diff --git a/pom.xml b/pom.xml index 7788415b5..14f4f3ceb 100644 --- a/pom.xml +++ b/pom.xml @@ -9,6 +9,7 @@ uk.ac.ebi.intact.maven intact-hibernate-master + 42 @@ -17,20 +18,15 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.3.3-SNAPSHOT + 4.2.4 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 @@ -93,7 +89,7 @@ - ${artifactId}-${version} + ${project.artifactId}-${project.version} @@ -129,7 +125,7 @@ 0 ${jetty.contextPath} - ${build.outputDirectory}/META-INF/jetty-env.xml + ${project.build.outputDirectory}/META-INF/jetty-env.xml @@ -138,7 +134,7 @@ - ${build.outputDirectory}/META-INF/jetty.xml + ${project.build.outputDirectory}/META-INF/jetty.xml @@ -186,9 +182,27 @@ org.apache.maven.plugins maven-compiler-plugin + 3.5.1 - 1.6 - 1.6 + 1.7 + 1.7 + + + + + org.apache.maven.plugins + maven-deploy-plugin + 2.8.2 + + true + + + + org.apache.maven.plugins + maven-install-plugin + 2.5.2 + + true @@ -196,6 +210,7 @@ org.jvnet.jaxb2.maven2 maven-jaxb2-plugin + 0.12.3 src/main/resources/META-INF/schema @@ -226,12 +241,20 @@ - 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 @@ -239,6 +262,16 @@ + + + disable-java8-doclint + + [1.8,) + + + -Xdoclint:none + + integration-tests @@ -914,19 +947,9 @@ - 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 - - - - 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/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/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 91a3b0d50..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 @@ -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 = 40; 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; @@ -125,6 +128,9 @@ public void searchOnLoad(ComponentSystemEvent evt) { userQuery.clearInteractionFilters(); doBinarySearch(userQuery.createSolrQuery()); } + if (this.currentQuery == null || !hasLoadedInteractorResults) { + doInteractorsSearch(); + } } } @@ -379,18 +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; @@ -409,6 +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() { @@ -437,7 +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); @@ -507,6 +525,29 @@ private void checkAndResumeInteractorTasks(Future 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/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/resources/Miriam.xml b/src/main/resources/Miriam.xml index 84ddd5297..dcd4a9a90 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 @@ -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 @@ -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..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 @@ -5,15 +5,15 @@ 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= 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} diff --git a/src/main/webapp/WEB-INF/extlinks.taglib.xml b/src/main/webapp/WEB-INF/extlinks.taglib.xml index df0b6a692..c135eb958 100644 --- a/src/main/webapp/WEB-INF/extlinks.taglib.xml +++ b/src/main/webapp/WEB-INF/extlinks.taglib.xml @@ -14,6 +14,10 @@ goChebi 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/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/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 @@
- + 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 000000000..035571065 Binary files /dev/null and b/src/main/webapp/images/logos/cp-logo.png differ diff --git a/src/main/webapp/pages/details/details_tab.xhtml b/src/main/webapp/pages/details/details_tab.xhtml index 2ab749d0b..a35681e3d 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 +341,10 @@
+ + +
+ @@ -352,6 +356,7 @@ target="_blank"> +
@@ -725,7 +730,7 @@
- +

Graphical Representation of Experimental Features

 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.
      • 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.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 @@ + + + + + + + + + + + + + + + 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..e0240d9c2 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 @@ +
      +

      +
      - + +
      +       + + +
      +       + + +
      -
      - + + + +