diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDao.java index eff66cd0d3..9a1afc0348 100644 --- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDao.java +++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDao.java @@ -48,10 +48,9 @@ public interface BioMaterialDao extends BaseVoEnabledDao findByFactor( ExperimentalFactor experimentalFactor ); /** - * @param bioMaterialId biomaterial id - * @return the experiment the biomaterial appears in + * Obtain all the experiments a biomaterial is used in. */ - ExpressionExperiment getExpressionExperiment( Long bioMaterialId ); + Collection getExpressionExperiments( BioMaterial bm ); /** * Thaw the given BioMaterial. diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDaoImpl.java index 39e3281077..9ab07d897e 100644 --- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDaoImpl.java +++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDaoImpl.java @@ -160,10 +160,12 @@ public Collection findByFactor( ExperimentalFactor experimentalFact } @Override - public ExpressionExperiment getExpressionExperiment( Long bioMaterialId ) { - return ( ExpressionExperiment ) this.getSessionFactory().getCurrentSession().createQuery( - "select distinct e from ExpressionExperiment e inner join e.bioAssays ba inner join ba.sampleUsed bm where bm.id =:bmid " ) - .setParameter( "bmid", bioMaterialId ).uniqueResult(); + public Collection getExpressionExperiments( BioMaterial bm ) { + //noinspection unchecked + return ( List ) this.getSessionFactory().getCurrentSession() + .createQuery( "select distinct e from ExpressionExperiment e join e.bioAssays ba join ba.sampleUsed bm where bm = :bm " ) + .setParameter( "bm", bm ) + .list(); } @Override diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialService.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialService.java index 31cfb77b16..79d2fcc943 100644 --- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialService.java +++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialService.java @@ -29,6 +29,7 @@ import ubic.gemma.persistence.service.BaseVoEnabledService; import javax.annotation.CheckReturnValue; +import javax.annotation.Nullable; import java.util.Collection; import java.util.Map; @@ -81,8 +82,9 @@ public interface BioMaterialService extends BaseService, BaseVoEnab @Secured({ "GROUP_USER", "ACL_SECURABLE_EDIT" }) void update( BioMaterial bioMaterial ); - @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" }) - ExpressionExperiment getExpressionExperiment( Long id ); + @Nullable + @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" }) + Collection getExpressionExperiments( BioMaterial bm ); @CheckReturnValue @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "ACL_SECURABLE__READ" }) diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialServiceImpl.java index ee52438896..9bf4ad3c03 100644 --- a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialServiceImpl.java +++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialServiceImpl.java @@ -85,8 +85,8 @@ public Collection findByFactor( ExperimentalFactor experimentalFact @Override @Transactional(readOnly = true) - public ExpressionExperiment getExpressionExperiment( Long id ) { - return this.bioMaterialDao.getExpressionExperiment( id ); + public Collection getExpressionExperiments( BioMaterial bm ) { + return this.bioMaterialDao.getExpressionExperiments( bm ); } @Override diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java index 4d5709ff59..8010443794 100644 --- a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java +++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java @@ -91,7 +91,9 @@ public DatabaseBackedGeneSetValueObject loadValueObject( GeneSet geneSet ) { @Override public DatabaseBackedGeneSetValueObject loadValueObjectById( Long id ) { DatabaseBackedGeneSetValueObject vo = loadValueObjectByIdLite( id ); - fillGeneIds( Collections.singletonList( vo ) ); + if ( vo != null ) { + fillGeneIds( Collections.singletonList( vo ) ); + } return vo; } diff --git a/gemma-rest/src/main/resources/restapidocs/index.jsp b/gemma-rest/src/main/resources/restapidocs/index.jsp index 07ecd4d01a..4ba09a3b9a 100644 --- a/gemma-rest/src/main/resources/restapidocs/index.jsp +++ b/gemma-rest/src/main/resources/restapidocs/index.jsp @@ -1,4 +1,5 @@ -<%@ page contentType="text/html;charset=UTF-8" %> +<%@ page pageEncoding="UTF-8" contentType="text/html;charset=UTF-8" trimDirectiveWhitespaces="true" %> + diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java index 8f0c783844..b39b5ba39d 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java +++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java @@ -495,9 +495,7 @@ public ModelAndView showArrayDesignByName( @RequestParam("name") String name ) { private ModelAndView showArrayDesignInternal( ArrayDesign arrayDesign ) { return new ModelAndView( "arrayDesign.detail" ) - .addObject( "arrayDesignId", arrayDesign.getId() ) - .addObject( "arrayDesignShortName", arrayDesign.getShortName() ) - .addObject( "arrayDesignName", arrayDesign.getName() ); + .addObject( "arrayDesign", arrayDesign ); } @RequestMapping(value = "/showCompositeSequenceSummary.html", method = { RequestMethod.GET, RequestMethod.HEAD }) diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java index 0b75b92fbd..4e4fa1d516 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java +++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java @@ -18,7 +18,6 @@ */ package ubic.gemma.web.controller.expression.bioAssay; -import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.springframework.beans.factory.annotation.Autowired; @@ -38,7 +37,6 @@ import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService; import ubic.gemma.web.util.EntityNotFoundException; -import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; import java.util.Map; @@ -66,6 +64,15 @@ public class BioAssayController { @Autowired private OutlierDetectionService outlierDetectionService; + @RequestMapping(value = { "/showBioAssay.html", "/" }, method = { RequestMethod.GET, RequestMethod.HEAD }) + public ModelAndView show( @RequestParam("id") Long id ) { + BioAssay bioAssay = bioAssayService.loadOrFail( id, EntityNotFoundException::new ); + bioAssay = bioAssayService.thaw( bioAssay ); + return new ModelAndView( "bioAssay.detail" ) + .addObject( "bioAssay", new BioAssayValueObject( bioAssay, false ) ); + } + + @SuppressWarnings("unused") // Is used in EEManager.js public Collection getBioAssays( Long eeId ) { ExpressionExperiment ee = eeService.loadAndThawLiteOrFail( eeId, EntityNotFoundException::new, "Could not load experiment with ID=" + eeId ); @@ -94,39 +101,4 @@ public String markOutlier( Collection ids ) { public String unmarkOutlier( Collection ids ) { return taskRunningService.submitTaskCommand( new BioAssayOutlierProcessingTaskCommand( ids, true ) ); } - - @RequestMapping(value = { "/showBioAssay.html", "/" }, method = { RequestMethod.GET, RequestMethod.HEAD }) - public ModelAndView show( @RequestParam("id") Long id ) { - BioAssay bioAssay = bioAssayService.load( id ); - if ( bioAssay == null ) { - throw new EntityNotFoundException( id + " not found" ); - } - bioAssay = bioAssayService.thaw( bioAssay ); - return new ModelAndView( "bioAssay.detail" ) - .addObject( "bioAssay", new BioAssayValueObject( bioAssay, false ) ); - } - - @RequestMapping(value = "/showAllBioAssays.html", method = { RequestMethod.GET, RequestMethod.HEAD }) - public ModelAndView showAllBioAssays( @RequestParam(value = "id", required = false) String sId ) { - Collection bioAssays = new ArrayList<>(); - if ( StringUtils.isBlank( sId ) ) { - /* - * Probably not desirable ... there are >380,000 of them - */ - bioAssays = bioAssayService.loadAll(); - } else { - String[] idList = StringUtils.split( sId, ',' ); - for ( String anIdList : idList ) { - Long id = Long.parseLong( anIdList ); - BioAssay bioAssay = bioAssayService.load( id ); - if ( bioAssay == null ) { - throw new EntityNotFoundException( id + " not found" ); - } - bioAssay = bioAssayService.thaw( bioAssay ); - bioAssays.add( bioAssay ); - } - } - return new ModelAndView( "bioAssays" ).addObject( "bioAssays", bioAssays ); - } - } diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/biomaterial/BioMaterialController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/biomaterial/BioMaterialController.java index 91d7792e34..c0a566b35d 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/controller/expression/biomaterial/BioMaterialController.java +++ b/gemma-web/src/main/java/ubic/gemma/web/controller/expression/biomaterial/BioMaterialController.java @@ -161,8 +161,9 @@ public Collection getFactorValues( EntityDelegator removeUserAndSessionGroups } @RequestMapping(value = "/showExpressionExperimentSet.html", method = { RequestMethod.GET, RequestMethod.HEAD }) - public ModelAndView showExpressionExperimentSet( HttpServletRequest request ) { - - ModelAndView mav = new ModelAndView( "expressionExperimentSet.detail" ); - StopWatch timer = new StopWatch(); - timer.start(); - - ExpressionExperimentSetValueObject eesvo = this.getExpressionExperimentSetFromRequest( request ); - - mav.addObject( "eeSetId", eesvo.getId() ); - mav.addObject( "eeSetName", eesvo.getName() ); - + public ModelAndView showExpressionExperimentSet( @RequestParam("id") Long id ) { + StopWatch timer = StopWatch.createStarted(); + ExpressionExperimentSetValueObject eesvo = expressionExperimentSetService.loadValueObjectById( id ); + if ( eesvo == null ) { + throw new EntityNotFoundException( "No experiment set with ID " + id ); + } if ( timer.getTime() > 200 ) { log.info( "Show experiment set was slow: id=" + eesvo.getId() + " " + timer.getTime() + "ms" ); } - - return mav; + return new ModelAndView( "expressionExperimentSet.detail" ) + .addObject( "eeSet", eesvo ); } /** @@ -454,31 +449,6 @@ private ExpressionExperimentSet create( ExpressionExperimentSetValueObject obj ) return expressionExperimentSetValueObjectHelper.create( obj ); } - /** - * @throws IllegalArgumentException if a matching EE can't be loaded - */ - private ExpressionExperimentSetValueObject getExpressionExperimentSetFromRequest( HttpServletRequest request ) { - - ExpressionExperimentSetValueObject set; - Long id; - - if ( request.getParameter( "id" ) != null ) { - try { - id = Long.parseLong( request.getParameter( "id" ) ); - } catch ( NumberFormatException e ) { - throw new IllegalArgumentException( "You must provide a valid numerical identifier" ); - } - set = expressionExperimentSetService.loadValueObjectById( id ); - - if ( set == null ) { - throw new EntityNotFoundException( "Unable to access experiment set with id=" + id ); - } - } else { - throw new IllegalArgumentException( "You must provide an id" ); - } - return set; - } - /** * Delete a EEset from the system. * diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneController.java index 6c1197e451..fe87c2ff99 100644 --- a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneController.java +++ b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneController.java @@ -145,15 +145,8 @@ public ModelAndView show( HttpServletRequest request ) { Long id = geneVO.getId(); assert id != null; - ModelAndView mav = new ModelAndView( "gene.detail" ); - mav.addObject( "geneId", id ); - mav.addObject( "geneOfficialSymbol", geneVO.getOfficialSymbol() ); - mav.addObject( "geneOfficialName", geneVO.getOfficialName() ); - mav.addObject( "geneNcbiId", geneVO.getNcbiId() ); - mav.addObject( "geneTaxonCommonName", geneVO.getTaxonCommonName() ); - mav.addObject( "geneTaxonId", geneVO.getTaxonId() ); - - return mav; + return new ModelAndView( "gene.detail" ) + .addObject( "gene", geneVO ); } @RequestMapping(value = "/downloadGeneList.html", method = { RequestMethod.GET, RequestMethod.HEAD }) diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java index cd03998444..63c25834af 100755 --- a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java +++ b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneSetController.java @@ -26,15 +26,16 @@ import org.springframework.stereotype.Controller; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestMethod; +import org.springframework.web.bind.annotation.RequestParam; import org.springframework.web.servlet.ModelAndView; -import ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject; -import ubic.gemma.persistence.service.genome.gene.GeneSetService; import ubic.gemma.core.search.ParseSearchException; import ubic.gemma.core.search.SearchException; import ubic.gemma.model.genome.TaxonValueObject; import ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject; import ubic.gemma.model.genome.gene.GeneSetValueObject; import ubic.gemma.model.genome.gene.GeneValueObject; +import ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject; +import ubic.gemma.persistence.service.genome.gene.GeneSetService; import ubic.gemma.web.persistence.SessionListManager; import ubic.gemma.web.util.EntityNotFoundException; @@ -357,20 +358,15 @@ public Collection removeUserAndSessionGroups( CollectionNote : Le contenu de ce site est accessible à tous les navigateurs, quelle que soit leur version. Cependant, ce navigateur peut ne pas prendre en charge certains standards courants du Web, empêchant l'affichage de certaines parties du design de notre site. Nous soutenons les actions de standardisation du Web, cf. campaign, en recommandant aux utilisateurs de mettre à jour leur navigateur. errors.conversion=Une erreur est apparue pendant la conversion des valeurs Web en valeurs typées. errors.twofields=Le champ {0} doit avoir la même valeur que le champ {1}. -errors.existing.user=L'identifiant ({0}) ou l'adresse de courriel ({1}) existe déjà. Veuillez essayer un autre identifiant. +errors.existing.user=L''identifiant ({0}) ou l''adresse de courriel ({1}) existe déjà. Veuillez essayer un autre identifiant. # -- success messages -- user.added=Les informations utilisateur pour {0} ont été ajoutées avec succès. @@ -45,7 +45,8 @@ reload.succeeded=Les options de rechargement sont completees avec succes. errorPage.title=Une erreur est apparue errorPage.heading=Oups ! 404.title=Page non trouvée -404.message=La page que vous avez demandée n'a pas été trouvée. Vous pouvez essayer de retourner à Main Menu. En attendant, pourquoi pas une belle image pour vous remonter le moral ? +# single quote must be doubled for {0} placeholder to work +404.message=La page que vous avez demandée n''a pas été trouvée. Vous pouvez essayer de retourner à Main Menu. En attendant, pourquoi pas une belle image pour vous remonter le moral ? 403.title=Accès refusé 403.message=Votre rôle actuel ne vous permet pas de voir cette page. Veuillez contacter votre administrateur système si vous pensez en avoir les droits d'accès. Entre temps, pourquoi pas une belle image pour vous remonter le moral ? @@ -56,7 +57,7 @@ login.rememberMe=Conserver ce mot de passe login.signup=Pas encore membre ? Demander un compte. login.passwordHint=Passeport oublié ? Obtenez votre mot de passe provisoire, envoyé par courriel. login.passwordHint.sent=Le mot de passe provisoire pour {0} a été envoyé à {1}. -login.passwordHint.error=L'utilisateur {0} n'a pas été trouvé dans l'annuaire. +login.passwordHint.error=L''utilisateur {0} n''a pas été trouvé dans l''annuaire. # -- welcome -- welcome.message= @@ -179,6 +180,7 @@ activeUsers.title=Utilisateurs actifs activeUsers.heading=Utilisateurs connectés activeUsers.message=Ci-dessous une liste des utilisateurs qui sont connectés et dont la session n'a pas expiré. activeUsers.fullName=Nom complet +personDetail.heading=Person Details diff --git a/gemma-web/src/main/resources/messages_nl.properties b/gemma-web/src/main/resources/messages_nl.properties index cc62470be5..f49eb614af 100644 --- a/gemma-web/src/main/resources/messages_nl.properties +++ b/gemma-web/src/main/resources/messages_nl.properties @@ -176,4 +176,5 @@ viewstream.heading=Stream informatie activeUsers.title=Actieve gebruikers activeUsers.heading=Huidige gebruikers activeUsers.message=De volgende gebruikers zijn ingelogd en hebben een geldige sessie. -activeUsers.fullName=Volledige naam \ No newline at end of file +activeUsers.fullName=Volledige naam +personDetail.heading=Person Details \ No newline at end of file diff --git a/gemma-web/src/main/resources/messages_pt_BR.properties b/gemma-web/src/main/resources/messages_pt_BR.properties index f07ad34a74..cfab4aee26 100644 --- a/gemma-web/src/main/resources/messages_pt_BR.properties +++ b/gemma-web/src/main/resources/messages_pt_BR.properties @@ -177,4 +177,5 @@ activeUsers.title=Usu activeUsers.heading=Usuários Corrente activeUsers.message=O seguinte é uma lista de usuários que se registraram e as suas sessões não expiraram. activeUsers.fullName=Todo Nome +personDetail.heading=Person Details diff --git a/gemma-web/src/main/webapp/common/analytics.jsp b/gemma-web/src/main/webapp/common/analytics.jsp index 1f5ea9b965..0c77570930 100644 --- a/gemma-web/src/main/webapp/common/analytics.jsp +++ b/gemma-web/src/main/webapp/common/analytics.jsp @@ -1,4 +1,6 @@ +<%@ page trimDirectiveWhitespaces="true" %> <%@ include file="/common/taglibs.jsp" %> + diff --git a/gemma-web/src/main/webapp/common/dwr.jsp b/gemma-web/src/main/webapp/common/dwr.jsp new file mode 100644 index 0000000000..758c1a9b64 --- /dev/null +++ b/gemma-web/src/main/webapp/common/dwr.jsp @@ -0,0 +1,15 @@ + + +<%-- for dwr creation of javascript objects to mirror java value objects; including one of these causes all the objects to be exposed.--%> + +<%-- We should use this as soon as we figure out how to set generateDtoClasses option to dtoall + script type="text/javascript" src="/Gemma/dwr/dtoall.js"> --%> +<%-- log javascript errors --%> + \ No newline at end of file diff --git a/gemma-web/src/main/webapp/common/header.inner.jsp b/gemma-web/src/main/webapp/common/header.inner.jsp index 2fa13d7051..1d904ed851 100644 --- a/gemma-web/src/main/webapp/common/header.inner.jsp +++ b/gemma-web/src/main/webapp/common/header.inner.jsp @@ -1,6 +1,6 @@ <%@ include file="/common/taglibs.jsp"%> - +
in English diff --git a/gemma-web/src/main/webapp/common/meta.jsp b/gemma-web/src/main/webapp/common/meta.jsp deleted file mode 100644 index 7590c3c945..0000000000 --- a/gemma-web/src/main/webapp/common/meta.jsp +++ /dev/null @@ -1,41 +0,0 @@ -<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %> -<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -"/> - - - diff --git a/gemma-web/src/main/webapp/common/taglibs.jsp b/gemma-web/src/main/webapp/common/taglibs.jsp index d442f1049d..45d2aebe16 100644 --- a/gemma-web/src/main/webapp/common/taglibs.jsp +++ b/gemma-web/src/main/webapp/common/taglibs.jsp @@ -1,5 +1,3 @@ -<%@ page language="java" errorPage="/pages/error/500.jsp" pageEncoding="UTF-8" - contentType="text/html; charset=utf-8"%> <%@ taglib uri="http://www.springframework.org/tags" prefix="spring"%> <%@ taglib uri="http://www.springframework.org/security/tags" prefix="security"%> <%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%> @@ -8,4 +6,4 @@ <%@ taglib uri="http://www.opensymphony.com/sitemesh/page" prefix="page"%> <%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%> <%@ taglib uri="/WEB-INF/Gemma.tld" prefix="Gemma"%> -<%@ taglib uri="http://jawr.net/tags" prefix="jwr"%> +<%@ taglib uri="http://jawr.net/tags" prefix="jwr"%> \ No newline at end of file diff --git a/gemma-web/src/main/webapp/common/userStatusVariables.jsp b/gemma-web/src/main/webapp/common/userStatusVariables.jsp index 29ab29fdaf..a8895ad415 100644 --- a/gemma-web/src/main/webapp/common/userStatusVariables.jsp +++ b/gemma-web/src/main/webapp/common/userStatusVariables.jsp @@ -1,35 +1,38 @@ -<%@ include file="/common/taglibs.jsp"%> - +<%@ include file="/common/taglibs.jsp" %> + <%-- Security fields used in Java script calls to hide or display information on pages, used to be in footer --%> - + - + - + - + - + - + - " /> + " /> - + <%-- dump some other useful settings --%> - - - + + + diff --git a/gemma-web/src/main/webapp/decorators/default.jsp b/gemma-web/src/main/webapp/decorators/default.jsp index b21f22d305..816da84ffb 100644 --- a/gemma-web/src/main/webapp/decorators/default.jsp +++ b/gemma-web/src/main/webapp/decorators/default.jsp @@ -1,77 +1,45 @@ +<%@ page pageEncoding="UTF-8" contentType="text/html; charset=utf-8" + trimDirectiveWhitespaces="true" %> +<%@ include file="/common/taglibs.jsp" %> + -<%-- Include common set of tag library declarations for each layout --%> -<%@ include file="/common/taglibs.jsp"%> - + -<%-- Include common set of meta tags for each layout --%> -<%@ include file="/common/meta.jsp"%> - - + + <decorator:title /> | <fmt:message key="webapp.name" /> - + +" /> +" /> + - - - - - - -<%-- for dwr creation of javascript objects to mirror java value objects; including one of these causes all the objects to be exposed.--%> - -<%-- We should use this as soon as we figure out how to set generateDtoClasses option to dtoall - script type='text/javascript' src='/Gemma/dwr/dtoall.js'> --%> - + <%-- for registration, possible from any page--%> - -<%-- log javascript errors --%> - - + + + + - - - - > - -
- -
- -
- - -
- - - -
- <%@ include file="/common/messages.jsp"%> - -

- -

- - - -
- - -
- - - - - -
- + + +
+
+ +
+
+
+ <%@ include file="/common/messages.jsp" %> + +
+
+
- - + \ No newline at end of file diff --git a/gemma-web/src/main/webapp/error.jsp b/gemma-web/src/main/webapp/error.jsp index 66705e1df2..13b9506391 100644 --- a/gemma-web/src/main/webapp/error.jsp +++ b/gemma-web/src/main/webapp/error.jsp @@ -1,12 +1,13 @@ +<%@ page isErrorPage="true" pageEncoding="UTF-8" contentType="text/html; charset=utf-8" + trimDirectiveWhitespaces="true" %> + <%@ include file="/common/taglibs.jsp" %> - - -<%@ page isErrorPage="true" %> +--%> @@ -38,7 +39,8 @@ If you can, avoid producing error this way and prefer raising an exception that

Unsupported Status Code

- There is no error page configured for the status code . + There is no error page configured for the status code .

<%@ include file="/common/exception.jsp" %> diff --git a/gemma-web/src/main/webapp/pages/admin/activeUsers.jsp b/gemma-web/src/main/webapp/pages/admin/activeUsers.jsp index d0cb97dcee..9ad1691e63 100644 --- a/gemma-web/src/main/webapp/pages/admin/activeUsers.jsp +++ b/gemma-web/src/main/webapp/pages/admin/activeUsers.jsp @@ -1,44 +1,41 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> + <fmt:message key="activeUsers.title" /> - - - -
-

Tasks

-
+

Tasks

+
-
+
-

- -

- +

+ +

+ : 
Signed in: ? - - -
-

FIXME table of authenticated users should go here.

- -

System Stats

- + + +
+

FIXME table of authenticated users should go here.

+ +

System Stats

+ Gemma version ${appConfig["gemma.version"] != null ? appConfig["gemma.version"] : "?"} built @@ -48,11 +45,11 @@ from ${appConfig["gemma.build.gitHash"]} + target="_blank" rel="noopener noreferrer">${appConfig["gemma.build.gitHash"]} - + - +
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/admin/geoRecordBrowser.jsp b/gemma-web/src/main/webapp/pages/admin/geoRecordBrowser.jsp index ec66fa6667..fb2f3e74c5 100644 --- a/gemma-web/src/main/webapp/pages/admin/geoRecordBrowser.jsp +++ b/gemma-web/src/main/webapp/pages/admin/geoRecordBrowser.jsp @@ -1,61 +1,56 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> GEO Record browser - - + + +
+ +
+ +
+

+ Displaying GEO records. +

+
+ +
+ +
+
+

+ Note: Records are not shown for taxa not in the Gemma system. If you + choose to load an experiment, please be careful: experiments that + have two (or more) array designs should be loaded using the regular + load form if you need to suppress the sample-matching functions. + Click on a row to display more information about the dataset, if available + from GEO, including information about platforms. This information is + often not available for a day or two after the data sets becomes + publicly available. +

+

+ To search GEO, type your query in the 'Search' field, e.g. Mus+musculus[ORGN]+AND+brain[ALL]. + For more information on how to construct queries, go to the + NCBI website. +

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

- Displaying GEO records. -

-
- -
- -
-
-

- Note: Records are not shown for taxa not in the Gemma system. If you - choose to load an experiment, please be careful: experiments that - have two (or more) array designs should be loaded using the regular - load form if you need to suppress the sample-matching functions. - Click on a row to display more information about the dataset, if available - from GEO, including information about platforms. This information is - often not available for a day or two after the data sets becomes - publicly available. -

-

- To search GEO, type your query in the 'Search' field, e.g. Mus+musculus[ORGN]+AND+brain[ALL]. - For more information on how to construct queries, go to the - NCBI website. -

-
- - \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/admin/indexer.jsp b/gemma-web/src/main/webapp/pages/admin/indexer.jsp index 07cbe29b35..e425fab1d5 100644 --- a/gemma-web/src/main/webapp/pages/admin/indexer.jsp +++ b/gemma-web/src/main/webapp/pages/admin/indexer.jsp @@ -1,31 +1,25 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - Index Gemma - - - - +Manage Search Indexes + - - - - -

- Choose the indexing options that are appropriate and then click - index. -

- -
-
- -
-
- - - +
+

Manage Search Indexes

+ +

+ Choose the indexing options that are appropriate and then click + index. +

+
+
+ +
+
+ +
diff --git a/gemma-web/src/main/webapp/pages/admin/loadExpressionExperimentForm.jsp b/gemma-web/src/main/webapp/pages/admin/loadExpressionExperimentForm.jsp index 604b558a3b..7baaeef307 100644 --- a/gemma-web/src/main/webapp/pages/admin/loadExpressionExperimentForm.jsp +++ b/gemma-web/src/main/webapp/pages/admin/loadExpressionExperimentForm.jsp @@ -1,181 +1,177 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - - - - - <fmt:message key="expressionExperimentLoad.title" /> + <fmt:message key="expressionExperimentLoad.title" /> + - - - -
- -
- +
+ +
- +
- - - - - + + + + + + + + + + + + +
- - - " /> - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - - - - - - - - -
+ + + " /> + -
- - - - - - "> - " value="true" - checked /> - +
+ + + + + + "> + " value="true" + checked /> + -
- - - - - - "> - " - value="true" id="loadPlatformOnly" - checked /> - +
+ + + + + + "> + " + value="true" id="loadPlatformOnly" + checked /> + -
- - - - - - "> - " value="true" - checked /> - +
+ + + + + + "> + " value="true" + checked /> + -
- - - - - - "> - " value="true" - checked /> - +
+ + + + + + "> + " value="true" + checked /> + -
- - - - - - "> - " value="true" - checked /> - +
+ + + + + + "> + " value="true" + checked /> + -
- - - - - - "> - " value="false" - checked /> - +
+ + + + + + "> + " value="false" + checked /> + -
- - -
-
-
-
+
+ + +
+
+
+
+ + + diff --git a/gemma-web/src/main/webapp/pages/admin/maintenanceMode.jsp b/gemma-web/src/main/webapp/pages/admin/maintenanceMode.jsp index 312b8be282..0704885602 100644 --- a/gemma-web/src/main/webapp/pages/admin/maintenanceMode.jsp +++ b/gemma-web/src/main/webapp/pages/admin/maintenanceMode.jsp @@ -1,13 +1,19 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> -

- Maintenance mode simply puts a notice on every page that things might - be broken. -

-
- + +Maintenance Mode + - -
\ No newline at end of file +
+

+ Maintenance mode simply puts a notice on every page that things might + be broken. +

+
+ + + +
+
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/admin/reIndexOntologies.jsp b/gemma-web/src/main/webapp/pages/admin/reIndexOntologies.jsp index 7010a17547..40ab600861 100755 --- a/gemma-web/src/main/webapp/pages/admin/reIndexOntologies.jsp +++ b/gemma-web/src/main/webapp/pages/admin/reIndexOntologies.jsp @@ -2,10 +2,7 @@ Index Gemma - - - diff --git a/gemma-web/src/main/webapp/pages/admin/systemStats.jsp b/gemma-web/src/main/webapp/pages/admin/systemStats.jsp index fdd7dff8c9..5d6612f1dc 100644 --- a/gemma-web/src/main/webapp/pages/admin/systemStats.jsp +++ b/gemma-web/src/main/webapp/pages/admin/systemStats.jsp @@ -1,7 +1,6 @@ <%@ include file="/common/taglibs.jsp"%> -System stats - +System Stats +
+ +

EE Page

+
+ +

ComboBoxes

+

DatasetGroup combo

+
+ +

DatasetGroupComboPanel

+
+

TaxonCombo

+
+ + +

FactorValueCombo

+
+ + +

Dataset search field

+
+
+ + +

CharacteristicCombo

+
+ +

Gene combo

+
+ +

Gene Group Combo

+
+ + +

MGEDCombo

+
+

ArrayDesignCombo

+
+ +

Panels

+ +

GeneChooserPanel

+
-

EE Page

-
+

DatasetGroupGridPanel with DatasetGroupEditToolbar

+
+

ExpressionExperiment Grid

+
-

ComboBoxes

-

DatasetGroup combo

-
-

DatasetGroupComboPanel

-
-

TaxonCombo

-
+

AuditTrailGrid

+
+

FilesUpload

+
-

FactorValueCombo

-
+

Visualization

+
-

Dataset search field

-
-
+

ProgressWidget

+
+

AnalysisResultsSearch

+
+
+
+
-

CharacteristicCombo

-
+

Widget

+
-

Gene combo

-
+

Font-awesome test

+

+ fa-camera-retro +

+
-

Gene Group Combo

-
+ \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/analysesResultsSearch.jsp b/gemma-web/src/main/webapp/pages/analysesResultsSearch.jsp index 1a48adbcf5..00c0c7fe2c 100755 --- a/gemma-web/src/main/webapp/pages/analysesResultsSearch.jsp +++ b/gemma-web/src/main/webapp/pages/analysesResultsSearch.jsp @@ -1,34 +1,23 @@ +<%@ include file="/common/taglibs.jsp" %> - - - Search Analyses Results - - - - - - + +Search Analyses Results + + + - - +
- - - +Ext.onReady( function() { + Ext.QuickTips.init(); -
- + new Gemma.GemmaViewPort( { + centerPanelConfig : new Gemma.AnalysisResultsSearch() + } ); +} ); + diff --git a/gemma-web/src/main/webapp/pages/arrayDesign.detail.jsp b/gemma-web/src/main/webapp/pages/arrayDesign.detail.jsp index 9f060caea1..9b14180eba 100644 --- a/gemma-web/src/main/webapp/pages/arrayDesign.detail.jsp +++ b/gemma-web/src/main/webapp/pages/arrayDesign.detail.jsp @@ -1,32 +1,27 @@ -<%@ include file="/common/taglibs.jsp"%> - +<%@ include file="/common/taglibs.jsp" %> + - - +${fn:escapeXml(arrayDesign.shortName)} - ${fn:escapeXml(arrayDesign.name)} + - -${arrayDesignShortName} - ${arrayDesignName } - - - - - - + + + \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/arrayDesign.edit.jsp b/gemma-web/src/main/webapp/pages/arrayDesign.edit.jsp index 36652cbf57..cfa91ab5ed 100644 --- a/gemma-web/src/main/webapp/pages/arrayDesign.edit.jsp +++ b/gemma-web/src/main/webapp/pages/arrayDesign.edit.jsp @@ -1,84 +1,90 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> -Edit Array Design ${arrayDesign.name} + +Edit ${arrayDesign.name} + - -
- - " alt="" class="icon" /> - -
- -
- + +
+ + " alt="" + class="icon" /> + +
+ +
+
" id="arrayDesignForm" - onsubmit="return validateArrayDesign(this)"> + onsubmit="return validateArrayDesign(this)"> - - - - - - - -
- - - - " id="name" /> - - -
- - - - " id="shortName" /> - + + + + + + + + - - - - - + + + + + + + - - - - - - - - + + + + + + + + -
+ + + + " id="name" /> + + +
+ + + + " id="shortName" /> + - -
- - - - - -
+ + + + + +
- - - - - - -
- " /> - " /> - -
+ + + + + + +
+ " /> + " /> + +
+
diff --git a/gemma-web/src/main/webapp/pages/arrayDesign.jsp b/gemma-web/src/main/webapp/pages/arrayDesign.jsp index 7288c13417..da9ca6bd9c 100644 --- a/gemma-web/src/main/webapp/pages/arrayDesign.jsp +++ b/gemma-web/src/main/webapp/pages/arrayDesign.jsp @@ -1,14 +1,6 @@ <%@ include file="/common/taglibs.jsp"%> - - <jsp:getProperty name="arrayDesign" property="shortName" /> - <jsp:getProperty name="arrayDesign" - property="name" /> - - - - - - + <jsp:getProperty name="arrayDesign" property="shortName" /> - <jsp:getProperty name="arrayDesign" property="name" />
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/arrayDesigns.jsp b/gemma-web/src/main/webapp/pages/arrayDesigns.jsp index ac6f766e0b..78fb8ed733 100644 --- a/gemma-web/src/main/webapp/pages/arrayDesigns.jsp +++ b/gemma-web/src/main/webapp/pages/arrayDesigns.jsp @@ -1,23 +1,16 @@ - -<%@ include file="/common/taglibs.jsp"%> - +Platforms + + - - - -Platforms - diff --git a/gemma-web/src/main/webapp/pages/bibRefList.jsp b/gemma-web/src/main/webapp/pages/bibRefList.jsp index 0e4a730539..d4e066aa2a 100644 --- a/gemma-web/src/main/webapp/pages/bibRefList.jsp +++ b/gemma-web/src/main/webapp/pages/bibRefList.jsp @@ -1,15 +1,14 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - +Bibliographic References + - Bibliographic References - diff --git a/gemma-web/src/main/webapp/pages/bioAssay.detail.jsp b/gemma-web/src/main/webapp/pages/bioAssay.detail.jsp index c00b37e60f..d6505e4352 100644 --- a/gemma-web/src/main/webapp/pages/bioAssay.detail.jsp +++ b/gemma-web/src/main/webapp/pages/bioAssay.detail.jsp @@ -1,45 +1,53 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> + <fmt:message key="bioAssay.details" /> + + -

- -

- - - - - - - - - +
+

+ +

+
- ${bioAssay.name}
+ + + + + + + + - - - - + + + + - - - - - - - - + + + + + + + + - - - - - - + + + + + + -
${bioAssay.name}
- ${bioAssay.description}
+ ${fn:escapeXml(bioAssay.description)}
Sample${bioAssay.sample.name}
Platform${bioAssay.arrayDesign.shortName}  - ${bioAssay.arrayDesign.name}
Sample + ${bioAssay.sample.name} +
Platform + ${bioAssay.arrayDesign.shortName} ${bioAssay.arrayDesign.name} +
Original platform${bioAssay.originalPlatform.shortName}  - ${bioAssay.originalPlatform.name}
Original Platform + ${bioAssay.originalPlatform.shortName} ${bioAssay.originalPlatform.name} +
+ +
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/bioAssaySet.jsp b/gemma-web/src/main/webapp/pages/bioAssaySet.jsp new file mode 100644 index 0000000000..80489a8c8c --- /dev/null +++ b/gemma-web/src/main/webapp/pages/bioAssaySet.jsp @@ -0,0 +1,13 @@ +<%@ include file="/common/taglibs.jsp" %> + +Assays for ${bioAssaySet.name} + +

Assays for ${bioAssaySet.name}

+ + + + + + + +
${bioAssay.name}
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/bioAssays.jsp b/gemma-web/src/main/webapp/pages/bioAssays.jsp deleted file mode 100644 index 3044dd0988..0000000000 --- a/gemma-web/src/main/webapp/pages/bioAssays.jsp +++ /dev/null @@ -1,57 +0,0 @@ -<%@ include file="/common/taglibs.jsp" %> - - <fmt:message key="bioAssays.title"/> - - - - - - - -
- -

- - for ${expressionExperiment.shortName} -

-

- View the Experimental - design -

- - - - - - - - -
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/bioMaterial.detail.jsp b/gemma-web/src/main/webapp/pages/bioMaterial.detail.jsp index cd0bab8fdd..09f00d5bd9 100644 --- a/gemma-web/src/main/webapp/pages/bioMaterial.detail.jsp +++ b/gemma-web/src/main/webapp/pages/bioMaterial.detail.jsp @@ -1,152 +1,158 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> + class="ubic.gemma.model.expression.biomaterial.BioMaterial" /> + -<fmt:message key="bioMaterial.details" /> - +${fn:escapeXml(bioMaterial.name)} + - - - -
-

- BioMaterial: ${bioMaterial.name} from - ${expressionExperiment.shortName} -

- - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - Description not available - -
- - - - - - - - Taxon not available - -
- - - - - - - - No external identifier - -
- Assays used in - - -
- -
- -

- -

- - - - - - -
- -

- -

-
- -
- -

Annotations

-
- - - - -
- - - - -
- -
- - - -
\ No newline at end of file +

${fn:escapeXml(bioMaterial.name)}

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + Description not available + +
+ + + + + + + Taxon not available + +
+ + + + + No external identifier + +
+ Assays used in + + +
Experiments used in + + ${experiment.shortName} + +
+ + +
+

+ + + + + + + + + + + + + + + +
NameDescriptionOrder Applied
${fn:escapeXml(treatment.name)}${fn:escapeXml(treatment.description)}${treatment.orderApplied}
+ + +
+ +

+ +

+
+ +
+ +

Annotations

+
+ + + + + +
+ + + +
+ +
+ + + +
+ + diff --git a/gemma-web/src/main/webapp/pages/characteristics.jsp b/gemma-web/src/main/webapp/pages/characteristics.jsp index b3a25e4904..0afa80dd8e 100644 --- a/gemma-web/src/main/webapp/pages/characteristics.jsp +++ b/gemma-web/src/main/webapp/pages/characteristics.jsp @@ -1,19 +1,13 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - <fmt:message key="characteristicBrowser.title" /> - - - - +<fmt:message key="characteristicBrowser.title" /> + -

- -

- -
-
- - +
+

+
+
+
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/compositeSequence.detail.jsp b/gemma-web/src/main/webapp/pages/compositeSequence.detail.jsp index 4744eff37f..c75858a073 100644 --- a/gemma-web/src/main/webapp/pages/compositeSequence.detail.jsp +++ b/gemma-web/src/main/webapp/pages/compositeSequence.detail.jsp @@ -1,59 +1,28 @@ + <%@ include file="/common/taglibs.jsp" %> - - - - <fmt:message key="compositeSequence.title"/> ${ compositeSequence.name} - - <%-- deprecated. We should replace this with something tidier --%> - - -

- - : ${ compositeSequence.name} on - - ${compositeSequence.arrayDesign.shortName} - - ${ compositeSequence.arrayDesign.name} - + ${fn:escapeXml(compositeSequence.name)} on + ${compositeSequence.arrayDesign.shortName}

- + - + - + - + - + - + - + - + + step="1"> + + + + +
- : - - : + title="Description for the probe, usually provided by the manufacturer. It might not match the sequence annotation!"> @@ -65,9 +34,7 @@
- Taxon : - Taxon: @@ -82,12 +49,10 @@
- Sequence Type : - Sequence Type: + title="The type of this sequence as recorded in our system"> @@ -107,12 +72,10 @@
- Sequence name : - Sequence name: + title='Name of the sequence in our system.'> @@ -123,12 +86,10 @@
- Sequence description : - Sequence description: + title='Description of the sequence in our system.'> @@ -141,12 +102,10 @@
- Sequence accession : - Sequence accession: + title='External accession for this sequence, if known'> @@ -157,27 +116,24 @@
- Sequence : - + title='Sequence, if known'> - + No sequence
- Sequence length : - Sequence length: @@ -196,6 +152,30 @@

Alignment information

- - + +<%-- deprecated. We should replace this with something tidier --%> + diff --git a/gemma-web/src/main/webapp/pages/contactUs.jsp b/gemma-web/src/main/webapp/pages/contactUs.jsp index f35bd91fe1..112931fd09 100644 --- a/gemma-web/src/main/webapp/pages/contactUs.jsp +++ b/gemma-web/src/main/webapp/pages/contactUs.jsp @@ -1,33 +1,26 @@ - -<%-- Decorator for the home page --%> - - -<%-- Include common set of tag library declarations for each layout --%> -<%@ include file="/common/taglibs.jsp"%> - +<%@ include file="/common/taglibs.jsp" %> + Contact Us - -
-
-

- Contacting us -

-

- For feature requests and bug reports, send us an email - here. -

-

- Please also keep an eye out for the feedback button-tab on the left - of some pages in Gemma. It looks like - this + +

+
+

+ Contacting us +

+

+ For feature requests and bug reports, send us an email + here. +

+

+ Please also keep an eye out for the feedback button-tab on the left + of some pages in Gemma. It looks like + this
- and is an easy way to give us in-context feedback! -

+ and is an easy way to give us in-context feedback! +

-
-
- - +
+
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/dataUpload.jsp b/gemma-web/src/main/webapp/pages/dataUpload.jsp index be55671c7e..b423adb1dc 100644 --- a/gemma-web/src/main/webapp/pages/dataUpload.jsp +++ b/gemma-web/src/main/webapp/pages/dataUpload.jsp @@ -1,32 +1,33 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - - Expression data upload - - - - - - +Upload Expression Data + + + + - -
-
-
- +
+

Upload Expression Data

+ + +
+
+
+ - - -

- Sorry, to upload data you must - login or - register. -

- + + +

+ Sorry, to upload data you must + login or + register. +

+ +
diff --git a/gemma-web/src/main/webapp/pages/error/403.jsp b/gemma-web/src/main/webapp/pages/error/403.jsp index 303c221631..0a783e0b4b 100644 --- a/gemma-web/src/main/webapp/pages/error/403.jsp +++ b/gemma-web/src/main/webapp/pages/error/403.jsp @@ -1,26 +1,24 @@ <%@ include file="/common/taglibs.jsp" %> -<fmt:message key="403.title"/> +<fmt:message key="403.title" /> - - - +
-

+

- +

diff --git a/gemma-web/src/main/webapp/pages/error/404.jsp b/gemma-web/src/main/webapp/pages/error/404.jsp index 3101a1311b..88282178cc 100644 --- a/gemma-web/src/main/webapp/pages/error/404.jsp +++ b/gemma-web/src/main/webapp/pages/error/404.jsp @@ -1,13 +1,11 @@ <%@ include file="/common/taglibs.jsp" %> -<fmt:message key="404.title"/> +<fmt:message key="404.title" /> - - - +
-

+

diff --git a/gemma-web/src/main/webapp/pages/experimentalDesign.detail.jsp b/gemma-web/src/main/webapp/pages/experimentalDesign.detail.jsp index 21b0b97253..1f18a1a6b6 100644 --- a/gemma-web/src/main/webapp/pages/experimentalDesign.detail.jsp +++ b/gemma-web/src/main/webapp/pages/experimentalDesign.detail.jsp @@ -1,175 +1,176 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> + class="ubic.gemma.model.expression.experiment.ExperimentalDesign" /> + class="ubic.gemma.model.expression.experiment.ExpressionExperiment" /> ${expressionExperiment.shortName} | <fmt:message key="experimentalDesign.details" /> - - - + value="${expressionExperiment.id}" /> + value="${experimentalDesign.id}" /> + value="${currentUserCanEdit}" />

-

- - for - - -

- - - - This experiment does not have any experimental - design details filled in. - - -

- Download design File: - Click - to start download - - -

- - - - -
- - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - (Name not available) - -
- - - - - - - (Description not available) - -
- - - - - - - (Database entry not available) - -
- - - - - - - (Primary publication not available) - -
+

+ + for + + + +

+ + + + This experiment does not have any experimental + design details filled in. + + +

+ Download design File: + Click + to start download + + +

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + (Name not available) + +
+ + + + + + + (Description not available) + +
+ + + + + + + (Database entry not available) + +
+ + + + + + + (Primary publication not available) + +
- - -
-

- Use the form below to populate the experimental design details. - Alternatively you can - upload - a design description file. Instructions are - here - . If you want to use the upload method, you can get a blank - template - file - to get started. -

-
- - - - - -

This experimental design needs attention, check in the tables below for more details.

- - -

- Here's another experimental design that needs attention: - ${randomExperimentalDesignThatNeedsAttentionShortName} -

- - - - - - <%-- This form element is needed for the checkboxes in the factor value panel --%> -
-
-
-
- -
- -
- -
\ No newline at end of file + + +
+

+ Use the form below to populate the experimental design details. + Alternatively you can + upload + a design description file. Instructions are + here + . If you want to use the upload method, you can get a blank + template + file + to get started. +

+
+ + + + + +

This experimental design needs attention, check in the tables below for more details.

+ + +

+ Here's another experimental design that needs attention: + ${randomExperimentalDesignThatNeedsAttentionShortName} +

+ + + + + + <%-- This form element is needed for the checkboxes in the factor value panel --%> +
+
+
+
+ +
+ +
+ +
+ + \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/expressionExperiment.bioAssays.jsp b/gemma-web/src/main/webapp/pages/expressionExperiment.bioAssays.jsp new file mode 100644 index 0000000000..5cb000fc17 --- /dev/null +++ b/gemma-web/src/main/webapp/pages/expressionExperiment.bioAssays.jsp @@ -0,0 +1,51 @@ +<%@ include file="/common/taglibs.jsp" %> + + +<fmt:message key="bioAssays.title" /> for ${expressionExperiment.shortName} + + + +
+

+ + for ${expressionExperiment.shortName} +

+

+ View the Experimental + design +

+ + + +
+ + diff --git a/gemma-web/src/main/webapp/pages/expressionExperiment.bioMaterials.jsp b/gemma-web/src/main/webapp/pages/expressionExperiment.bioMaterials.jsp new file mode 100644 index 0000000000..6c47c5cfba --- /dev/null +++ b/gemma-web/src/main/webapp/pages/expressionExperiment.bioMaterials.jsp @@ -0,0 +1,16 @@ +<%@ include file="/common/taglibs.jsp" %> + + +Biomaterials for ${expressionExperiment.shortName} + +

Biomaterials for ${expressionExperiment.shortName}

+ + + + + + + +
${bioMaterial.name}
diff --git a/gemma-web/src/main/webapp/pages/expressionExperiment.detail.jsp b/gemma-web/src/main/webapp/pages/expressionExperiment.detail.jsp index 55c7ebcd02..966a6017bd 100644 --- a/gemma-web/src/main/webapp/pages/expressionExperiment.detail.jsp +++ b/gemma-web/src/main/webapp/pages/expressionExperiment.detail.jsp @@ -1,36 +1,39 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> -${expressionExperiment.shortName} Details - - - - - - - +${fn:escapeXml(expressionExperiment.shortName)} - ${fn:escapeXml(expressionExperiment.name)} + + - - + + - + + + + + +
-
+
-
+ \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/expressionExperiment.edit.jsp b/gemma-web/src/main/webapp/pages/expressionExperiment.edit.jsp index 3ebeed5ea3..f2378b8465 100644 --- a/gemma-web/src/main/webapp/pages/expressionExperiment.edit.jsp +++ b/gemma-web/src/main/webapp/pages/expressionExperiment.edit.jsp @@ -1,24 +1,26 @@ <%@ include file="/common/taglibs.jsp" %> + + + - - +Edit ${expressionExperiment.shortName} + -
- -
+ +
-<fmt:message key="expressionExperiment.title"/> ${expressionExperiment.shortName} +<fmt:message key="expressionExperiment.title" /> ${expressionExperiment.shortName}
"> @@ -50,50 +52,50 @@
" - value=""/> + value="" /> " - value=""/> + value="" /> checked="checked" /> + checked="checked" /> "> checked="checked" /> + checked="checked" /> "> checked="checked" /> + checked="checked" /> "> checked="checked" /> + checked="checked" /> "> checked="checked" /> + checked="checked" /> "> checked="checked" /> + checked="checked" /> "> checked="checked" /> + checked="checked" /> "> @@ -152,15 +154,15 @@
+ value="Unmatch all bioassays" />
- +
- "/> - "/> + " /> + " />
diff --git a/gemma-web/src/main/webapp/pages/expressionExperimentLinkSummary.jsp b/gemma-web/src/main/webapp/pages/expressionExperimentLinkSummary.jsp index d5bc6a7a95..3141b898c0 100644 --- a/gemma-web/src/main/webapp/pages/expressionExperimentLinkSummary.jsp +++ b/gemma-web/src/main/webapp/pages/expressionExperimentLinkSummary.jsp @@ -1,28 +1,24 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - - Dataset manager - - +Dataset manager - - + diff --git a/gemma-web/src/main/webapp/pages/expressionExperimentSet.detail.jsp b/gemma-web/src/main/webapp/pages/expressionExperimentSet.detail.jsp index e1a3d342d2..275e658c07 100644 --- a/gemma-web/src/main/webapp/pages/expressionExperimentSet.detail.jsp +++ b/gemma-web/src/main/webapp/pages/expressionExperimentSet.detail.jsp @@ -1,38 +1,39 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> + - ${eeSetName} Details - +${fn:escapeXml(eeSet.name)} + - - - - + + - +
-
+
diff --git a/gemma-web/src/main/webapp/pages/expressionExperimentSetManager.jsp b/gemma-web/src/main/webapp/pages/expressionExperimentSetManager.jsp index 228ae87dd0..e2ebe97519 100644 --- a/gemma-web/src/main/webapp/pages/expressionExperimentSetManager.jsp +++ b/gemma-web/src/main/webapp/pages/expressionExperimentSetManager.jsp @@ -1,43 +1,40 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> Dataset Group Manager - - - - + - - -

Sorry, you must be logged in to use this tool.

+ + +

Sorry, you must be logged in to use this tool.

 -
- - - - +
+ + + + diff --git a/gemma-web/src/main/webapp/pages/expressionExperimentsWithQC.jsp b/gemma-web/src/main/webapp/pages/expressionExperimentsWithQC.jsp index 82b8c6ac42..b78ac3c591 100644 --- a/gemma-web/src/main/webapp/pages/expressionExperimentsWithQC.jsp +++ b/gemma-web/src/main/webapp/pages/expressionExperimentsWithQC.jsp @@ -2,7 +2,6 @@ Expression Experiments with QC Issues - diff --git a/gemma-web/src/main/webapp/pages/gene.detail.jsp b/gemma-web/src/main/webapp/pages/gene.detail.jsp index e61962bd16..1de543d0f8 100644 --- a/gemma-web/src/main/webapp/pages/gene.detail.jsp +++ b/gemma-web/src/main/webapp/pages/gene.detail.jsp @@ -1,45 +1,40 @@ -<%@ include file="/common/taglibs.jsp"%> - - - - +<%@ include file="/common/taglibs.jsp" %> + -<c:if test="${not empty geneOfficialSymbol}"> - ${geneOfficialSymbol} - </c:if> <fmt:message key="gene.details" /> + +${fn:escapeXml(gene.name)} - ${fn:escapeXml(gene.officialName)} + - - - - - - - - + + + + + + -
+
- \ No newline at end of file + \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/geneGroupManager.jsp b/gemma-web/src/main/webapp/pages/geneGroupManager.jsp index 9388ad8380..aa6402d18a 100644 --- a/gemma-web/src/main/webapp/pages/geneGroupManager.jsp +++ b/gemma-web/src/main/webapp/pages/geneGroupManager.jsp @@ -3,7 +3,6 @@ Manage Gene Groups - diff --git a/gemma-web/src/main/webapp/pages/geneSet.detail.jsp b/gemma-web/src/main/webapp/pages/geneSet.detail.jsp index 3217207432..0c48cf2fce 100644 --- a/gemma-web/src/main/webapp/pages/geneSet.detail.jsp +++ b/gemma-web/src/main/webapp/pages/geneSet.detail.jsp @@ -1,39 +1,40 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> + - ${geneSetName} Details - +${fn:escapeXml(geneSet.name)} Details + - - - - - + + - +
-
+
+ + + diff --git a/gemma-web/src/main/webapp/pages/generalSearch.jsp b/gemma-web/src/main/webapp/pages/generalSearch.jsp index 852a933ea4..f65d29647a 100644 --- a/gemma-web/src/main/webapp/pages/generalSearch.jsp +++ b/gemma-web/src/main/webapp/pages/generalSearch.jsp @@ -1,23 +1,9 @@ -<%@ include file="/common/taglibs.jsp"%> - +<%@ include file="/common/taglibs.jsp" %> - <fmt:message key="generalSearch.title" /> - - - - +
@@ -25,3 +11,13 @@
+ diff --git a/gemma-web/src/main/webapp/pages/home.jsp b/gemma-web/src/main/webapp/pages/home.jsp index a9052289c5..adfd967d43 100755 --- a/gemma-web/src/main/webapp/pages/home.jsp +++ b/gemma-web/src/main/webapp/pages/home.jsp @@ -3,32 +3,10 @@ <%@ include file="/common/taglibs.jsp" %> Home - - <%-- --%> - - <%-- jshowoff.css is included in the bundle --%> @@ -152,7 +130,7 @@ $.getJSON( '${pageContext.request.contextPath}' + '/rest/v2/datasets/count', fun
Copyright © 2007-2024
- Terms and conditions + Terms and conditions
@@ -161,4 +139,24 @@ $.getJSON( '${pageContext.request.contextPath}' + '/rest/v2/datasets/count', fun src="https://i.creativecommons.org/l/by-nc/4.0/80x15.png" width="80" height="15" /> - \ No newline at end of file + + + \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/invalidGeoAccession.jsp b/gemma-web/src/main/webapp/pages/invalidGeoAccession.jsp index 3872bfc31b..fcfadf6525 100644 --- a/gemma-web/src/main/webapp/pages/invalidGeoAccession.jsp +++ b/gemma-web/src/main/webapp/pages/invalidGeoAccession.jsp @@ -1,23 +1,13 @@ -<%@ include file="/common/taglibs.jsp"%> -<%@ page language="java" isErrorPage="true"%> - - +<%@ page isErrorPage="true" %> +<%@ include file="/common/taglibs.jsp" %> <%-- This is not being used. --%> - - Invalid GEO accession - - - - Invalid GEO accession - - - « Back - - - -

- Either that accession does not exist in GEO, or if you entered a GDS number, Gemma could not locate a matching series - (GSE) on the GEO web site. Please check the - GEO web site to make sure you selected a valid accession. -

- +Invalid GEO accession + +

Invalid GEO accession

+« Back + +

+ Either that accession does not exist in GEO, or if you entered a GDS number, Gemma could not locate a matching + series (GSE) on the GEO web site. Please check theGEO website to + make sure you selected a valid accession. +

diff --git a/gemma-web/src/main/webapp/pages/manageGroups.jsp b/gemma-web/src/main/webapp/pages/manageGroups.jsp index a020f82d2d..8070de825b 100644 --- a/gemma-web/src/main/webapp/pages/manageGroups.jsp +++ b/gemma-web/src/main/webapp/pages/manageGroups.jsp @@ -1,38 +1,27 @@ -<%@ include file="/common/taglibs.jsp"%> - +<%@ include file="/common/taglibs.jsp" %> - Manage groups - - +Manage groups + - -

- Manage groups -

- -

- A 'Group' is a set of Gemma users who have a common set of permissions. This page allows you to see what Groups you - belong to, create groups, and change who is in groups you control. -

- -

- For additional controls on which groups can view or edit your data sets, visit the - ">Data Manager. If - you want to manage Gene Groups go to the - ">Gene Group Manager. To manage Expression Dataset Groups go to - the - ">Dataset Group Manager. -

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

Manage groups

+ +

+ A 'Group' is a set of Gemma users who have a common set of permissions. This page allows you to see what Groups you + belong to, create groups, and change who is in groups you control. +

+ +

+ For additional controls on which groups can view or edit your data sets, visit the + ">Data Manager. If + you want to manage Gene Groups go to the + ">Gene Group Manager. To manage Expression Dataset Groups go to + the + ">Dataset Group Manager. +

+ +
+
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/metaAnalysisManager.jsp b/gemma-web/src/main/webapp/pages/metaAnalysisManager.jsp index 42ad896107..cbdf29a7ea 100644 --- a/gemma-web/src/main/webapp/pages/metaAnalysisManager.jsp +++ b/gemma-web/src/main/webapp/pages/metaAnalysisManager.jsp @@ -1,8 +1,6 @@ <%@ include file="/common/taglibs.jsp"%> Meta-analysis Manager - - diff --git a/gemma-web/src/main/webapp/pages/metaheatmap.jsp b/gemma-web/src/main/webapp/pages/metaheatmap.jsp index 8c80990a8a..40b03e1d4f 100644 --- a/gemma-web/src/main/webapp/pages/metaheatmap.jsp +++ b/gemma-web/src/main/webapp/pages/metaheatmap.jsp @@ -1,59 +1,59 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - - - - - - +Meta-analysis Heatmap + + -Start a new search

-
\ No newline at end of file + +Start a new search

+
+ + diff --git a/gemma-web/src/main/webapp/pages/passwordHint.jsp b/gemma-web/src/main/webapp/pages/passwordHint.jsp index 54d176fd61..b2def77de9 100644 --- a/gemma-web/src/main/webapp/pages/passwordHint.jsp +++ b/gemma-web/src/main/webapp/pages/passwordHint.jsp @@ -1,16 +1,8 @@ -<%-- -author: keshav - ---%> - -<%@ include file="/common/taglibs.jsp"%> - +<%-- author: keshav --%> +<%@ include file="/common/taglibs.jsp" %> Password reset - - + -
- diff --git a/gemma-web/src/main/webapp/pages/personForm.jsp b/gemma-web/src/main/webapp/pages/personForm.jsp index bd43291bfe..83f9039c28 100644 --- a/gemma-web/src/main/webapp/pages/personForm.jsp +++ b/gemma-web/src/main/webapp/pages/personForm.jsp @@ -1,98 +1,101 @@ -<%@ include file="/common/taglibs.jsp"%> -<fmt:message key="personDetail.title" /> - - -

- -

- +<%@ include file="/common/taglibs.jsp" %> + +<fmt:message key="personDetail.title" /> + + +

- - - +
- -
+ + - - + - + + + - - + + - - + - + + + - + - + - - + - + + + - - - - - -
+ + - First Name - - - <%-- + + First Name + + + <%-- " id="" value="" /> --%> - " value="" /> - + " + value="" /> + - -
- -
+ + - Middle Name: - - - <%-- + + Middle Name: + + + <%-- " id="" value="" /> --%> - " value="" /> - + " + value="" /> + - -
- - + + - Last Name: - - - <%-- + + Last Name: + + + <%-- " id="" value="" /> --%> - " value="" /> - + " + value="" /> + - -
- " /> - " /> - " /> -
+
+ " /> + " /> + " /> +
diff --git a/gemma-web/src/main/webapp/pages/processProgress.jsp b/gemma-web/src/main/webapp/pages/processProgress.jsp index 035a9ba86f..47f727f315 100644 --- a/gemma-web/src/main/webapp/pages/processProgress.jsp +++ b/gemma-web/src/main/webapp/pages/processProgress.jsp @@ -1,22 +1,23 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> <%-- DEPRECATED, please use form-page-embedded ajaxified progress bar instead; see loadExpressionExperiment.js for some pointers. --%> -<fmt:message key="processProgress.title" /> - - - -

- -

+ +<fmt:message key="processProgress.title" /> + +

+Ext.onReady( function() { + var p = new progressbar(); + p.createIndeterminateProgressBar(); + p.on( 'fail', function( error ) { + alert( error ); + } ); + p.on( 'cancel', function( cancel ) { + alert( cancel ); + } ); + p.startProgress(); +} ); +
diff --git a/gemma-web/src/main/webapp/pages/register.jsp b/gemma-web/src/main/webapp/pages/register.jsp index ffdc635996..1c117222bc 100644 --- a/gemma-web/src/main/webapp/pages/register.jsp +++ b/gemma-web/src/main/webapp/pages/register.jsp @@ -2,6 +2,5 @@ Registration - \ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/systemNotices.jsp b/gemma-web/src/main/webapp/pages/systemNotices.jsp index 152c127c9c..a0a25cceb9 100644 --- a/gemma-web/src/main/webapp/pages/systemNotices.jsp +++ b/gemma-web/src/main/webapp/pages/systemNotices.jsp @@ -1,26 +1,14 @@ -<%@ include file="/common/taglibs.jsp"%> +<%@ include file="/common/taglibs.jsp" %> - System stats +System stats - -

- Compute grid status -

- -

- This page has information about the status of the Gemma compute grid. Hit 'refresh' in your browser to see updated - information. -

- - - -
-

- ${status} -

-
- - - +

Compute grid status

+

+ This page has information about the status of the Gemma compute grid. Hit 'refresh' in your browser to see updated + information. +

+
+

${status}

+
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/pages/userProfile.jsp b/gemma-web/src/main/webapp/pages/userProfile.jsp index cb92c1998d..9ff30952ed 100644 --- a/gemma-web/src/main/webapp/pages/userProfile.jsp +++ b/gemma-web/src/main/webapp/pages/userProfile.jsp @@ -1,14 +1,15 @@ -<%@ include file="/common/taglibs.jsp"%> - +<%@ include file="/common/taglibs.jsp" %> - Edit your profile - - +Edit your profile + -

- Change your email address or password. You must enter your current password. -

-
-
+
+

User Profile

+

+ Change your email address or password. You must enter your current password. +

+
+
+
\ No newline at end of file diff --git a/gemma-web/src/main/webapp/scripts/api/entities/platform/PlatformElementGrid.js b/gemma-web/src/main/webapp/scripts/api/entities/platform/PlatformElementGrid.js index 8036f55080..38f5c03dfe 100644 --- a/gemma-web/src/main/webapp/scripts/api/entities/platform/PlatformElementGrid.js +++ b/gemma-web/src/main/webapp/scripts/api/entities/platform/PlatformElementGrid.js @@ -1,7 +1,7 @@ Ext.namespace( 'Gemma' ); /** - * + * * @class Gemma.PlatformElementGrid * @extends Ext.grid.GridPanel */ @@ -26,7 +26,7 @@ Gemma.PlatformElementGrid = Ext /** * Show first batch of data. - * + * * @param {Object} * isArrayDesign * @param {Object} @@ -168,6 +168,9 @@ Gemma.PlatformElementGrid = Ext header : "Element Name", width : 130, dataIndex : "compositeSequenceName", + renderer : ( data, metadata, record ) => { + return '' + data + ''; + }, tooltip : "Element or probe name" }, { @@ -269,7 +272,7 @@ Gemma.PlatformElementGrid = Ext /** * Event handler for searches. Update the lower grid. - * + * * @param {Object} * event */