Merge branch 'merge-12.1.5' into 'master'

Merge 12.1.5 into master

See merge request !573

.gitlab-ci.yml

@@ -18,7 +18,7 @@ test_frontend:
     - npm test
 
 test_backend 1 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
 #xvfb is for X11 connection used by some parts of the java code: https://stackoverflow.com/a/47575851/1127920
@@ -31,7 +31,7 @@ test_backend 1 15:
     - mvn test -pl commons
 
 test_backend 2 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -43,35 +43,35 @@ test_backend 2 15:
     - mvn test -pl annotation
 
 test_backend 3 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl CellDesigner-plugin -am
     - mvn test -pl CellDesigner-plugin
 
 test_backend 4 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl converter -am
     - mvn test -pl converter
 
 test_backend 5 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl converter-graphics -am
     - mvn test -pl converter-graphics
 
 test_backend 6 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl converter-CellDesigner -am
     - mvn test -pl converter-CellDesigner
 
 test_backend 7 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -82,35 +82,35 @@ test_backend 7 15:
     - mvn test -pl converter-SBGNML
 
 test_backend 8 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl converter-sbml -am
     - mvn test -pl converter-sbml
 
 test_backend 9 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl model -am
     - mvn test -pl model
 
 test_backend 10 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl model-command -am
     - mvn test -pl model-command
 
 test_backend 11 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - mvn -DskipTests=true clean install -pl pathvisio -am
     - mvn test -pl pathvisio
 
 test_backend 12 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -121,7 +121,7 @@ test_backend 12 15:
     - mvn test -pl persist
 
 test_backend 13 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -132,7 +132,7 @@ test_backend 13 15:
     - mvn test -pl reactome
 
 test_backend 14 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -143,7 +143,7 @@ test_backend 14 15:
     - mvn test -pl rest-api
 
 test_backend 15 15:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   services:
     - postgres:9.6
   stage: test
@@ -154,7 +154,7 @@ test_backend 15 15:
     - mvn test -pl service
 
 build_war:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: build
   only:
     - tags
@@ -173,7 +173,7 @@ build_war:
     - cp web/target/web-1.0.war minerva.war
 
 dependency_conflict_check:
-  image: maven:latest
+  image: maven:3.6.0-jdk-8
   stage: test
   script:
     - apt-get update

CHANGELOG

@@ -7,6 +7,13 @@ minerva (12.2.0~alpha.0) stable; urgency=medium
     highligh
 
 
+minerva (12.1.5) stable; urgency=medium
+  * Bug fix: Drugbank changed output format which crashed drug connector
+  * Bug fix: word wrapping fixed in overlay table for long overlay names
+    in Firefox browser
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 10 Janc 2019 14:00:00 +0200
+
 minerva (12.1.4) stable; urgency=medium
   * Bug fix: no check for limit on custom data overlays fixed
   * Bug fix: error message improved when there is privilege problem during

annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java

@@ -86,17 +86,17 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
   /**
    * Url used for accessing information about target synonyms.
    */
-  static final String URLPEP = "https://www.drugbank.ca/biodb/polypeptides/";
+  static final String URLPEP = "https://www.drugbank.ca/polypeptides/";
 
   /**
    * Url that allows to search for drugs using target hgnc name.
    */
-  static final String URL_TARGETS = "https://www.drugbank.ca/search?utf8=%E2%9C%93&searcher=targets&query=";
+  static final String URL_TARGETS = "https://www.drugbank.ca/search?utf8=%E2%9C%93&searcher=bio_entities&query=";
 
   /**
    * Url that helps finding drug name for given target identifier.
    */
-  static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/biodb/bio_entities/";
+  static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/bio_entities/";
 
   /**
    * Pattern used to get information about {@link Drug#bloodBrainBarrier blood
@@ -108,7 +108,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
    * Pattern that extract information about target identifier when searching for
    * targets with given set of HGNC names.
    */
-  private Pattern targetPattern = Pattern.compile("(?<=\"/biodb/bio_entities/)([\\s\\S]*?)(?=\")");
+  private Pattern targetPattern = Pattern.compile("(?<=\"/bio_entities/)([\\s\\S]*?)(?=\")");
 
   /**
    * Constructor.
@@ -375,7 +375,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
       type = htmlPage.substring(kindIndex, endKindIndex);
     }
     if (type.trim().equalsIgnoreCase("Protein")) {
-      int uniprotIdStart = htmlPage.indexOf("/biodb/polypeptides/") + "/biodb/polypeptides/".length();
+      int uniprotIdStart = htmlPage.indexOf("\"/polypeptides/") + "\"/polypeptides/".length();
       Target result = new Target();
       result.setType(TargetType.SINGLE_PROTEIN);
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java

@@ -84,6 +84,9 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
     if (term == null || "".equals(term.trim())) {
       return null;
     }
+    if (term.equalsIgnoreCase("Humans")) {
+	  term="Human";
+	}
     String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
     if (res != null) {
       if (res.equals("null")) {

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java

@@ -43,7 +43,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
 	/**
 	 * Version of the rest API that is supported by this annotator.
 	 */
-	static final String					SUPPORTED_VERSION				 = "8.0";
+	static final String					SUPPORTED_VERSION				 = "9.0";
 
 	/**
 	 * Url address of ensembl restful service.

annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java

@@ -780,12 +780,12 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
     }
 
   }
-  
+
   @Test
   public void testExtractTargetsFromPageContent() throws Exception {
     try {
       String pageContent = " Details</a>blablablablabla Details</a>";
-      List<Target> result = drugBankHTMLParser.extractTargetsFromPageContent(pageContent,2,3);
+      List<Target> result = drugBankHTMLParser.extractTargetsFromPageContent(pageContent, 2, 3);
 
       assertEquals(0, result.size());
 
@@ -795,7 +795,5 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
     }
 
   }
-  
-  
 
 }

annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java

@@ -43,6 +43,17 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testByHumansName() throws Exception {
+    try {
+      MiriamData md = taxonomyBackend.getByName("Humans");
+      assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testByComplexName() throws Exception {
     try {

annotation/testFiles/drugbank/target-html-part.html

- Details</a><strong>1. <a href="/biodb/polypeptides/P21430">Matrix protein 2</a></strong></div><div class="card-body"><div class="row"><div class="col-sm-12 col-lg-5"><dl><dt class="col-md-5 col-sm-6">Kind</dt><dd class="col-md-7 col-sm-6">Protein</dd><dt class="col-md-5 col-sm-6">Organism</dt><dd class="col-md-7 col-sm-6">Influenza A virus (strain A/Ann Arbor/6/1960 H2N2)</dd><dt class="col-md-5 col-sm-6">Pharmacological action</dt><dd class="col-md-7 col-sm-6"><div class="badge badge badge-yes">Yes</div></dd><dt class="col-md-5 col-sm-6">Actions</dt><dd class="col-md-7 col-sm-6"><div class="badge badge-pill badge-action">Inhibitor</div></dd></dl></div><div class="col-sm-12 col-lg-7"><dl><dt class="col-md-5 col-sm-6">General Function</dt><dd class="col-md-7 col-sm-6">Ion channel activity</dd><dt class="col-md-5 col-sm-6">Specific Function</dt><dd class="col-md-7 col-sm-6">Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytos...</dd><dt class="col-md-5 col-sm-6">Gene Name</dt><dd class="col-md-7 col-sm-6">M</dd><dt class="col-md-5 col-sm-6">Uniprot ID</dt><dd class="col-md-7 col-sm-6"><a target="_blank" href="http://www.uniprot.org/uniprot/P21430">P21430</a></dd><dt class="col-md-5 col-sm-6">Uniprot Name</dt><dd class="col-md-7 col-sm-6">Matrix protein 2</dd><dt class="col-md-5 col-sm-6">Molecular Weight</dt><dd class="col-md-7 col-sm-6">11165.62 Da</dd></dl></div></div><h5>References</h5><div class="references"><ol class="cite-this-references"><li id="reference-A10951">Wang C, Takeuchi K, Pinto LH, Lamb RA: Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block. J Virol. 1993 Sep;67(9):5585-94. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/7688826">PubMed:7688826</a>] </li><li id="reference-A4968">Jing X, Ma C, Ohigashi Y, Oliveira FA, Jardetzky TS, Pinto LH, Lamb RA: Functional studies indicate amantadine binds to the pore of the influenza A virus M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10967-72. doi: 10.1073/pnas.0804958105. Epub 2008 Jul 31. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18669647">PubMed:18669647</a>] </li><li id="reference-A10952">Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M: Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc. 2009 Jun 17;131(23):8066-76. doi: 10.1021/ja900063s. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/19469531">PubMed:19469531</a>] </li><li id="reference-A3946">Beigel J, Bray M: Current and future antiviral therapy of severe seasonal and avian influenza. Antiviral Res. 2008 Apr;78(1):91-102. doi: 10.1016/j.antiviral.2008.01.003. Epub 2008 Feb 4. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18328578">PubMed:18328578</a>] </li><li id="reference-A10953">Lear JD: Proton conduction through the M2 protein of the influenza A virus; a quantitative, mechanistic analysis of experimental data. FEBS Lett. 2003 Sep 18;552(1):17-22. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/12972146">PubMed:12972146</a>] </li><li id="reference-A10954">Salom D, Hill BR, Lear JD, DeGrado WF: pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus. Biochemistry. 2000 Nov 21;39(46):14160-70. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/11087364">PubMed:11087364</a>] </li></ol></div></div></div><div class="bond card" id="BE0000641"><div class="card-header"><a class="btn btn-drugbank-secondary btn-sm bond-details-link ml-3" href="/biodb/polypeptides/Q8TCU5">
+ Details</a><strong>1. <a href="/polypeptides/P21430">Matrix protein 2</a></strong></div><div class="card-body"><div class="row"><div class="col-sm-12 col-lg-5"><dl><dt class="col-md-5 col-sm-6">Kind</dt><dd class="col-md-7 col-sm-6">Protein</dd><dt class="col-md-5 col-sm-6">Organism</dt><dd class="col-md-7 col-sm-6">Influenza A virus (strain A/Ann Arbor/6/1960 H2N2)</dd><dt class="col-md-5 col-sm-6">Pharmacological action</dt><dd class="col-md-7 col-sm-6"><div class="badge badge badge-yes">Yes</div></dd><dt class="col-md-5 col-sm-6">Actions</dt><dd class="col-md-7 col-sm-6"><div class="badge badge-pill badge-action">Inhibitor</div></dd></dl></div><div class="col-sm-12 col-lg-7"><dl><dt class="col-md-5 col-sm-6">General Function</dt><dd class="col-md-7 col-sm-6">Ion channel activity</dd><dt class="col-md-5 col-sm-6">Specific Function</dt><dd class="col-md-7 col-sm-6">Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytos...</dd><dt class="col-md-5 col-sm-6">Gene Name</dt><dd class="col-md-7 col-sm-6">M</dd><dt class="col-md-5 col-sm-6">Uniprot ID</dt><dd class="col-md-7 col-sm-6"><a target="_blank" href="http://www.uniprot.org/uniprot/P21430">P21430</a></dd><dt class="col-md-5 col-sm-6">Uniprot Name</dt><dd class="col-md-7 col-sm-6">Matrix protein 2</dd><dt class="col-md-5 col-sm-6">Molecular Weight</dt><dd class="col-md-7 col-sm-6">11165.62 Da</dd></dl></div></div><h5>References</h5><div class="references"><ol class="cite-this-references"><li id="reference-A10951">Wang C, Takeuchi K, Pinto LH, Lamb RA: Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block. J Virol. 1993 Sep;67(9):5585-94. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/7688826">PubMed:7688826</a>] </li><li id="reference-A4968">Jing X, Ma C, Ohigashi Y, Oliveira FA, Jardetzky TS, Pinto LH, Lamb RA: Functional studies indicate amantadine binds to the pore of the influenza A virus M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10967-72. doi: 10.1073/pnas.0804958105. Epub 2008 Jul 31. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18669647">PubMed:18669647</a>] </li><li id="reference-A10952">Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M: Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc. 2009 Jun 17;131(23):8066-76. doi: 10.1021/ja900063s. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/19469531">PubMed:19469531</a>] </li><li id="reference-A3946">Beigel J, Bray M: Current and future antiviral therapy of severe seasonal and avian influenza. Antiviral Res. 2008 Apr;78(1):91-102. doi: 10.1016/j.antiviral.2008.01.003. Epub 2008 Feb 4. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18328578">PubMed:18328578</a>] </li><li id="reference-A10953">Lear JD: Proton conduction through the M2 protein of the influenza A virus; a quantitative, mechanistic analysis of experimental data. FEBS Lett. 2003 Sep 18;552(1):17-22. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/12972146">PubMed:12972146</a>] </li><li id="reference-A10954">Salom D, Hill BR, Lear JD, DeGrado WF: pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus. Biochemistry. 2000 Nov 21;39(46):14160-70. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/11087364">PubMed:11087364</a>] </li></ol></div></div></div><div class="bond card" id="BE0000641"><div class="card-header"><a class="btn btn-drugbank-secondary btn-sm bond-details-link ml-3" href="/polypeptides/Q8TCU5">
\ No newline at end of file

frontend-js/src/main/css/global.css

@@ -926,8 +926,15 @@ https://www.w3schools.com/css/tryit.asp?filename=trycss_tooltip
     overflow-x: hidden;
 }
 
-.minerva-overlay-panel td, .minerva-overlay-panel th {
-    word-break: break-word;
+.minerva-overlay-panel td.word_wrap, .minerva-overlay-panel th.word_wrap {
+    /* For Firefox */
+    white-space: pre-wrap;
+    word-break: break-all;
+
+    /* For Chrome */
+    word-wrap: break-word;
+
+    min-width: 50px;
 }
 
 .minerva-search-data-hidden {

frontend-js/src/main/js/gui/AddOverlayDialog.js

@@ -297,7 +297,7 @@ AddOverlayDialog.prototype.open = function () {
               var errorMessage = JSON.parse(error.content);
               GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
             } else if (error instanceof SecurityError) {
-              GuiConnector.alert("You cannot add more overlays");
+              GuiConnector.alert("You cannot add more overlays, Custom Overlay limit is reached.");
             } else {
               GuiConnector.alert(error);
             }

frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js

@@ -604,7 +604,8 @@ OverlayPanel.prototype.init = function () {
       type: 'num',
       className: "no_padding"
     }, {
-      title: 'Name'
+      title: 'Name',
+      className: "word_wrap"
     }, {
       title: 'View',
       orderable: false,

persist/src/main/resources/db/migration/12.1.5/V12.1.0.20190109__drug_bank_cache_purge.sql

+delete from cachequery where type = (select iddb from cache_type where classname = 'lcsb.mapviewer.annotation.services.DrugbankHTMLParser') and (query like 'http%' or accessed > '2019-01-08');