From eb0404aeb348f528070a0bf07a67c6d42229e51f Mon Sep 17 00:00:00 2001 From: noedelta Date: Thu, 7 Jul 2016 17:29:56 +0100 Subject: [PATCH 01/14] Added new release plugin - jgitflow. Updated hibernate master version to the latest. Updated the name of the intact-view repository in SCM. --- pom.xml | 45 +++++++++++++++++++-------------------------- 1 file changed, 19 insertions(+), 26 deletions(-) diff --git a/pom.xml b/pom.xml index 7788415b5..a0e3e1d9b 100644 --- a/pom.xml +++ b/pom.xml @@ -9,7 +9,7 @@ uk.ac.ebi.intact.maven intact-hibernate-master - 42 + 44 4.0.0 @@ -21,16 +21,11 @@ IntAct Services :: View - - - - - - scm:git:https://github.com/EBI-IntAct/IntAct-View.git - scm:git:https://github.com/EBI-IntAct/IntAct-View.git - https://github.com/EBI-IntAct/IntAct-View + scm:git:https://github.com/EBI-IntAct/intact-view.git + scm:git:https://github.com/EBI-IntAct/intact-view.git + https://github.com/EBI-IntAct/intact-view HEAD @@ -226,12 +221,20 @@ - org.apache.maven.plugins - maven-release-plugin - 2.5 + external.atlassian.jgitflow + jgitflow-maven-plugin + 1.0-m5.1 - true - deploy + + master + develop + feature- + release- + hotfix- + ${project.artifactId}- + + + true @@ -914,19 +917,9 @@ - intact.nexus - IntAct Nexus - http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public + nexus-ebi-release-repo + http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ - - - intact.nexus - IntAct Nexus - http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public - - - - From ed5a6b4ffae0174e964c4952c95980b8be948a51 Mon Sep 17 00:00:00 2001 From: noedelta Date: Thu, 7 Jul 2016 17:45:19 +0100 Subject: [PATCH 02/14] Create the option to link directly from uniprot to the interactor list in intact-view. With this option the users from uniprot can understand better the DR lines generated by intact. --- .../controller/search/SearchController.java | 3 +++ src/main/webapp/WEB-INF/faces-config.xml | 2 +- src/main/webapp/WEB-INF/pretty-config.xml | 5 +++++ src/main/webapp/pages/list/list.xhtml | 21 +++++++++++++++++++ 4 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 src/main/webapp/pages/list/list.xhtml diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java index 91a3b0d50..2b0accfe3 100644 --- a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java @@ -125,6 +125,9 @@ public void searchOnLoad(ComponentSystemEvent evt) { userQuery.clearInteractionFilters(); doBinarySearch(userQuery.createSolrQuery()); } + if (this.currentQuery == null || !hasLoadedInteractorResults) { + doInteractorsSearch(); + } } } diff --git a/src/main/webapp/WEB-INF/faces-config.xml b/src/main/webapp/WEB-INF/faces-config.xml index 185f6ad84..e8c5096ea 100644 --- a/src/main/webapp/WEB-INF/faces-config.xml +++ b/src/main/webapp/WEB-INF/faces-config.xml @@ -93,7 +93,7 @@ * list - /pages/list/list_tab.xhtml + /pages/list/list.xhtml diff --git a/src/main/webapp/WEB-INF/pretty-config.xml b/src/main/webapp/WEB-INF/pretty-config.xml index dc6d99d04..5ac4f8c92 100644 --- a/src/main/webapp/WEB-INF/pretty-config.xml +++ b/src/main/webapp/WEB-INF/pretty-config.xml @@ -29,6 +29,11 @@ /pages/interactions/interactions.xhtml + + + /pages/list/list.xhtml + + diff --git a/src/main/webapp/pages/list/list.xhtml b/src/main/webapp/pages/list/list.xhtml new file mode 100644 index 000000000..8bed3b76f --- /dev/null +++ b/src/main/webapp/pages/list/list.xhtml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + From 73a461e8c7365639e3a49330610bb2e622a3174f Mon Sep 17 00:00:00 2001 From: noedelta Date: Fri, 8 Jul 2016 09:10:26 +0100 Subject: [PATCH 03/14] Removes dome warning from the pom.xml file. --- pom.xml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/pom.xml b/pom.xml index a0e3e1d9b..49fc13254 100644 --- a/pom.xml +++ b/pom.xml @@ -88,7 +88,7 @@ - ${artifactId}-${version} + ${project.artifactId}-${project.version} @@ -124,7 +124,7 @@ 0 ${jetty.contextPath} - ${build.outputDirectory}/META-INF/jetty-env.xml + ${project.build.outputDirectory}/META-INF/jetty-env.xml @@ -133,7 +133,7 @@ - ${build.outputDirectory}/META-INF/jetty.xml + ${project.build.outputDirectory}/META-INF/jetty.xml @@ -181,9 +181,10 @@ org.apache.maven.plugins maven-compiler-plugin + 3.5.1 - 1.6 - 1.6 + 1.7 + 1.7 @@ -191,6 +192,7 @@ org.jvnet.jaxb2.maven2 maven-jaxb2-plugin + 0.12.3 src/main/resources/META-INF/schema From 2ee843d7348b242debc5dcfb0af7b7b2c6a2c9ef Mon Sep 17 00:00:00 2001 From: noedelta Date: Fri, 8 Jul 2016 14:02:05 +0100 Subject: [PATCH 04/14] Fixed some death links in the the downloads page. Fixed a problem introduce in the pom.xml due to the update of the hibernate master. --- pom.xml | 3 ++- src/main/resources/META-INF/beans.spring.xml | 1 + .../pages/documentation/downloads_content.xhtml | 13 ++++++++++--- 3 files changed, 13 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index 49fc13254..a88ebd760 100644 --- a/pom.xml +++ b/pom.xml @@ -9,7 +9,8 @@ uk.ac.ebi.intact.maven intact-hibernate-master - 44 + + 42 4.0.0 diff --git a/src/main/resources/META-INF/beans.spring.xml b/src/main/resources/META-INF/beans.spring.xml index 361b6a672..c5e0ab0c6 100644 --- a/src/main/resources/META-INF/beans.spring.xml +++ b/src/main/resources/META-INF/beans.spring.xml @@ -28,6 +28,7 @@ + diff --git a/src/main/webapp/pages/documentation/downloads_content.xhtml b/src/main/webapp/pages/documentation/downloads_content.xhtml index 75a9bfe42..e814000fb 100644 --- a/src/main/webapp/pages/documentation/downloads_content.xhtml +++ b/src/main/webapp/pages/documentation/downloads_content.xhtml @@ -23,6 +23,9 @@
  • cv: controlled vocabularies.
  • psi25: IntAct data in PSI-MI 2.5 format. +
    + psi30: IntAct data in PSI-MI 3.0 format. +
    See the PSI website for a detailed format description. @@ -35,8 +38,8 @@ intact.zip: entire contents of the database in a single file.
    - pmidMITAB.zip: entire contents of the database, each file represents a publication. + pmidMITAB27.zip: entire contents of the database, each file represents a publication.
  • various: Data subsets for exchange with collaborating databases. @@ -50,7 +53,11 @@
    • psi25: IntAct complexes in PSI-MI 2.5 format. - See the + psi30: IntAct complexes in PSI-MI 3.0 format. +
      + See the PSI website for a detailed format description.
      • From c249b11aa937edc856b07d8574f1187224c99b2a Mon Sep 17 00:00:00 2001 From: noedelta Date: Fri, 8 Jul 2016 14:04:15 +0100 Subject: [PATCH 05/14] merging 'feature-GENISSUES-69' into 'develop' From 81096e178199a96e2c1527876d96570cce52658d Mon Sep 17 00:00:00 2001 From: noedelta Date: Fri, 8 Jul 2016 14:24:07 +0100 Subject: [PATCH 06/14] Updates OLS url to the new website --- src/main/resources/Miriam.xml | 42 +++++++++---------- .../default-xref-links.properties | 2 +- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/src/main/resources/Miriam.xml b/src/main/resources/Miriam.xml index 84ddd5297..05a22b962 100644 --- a/src/main/resources/Miriam.xml +++ b/src/main/resources/Miriam.xml @@ -66,9 +66,9 @@ - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ CHEBI:36927 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id ChEBI through OLS European Bioinformatics Institute, Cambridge @@ -1183,9 +1183,9 @@ United Kingdom - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ SBO:0000262 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id SBO through OLS European Bioinformatics Institute @@ -2547,9 +2547,9 @@ - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ ECO:0000006 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Evidence Codes via the Ontology Lookup Service (OLS) European Bioinformatics Institute United Kingdom @@ -2588,9 +2588,9 @@ - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ MOD:00001 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Protein modifications ontology via the Ontology Lookup Service (OLS) European Bioinformatics Institute @@ -3021,10 +3021,10 @@ - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ FMA:67112 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Foundational Model of Anatomy via Ontology Lookup Service (OLS) European Bioinformatics Institute United Kingdom @@ -4584,9 +4584,9 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ MI:0308 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Molecular Interactions Ontology through OLS European Bioinformatics Institute @@ -4625,9 +4625,9 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ CL:0000232 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Cell Type Ontology through OLS European Bioinformatics Institute @@ -4674,9 +4674,9 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ BTO:0000146 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Brenda Tissue Ontology through OLS European Bioinformatics Institute @@ -4721,9 +4721,9 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ PATO:0001998 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id PATO through OLS European Bioinformatics Institute UK @@ -5671,7 +5671,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit UO:0000080 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id Unit Ontology via Ontology Lookup Service European Bioinformatics Institute United Kingdom @@ -7618,9 +7618,9 @@ Note: Currently, direct access to RNA products is restricted. This is expected t - http://www.ebi.ac.uk/ontology-lookup/ + http://www.ebi.ac.uk/ols/ EDAM:0001163 - http://www.ebi.ac.uk/ontology-lookup/?termId=$id + http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id EDAM via OLS EMBL-EBI diff --git a/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties b/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties index ca7c3a92c..fdf8acf48 100644 --- a/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties +++ b/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties @@ -13,7 +13,7 @@ biogrid= europePubmedCentral=http://europepmc.org/abstract/MED/{0} hierarchView=http://www.ebi.ac.uk/tc-test/intact/hierarchView/display.jsp?AC={0}&depth=1&method=All -ols=http://www.ebi.ac.uk/ontology-lookup/?termId={0} +ols=http://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id={0} uniprotkb=http://www.ebi.uniprot.org/entry/{0} uniparc=http://www.ebi.uniprot.org/entry/{0} chebi=http://www.ebi.ac.uk/chebi/searchId.do?chebiId={0} From 3a74f6fd937081fdeb4259fab020a09ab997461a Mon Sep 17 00:00:00 2001 From: noedelta Date: Mon, 18 Jul 2016 14:45:07 +0100 Subject: [PATCH 07/14] Updates matrix db URL. --- src/main/resources/Miriam.xml | 4 ++-- .../ac/ebi/intact/binarysearch/default-xref-links.properties | 4 ++-- src/main/webapp/home_content.xhtml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/resources/Miriam.xml b/src/main/resources/Miriam.xml index 05a22b962..dcd4a9a90 100644 --- a/src/main/resources/Miriam.xml +++ b/src/main/resources/Miriam.xml @@ -3068,9 +3068,9 @@ - http://matrixdb.ibcp.fr/ + http://matrixdb.univ-lyon1.fr/ P00747_P07355 - http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association + http://matrixdb.univ-lyon1.fr/cgi-bin/model/report/default?name=$id&class=Association MatrixDB Association Institut de Biologie et Chimie des Protéines, Lyon University diff --git a/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties b/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties index fdf8acf48..b759c6271 100644 --- a/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties +++ b/src/main/resources/uk/ac/ebi/intact/binarysearch/default-xref-links.properties @@ -5,8 +5,8 @@ intact=http://www.ebi.ac.uk/intact/interaction/{0} mint=http://mint.bio.uniroma2.it/mint/search/interaction.do?ac={0} -matrixdb_interaction=http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name={0}&class=Association -matrixdb_molecule=http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name={0}&class=BioMolecule +matrixdb_interaction=http://matrixdb.univ-lyon1.fr/cgi-bin/model/report/default?name={0}&class=Association +matrixdb_molecule=http://matrixdb.univ-lyon1.fr/cgi-bin/model/report/default?name={0}&class=BioMolecule mpidb= irefindex= biogrid= diff --git a/src/main/webapp/home_content.xhtml b/src/main/webapp/home_content.xhtml index da607b34c..050021de2 100644 --- a/src/main/webapp/home_content.xhtml +++ b/src/main/webapp/home_content.xhtml @@ -153,7 +153,7 @@
      - + From 84219cdb9b217d80044618bba84fe7938db3917b Mon Sep 17 00:00:00 2001 From: noedelta Date: Mon, 18 Jul 2016 14:47:47 +0100 Subject: [PATCH 08/14] Creates links for complex portal and adds complex category in the interactors tab. --- .../OntologyInteractorTypeConfig.java | 44 ++++++++++ .../list/ComplexListController.java | 36 ++++++++ .../controller/search/SearchController.java | 63 +++++++++++++- src/main/webapp/WEB-INF/extlinks.taglib.xml | 4 + src/main/webapp/WEB-INF/extlinks.tld | 11 +++ .../components/links/GoComplexPortal.xhtml | 7 ++ src/main/webapp/images/logos/cp-logo.png | Bin 0 -> 2532 bytes .../webapp/pages/list/complex_list_tab.xhtml | 82 ++++++++++++++++++ src/main/webapp/pages/list/list_tab.xhtml | 11 +++ .../intactview/interactorLinkLogos.xhtml | 27 ++++-- 10 files changed, 274 insertions(+), 11 deletions(-) create mode 100644 src/main/java/uk/ac/ebi/intact/view/webapp/controller/list/ComplexListController.java create mode 100644 src/main/webapp/WEB-INF/facelets/components/links/GoComplexPortal.xhtml create mode 100644 src/main/webapp/images/logos/cp-logo.png create mode 100644 src/main/webapp/pages/list/complex_list_tab.xhtml diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/application/OntologyInteractorTypeConfig.java b/src/main/java/uk/ac/ebi/intact/view/webapp/application/OntologyInteractorTypeConfig.java index eec0b5b96..0b08902bd 100644 --- a/src/main/java/uk/ac/ebi/intact/view/webapp/application/OntologyInteractorTypeConfig.java +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/application/OntologyInteractorTypeConfig.java @@ -36,11 +36,13 @@ public class OntologyInteractorTypeConfig implements InitializingBean{ private IntactViewConfiguration viewConfiguration; private String [] proteinTypes; + private String [] complexTypes; private String [] compoundTypes; private String [] nucleicAcidTypes; private String[] geneTypes; private boolean proteinTypesInitialized; + private boolean complexTypesInitialized; private boolean compoundTypesInitialized; private boolean nucleicAcidTypesInitialized; private boolean geneTypesInitialized; @@ -55,6 +57,10 @@ public void afterPropertiesSet() throws Exception { log.info("Loading protein types..."); loadProteins(ontologySearcher); + // load complexes + log.info("Loading complex types..."); + loadComplexes(ontologySearcher); + // load nucleic acids log.info("Loading nucleic acid types..."); loadNucleicAcids(ontologySearcher); @@ -76,6 +82,11 @@ public void refreshTypes(){ log.info("Loading protein types..."); loadProteins(ontologySearcher); + // load complexes + log.info("Loading complexes types..."); + loadComplexes(ontologySearcher); + + // load nucleic acids log.info("Loading nucleic acid types..."); loadNucleicAcids(ontologySearcher); @@ -121,6 +132,30 @@ private void loadProteins(OntologySearcher ontologySearcher){ } } + private void loadComplexes(OntologySearcher ontologySearcher){ + try{ + OntologyTerm bioActiveEntity = new LazyLoadedOntologyTerm( ontologySearcher, "MI:0314", "complex" ); + + List complexChildren = loadChildrenFor(bioActiveEntity); + + this.complexTypes = new String[1+complexChildren.size()]; + + this.complexTypes[0] = bioActiveEntity.getId(); + + int index = 1; + for (OntologyTerm term : complexChildren){ + this.complexTypes[index] = term.getId(); + index++; + } + complexTypesInitialized = true; + } + catch (SolrServerException e){ + log.error("Could not load complexes types from SOLR index. Use defaults.", e); + complexTypesInitialized = false; + complexTypes = new String[]{"MI:0314", "MI:1302"}; + } + } + private void loadCompounds(OntologySearcher ontologySearcher){ try{ OntologyTerm bioActiveEntity = new LazyLoadedOntologyTerm( ontologySearcher, "MI:1100", "bioactive entity" ); @@ -218,6 +253,15 @@ public String[] getProteinTypes() { return proteinTypes; } + public String[] getComplexTypes() { + if (!complexTypesInitialized){ + final SolrServer ontologySolrServer = viewConfiguration.getOntologySolrServer(); + OntologySearcher ontologySearcher = new OntologySearcher(ontologySolrServer); + loadComplexes(ontologySearcher); + } + return complexTypes; + } + public String[] getCompoundTypes() { if (!compoundTypesInitialized){ final SolrServer ontologySolrServer = viewConfiguration.getOntologySolrServer(); diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/list/ComplexListController.java b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/list/ComplexListController.java new file mode 100644 index 000000000..50da1da01 --- /dev/null +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/list/ComplexListController.java @@ -0,0 +1,36 @@ +/** + * Copyright 2008 The European Bioinformatics Institute, and others. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package uk.ac.ebi.intact.view.webapp.controller.list; + + +import org.apache.myfaces.orchestra.conversation.annotations.ConversationName; +import org.springframework.context.annotation.Scope; +import org.springframework.stereotype.Controller; + +/** + * Controller for ProteinList View + * + * @author Bruno Aranda (baranda@ebi.ac.uk) + * @version $Id$ + * @since 0.9 + */ +@Controller +@Scope( "conversation.access" ) +@ConversationName( "general" ) +public class ComplexListController extends InteractorListController { + + +} \ No newline at end of file diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java index 2b0accfe3..d63cb3cf8 100644 --- a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java @@ -64,7 +64,8 @@ public class SearchController extends JpaBaseController { private int smallMoleculeTotalResults; private int geneTotalResults; private int nucleicAcidTotalResults; - private int threadTimeOut = 10; + private int complexTotalResults; + private int threadTimeOut = 20; private String currentQuery; private String selectedInteractor; private boolean hasLoadedSearchControllerResults = false; @@ -75,6 +76,8 @@ public class SearchController extends JpaBaseController { private InteractorSearchResultDataModel smallMoleculeResults; private InteractorSearchResultDataModel nucleicAcidResults; private InteractorSearchResultDataModel geneResults; + private InteractorSearchResultDataModel complexResults; + // io private String exportFormat; private String userSortColumn = DEFAULT_SORT_COLUMN; @@ -382,18 +385,20 @@ public void doInteractorsSearch() { final int pageSize = getUserQuery().getPageSize(); Callable proteinRunnable = createProteinSearchRunnable(config, solrQuery, solrServer, pageSize); + Callable complexRunnable = createComplexSearchRunnable(config, solrQuery, solrServer, pageSize); Callable compoundRunnable = createSmallMoleculeSearchRunnable(config, solrQuery, solrServer, pageSize); Callable nucleicAcidRunnable = createNucleicAcidSearchRunnable(config, solrQuery, solrServer, pageSize); Callable geneRunnable = createGeneSearchRunnable(config, solrQuery, solrServer, pageSize); Future proteinFuture = executorService.submit(proteinRunnable); + Future complexFuture = executorService.submit(complexRunnable); Future compoundFuture = executorService.submit(compoundRunnable); Future nucleicAcidFuture = executorService.submit(nucleicAcidRunnable); Future geneFuture = executorService.submit(geneRunnable); - checkAndResumeInteractorTasks(proteinFuture, compoundFuture, nucleicAcidFuture, geneFuture); + checkAndResumeInteractorTasks(proteinFuture, compoundFuture, complexFuture, nucleicAcidFuture, geneFuture); - interactorTotalResults = smallMoleculeTotalResults + proteinTotalResults + nucleicAcidTotalResults + geneTotalResults; + interactorTotalResults = smallMoleculeTotalResults + proteinTotalResults + complexTotalResults + nucleicAcidTotalResults + geneTotalResults; // loaded browse results hasLoadedInteractorResults = true; @@ -412,6 +417,15 @@ public InteractorSearchResultDataModel call() { }; } + private Callable createComplexSearchRunnable(final OntologyInteractorTypeConfig typeConfig, final SolrQuery solrQuery, final SolrServer solrServer, final int pageSize) { + return new Callable() { + public InteractorSearchResultDataModel call() { + + return doInteractorSearch(typeConfig.getComplexTypes(), solrQuery, solrServer, pageSize); + } + }; + } + private Callable createSmallMoleculeSearchRunnable(final OntologyInteractorTypeConfig typeConfig, final SolrQuery solrQuery, final SolrServer solrServer, final int pageSize) { return new Callable() { public InteractorSearchResultDataModel call() { @@ -440,7 +454,8 @@ public InteractorSearchResultDataModel call() { } private void checkAndResumeInteractorTasks(Future proteinFuture, Future compoundFuture, - Future nucleicAcidFuture, Future geneFuture) { + Future complexFuture, Future nucleicAcidFuture, + Future geneFuture) { if (proteinFuture != null) { try { this.proteinResults = proteinFuture.get(threadTimeOut, TimeUnit.SECONDS); @@ -510,6 +525,29 @@ private void checkAndResumeInteractorTasks(FuturegoChebi facelets/components/links/GoChebi.xhtml + + goComplexPortal + facelets/components/links/GoComplexPortal.xhtml + goDrugbank facelets/components/links/GoDrugbank.xhtml diff --git a/src/main/webapp/WEB-INF/extlinks.tld b/src/main/webapp/WEB-INF/extlinks.tld index 547011f84..77bb400cd 100644 --- a/src/main/webapp/WEB-INF/extlinks.tld +++ b/src/main/webapp/WEB-INF/extlinks.tld @@ -28,6 +28,17 @@ + + goComplexPortal + + query + true + + + onlyLogo + + + goDrugbank diff --git a/src/main/webapp/WEB-INF/facelets/components/links/GoComplexPortal.xhtml b/src/main/webapp/WEB-INF/facelets/components/links/GoComplexPortal.xhtml new file mode 100644 index 000000000..ea3ffdec2 --- /dev/null +++ b/src/main/webapp/WEB-INF/facelets/components/links/GoComplexPortal.xhtml @@ -0,0 +1,7 @@ + + + + + + \ No newline at end of file diff --git a/src/main/webapp/images/logos/cp-logo.png b/src/main/webapp/images/logos/cp-logo.png new file mode 100644 index 0000000000000000000000000000000000000000..ae6d4092eaee24b931bb1deb7aaac4e7fb67c8ca GIT binary patch literal 2532 zcmZ8jcU0477ycnK3|pj(2!tVGN;&{+b3-YM01yWUfMtJf zE*$`*qf6RdEVvKHq8&WR0031v6dqc&RXhOj1c%}96grGXf7H6 zENEt2Gm1b7fY72MiDWYxLisO*8P`4x!;~R^K`0RjWjqE8u_470Acjx_C|ubR1c5*- zVuLT5xuWd8rE@)mawvroZ3cr;sZ=OcA4-Z1f$5o=n!@0xVW&^)auK@Z1R^DXrb{HN z{9WXqIw%4;C^jsb5=J6I4(kR4lHw=`W#z+0|DJDiMn(VIh)Dj%ipvj13y6m4LE*4} zD{~VqxE#%FVhI5hQY?-{inK%?E&+m$3J4*%5(0t~EMWhS_}0<_b~wlX%=I_vzoJ~$ zmLP8CKO3|Jg~Q<<03fi8Mj>&bd@Ei;S-4Tz{a2=6^qT(=!uq?sIciv}ysVsg0`H?E zc8>|EKt&A_TW+N^Mb$!5JyYw?pakQFx4T1bZPmIDjrCxv8&q4F`M*^e7+O%8`)5)+ z8eXzXFRhwhS%6XrrA6~>Hq&6BEO>!k@~QkFX<_F;|A4xxQ?(xsbA~EQCI9e)=SW>y zh1BPjy${9nD|cFdtB^=K-aAlmXSWCtEdQm<=c`FyJ$3lmxyht4me~73u$siWK;|$; 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z=VC?cPOlZlca0JS{*h8xcRoPo9iLK1p{U}NE$qPQpnYng(5gFnY2v114kLnRs6t=; i{9qp0Io;-~PZy8OhmnmnsqKTqzZBZm8TH_df9jtS#cKWl literal 0 HcmV?d00001 diff --git a/src/main/webapp/pages/list/complex_list_tab.xhtml b/src/main/webapp/pages/list/complex_list_tab.xhtml new file mode 100644 index 000000000..07b75df77 --- /dev/null +++ b/src/main/webapp/pages/list/complex_list_tab.xhtml @@ -0,0 +1,82 @@ + + + + + + + + + +    + + + + + + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +       + + + + + + + + + + + + + + + + +       + +       \ No newline at end of file diff --git a/src/main/webapp/pages/list/list_tab.xhtml b/src/main/webapp/pages/list/list_tab.xhtml index aaca5e892..fc636e049 100644 --- a/src/main/webapp/pages/list/list_tab.xhtml +++ b/src/main/webapp/pages/list/list_tab.xhtml @@ -21,6 +21,17 @@ + +
      + + What is this view + + +
      + + +       +
      diff --git a/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml b/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml index 87a8e50e5..c1cb6cddd 100644 --- a/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml +++ b/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml @@ -1,11 +1,8 @@ @@ -24,23 +21,39 @@ +
      +

      +
      - + +
      +       + + +
      +       + + +
      -
      - + + + + From ceed3ee29afa90042ab1cdd56cf5c65b615a4e9d Mon Sep 17 00:00:00 2001 From: noedelta Date: Mon, 18 Jul 2016 15:06:24 +0100 Subject: [PATCH 09/14] updating poms for 4.2.4 branch with snapshot versions --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a88ebd760..92478dae7 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,7 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.3.3-SNAPSHOT + 4.2.4-SNAPSHOT IntAct Services :: View From 548a5a0a0d287354f90cdea083407e642fc8d68a Mon Sep 17 00:00:00 2001 From: noedelta Date: Tue, 19 Jul 2016 11:54:05 +0100 Subject: [PATCH 10/14] Reduces the size of the CP logo --- src/main/webapp/images/logos/cp-logo.png | Bin 2532 -> 1993 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/src/main/webapp/images/logos/cp-logo.png b/src/main/webapp/images/logos/cp-logo.png index ae6d4092eaee24b931bb1deb7aaac4e7fb67c8ca..0355710657ee86c00473146a5eca4a3f25560753 100644 GIT binary patch delta 1563 zcmV+$2ITqV6Uh%DiBL{Q4GJ0x0000DNk~Le0000R0000e2nGNE01rBWR@`$rv07SO(drpoIDsu6h-%)qAk$&$g~W z{lS!CST|`jZ2k;5N(d;IjB4W@_Bg4V^b?4{mHWW?yO_84JHOOw_fkvNSAW?^53eDx zGBTFtMU#Z%De18WH(3|~V;F(-!~UKX*mI#dl~FU*q&LSx7NqP63JZeL)|KeA>KqA` z1uJ0tEhS4nVuuwJy9r7sUA;cqX)bB#50Xztr941WC^AZ0v z7VT?8gI9d8Qk#g3S=x)4*4VcS&i8zM)WyQq05!ER z3W*c1Zv%rs^iQzgLPAxR=hRibIH0NCaO4p-xH{4qRQuH~KaPCb>K#s-6hvr&X|TzG z7;2bQn--2eUA19&WGYnPamrOjoUSNZrLLeEpU=LYcz`wxaLKOPF@Lt>i`>Zeg^yIZ>-$CQ>Al*@5ad%~7(qA`sEqTO7lB1ri_EyH z7A{+Z7HnnpQ185L%~xh(k1lNDd?o5hu%tZOrJ=%O#GYre{kW}f&~nszi#fD-X!Wh zW{`M2(aq>JZL$CZcZK+ss?)W&(Iu#E@E{`$;WqSWyL1k1P7~-%rjGCx4@CDGr!(A< zr;I0Zhwci&h<_N|D5NOUwWjX2glG_(qPGQFY^QDe&dkj9W3y*Phg#>34(L%sjmP>k z%P<*zA0?@Q>HeZ<$ejyPh}FC)TCPW))D@RcCc{rsN+0ILf9^H9;z}t?isKDReOz|` zn7X6cIggSz#SqqkQNa^CDvDR-WTZ9Eh8-**!`jn0bAL$UO<=c(xtq*^HM=!PJD48) zQCb>EYaLlaeE6Kn*(BQ)wcK?+Tv{;bm$d^6ra)OUh!!&861SR^LziDdi?wZW{V9}uFV33X& zIRwNq5Pxobk-k!TLHh_9I2o3Wl`HZ;I{o~xJ(q1$9AtxPFLo@9KcxioUaj39#?|oq z^o3OhNrdJS(UI}8@Xg&s4WnA|@Y2XhQqw_*3H%@Fx8h?I|9_!M2$M*3`cfc)_+Yzi$pFWz5 z{0sJm9Z;O3^@iE@3I8;vU3RFP8@ygJG{JQNs^5D(hf6TL9%%i z6TCFOHnFU$I}uwq<(tion9%oo@Vpbm76C+CUI9C_1uN#Jq^49>{{a>l70xSXVrKvV N002ovPDHLkV1jyS<7WT> delta 2107 zcmV-B2*mfv59AXeiBL{Q4GJ0x0000DNk~Le0000e0000w2nGNE0K(uK{jnj#0e=VT zNklUHrLZKn#+1sVG&MYQv&-UwyRgj8oqO*&e&;TCWu2Mj z&d$a(&7NfE&Ybg~|9t2B|1hi z<>F}oU@mNBvK?SB6Dzs&{a-OC@cos4>+%6L5v@gMkW)KxcsHX@NrRxvo%SJBTiRHb zj!3KRA6skLNx6l*)Ou8sX0kzmE?ZHXwzY$$S}5UfusE+%Z;};d`hR&>Iez`}ACs_Z zVjdkUYCW@&t^C9x-(EzD-48ZmfoRB97qoZHnp6%+wuKz3Q)BkpR9>)D88nh9xrtqN zczbU^vjS|Kw)|>ai6xBjI|Sp!8iVxZu|XcM``SM7>d5MUUyh0jbz@8gna>*fHYay8U3PR2riC85F{c4MQdv_r zNDP{flD;Cwjp0e@K^S+<6Hr-}5D?4$KGUH!?@rpkb3w&dv&oMyfs7g#XhZE<=b0xD zkV~7lvQzKgS#f+SmGafd-*H-SsIyXm>8RVVO;HOmxsF_O8-KgvKTX}}@TME!(J3ni zo2K|_jCeJ6ceSs@3;wzd&Y5L%fK*Bf#deh@#K!S+cmLy`7x@dwHx`ppAVk$&d8+-@ zy;GVd(hzGgRQDA46e^WQP~eprSVf;}MSEpRzQn!MD{O4zNj<0~3TvLayi#!SsLhSZ zjImg!@4+^+Gk-lvj~GaNn;9Bto0(F7l#cUM@#2O!wF$1q9qOQA)@mx|H-pW=U=)ku_uwpWfM2C^7BP$BUeb zVM7O}%-K#~>s)zNp{Bhf^A; zE?K!YU4QE09BNB?O+%8&y>zDK5IJ5GLtPC-K#mR>ln}ER>OJdFDY>0Lx5Jv_N_QS= z@J^HQR9u*m_~h7C0c-*AG3Oeors(Cu zu}6;SCDYdbeCi{kin+QAN_v^e#RU$eS14F@uG+$Yc=rDrb34}jYuH5}PM%mf3x#+o zXn(pET2T88Dm`MphY}?lKOXb+2iHyfU!yn}2s3F>xPmf)F}hfIGc!fpty$_EjgAf!R_f$mPE$ zM?9ydR}P_zFI=jGS;joMnLa!G2X;sH=Y_oj3|IQ{hrf(hR81e%T0Hb8*yFvB@PDJo z)xaX^DjiEx1H}XN4)$6ZZ+z|3*-MU&oY0gA*T{B_1TdKVSi|FF*!V33pj;=Lzux-| z8=(i-&eSHVom|tqao1>sFMzXdlsh!YF&)yrHa%D3AaQ?aR2Mk_WLhmp^_$&JA0!pt zcxE>XN1_7^XME4s0f6}uKEU7rgMZx&=wCMbt3laBbrn4aA(+XEp~gq{osL0IHBn6@ z9$!Xm(E*ac6VlH20~Ml`O0F$XH@Fu_CH@4FQ5SW3ZgkZCxtLhdT>R2r11WV?Q2L-3 zweHE<0$^B1$$jK{o2b)yi+(dB@;_YU1~5divVJ(lt>w^s^P!eU23jxx8h;w#3Sk>) zLSHtM=e$iu;z@es#^!S@BE9V!z|i%YhH1#m2cQpU1==uFIa;+SzY{v}LkQB%R9jge zPRaF}A3(iY?VA>{5tU$U6;M?L02tc^A-k3iAKpbT|4je7-shG-z;Nl>k4ll7YXQ=r lGbdKjlXFglL-}040T|)b@(}P9`u_j`002ovPDHLkV1lep^U(kR From 131fa20f4ce214c045100111ee32f1bf2211995e Mon Sep 17 00:00:00 2001 From: noedelta Date: Tue, 19 Jul 2016 11:54:45 +0100 Subject: [PATCH 11/14] Disable features widget if one of the participant is a complex --- src/main/webapp/pages/details/details_tab.xhtml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/pages/details/details_tab.xhtml b/src/main/webapp/pages/details/details_tab.xhtml index 2ab749d0b..acd3ced4a 100644 --- a/src/main/webapp/pages/details/details_tab.xhtml +++ b/src/main/webapp/pages/details/details_tab.xhtml @@ -10,8 +10,8 @@ xmlns:iam="http://intact.ebi.ac.uk/miscel" xmlns:iaf="http://intact.ebi.ac.uk/functions" - xmlns:iax="http://intact.ebi.ac.uk/extlinks" - > + xmlns:iax="http://intact.ebi.ac.uk/extlinks" xmlns:c="http://java.sun.com/jsp/jstl/core" +> @@ -341,6 +341,11 @@
      + + + +
      +       @@ -352,6 +357,7 @@ target="_blank"> +
      @@ -725,7 +731,7 @@
      - +

      Graphical Representation of Experimental Features

       From 044b36c29f37b1d6cbdf0ea6959f10725884611f Mon Sep 17 00:00:00 2001 From: noedelta Date: Tue, 19 Jul 2016 15:59:44 +0100 Subject: [PATCH 12/14] Enables link to complex portal and disables features widget (if one of the participant is a complex) in teh detail view. --- .../controller/details/DetailsController.java | 16 ++++++++++++++++ .../controller/search/SearchController.java | 2 +- .../view/webapp/model/ParticipantWrapper.java | 8 ++++++++ src/main/webapp/pages/details/details_tab.xhtml | 3 +-- .../intactview/interactorLinkLogos.xhtml | 4 ++-- 5 files changed, 28 insertions(+), 5 deletions(-) diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/details/DetailsController.java b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/details/DetailsController.java index 3bc5da3b4..bfdbcde6b 100644 --- a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/details/DetailsController.java +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/details/DetailsController.java @@ -39,6 +39,7 @@ import uk.ac.ebi.intact.view.webapp.controller.search.SearchController; import uk.ac.ebi.intact.view.webapp.controller.search.UserQuery; import uk.ac.ebi.intact.view.webapp.model.ParticipantLazyDataModel; +import uk.ac.ebi.intact.view.webapp.model.ParticipantWrapper; import javax.faces.context.FacesContext; import javax.persistence.Query; @@ -92,6 +93,8 @@ public class DetailsController extends JpaBaseController { private Experiment experiment; private int numberInteractions=0; private int numberParticipants=0; + private boolean containComplexes=false; + private ParticipantLazyDataModel participants; private boolean featureAvailable; private int numberOfInteractorsInExperiment=0; @@ -751,6 +754,19 @@ else if (exp != null && exp.getFullName() != null){ return "-"; } + public boolean isContainComplexes() { + + containComplexes =false; + for (ParticipantWrapper participant : participants) { + if (participant.getInteractorTypeShortlabel().contains("complex")) { + containComplexes = true; + break; + } + } + + return containComplexes; + } + public ParticipantLazyDataModel getParticipants() { return participants; } diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java index d63cb3cf8..130e41cf5 100644 --- a/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/controller/search/SearchController.java @@ -65,7 +65,7 @@ public class SearchController extends JpaBaseController { private int geneTotalResults; private int nucleicAcidTotalResults; private int complexTotalResults; - private int threadTimeOut = 20; + private int threadTimeOut = 40; private String currentQuery; private String selectedInteractor; private boolean hasLoadedSearchControllerResults = false; diff --git a/src/main/java/uk/ac/ebi/intact/view/webapp/model/ParticipantWrapper.java b/src/main/java/uk/ac/ebi/intact/view/webapp/model/ParticipantWrapper.java index 5bbc08995..65fb9bf79 100644 --- a/src/main/java/uk/ac/ebi/intact/view/webapp/model/ParticipantWrapper.java +++ b/src/main/java/uk/ac/ebi/intact/view/webapp/model/ParticipantWrapper.java @@ -31,6 +31,8 @@ public class ParticipantWrapper { private Collection interactorXrefs; private Collection interactorAliases; private CvInteractorType interactorType; + private String interactorTypeShortlabel; + private String bioSourceAc; private String bioSourceShortLabel; @@ -69,6 +71,8 @@ public ParticipantWrapper(Component component){ interactorXrefs = Functions.extractIdentityXrefs(interactor.getXrefs()); interactorAliases = new ArrayList(interactor.getAliases()); interactorType = interactor.getCvInteractorType(); + interactorTypeShortlabel = interactorType.getShortLabel(); + Hibernate.initialize(interactorType.getAnnotations()); Hibernate.initialize(interactorType.getXrefs()); @@ -200,4 +204,8 @@ public Collection getConfidences() { public String getInteractorAc() { return interactorAc; } + + public String getInteractorTypeShortlabel() { + return interactorTypeShortlabel; + } } diff --git a/src/main/webapp/pages/details/details_tab.xhtml b/src/main/webapp/pages/details/details_tab.xhtml index acd3ced4a..a35681e3d 100644 --- a/src/main/webapp/pages/details/details_tab.xhtml +++ b/src/main/webapp/pages/details/details_tab.xhtml @@ -342,7 +342,6 @@       -
      @@ -731,7 +730,7 @@
      - +

      Graphical Representation of Experimental Features

       diff --git a/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml b/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml index c1cb6cddd..e0240d9c2 100644 --- a/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml +++ b/src/main/webapp/resources/intactview/interactorLinkLogos.xhtml @@ -39,11 +39,11 @@
      - +
      - +
      From 00d729488c23b39c4ba8a1b967ffc1626ce48c9c Mon Sep 17 00:00:00 2001 From: noedelta Date: Mon, 25 Jul 2016 09:31:29 +0100 Subject: [PATCH 13/14] Simplified the release skipping install and deploy phase. Disable doclint for java8 --- pom.xml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/pom.xml b/pom.xml index 92478dae7..91fad7e92 100644 --- a/pom.xml +++ b/pom.xml @@ -188,6 +188,23 @@ 1.7 + + + org.apache.maven.plugins + maven-deploy-plugin + 2.8.2 + + true + + + + org.apache.maven.plugins + maven-install-plugin + 2.5.2 + + true + + @@ -245,6 +262,16 @@ + + + disable-java8-doclint + + [1.8,) + + + -Xdoclint:none + + integration-tests From 6d4a7752a7ad12c955628593b879c0b83bed5969 Mon Sep 17 00:00:00 2001 From: noedelta Date: Mon, 25 Jul 2016 09:33:08 +0100 Subject: [PATCH 14/14] updating poms for branch'release-4.2.4' with non-snapshot versions --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 91fad7e92..14f4f3ceb 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,7 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.4-SNAPSHOT + 4.2.4 IntAct Services :: View