubmapById = function(identifier) {
return null;
};
-CustomMap.prototype.removeSelection = function() {
+CustomMap.prototype.removeSelection = function () {
var model = this.getSubmapById(this.getActiveSubmapId());
if (model !== null) {
model._removeSelection();
@@ -507,12 +507,12 @@ CustomMap.prototype.removeSelection = function() {
/**
* Removes layout from visualization.
- *
+ *
* @param identifier
* identifier of layout to remove
- *
+ *
*/
-CustomMap.prototype.removeSelectedLayout = function(identifier) {
+CustomMap.prototype.removeSelectedLayout = function (identifier) {
var self = this;
logger.debug("Removing layout: " + identifier);
@@ -521,9 +521,9 @@ CustomMap.prototype.removeSelectedLayout = function(identifier) {
return Promise.resolve();
} else {
self._selectedOverlays[identifier] = false;
- return self.refreshSelectedLayouts().then(function() {
+ return self.refreshSelectedLayouts().then(function () {
return self.getVisibleDataOverlays();
- }).then(function(visibleDataOverlays) {
+ }).then(function (visibleDataOverlays) {
var ids = [];
for (var i = 0; i < visibleDataOverlays.length; i++) {
ids.push(visibleDataOverlays[i].getId());
@@ -537,10 +537,10 @@ CustomMap.prototype.removeSelectedLayout = function(identifier) {
/**
* Refresh visualization of selected layouts.
*/
-CustomMap.prototype.refreshSelectedLayouts = function() {
+CustomMap.prototype.refreshSelectedLayouts = function () {
logger.debug("Refreshing layouts");
var self = this;
- return self.getVisibleDataOverlays().then(function(visibleDataOverlays) {
+ return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
// show layouts that should be visualized (resize or show them)
var promises = [];
for (var i = 0; i < visibleDataOverlays.length; i++) {
@@ -552,9 +552,9 @@ CustomMap.prototype.refreshSelectedLayouts = function() {
promises.push(self.showSelectedLayout(layoutId, i, visibleDataOverlays.length));
}
}
- return Promise.all(promises).then(function() {
+ return Promise.all(promises).then(function () {
// remove layouts that were
- for ( var key in self.selectedLayoutOverlays) {
+ for (var key in self.selectedLayoutOverlays) {
if (!self._selectedOverlays.hasOwnProperty(key) || self._selectedOverlays[key] === false) {
if (self.layoutContainsOverlays(key)) {
self.hideSelectedLayout(key);
@@ -568,11 +568,11 @@ CustomMap.prototype.refreshSelectedLayouts = function() {
/**
* Hides layout from the map and all submaps
- *
+ *
* @param layoutId
* identifier of a layout to hide
*/
-CustomMap.prototype.hideSelectedLayout = function(layoutId) {
+CustomMap.prototype.hideSelectedLayout = function (layoutId) {
this._hideSelectedLayout(layoutId);
for (var i = 0; i < this.submaps.length; i++) {
this.submaps[i]._hideSelectedLayout(layoutId);
@@ -582,7 +582,7 @@ CustomMap.prototype.hideSelectedLayout = function(layoutId) {
/**
* Resize(refresh) layout on the map and all submaps. Resizing should be called
* when number of layouts to visualize change.
- *
+ *
* @param layoutId
* identifier of layout to refresh
* @param index
@@ -590,7 +590,7 @@ CustomMap.prototype.hideSelectedLayout = function(layoutId) {
* @param length
* number of layouts that we currently visualize
*/
-CustomMap.prototype.resizeSelectedLayout = function(layoutId, index, length) {
+CustomMap.prototype.resizeSelectedLayout = function (layoutId, index, length) {
logger.debug("Resize layout: " + layoutId);
var promises = [];
promises.push(this._resizeSelectedLayout(layoutId, index, length));
@@ -602,7 +602,7 @@ CustomMap.prototype.resizeSelectedLayout = function(layoutId, index, length) {
/**
* Show layout on the map and all submaps.
- *
+ *
* @param layoutId
* identifier of layout to show
* @param index
@@ -610,7 +610,7 @@ CustomMap.prototype.resizeSelectedLayout = function(layoutId, index, length) {
* @param length
* number of layouts that we currently visualize
*/
-CustomMap.prototype.showSelectedLayout = function(layoutId, index, length) {
+CustomMap.prototype.showSelectedLayout = function (layoutId, index, length) {
logger.debug("Resize layout: " + layoutId);
var promises = [];
promises.push(this._showSelectedLayout(layoutId, index, length));
@@ -624,13 +624,13 @@ CustomMap.prototype.showSelectedLayout = function(layoutId, index, length) {
/**
* This method checks if the layout contains any overlays (like AliasSurface or
* ReactionSurface) that is currently visible on the map.
- *
+ *
* @param layoutId
* identifier of the layout
* @returns {Boolean}: <code>true</code> if the layout contains overlays to
* visualize, <code>false</code> otherwise
*/
-CustomMap.prototype.layoutContainsOverlays = function(layoutId) {
+CustomMap.prototype.layoutContainsOverlays = function (layoutId) {
// first, check top map
if (this.selectedLayoutOverlays.hasOwnProperty(layoutId) && this.selectedLayoutOverlays[layoutId].length > 0) {
@@ -641,7 +641,7 @@ CustomMap.prototype.layoutContainsOverlays = function(layoutId) {
for (var i = 0; i < this.submaps.length; i++) {
if (this.submaps[i].initialized) {
if (this.submaps[i].selectedLayoutOverlays.hasOwnProperty(layoutId)
- && this.submaps[i].selectedLayoutOverlays[layoutId].length > 0) {
+ && this.submaps[i].selectedLayoutOverlays[layoutId].length > 0) {
return true;
}
}
@@ -652,7 +652,7 @@ CustomMap.prototype.layoutContainsOverlays = function(layoutId) {
/**
* Refresh content of all {@link AliasInfoWindow} in this map and all submaps.
*/
-CustomMap.prototype.refreshInfoWindows = function() {
+CustomMap.prototype.refreshInfoWindows = function () {
var promises = [];
promises.push(this._refreshInfoWindows());
// now check all submaps
@@ -664,13 +664,13 @@ CustomMap.prototype.refreshInfoWindows = function() {
/**
* Opens {@link AliasInfoWindow} for an {@link Alias} in a given model/submodel.
- *
+ *
* @param aliasId
* identifier of {@link Alias}
* @param modelId
* identifier of {@link AbstractCustomMap}
*/
-CustomMap.prototype.openInfoWindowForAlias = function(alias, marker) {
+CustomMap.prototype.openInfoWindowForAlias = function (alias, marker) {
logger.debug("Opening info window for alias: " + alias.getId() + ", model: " + alias.getModelId());
var submap = this.getSubmapById(alias.getModelId());
return submap._openInfoWindowForAlias(alias, marker);
@@ -678,14 +678,14 @@ CustomMap.prototype.openInfoWindowForAlias = function(alias, marker) {
/**
* Renders markers, lines, etc. for elements highlighted in OverlayCollection.
- *
+ *
* @param overlayCollection
* {@link OverlayCollection} to be processed
* @param fitBounds
* <code>true</code> if the borders should fit bounds after creating
* all elements
*/
-CustomMap.prototype.renderOverlayCollection = function(params) {
+CustomMap.prototype.renderOverlayCollection = function (params) {
var self = this;
var fitBounds = params.fitBounds;
var overlayCollection = params.overlayCollection;
@@ -693,33 +693,52 @@ CustomMap.prototype.renderOverlayCollection = function(params) {
var elements;
var markers = [];
- return overlayCollection.getIdentifiedElements().then(function(identifiedElements) {
+ return overlayCollection.getIdentifiedElements().then(function (identifiedElements) {
elements = identifiedElements;
- return Promise.each(elements, function(element) {
+ var elementsByModelId = [];
+ var modelId;
+
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ modelId = element.getModelId();
+ if (elementsByModelId[modelId] === undefined) {
+ elementsByModelId[modelId] = [];
+ }
+ elementsByModelId[modelId].push(element);
+ }
+ var promises = [];
+ for (modelId in elementsByModelId) {
+ if (elementsByModelId.hasOwnProperty(modelId)) {
+ promises.push(self.getModel().getSubmodelById(parseInt(modelId)).getByIdentifiedElements(elementsByModelId[modelId], false));
+ }
+ }
+ return Promise.all(promises);
+ }).then(function () {
+ return Promise.each(elements, function (element) {
var icon = element.getIcon();
if (icon !== null && icon !== undefined) {
- return self.createMarkerForDbOverlay(element, overlayCollection).then(function(marker) {
+ return self.createMarkerForDbOverlay(element, overlayCollection).then(function (marker) {
markers.push(marker);
});
} else {
- return self.createSurfaceForDbOverlay(element, overlayCollection).then(function(mapOverlay) {
+ return self.createSurfaceForDbOverlay(element, overlayCollection).then(function (mapOverlay) {
markers.push(mapOverlay);
});
}
});
- }).then(function() {
+ }).then(function () {
self.removeUnmodifiedMarkersAndSurfaces(markers, overlayCollection);
- return Promise.each(elements, function(element) {
+ return Promise.each(elements, function (element) {
var infoWindow = self.getInfoWindowForIdentifiedElement(element);
if (infoWindow !== null && infoWindow !== undefined) {
- return self.retrieveOverlayDetailDataForElement(element, infoWindow.getOverlayFullViewArray()).then(function() {
+ return self.retrieveOverlayDetailDataForElement(element, infoWindow.getOverlayFullViewArray()).then(function () {
return self.updateInfoWindowForIdentifiedElement(element);
});
}
});
- }).then(function() {
+ }).then(function () {
if (elements.length > 0 && fitBounds) {
self.fitBounds(markers);
for (var j = 0; j < self.submaps.length; j++) {
@@ -729,16 +748,16 @@ CustomMap.prototype.renderOverlayCollection = function(params) {
});
};
-CustomMap.prototype.removeUnmodifiedMarkersAndSurfaces = function(modifiedMarkersAndSurfaces, dbOverlay) {
+CustomMap.prototype.removeUnmodifiedMarkersAndSurfaces = function (modifiedMarkersAndSurfaces, dbOverlay) {
var modifiedMarkers = {
- "ALIAS" : [],
- "REACTION" : [],
- "POINT" : [],
+ "ALIAS": [],
+ "REACTION": [],
+ "POINT": [],
};
var modifiedSurfaces = {
- "ALIAS" : [],
- "REACTION" : [],
- "POINT" : [],
+ "ALIAS": [],
+ "REACTION": [],
+ "POINT": [],
};
for (var i = 0; i < modifiedMarkersAndSurfaces.length; i++) {
@@ -781,17 +800,17 @@ CustomMap.prototype.removeUnmodifiedMarkersAndSurfaces = function(modifiedMarker
/**
* Opens {@link AbstractInfoWindow} for a marker.
- *
+ *
* @param marker
* {@link AbstractMarker} for which info window should be opened
*/
-CustomMap.prototype.openInfoWindowForIdentifiedElement = function(element, marker) {
+CustomMap.prototype.openInfoWindowForIdentifiedElement = function (element, marker) {
var self = this;
var submap = self.getSubmapById(element.getModelId());
logger.debug(element + ": Opening info window");
// open AliasInfoWindow in a right model
- return submap._openInfoWindowForIdentifiedElement(element, marker).then(function() {
+ return submap._openInfoWindowForIdentifiedElement(element, marker).then(function () {
var infoWindow = submap.returnInfoWindowForIdentifiedElement(element);
return self.retrieveOverlayDetailDataForElement(element, infoWindow.getOverlayFullViewArray());
});
@@ -801,17 +820,17 @@ CustomMap.prototype.openInfoWindowForIdentifiedElement = function(element, marke
/**
* Sends requestes to download detailed data about element in all
* {@link OverlayCollection}.
- *
+ *
* @param element
* element for which we want to have detailed information
*/
-CustomMap.prototype.retrieveOverlayDetailDataForElement = function(element, general) {
+CustomMap.prototype.retrieveOverlayDetailDataForElement = function (element, general) {
var promises = [];
if (general === undefined) {
logger.warn("general param is undefined!");
general = [];
}
- for ( var overlayName in this.overlayCollections) {
+ for (var overlayName in this.overlayCollections) {
if (this.overlayCollections.hasOwnProperty(overlayName)) {
var overlay = this.overlayCollections[overlayName];
@@ -830,11 +849,11 @@ CustomMap.prototype.retrieveOverlayDetailDataForElement = function(element, gene
/**
* Updates info window identified by element given as a parameter.
- *
+ *
* @param identifiedElement
* element for which info window should be updated
*/
-CustomMap.prototype.updateInfoWindowForIdentifiedElement = function(identifiedElement) {
+CustomMap.prototype.updateInfoWindowForIdentifiedElement = function (identifiedElement) {
var infoWindow = this.getInfoWindowForIdentifiedElement(identifiedElement);
if (infoWindow === null || infoWindow === undefined) {
return Promise.resolve();
@@ -845,7 +864,7 @@ CustomMap.prototype.updateInfoWindowForIdentifiedElement = function(identifiedEl
/**
* Returns data from all {@link OverlayCollection} for a given alias.
- *
+ *
* @param alias
* {@link Alias} for which overlay data will be returned
* @param general
@@ -853,14 +872,14 @@ CustomMap.prototype.updateInfoWindowForIdentifiedElement = function(identifiedEl
* availble right now in the overlay
* @returns data from all {@link OverlayCollection} for a given alias
*/
-CustomMap.prototype.getOverlayDataForAlias = function(alias, general) {
+CustomMap.prototype.getOverlayDataForAlias = function (alias, general) {
var identifiedElement = new IdentifiedElement(alias);
return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
};
/**
* Returns data from all {@link OverlayCollection} for a given reaction.
- *
+ *
* @param reaction
* {@link Reaction} for which overlay data will be returned
* @param general
@@ -868,20 +887,20 @@ CustomMap.prototype.getOverlayDataForAlias = function(alias, general) {
* availble right now in the overlay
* @returns data from all {@link OverlayCollection} for a given alias
*/
-CustomMap.prototype.getOverlayDataForReaction = function(reaction, general) {
+CustomMap.prototype.getOverlayDataForReaction = function (reaction, general) {
var identifiedElement = new IdentifiedElement(reaction);
return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
};
/**
* Returns data from all {@link OverlayCollection} for a given {@link PointData}
- *
+ *
* @param point
* {@link PointData} for which overlay data will be returned
* @returns data from all {@link OverlayCollection} for a given
* {@link PointData}
*/
-CustomMap.prototype.getOverlayDataForPoint = function(point, general) {
+CustomMap.prototype.getOverlayDataForPoint = function (point, general) {
var identifiedElement = new IdentifiedElement(point);
return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
};
@@ -889,20 +908,20 @@ CustomMap.prototype.getOverlayDataForPoint = function(point, general) {
/**
* Returns data from all {@link OverlayCollection} for element identified by the
* parameter
- *
+ *
* @param identifiedElement
* {@link IdentifiedElement} for which overlay data will be returned
* @returns data from all {@link OverlayCollection} for a given
* {@link IdentifiedElement}
*/
-CustomMap.prototype.getOverlayDataForIdentifiedElement = function(identifiedElement, general) {
+CustomMap.prototype.getOverlayDataForIdentifiedElement = function (identifiedElement, general) {
if (general === undefined) {
logger.warn("general parameter must be defined");
general = [];
}
var promises = [];
var overlays = [];
- for ( var overlayName in this.overlayCollections) {
+ for (var overlayName in this.overlayCollections) {
if (this.overlayCollections.hasOwnProperty(overlayName)) {
var overlay = this.overlayCollections[overlayName];
if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
@@ -913,29 +932,29 @@ CustomMap.prototype.getOverlayDataForIdentifiedElement = function(identifiedElem
}
overlays.push(overlay);
promises.push(overlay.getDetailDataByIdentifiedElement(identifiedElement, !overlay.allowSearchById()
- || generalFlag));
+ || generalFlag));
}
}
}
- return Promise.all(promises).then(function(values) {
+ return Promise.all(promises).then(function (values) {
var result = [];
for (var i = 0; i < values.length; i++) {
result.push({
- overlay : overlays[i],
- data : values[i]
+ overlay: overlays[i],
+ data: values[i]
});
}
return result;
});
};
-CustomMap.prototype.getOverlayByName = function(name) {
+CustomMap.prototype.getOverlayByName = function (name) {
return this.overlayCollections[name];
};
-CustomMap.prototype.getDbOverlays = function() {
+CustomMap.prototype.getDbOverlays = function () {
var result = [];
- for ( var overlayName in this.overlayCollections) {
+ for (var overlayName in this.overlayCollections) {
if (this.overlayCollections.hasOwnProperty(overlayName)) {
result.push(this.overlayCollections[overlayName]);
}
@@ -945,13 +964,13 @@ CustomMap.prototype.getDbOverlays = function() {
/**
* Returns {@link AbstractInfoWindow} for element identified by the parameter.
- *
+ *
* @param identifiedElement
* {@link IdentifiedElement} that determines for which element we want
* {@link AbstractInfoWindow}
* @returns {@link AbstractInfoWindow} for element identified by the parameter
*/
-CustomMap.prototype.getInfoWindowForIdentifiedElement = function(identifiedElement) {
+CustomMap.prototype.getInfoWindowForIdentifiedElement = function (identifiedElement) {
var model = this.getSubmapById(identifiedElement.modelId);
var infoWindow = null;
if (identifiedElement.type === "ALIAS") {
@@ -966,25 +985,25 @@ CustomMap.prototype.getInfoWindowForIdentifiedElement = function(identifiedEleme
return infoWindow;
};
-CustomMap.prototype.getActiveSubmapId = function() {
+CustomMap.prototype.getActiveSubmapId = function () {
return this._activeSubmapId;
};
-CustomMap.prototype.setActiveSubmapId = function(submapId) {
+CustomMap.prototype.setActiveSubmapId = function (submapId) {
this._activeSubmapId = submapId;
};
-CustomMap.prototype.setActiveSubmapClickCoordinates = function(coordinates) {
+CustomMap.prototype.setActiveSubmapClickCoordinates = function (coordinates) {
if (!(coordinates instanceof google.maps.Point)) {
throw new Error("Coordinates must be provided as google.maps.Point object, but found: " + coordinates);
}
this._activeSubmapCoordinates = coordinates;
};
-CustomMap.prototype.getActiveSubmapClickCoordinates = function() {
+CustomMap.prototype.getActiveSubmapClickCoordinates = function () {
return this._activeSubmapCoordinates;
};
-CustomMap.prototype.getReferenceGenome = function(type, version) {
+CustomMap.prototype.getReferenceGenome = function (type, version) {
var self = this;
if (self.getProject().getOrganism() === undefined) {
return Promise.resolve(new ReferenceGenome(null));
@@ -995,10 +1014,10 @@ CustomMap.prototype.getReferenceGenome = function(type, version) {
}
if (self._referenceGenome[type][version] === undefined) {
return ServerConnector.getReferenceGenome({
- type : type,
- version : version,
- organism : self.getProject().getOrganism().getResource(),
- }).then(function(genome) {
+ type: type,
+ version: version,
+ organism: self.getProject().getOrganism().getResource(),
+ }).then(function (genome) {
self._referenceGenome[type][version] = genome;
return genome;
});
@@ -1007,22 +1026,22 @@ CustomMap.prototype.getReferenceGenome = function(type, version) {
}
};
-CustomMap.prototype.getTopMap = function() {
+CustomMap.prototype.getTopMap = function () {
return this;
};
-CustomMap.prototype.setProject = function(project) {
+CustomMap.prototype.setProject = function (project) {
this._project = project;
};
-CustomMap.prototype.getProject = function() {
+CustomMap.prototype.getProject = function () {
return this._project;
};
-CustomMap.prototype.getTopOverviewImage = function() {
+CustomMap.prototype.getTopOverviewImage = function () {
return this.getProject().getTopOverviewImage();
};
-CustomMap.prototype.addControl = function(element) {
+CustomMap.prototype.addControl = function (element) {
if (this._controls[element.id] !== undefined) {
throw new Error("Element with id " + element.id + " already added to controls");
}
@@ -1032,52 +1051,52 @@ CustomMap.prototype.addControl = function(element) {
this._controls[element.id] = element;
};
-CustomMap.prototype.getControl = function(type) {
+CustomMap.prototype.getControl = function (type) {
if (ControlType[type] === undefined) {
throw new Error("Unknown control type: " + type);
}
return this._controls[type];
};
-CustomMap.prototype.setCommentDialog = function(commentDialog) {
+CustomMap.prototype.setCommentDialog = function (commentDialog) {
this._commentDialog = commentDialog;
};
-CustomMap.prototype.getCommentDialog = function() {
+CustomMap.prototype.getCommentDialog = function () {
return this._commentDialog;
};
-CustomMap.prototype.setContextMenu = function(contextMenu) {
+CustomMap.prototype.setContextMenu = function (contextMenu) {
this._contextMenu = contextMenu;
};
-CustomMap.prototype.getContextMenu = function() {
+CustomMap.prototype.getContextMenu = function () {
return this._contextMenu;
};
-CustomMap.prototype.setSelectionContextMenu = function(selectionContextMenu) {
+CustomMap.prototype.setSelectionContextMenu = function (selectionContextMenu) {
this._selectionContextMenu = selectionContextMenu;
};
-CustomMap.prototype.getSelectionContextMenu = function() {
+CustomMap.prototype.getSelectionContextMenu = function () {
return this._selectionContextMenu;
};
-CustomMap.prototype.openCommentDialog = function() {
+CustomMap.prototype.openCommentDialog = function () {
var self = this;
return ServerConnector.getClosestElementsByCoordinates({
- modelId : this.getActiveSubmapId(),
- coordinates : this.getActiveSubmapClickCoordinates()
- }).then(function(elements) {
+ modelId: this.getActiveSubmapId(),
+ coordinates: this.getActiveSubmapClickCoordinates()
+ }).then(function (elements) {
var commentDialog = self.getCommentDialog();
if (commentDialog === undefined) {
var div = Functions.createElement({
- type : "div"
+ type: "div"
});
self.getElement().appendChild(div);
commentDialog = new CommentDialog({
- element : div,
- customMap : self
+ element: div,
+ customMap: self
});
self.setCommentDialog(commentDialog);
}
@@ -1087,7 +1106,7 @@ CustomMap.prototype.openCommentDialog = function() {
});
};
-CustomMap.prototype.fetchIdentifiedElements = function(elements, complete) {
+CustomMap.prototype.fetchIdentifiedElements = function (elements, complete) {
var modelIds = [];
var modelElements = [];
var i;
@@ -1109,10 +1128,10 @@ CustomMap.prototype.fetchIdentifiedElements = function(elements, complete) {
};
-CustomMap.prototype.refreshSearchAutocomplete = function() {
+CustomMap.prototype.refreshSearchAutocomplete = function () {
var self = this;
self._searchAutocomplete = [];
- return ServerConnector.getSuggestedQueryList().then(function(queries) {
+ return ServerConnector.getSuggestedQueryList().then(function (queries) {
for (var i = 0; i < queries.length; i++) {
var mainString = queries[i];
for (var j = 0; j < mainString.length; j++) {
@@ -1137,7 +1156,7 @@ CustomMap.prototype.refreshSearchAutocomplete = function() {
});
};
-CustomMap.prototype.getSearchAutocomplete = function(query) {
+CustomMap.prototype.getSearchAutocomplete = function (query) {
if (this._searchAutocomplete === undefined) {
this.refreshSearchAutocomplete();
return [];
@@ -1146,15 +1165,15 @@ CustomMap.prototype.getSearchAutocomplete = function(query) {
return this._searchAutocomplete[query];
};
-CustomMap.prototype.setSelectedPolygon = function(polygonData) {
+CustomMap.prototype.setSelectedPolygon = function (polygonData) {
this._selectedPolygon = polygonData;
};
-CustomMap.prototype.getSelectedPolygon = function() {
+CustomMap.prototype.getSelectedPolygon = function () {
return this._selectedPolygon;
};
-CustomMap.prototype.getDistance = function(params) {
+CustomMap.prototype.getDistance = function (params) {
var self = this;
var ie = params.element;
var model = self.getSubmapById(ie.getModelId()).getModel();
@@ -1164,21 +1183,21 @@ CustomMap.prototype.getDistance = function(params) {
var x = params.coordinates.x;
var y = params.coordinates.y;
var p1 = new google.maps.Point(x, y);
- return model.getByIdentifiedElement(ie).then(function(element) {
+ return model.getByIdentifiedElement(ie).then(function (element) {
if (element instanceof Alias) {
if (element.getX() <= x && element.getX() + element.getWidth() >= x) {
if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
return 0;
} else {
return Math.min( //
- Math.abs(element.getY() - y), //
- Math.abs(element.getY() + element.getHeight() - y) //
+ Math.abs(element.getY() - y), //
+ Math.abs(element.getY() + element.getHeight() - y) //
);
}
} else if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
return Math.min( //
- Math.abs(element.getX() - x), //
- Math.abs(element.getX() + element.getWidth() - x) //
+ Math.abs(element.getX() - x), //
+ Math.abs(element.getX() + element.getWidth() - x) //
);
} else {
var elementX = element.getX();
@@ -1186,10 +1205,10 @@ CustomMap.prototype.getDistance = function(params) {
var elementWidth = element.getWidth();
var elementHeight = element.getHeight();
return Math.min( //
- Functions.distance(p1, new google.maps.Point(elementX, y)), //
- Functions.distance(p1, new google.maps.Point(elementX + elementWidth, elementY)), //
- Functions.distance(p1, new google.maps.Point(elementX, elementY + elementHeight)), //
- Functions.distance(p1, new google.maps.Point(elementX + elementWidth, elementY + elementHeight)) //
+ Functions.distance(p1, new google.maps.Point(elementX, y)), //
+ Functions.distance(p1, new google.maps.Point(elementX + elementWidth, elementY)), //
+ Functions.distance(p1, new google.maps.Point(elementX, elementY + elementHeight)), //
+ Functions.distance(p1, new google.maps.Point(elementX + elementWidth, elementY + elementHeight)) //
);
}
} else if (element instanceof Reaction) {
@@ -1205,7 +1224,7 @@ CustomMap.prototype.getDistance = function(params) {
});
};
-CustomMap.prototype.getSubmaps = function() {
+CustomMap.prototype.getSubmaps = function () {
var submaps = this.submaps;
if (submaps === undefined) {
submaps = [];
@@ -1213,7 +1232,7 @@ CustomMap.prototype.getSubmaps = function() {
return submaps;
};
-CustomMap.prototype.destroy = function() {
+CustomMap.prototype.destroy = function () {
var self = this;
var commentDialog = self.getCommentDialog();
if (commentDialog !== undefined) {
@@ -1221,11 +1240,11 @@ CustomMap.prototype.destroy = function() {
}
};
-CustomMap.prototype.getVisibleDataOverlays = function() {
+CustomMap.prototype.getVisibleDataOverlays = function () {
var dataOverlayPromises = [];
// get list of layouts
- for ( var key in this._selectedOverlays) {
+ for (var key in this._selectedOverlays) {
if (this._selectedOverlays.hasOwnProperty(key) && this._selectedOverlays[key] === true) {
dataOverlayPromises.push(this.getModel().getLayoutDataById(key));
}
@@ -1234,7 +1253,7 @@ CustomMap.prototype.getVisibleDataOverlays = function() {
return Promise.all(dataOverlayPromises);
};
-CustomMap.prototype.createMarkerForDbOverlay = function(element, dbOverlay) {
+CustomMap.prototype.createMarkerForDbOverlay = function (element, dbOverlay) {
var self = this;
var result = dbOverlay.markers[element.getType()][element.getId()];
@@ -1255,21 +1274,21 @@ CustomMap.prototype.createMarkerForDbOverlay = function(element, dbOverlay) {
throw new Error("Unknown type of the element in overlay: " + element.type);
}
result = new MarkerConstructor({
- element : element,
- map : submap,
- onClick : [ function() {
+ element: element,
+ map: submap,
+ onClick: [function () {
return self._openInfoWindowForIdentifiedElement(element, result.getGoogleMarker());
- }, function() {
+ }, function () {
return self.callListeners("onBioEntityClick", element);
- }, ]
+ },]
});
- return result.init().then(function() {
+ return result.init().then(function () {
dbOverlay.markers[element.getType()][element.getId()] = result;
return result;
});
};
-CustomMap.prototype.createSurfaceForDbOverlay = function(element, dbOverlay) {
+CustomMap.prototype.createSurfaceForDbOverlay = function (element, dbOverlay) {
var self = this;
var result = dbOverlay.mapOverlays[element.getType()][element.getId()];
@@ -1281,30 +1300,30 @@ CustomMap.prototype.createSurfaceForDbOverlay = function(element, dbOverlay) {
var map = self.getSubmapById(element.getModelId());
if (element.getType() === "ALIAS") {
return AliasSurface.createFromIdentifiedElement({
- element : element,
- map : self,
- onClick : [ function() {
+ element: element,
+ map: self,
+ onClick: [function () {
return self.openInfoWindowForIdentifiedElement(element, result.getGoogleMarker());
- }, function() {
+ }, function () {
return self.callListeners("onBioEntityClick", element);
- } ]
- }).then(function(surface) {
+ }]
+ }).then(function (surface) {
result = surface;
dbOverlay.mapOverlays[element.getType()][element.getId()] = result;
return result;
});
} else if (element.getType() === "REACTION") {
- return map.getModel().getReactionById(element.getId()).then(function(reactionData) {
+ return map.getModel().getReactionById(element.getId()).then(function (reactionData) {
var result = new ReactionSurface({
- reaction : reactionData,
- map : map,
- customized : true,
- color : element.getColor(),
- onClick : [ function() {
+ reaction: reactionData,
+ map: map,
+ customized: true,
+ color: element.getColor(),
+ onClick: [function () {
return self.openInfoWindowForIdentifiedElement(element, result.getGoogleMarker());
- }, function() {
+ }, function () {
return self.callListeners("onBioEntityClick", element);
- } ]
+ }]
});
result.show();
dbOverlay.mapOverlays[element.getType()][element.getId()] = result;
@@ -1319,21 +1338,21 @@ 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) {
+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.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.getModel().getByIdentifiedElement(element).then(function (reaction) {
return submap._openInfoWindowForReaction(reaction, googleMarker);
});
} else {
diff --git a/frontend-js/src/main/js/map/data/IdentifiedElement.js b/frontend-js/src/main/js/map/data/IdentifiedElement.js
index caa6ef2d22e5905e2006c75bb849dfdc9de85f15..727425d6611892b1f64a0fee59f72e9d816bb65a 100644
--- a/frontend-js/src/main/js/map/data/IdentifiedElement.js
+++ b/frontend-js/src/main/js/map/data/IdentifiedElement.js
@@ -3,6 +3,7 @@
var Alias = require('./Alias');
var LayoutAlias = require('./LayoutAlias');
var Reaction = require('./Reaction');
+var LayoutReaction = require('./LayoutReaction');
var PointData = require('./PointData');
var logger = require('../../logger');
@@ -32,6 +33,10 @@ function IdentifiedElement(javaObject) {
this.setId(javaObject.getId());
this.setModelId(javaObject.getModelId());
this.setType("REACTION");
+ } else if (javaObject instanceof LayoutReaction) {
+ this.setId(javaObject.getId());
+ this.setModelId(javaObject.getModelId());
+ this.setType("REACTION");
} else if (javaObject instanceof PointData) {
this.setId(javaObject.getId());
this.setModelId(javaObject.getModelId());
@@ -77,11 +82,11 @@ function IdentifiedElement(javaObject) {
/**
* Returns point where it should be visualized when the type of object is
* "POINT".
- *
+ *
* @returns {@linke google.maps.Point} where it should be visualized when the
* type of object is "POINT".
*/
-IdentifiedElement.prototype.getPoint = function() {
+IdentifiedElement.prototype.getPoint = function () {
if (this._point === undefined || this._point === null) {
logger.warn("No point associated with IdentifiedElement");
return null;
@@ -92,15 +97,15 @@ IdentifiedElement.prototype.getPoint = function() {
/**
* Returns element identifier.
- *
+ *
* @returns element identifier
*/
-IdentifiedElement.prototype.getId = function() {
+IdentifiedElement.prototype.getId = function () {
return this.id;
};
-IdentifiedElement.prototype.setId = function(id) {
- // some elements are identfied by id that is not a number (like point on the
+IdentifiedElement.prototype.setId = function (id) {
+ // some elements are identified by id that is not a number (like point on the
// map)
if (!isNaN(id)) {
id = parseInt(id);
@@ -108,7 +113,7 @@ IdentifiedElement.prototype.setId = function(id) {
this.id = id;
};
-IdentifiedElement.prototype.setModelId = function(modelId) {
+IdentifiedElement.prototype.setModelId = function (modelId) {
if (modelId === undefined || modelId === null) {
throw new Error("ModelId is invalid");
}
@@ -117,10 +122,10 @@ IdentifiedElement.prototype.setModelId = function(modelId) {
/**
* Returns model identifier where element is placed.
- *
+ *
* @returns model identifier
*/
-IdentifiedElement.prototype.getModelId = function() {
+IdentifiedElement.prototype.getModelId = function () {
return this.modelId;
};
@@ -132,14 +137,14 @@ IdentifiedElement.prototype.getModelId = function() {
* <li>"POINT" - for any point on the map, the data connected to this kind of
* objects are stored in {@link PointData}</li>
* </ul>
- *
+ *
* @returns type of the element
*/
-IdentifiedElement.prototype.getType = function() {
+IdentifiedElement.prototype.getType = function () {
return this.type;
};
-IdentifiedElement.prototype.setType = function(type) {
+IdentifiedElement.prototype.setType = function (type) {
if (type === undefined || type === null) {
throw new Error("Type not defined");
}
@@ -149,77 +154,77 @@ IdentifiedElement.prototype.setType = function(type) {
/**
* Returns icon that should be used for visualization.
- *
+ *
* @returns icon that should be used for visualization
*/
-IdentifiedElement.prototype.getIcon = function() {
+IdentifiedElement.prototype.getIcon = function () {
return this._visualizationdata._icon;
};
-IdentifiedElement.prototype.setIcon = function(icon) {
+IdentifiedElement.prototype.setIcon = function (icon) {
this._visualizationdata._icon = icon;
};
-IdentifiedElement.prototype.getColor = function() {
+IdentifiedElement.prototype.getColor = function () {
return this._visualizationdata._color;
};
-IdentifiedElement.prototype.setColor = function(color) {
+IdentifiedElement.prototype.setColor = function (color) {
this._visualizationdata._color = color;
};
-IdentifiedElement.prototype.getOpacity = function() {
+IdentifiedElement.prototype.getOpacity = function () {
return this._visualizationdata._opacity;
};
-IdentifiedElement.prototype.setOpacity = function(opacity) {
+IdentifiedElement.prototype.setOpacity = function (opacity) {
this._visualizationdata._opacity = opacity;
};
-IdentifiedElement.prototype.getLineWeight = function() {
+IdentifiedElement.prototype.getLineWeight = function () {
return this._visualizationdata._lineWeight;
};
-IdentifiedElement.prototype.setLineWeight = function(lineWeight) {
+IdentifiedElement.prototype.setLineWeight = function (lineWeight) {
this._visualizationdata._lineWeight = lineWeight;
};
-IdentifiedElement.prototype.getLineOpacity = function() {
+IdentifiedElement.prototype.getLineOpacity = function () {
return this._visualizationdata._lineOpacity;
};
-IdentifiedElement.prototype.setLineOpacity = function(lineOpacity) {
+IdentifiedElement.prototype.setLineOpacity = function (lineOpacity) {
this._visualizationdata._lineOpacity = lineOpacity;
};
-IdentifiedElement.prototype.getLineColor = function() {
+IdentifiedElement.prototype.getLineColor = function () {
return this._visualizationdata._lineColor;
};
-IdentifiedElement.prototype.setLineColor = function(lineColor) {
+IdentifiedElement.prototype.setLineColor = function (lineColor) {
this._visualizationdata._lineColor = lineColor;
};
-IdentifiedElement.prototype.getOnClickHandler = function() {
+IdentifiedElement.prototype.getOnClickHandler = function () {
return this._visualizationdata._onClickHandler;
};
-IdentifiedElement.prototype.setOnClickHandler = function(onClickHandler) {
+IdentifiedElement.prototype.setOnClickHandler = function (onClickHandler) {
this._visualizationdata._onClickHandler = onClickHandler;
};
-IdentifiedElement.prototype.equals = function(argument) {
+IdentifiedElement.prototype.equals = function (argument) {
if (argument instanceof IdentifiedElement) {
return (this.getType() === argument.getType() && //
- this.getId() === argument.getId() && //
- this.getModelId() === argument.getModelId());
+ this.getId() === argument.getId() && //
+ this.getModelId() === argument.getModelId());
} else {
return false;
}
};
-IdentifiedElement.prototype.toString = function() {
+IdentifiedElement.prototype.toString = function () {
var self = this;
return "[" + IdentifiedElement.prototype.constructor.name + "] " + self.getType() + " " + self.getId() + " (model: "
- + self.getModelId() + ")";
+ + self.getModelId() + ")";
};
module.exports = IdentifiedElement;
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index b649df92467375a69e77ebbc148bfe9967b01334..1e4e53b9f6ff0d03d8c6e9288c8078043b270ec9 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -276,7 +276,7 @@ MapModel.prototype.getMissingElements = function(elements) {
var reactions = layout.getReactions();
for (var k = 0; k < reactions.length; k++) {
- var reaction = reactions[j];
+ var reaction = reactions[k];
if (this._reactions[reaction.getId()] === undefined && this._missingReactions[reaction.getId()] === undefined) {
this._missingReactions[reaction.getId()] = reaction.getId();
reactionIds.push(reaction.getId());
@@ -682,7 +682,7 @@ MapModel.prototype.getByIdentifiedElements = function(identifiedElements, comple
return self.getMissingElements({
aliasIds : missingAliases,
reactionIds : missingReactions,
- complete : true
+ complete : complete
}).then(function() {
var promises = [];
for (var i = 0; i < identifiedElements.length; i++) {
@@ -699,6 +699,14 @@ MapModel.prototype.isAvailable = function(ie, complete) {
element = this._aliases[ie.getId()];
} else if (ie.getType() === "REACTION") {
element = this._reactions[ie.getId()];
+ } else if (ie.getType() === "POINT") {
+ var id = this._pointToId(ie.getId());
+ var result = this._pointsData[id];
+ if (result === undefined) {
+ result = new PointData(ie);
+ this._pointsData[id] = result;
+ }
+ element = this._pointsData[id];
} else {
throw new Error("Unknown type: " + ie.getType(), complete);
}
diff --git a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
index 57da91aee6f24955c95bc6ff1bafaa9a017d52af..6aca213bd7a5f8010fcdcc9ba4d2a8213e018402 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
@@ -41,77 +41,84 @@ AbstractDbOverlay.prototype = Object.create(ObjectWithListeners.prototype);
AbstractDbOverlay.prototype.constructor = AbstractDbOverlay;
AbstractDbOverlay.QueryType = {
- SEARCH_BY_COORDINATES : "SEARCH_BY_COORDINATES",
- SEARCH_BY_TARGET : "SEARCH_BY_TARGET",
- SEARCH_BY_QUERY : "SEARCH_BY_QUERY",
+ SEARCH_BY_COORDINATES: "SEARCH_BY_COORDINATES",
+ SEARCH_BY_TARGET: "SEARCH_BY_TARGET",
+ SEARCH_BY_QUERY: "SEARCH_BY_QUERY",
};
-AbstractDbOverlay.prototype.encodeQuery = function(type, arg0, arg1, arg2) {
+AbstractDbOverlay.prototype.encodeQuery = function (type, arg0, arg1, arg2) {
if (type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
var modelId = arg0;
var coordinates = arg1;
var zoom = arg2;
return JSON.stringify({
- type : type,
- modelId : modelId,
- coordinates : coordinates,
- zoom : zoom,
+ type: type,
+ modelId: modelId,
+ coordinates: coordinates,
+ zoom: zoom,
});
} else if (type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
var target = arg0;
return JSON.stringify({
- type : type,
- target : target,
+ type: type,
+ target: target,
});
} else if (type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
var query = arg0;
var perfect = arg1;
return JSON.stringify({
- type : type,
- query : query,
- perfect : perfect,
+ type: type,
+ query: query,
+ perfect: perfect,
});
} else {
throw new Error("Unknown query type: " + type);
}
};
-AbstractDbOverlay.prototype.decodeQuery = function(query) {
+AbstractDbOverlay.prototype.decodeQuery = function (query) {
return JSON.parse(query);
};
-AbstractDbOverlay.prototype.searchByQuery = function(originalQuery, perfect, fitBounds) {
+AbstractDbOverlay.prototype.searchByQuery = function (originalQuery, perfect, fitBounds) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
ServerConnector.getSessionData().setQuery({
- type : self.getName(),
- query : query
+ type: self.getName(),
+ query: query
});
- var queries = self.splitQuery(originalQuery);
-
+ var res;
var encodedQueries = [];
- var promises = [];
- for (var i = 0; i < queries.length; i++) {
- encodedQueries.push(self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, queries[i], perfect));
- promises.push(self.searchBySingleQuery(queries[i], perfect));
- }
+ return self.searchBySingleQuery(originalQuery, perfect).then(function (results) {
+ if (results.length > 0) {
+ encodedQueries.push(query);
+ return [results];
+ } else {
+ var queries = self.splitQuery(originalQuery);
+
+ var promises = [];
+ for (var i = 0; i < queries.length; i++) {
+ encodedQueries.push(self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, queries[i], perfect));
+ promises.push(self.searchBySingleQuery(queries[i], perfect));
+ }
- var res;
- return Promise.all(promises).then(function(results) {
+ return Promise.all(promises);
+ }
+ }).then(function (results) {
self.setQueries(encodedQueries);
res = results;
return self.callListeners('onSearch', {
- fitBounds : fitBounds,
- identifiedElements : res,
- type : AbstractDbOverlay.QueryType.SEARCH_BY_QUERY,
+ fitBounds: fitBounds,
+ identifiedElements: res,
+ type: AbstractDbOverlay.QueryType.SEARCH_BY_QUERY,
});
- }).then(function() {
+ }).then(function () {
return res;
});
};
-AbstractDbOverlay.prototype.searchNamesByTarget = function(element) {
+AbstractDbOverlay.prototype.searchNamesByTarget = function (element) {
var self = this;
var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
@@ -119,23 +126,23 @@ AbstractDbOverlay.prototype.searchNamesByTarget = function(element) {
return Promise.resolve(self._elementsByQuery[query]);
} else {
return self.getNamesByTargetFromServer({
- target : element
- }).then(function(drugNames) {
+ target: element
+ }).then(function (drugNames) {
self._elementsByQuery[query] = drugNames;
return self._elementsByQuery[query];
});
}
};
-AbstractDbOverlay.prototype.setQueries = function(queries) {
+AbstractDbOverlay.prototype.setQueries = function (queries) {
this._queries = queries;
};
-AbstractDbOverlay.prototype.getQueries = function() {
+AbstractDbOverlay.prototype.getQueries = function () {
return this._queries;
};
-AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function(targetingElement, colourId) {
+AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function (targetingElement, colourId) {
var self = this;
var result = [];
var iconCounter = 1;
@@ -160,11 +167,11 @@ AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function
return result;
};
-AbstractDbOverlay.prototype.refresh = function() {
+AbstractDbOverlay.prototype.refresh = function () {
throw new Error("Refreshing shouldn't be called");
};
-AbstractDbOverlay.prototype.searchByEncodedQuery = function(originalQuery, fitBounds) {
+AbstractDbOverlay.prototype.searchByEncodedQuery = function (originalQuery, fitBounds) {
var query = this.decodeQuery(originalQuery);
query.fitBounds = fitBounds;
if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
@@ -179,9 +186,9 @@ AbstractDbOverlay.prototype.searchByEncodedQuery = function(originalQuery, fitBo
}
};
-AbstractDbOverlay.prototype.clear = function() {
+AbstractDbOverlay.prototype.clear = function () {
var self = this;
- return self.searchByQuery("").then(function() {
+ return self.searchByQuery("").then(function () {
return self.callListeners('onClear');
});
};
@@ -189,38 +196,38 @@ AbstractDbOverlay.prototype.clear = function() {
/**
* Returns true if overlay allows to get general data for element.
*/
-AbstractDbOverlay.prototype.allowGeneralSearch = function() {
+AbstractDbOverlay.prototype.allowGeneralSearch = function () {
return this._allowGeneralSearch;
};
-AbstractDbOverlay.prototype.getName = function() {
+AbstractDbOverlay.prototype.getName = function () {
return this.name;
};
/**
* Returns true if overlay allows to get data for element by search id.
*/
-AbstractDbOverlay.prototype.allowSearchById = function() {
+AbstractDbOverlay.prototype.allowSearchById = function () {
return this._allowSearchById;
};
-AbstractDbOverlay.prototype.setMap = function(map) {
+AbstractDbOverlay.prototype.setMap = function (map) {
this._map = map;
};
-AbstractDbOverlay.prototype.getMap = function() {
+AbstractDbOverlay.prototype.getMap = function () {
return this._map;
};
-AbstractDbOverlay.prototype.setName = function(name) {
+AbstractDbOverlay.prototype.setName = function (name) {
this.name = name;
};
-AbstractDbOverlay.prototype.getName = function() {
+AbstractDbOverlay.prototype.getName = function () {
return this.name;
};
-AbstractDbOverlay.prototype.setAllowSearchById = function(allowSearchById) {
+AbstractDbOverlay.prototype.setAllowSearchById = function (allowSearchById) {
// configure if the overlay can contain detailed data about elements that
// should be visualized in detailed mode of the Info Window
if (typeof allowSearchById === "boolean") {
@@ -232,7 +239,7 @@ AbstractDbOverlay.prototype.setAllowSearchById = function(allowSearchById) {
}
};
-AbstractDbOverlay.prototype.setAllowGeneralSearch = function(allowGeneralSearch) {
+AbstractDbOverlay.prototype.setAllowGeneralSearch = function (allowGeneralSearch) {
if (typeof allowGeneralSearch === "boolean") {
this._allowGeneralSearch = allowGeneralSearch;
} else if (allowGeneralSearch === undefined) {
@@ -242,22 +249,22 @@ AbstractDbOverlay.prototype.setAllowGeneralSearch = function(allowGeneralSearch)
}
};
-AbstractDbOverlay.prototype.setIconType = function(iconType) {
+AbstractDbOverlay.prototype.setIconType = function (iconType) {
this._iconType = iconType;
};
-AbstractDbOverlay.prototype.setIconStart = function(iconStart) {
+AbstractDbOverlay.prototype.setIconStart = function (iconStart) {
this._iconStart = iconStart;
};
-AbstractDbOverlay.IconColors = [ "red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange" ];
+AbstractDbOverlay.IconColors = ["red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange"];
-AbstractDbOverlay.prototype.getColor = function(colorId) {
+AbstractDbOverlay.prototype.getColor = function (colorId) {
var id = colorId + this._iconStart;
id %= AbstractDbOverlay.IconColors.length;
return AbstractDbOverlay.IconColors[id];
};
-AbstractDbOverlay.prototype.getIcon = function(colorId, id) {
+AbstractDbOverlay.prototype.getIcon = function (colorId, id) {
if (id >= 100) {
id = 1;
}
@@ -265,7 +272,7 @@ AbstractDbOverlay.prototype.getIcon = function(colorId, id) {
return "marker/" + this._iconType + "/" + this._iconType + "_" + color + "_" + id + ".png";
};
-AbstractDbOverlay.prototype.splitQuery = function(query, useFullName) {
+AbstractDbOverlay.prototype.splitQuery = function (query, useFullName) {
var result = [];
if (query.indexOf(";") >= 0) {
result = query.split(";");
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index caf31be8d1bfd7f3797bc413c4e50db0ab7cd638..947e0cd77818364a27696614efef19a550a9d28b 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -34,80 +34,81 @@ function Helper(configuration) {
}
this.setConfiguration(configuration);
this.idCounter = 1000000;
+ this.EPSILON = Helper.EPSILON;
}
-Helper.prototype.setConfiguration = function(configuration) {
+Helper.prototype.setConfiguration = function (configuration) {
this._configuration = configuration;
};
-Helper.prototype.getConfiguration = function() {
+Helper.prototype.getConfiguration = function () {
return this._configuration;
};
-Helper.prototype.createCommentDbOverlay = function(map) {
+Helper.prototype.createCommentDbOverlay = function (map) {
var result = new CommentDbOverlay({
- map : map,
- name : "comment",
- allowGeneralSearch : true
+ map: map,
+ name: "comment",
+ allowGeneralSearch: true
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createSearchDbOverlay = function(map) {
+Helper.prototype.createSearchDbOverlay = function (map) {
var result = new SearchDbOverlay({
- map : map,
- name : "search",
+ map: map,
+ name: "search",
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createDbOverlay = function(map) {
+Helper.prototype.createDbOverlay = function (map) {
var result = new AbstractDbOverlay({
- map : map,
- name : "search",
+ map: map,
+ name: "search",
});
- result.clear = function() {
+ result.clear = function () {
logger.debug("Clear mock");
};
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createDrugDbOverlay = function(map) {
+Helper.prototype.createDrugDbOverlay = function (map) {
var result = new DrugDbOverlay({
- map : map,
- name : "drug",
- allowGeneralSearch : true,
- allowSearchById : true,
+ map: map,
+ name: "drug",
+ allowGeneralSearch: true,
+ allowSearchById: true,
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createChemicalDbOverlay = function(map) {
+Helper.prototype.createChemicalDbOverlay = function (map) {
var result = new ChemicalDbOverlay({
- map : map,
- name : "chemical",
- allowGeneralSearch : true,
- allowSearchById : true,
+ map: map,
+ name: "chemical",
+ allowGeneralSearch: true,
+ allowSearchById: true,
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createMiRnaDbOverlay = function(map) {
+Helper.prototype.createMiRnaDbOverlay = function (map) {
var result = new MiRnaDbOverlay({
- map : map,
- name : "mirna",
- allowGeneralSearch : true,
- allowSearchById : true,
+ map: map,
+ name: "mirna",
+ allowGeneralSearch: true,
+ allowSearchById: true,
});
map.registerDbOverlay(result);
return result;
};
-Helper.prototype.createComment = function(element) {
+Helper.prototype.createComment = function (element) {
var elementType = "ALIAS";
var elementId = this.idCounter++;
var id = this.idCounter++;
@@ -124,25 +125,25 @@ Helper.prototype.createComment = function(element) {
}
var result = new Comment({
- elementId : elementId,
- type : elementType,
- modelId : modelId,
- icon : "icons/comment.png",
- id : id,
- pinned : true,
- coord : {
- x : 321.5,
- y : 289.0
+ elementId: elementId,
+ type: elementType,
+ modelId: modelId,
+ icon: "icons/comment.png",
+ id: id,
+ pinned: true,
+ coord: {
+ x: 321.5,
+ y: 289.0
},
- removed : false,
- title : "title fo comment: " + id,
- content : "content of the comment # " + id
+ removed: false,
+ title: "title fo comment: " + id,
+ content: "content of the comment # " + id
});
return result;
};
-Helper.prototype.createProject = function() {
+Helper.prototype.createProject = function () {
var result = new Project();
result.setProjectId("testId");
result.setId(this.idCounter++);
@@ -150,17 +151,17 @@ Helper.prototype.createProject = function() {
return result;
};
-Helper.prototype.createUser = function() {
+Helper.prototype.createUser = function () {
var result = new User({
- login : "testlogin",
- id : this.idCounter++,
- name : "some name",
- surname : "surn",
+ login: "testlogin",
+ id: this.idCounter++,
+ name: "some name",
+ surname: "surn",
});
return result;
};
-Helper.prototype.createAlias = function(map) {
+Helper.prototype.createAlias = function (map) {
var mapId;
if (map === undefined) {
mapId = this.idCounter++;
@@ -168,17 +169,17 @@ Helper.prototype.createAlias = function(map) {
mapId = map.getId();
}
var result = new Alias({
- idObject : this.idCounter++,
- name : "Test element",
- type : "RNA",
- modelId : mapId,
- bounds : {
- x : 10.0,
- y : 20.0,
- width : 30.0,
- height : 40.0,
+ idObject: this.idCounter++,
+ name: "Test element",
+ type: "RNA",
+ modelId: mapId,
+ bounds: {
+ x: 10.0,
+ y: 20.0,
+ width: 30.0,
+ height: 40.0,
},
- references : [],
+ references: [],
});
if (map !== undefined) {
map.getModel().addAlias(result);
@@ -186,55 +187,63 @@ Helper.prototype.createAlias = function(map) {
return result;
};
-Helper.prototype.createLayoutAlias = function(alias) {
+Helper.prototype.createLayoutAlias = function (alias) {
var id;
+ var modelId;
if (alias instanceof Alias) {
id = alias.getId();
+ modelId = alias.getModelId();
} else {
id = this.idCounter++;
+ modelId = this.idCounter++;
}
var result = new LayoutAlias({
- idObject : id,
- value : 0.2,
- color : {
- a : 23
+ idObject: id,
+ value: 0.2,
+ color: {
+ a: 23
},
- geneVariations : [ {} ]
+ modelId: modelId,
+ geneVariations: [{}]
});
return result;
};
-Helper.prototype.createLayoutReaction = function(reaction) {
+Helper.prototype.createLayoutReaction = function (reaction) {
var reactionId;
+ var modelId;
if (reaction instanceof Reaction) {
reactionId = reaction.getId();
+ modelId = reaction.getModelId();
} else {
reactionId = this.idCounter++;
+ modelId = this.idCounter++;
}
var result = new LayoutReaction({
- idObject : reactionId,
- width : 3.4,
- color : {
- a : 24,
+ idObject: reactionId,
+ modelId: modelId,
+ width: 3.4,
+ color: {
+ a: 24,
},
- reverse : true
+ reverse: true
});
return result;
};
-Helper.prototype.createIdentifiedElement = function(element) {
+Helper.prototype.createIdentifiedElement = function (element) {
if (element === undefined) {
return new IdentifiedElement({
- type : "ALIAS",
- id : this.idCounter++,
- modelId : this.idCounter++,
+ type: "ALIAS",
+ id: this.idCounter++,
+ modelId: this.idCounter++,
});
}
return new IdentifiedElement(element);
};
-Helper.prototype.createReaction = function(map) {
+Helper.prototype.createReaction = function (map) {
var mapId = null;
if (map !== undefined) {
mapId = map.getId();
@@ -242,49 +251,49 @@ Helper.prototype.createReaction = function(map) {
mapId = this.idCounter++;
}
var result = new Reaction({
- idObject : this.idCounter++,
- lines : [ {
- start : {
- x : 434.8904109589041,
- y : 85.0
+ idObject: this.idCounter++,
+ lines: [{
+ start: {
+ x: 434.8904109589041,
+ y: 85.0
},
- end : {
- x : 410.8341500923087,
- y : 104.95576185524392
+ end: {
+ x: 410.8341500923087,
+ y: 104.95576185524392
},
- type : "START"
+ type: "START"
}, {
- start : {
- x : 404.6769250286157,
- y : 110.06345991944379
+ start: {
+ x: 404.6769250286157,
+ y: 110.06345991944379
},
- end : {
- x : 380.62066416202026,
- y : 130.0192217746877
+ end: {
+ x: 380.62066416202026,
+ y: 130.0192217746877
},
- type : "END"
- } ],
- centerPoint : new google.maps.Point(0, 0),
- modelId : mapId,
- references : [],
+ type: "END"
+ }],
+ centerPoint: new google.maps.Point(0, 0),
+ modelId: mapId,
+ references: [],
});
return result;
};
-Helper.prototype.createOptions = function(project) {
+Helper.prototype.createOptions = function (project) {
if (project === undefined) {
project = this.createProject();
}
var options = {
- mapDiv : testDiv,
- element : testDiv,
- project : project,
+ mapDiv: testDiv,
+ element: testDiv,
+ project: project,
};
return options;
};
-Helper.prototype.createModel = function() {
+Helper.prototype.createModel = function () {
var result = new Model();
result.setId(this.idCounter++);
result.setTileSize(256);
@@ -293,16 +302,16 @@ Helper.prototype.createModel = function() {
result.setMaxZoom(8);
result.setMinZoom(2);
result.setCenterLatLng({
- lat : 10,
- lng : 20
+ lat: 10,
+ lng: 20
});
result.setTopLeftLatLng({
- lat : 8,
- lng : 8
+ lat: 8,
+ lng: 8
});
result.setBottomRightLatLng({
- lat : 30,
- lng : 30
+ lat: 30,
+ lng: 30
});
var layout = this.createLayout();
@@ -310,51 +319,51 @@ Helper.prototype.createModel = function() {
return result;
};
-Helper.prototype.createLayout = function() {
+Helper.prototype.createLayout = function () {
var id = this.idCounter++;
var layout = new LayoutData({
- idObject : id,
- name : "testLayout" + id,
+ idObject: id,
+ name: "testLayout" + id,
});
return layout;
};
-Helper.prototype.createGoogleMap = function() {
+Helper.prototype.createGoogleMap = function () {
var result = new google.maps.Map(testDiv, {
- center : {
- lat : -34.397,
- lng : 150.644
+ center: {
+ lat: -34.397,
+ lng: 150.644
},
- scrollwheel : false,
- zoom : 8
+ scrollwheel: false,
+ zoom: 8
});
return result;
};
-Helper.prototype.createCustomMapOptions = function(project) {
+Helper.prototype.createCustomMapOptions = function (project) {
if (project === undefined) {
project = this.createProject();
}
var result = new CustomMapOptions({
- markerOptimization : true,
- project : project,
- element : testDiv,
- mapDiv : testDiv,
- configuration : this.getConfiguration(),
+ markerOptimization: true,
+ project: project,
+ element: testDiv,
+ mapDiv: testDiv,
+ configuration: this.getConfiguration(),
});
return result;
};
-Helper.prototype.createAbstractCustomMap = function() {
+Helper.prototype.createAbstractCustomMap = function () {
var options = this.createCustomMapOptions();
var result = new AbstractCustomMap(options.getProject().getModel(), options);
return result;
};
-Helper.prototype.createCustomMap = function(project) {
+Helper.prototype.createCustomMap = function (project) {
if (project === null) {
throw new Error("Project cannot be null");
}
@@ -366,12 +375,12 @@ Helper.prototype.createCustomMap = function(project) {
/**
* Changes url but saves the cookies.
*/
-Helper.prototype.setUrl = function(url) {
+Helper.prototype.setUrl = function (url) {
var cookies = Cookies.get();
global.dom.reconfigure({
- url : url
+ url: url
});
- for ( var cookie in cookies) {
+ for (var cookie in cookies) {
Cookies.set(cookie, cookies[cookie]);
}
GuiConnector.init();
diff --git a/frontend-js/src/test/js/map/CustomMap-test.js b/frontend-js/src/test/js/map/CustomMap-test.js
index 3c434c3198f62fb471c0981e85acc049982341f4..ccef0aab0a0865668b57ecfe6558b6255ab7d577 100644
--- a/frontend-js/src/test/js/map/CustomMap-test.js
+++ b/frontend-js/src/test/js/map/CustomMap-test.js
@@ -116,24 +116,19 @@ describe('CustomMap', function() {
it("simple", function() {
var map = helper.createCustomMap();
- var alias = helper.createAlias();
- alias.setModelId(map.getId());
+ var alias = helper.createAlias(map);
map.getModel().addAlias(alias);
- var reaction = helper.createReaction();
+ var reaction = helper.createReaction(map);
map.getModel().addReaction(reaction);
var layout = helper.createLayout();
layout.setInputDataAvailable(true);
layout.setInitialized(true);
- var layoutAlias = helper.createLayoutAlias();
- layoutAlias.setId(alias.getId());
- layoutAlias.setModelId(map.getId());
+ var layoutAlias = helper.createLayoutAlias(alias);
layout.addAlias(layoutAlias);
- var layoutReaction = helper.createLayoutReaction();
- layoutReaction.setId(reaction.getId());
- layoutReaction.setModelId(map.getId());
+ var layoutReaction = helper.createLayoutReaction(reaction);
layout.addReaction(layoutReaction);
map.getModel().addLayout(layout);
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index 6c14d02b8595aebd12e4ca6bf3d728052006e710..760c1f6b464c67fe5a9eae6b44688c009294512e 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -1,7 +1,5 @@
"use strict";
-var Helper = require('./helper');
-
require("./mocha-config.js");
var Alias = require('../../main/js/map/data/Alias');
@@ -408,8 +406,8 @@ describe('minerva global', function() {
var sessionData = ServerConnectorMock.getSessionData(globalResult.getProject());
var center = sessionData.getCenter(globalResult.getProject().getModel());
assert.ok(center instanceof google.maps.Point);
- assert.closeTo(parseFloat(center.x), 10, Helper.EPSILON);
- assert.closeTo(parseFloat(center.y), 20, Helper.EPSILON);
+ assert.closeTo(parseFloat(center.x), 10, helper.EPSILON);
+ assert.closeTo(parseFloat(center.y), 20, helper.EPSILON);
}).then(function() {
globalResult.destroy();
});
diff --git a/frontend-js/src/test/js/mocha-config.js b/frontend-js/src/test/js/mocha-config.js
index b04d4694da8de0eb0f88dfa7cc40a140f3b9fdb4..2386f2d30d9a31862b0f3c8e1843f9e5a9bd10a3 100644
--- a/frontend-js/src/test/js/mocha-config.js
+++ b/frontend-js/src/test/js/mocha-config.js
@@ -3,7 +3,7 @@
var Promise = require("bluebird");
var Cookies = require('js-cookie');
-var Helper = require('./Helper');
+var Helper = require('./helper');
// GLOBAL configuration
global.navigator = {
@@ -18,7 +18,7 @@ global.dom = new jsdom.JSDOM();
global.window = global.dom.window;
global.document = window.document;
-global.$ = require('jQuery');
+global.$ = require('jquery');
global.jQuery = $;
global.window.$ = $;
diff --git a/frontend-js/testFiles/apiCalls/doLogout b/frontend-js/testFiles/apiCalls/doLogout
new file mode 100644
index 0000000000000000000000000000000000000000..1a36cf5fc27a0920a9f3668225f9d7aec239566e
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/doLogout
@@ -0,0 +1 @@
+{"status":"ok"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/bioEntities/elements/329173/POST_coordinates=2.00%2C12.00&pinned=false&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/bioEntities/elements/329173/POST_coordinates=2.00%2C12.00&pinned=true&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/bioEntities/elements/329173/POST_coordinates=2.00%2C12.00&pinned=false&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/bioEntities/elements/329173/POST_coordinates=2.00%2C12.00&pinned=true&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/points/2.00,12.00/POST_pinned=false&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/points/2.00,12.00/POST_pinned=true&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/points/2.00,12.00/POST_pinned=false&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/comments/models/15781/points/2.00,12.00/POST_pinned=true&token=MOCK_TOKEN_ID&
diff --git a/persist/src/db/11/fix_db_20170616.sql b/persist/src/db/11.0.0/fix_db_20170616.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170616.sql
rename to persist/src/db/11.0.0/fix_db_20170616.sql
diff --git a/persist/src/db/11/fix_db_20170627.sql b/persist/src/db/11.0.0/fix_db_20170627.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170627.sql
rename to persist/src/db/11.0.0/fix_db_20170627.sql
diff --git a/persist/src/db/11/fix_db_20170628.sql b/persist/src/db/11.0.0/fix_db_20170628.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170628.sql
rename to persist/src/db/11.0.0/fix_db_20170628.sql
diff --git a/persist/src/db/11/fix_db_20170629.sql b/persist/src/db/11.0.0/fix_db_20170629.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170629.sql
rename to persist/src/db/11.0.0/fix_db_20170629.sql
diff --git a/persist/src/db/11/fix_db_20170705.sql b/persist/src/db/11.0.0/fix_db_20170705.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170705.sql
rename to persist/src/db/11.0.0/fix_db_20170705.sql
diff --git a/persist/src/db/11/fix_db_20170714.sql b/persist/src/db/11.0.0/fix_db_20170714.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170714.sql
rename to persist/src/db/11.0.0/fix_db_20170714.sql
diff --git a/persist/src/db/11/fix_db_20170725.sql b/persist/src/db/11.0.0/fix_db_20170725.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170725.sql
rename to persist/src/db/11.0.0/fix_db_20170725.sql
diff --git a/persist/src/db/11/fix_db_20170731.sql b/persist/src/db/11.0.0/fix_db_20170731.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20170731.sql
rename to persist/src/db/11.0.0/fix_db_20170731.sql
diff --git a/persist/src/db/11.0.1/fix_db_20170908.sql b/persist/src/db/11.0.1/fix_db_20170908.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/11.0.1/fix_db_20170908.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index 621a0dd6d64839e716e89d2742381313bec10858..f35425bd3b5820f29dfe956e03c341f7434278e7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -103,11 +103,27 @@ public class UserController extends BaseController {
}
@RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token) throws SecurityException {
+ public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ HttpServletResponse response //
+ ) throws SecurityException, IOException {
userService.logout(token);
- Map<String, String> response = new HashMap<>();
- response.put("status", "OK");
- return response;
+ Map<String, String> result = new HashMap<>();
+ result.put("status", "OK");
+
+ final Boolean useSecureCookie = false;
+ final String cookiePath = "/";
+
+ Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
+
+ cookie.setSecure(useSecureCookie);
+ cookie.setMaxAge(0);
+ cookie.setPath(cookiePath);
+
+ response.addCookie(cookie);
+ response.getWriter().write("{\"status\":\"OK\"}");
+ response.getWriter().flush();
+ response.getWriter().close();
+ return result;
}
/**