From 19f85bf175170c6ab5c4ce1b254c0fe10738e8ea Mon Sep 17 00:00:00 2001 From: Ben Alexander Date: Tue, 25 Feb 2020 15:02:27 -0500 Subject: [PATCH 01/10] Multiple mouse records were showing the same pop-up data. They were incorrectly incorporating the gene name into the target field for the pop-up --- grails-app/views/templates/dynamicUi/_MOD.gsp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/grails-app/views/templates/dynamicUi/_MOD.gsp b/grails-app/views/templates/dynamicUi/_MOD.gsp index 7baad1090..0d957434a 100644 --- a/grails-app/views/templates/dynamicUi/_MOD.gsp +++ b/grails-app/views/templates/dynamicUi/_MOD.gsp @@ -24,8 +24,8 @@ records={{numberRecords}}
{{cellPresentationString}} -
+ class="cellExpander" data-target="#mod_data_{{gene}}" style="color:black">{{cellPresentationString}} +
{{#recordsExist}} {{#geneName}}
{{.}}
From 6cf7067cc7220654bb036cce217ff334c3caaed2 Mon Sep 17 00:00:00 2001 From: mariacos Date: Thu, 27 Feb 2020 10:36:26 -0500 Subject: [PATCH 02/10] added missing translation --- grails-app/i18n/metadata.properties | 1 + 1 file changed, 1 insertion(+) diff --git a/grails-app/i18n/metadata.properties b/grails-app/i18n/metadata.properties index c87af595d..a161e4026 100755 --- a/grails-app/i18n/metadata.properties +++ b/grails-app/i18n/metadata.properties @@ -3698,6 +3698,7 @@ metadata.GWAS_UKBB_mdv112=UK Biobank Sleep Traits GWAS: Self-report metadata.GWAS_UKBB_eu_mdv112=UK Biobank Sleep Traits GWAS: Self-report metadata.GWAS_DIAGRAMimputed_mdv112=DIAGRAM 1000G GWAS metadata.GWAS_GiantUKBB_mdv112=GIANT UK Biobank GWAS +metadata.GWAS_GiantUKBB_eu_mdv112=GIANT UK Biobank GWAS metadata.GWAS_BFpercent_mdv112=Body fat percentage GWAS metadata.GWAS_EGGC_mdv112=Early Growth Genetics Consortium GWAS metadata.GWAS_HRgene_mdv112=Heart rate GWAS From de08138c008f56d67a4999347ee575eaab1b0e8c Mon Sep 17 00:00:00 2001 From: mariacos Date: Thu, 27 Feb 2020 11:29:08 -0500 Subject: [PATCH 03/10] updated dataset name translations --- grails-app/i18n/metadata.properties | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/grails-app/i18n/metadata.properties b/grails-app/i18n/metadata.properties index a161e4026..1f40cc8cb 100755 --- a/grails-app/i18n/metadata.properties +++ b/grails-app/i18n/metadata.properties @@ -3622,14 +3622,15 @@ metadata.GWAS_MAGIC-Metabochip_eu_mdv111=MAGIC Metabochip GWAS #mdv112 metadata.GWAS_CARDIoGRAM_mdv112=CARDIoGRAMplusC4D GWAS -metadata.GWAS_CKDGenConsortium_mdv112=CKDGen GWAS -metadata.GWAS_CKDGenConsortium-UACR_mdv112=CKDGen GWAS - stratified UACR associations -metadata.GWAS_CKDGenConsortium-UACR_DM_mdv112=CKDGen GWAS: individuals with T2D -metadata.GWAS_CKDGenConsortium-UACR_nonDM_mdv112=CKDGen GWAS: individuals without T2D -metadata.GWAS_CKDGenConsortium-eGFRcrea_mdv112=CKDGen GWAS - stratified serum creatinine associations -metadata.GWAS_CKDGenConsortium-eGFRcrea_aa_mdv112=CKDGen GWAS: African Americans -metadata.GWAS_CKDGenConsortium-eGFRcrea_nonDM_mdv112=CKDGen GWAS: individuals without T2D -metadata.GWAS_CKDGenConsortium-eGFRcrea_DM_mdv112=CKDGen GWAS: individuals with T2D +metadata.GWAS_CKDGenConsortium_mdv112=CKDGen 1000G GWAS + +metadata.GWAS_CKDGenConsortium-UACR_mdv112=CKDGen 1000G GWAS - stratified UACR associations +metadata.GWAS_CKDGenConsortium-UACR_DM_mdv112=CKDGen 1000G GWAS: individuals with T2D +metadata.GWAS_CKDGenConsortium-UACR_nonDM_mdv112=CKDGen 1000G GWAS: individuals without T2D +metadata.GWAS_CKDGenConsortium-eGFRcrea_mdv112=CKDGen 1000G GWAS - stratified serum creatinine associations +metadata.GWAS_CKDGenConsortium-eGFRcrea_aa_mdv112=CKDGen 1000G GWAS: African Americans +metadata.GWAS_CKDGenConsortium-eGFRcrea_nonDM_mdv112=CKDGen 1000G GWAS: individuals without T2D +metadata.GWAS_CKDGenConsortium-eGFRcrea_DM_mdv112=CKDGen 1000G GWAS: individuals with T2D metadata.GWAS_DIAGRAM_mdv112=DIAGRAM Transethnic meta-analysis metadata.GWAS_DIAGRAM_eu_mdv112=DIAGRAM GWAS + MetaboChip metadata.GWAS_DIAGRAM_eu_females_mdv112=DIAGRAM GWAS + MetaboChip: females From 3a6abb25563fdc604126810696f55b5d8a2a1ae4 Mon Sep 17 00:00:00 2001 From: Preeti Date: Thu, 27 Feb 2020 11:34:16 -0500 Subject: [PATCH 04/10] add tissue panel for osteoclast atac seq and osteoclast dnase (#189) --- grails-app/conf/Config.groovy | 125 +++++++++--------- .../mpg/RegionInfoController.groovy | 4 +- .../broadinstitute/mpg/WidgetService.groovy | 2 + 3 files changed, 68 insertions(+), 63 deletions(-) diff --git a/grails-app/conf/Config.groovy b/grails-app/conf/Config.groovy index 80c5e2c58..39708c0a6 100755 --- a/grails-app/conf/Config.groovy +++ b/grails-app/conf/Config.groovy @@ -596,68 +596,69 @@ grails.plugin.springsecurity.userLookup.authorityJoinClassName = 'org.broadinsti grails.plugin.springsecurity.authority.className = 'org.broadinstitute.mpg.people.Role' -portal.type.override = "t2d" // options are "t2d", "stroke", "mi", "ibd", "epilepsy", or "sleep". What is the portal type for all nonsystem users? - - -portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for this portal type - "T2D", // displayable label for this portal type - "mdv43", // the MDV number for this portal - "T2DKP", // name of KB data we want - "T2D", // the default phenotype for this portal - "ExSeq_19k_mdv28", // default data set. Used rarely. - ["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"], - ["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"], +portal.type.override = "bone" // options are "t2d", "stroke", "mi", "ibd", "epilepsy", or "sleep". What is the portal type for all nonsystem users? + + +portal.data.versionDesignator = [ new PortalVersionBean + ("t2d", // label for this portal type + "T2D", // displayable label for this portal type + "mdv43", // the MDV number for this portal + "T2DKP", // name of KB data we want + "T2D", // the default phenotype for this portal + "ExSeq_19k_mdv28", // default data set. Used rarely. + ["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"], + ["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"], ["Islets","Liver","SkeletalMuscle","Adipose"], // tissues to display beneath a LocusZoom plot -- use these for the DCC - // ["islet of Langerhans","liver","adipocyte"], // tissues to display beneath a LocusZoom plot -- use these for UCSD - ["GLYCEMIC", "ANTHROPOMETRIC", "RENAL", "HEPATIC", "LIPIDS", "CARDIOVASCULAR", "BLOOD PRESSURE"], // most important phenotype group name - [], // any data sets that should be omitted from LZ display - "[3]", // the assays we should search - "ExSeq_13k_mdv23", - "images/t2d/front_T2DKP_logo_2019.svg", - "portal.header.tagline", - "portal.header.title.short", - ["English", "Spanish"], - ["SLC30A8"], - ["rs13266634"], - ["chr9:21,940,000-22,190,000"], - "images/t2d/T2DKP_bg_2019.png", - "pheno.help.text", - "images/t2d/header_T2DKP_logo.svg", - "images/menu_bg_2017_5.png", - "true", - "gene.genePage.warning", - "", - '5010306206573083521', - 'http://raremetal.type2diabeteskb.org/aggregation/covariance',//URL for UMich aggregation tests - 'http://raremetal.type2diabeteskb.org/aggregation/metadata',//URL for metadata needed by aggregation tests - 1, // expose the common variant tab have on the gene page - 1, // expose the high-impact variant tab on the gene page - 1, // do we have parent level associations to show - 1, // Do we have gene level associations to show? - 1, // add a link to the GRS module into the headers. Note that the GRS module is available whether or not the link is in place - 1, // no longer used? - 0, // if true then entering a gene takes you to a region page around that chain - 1, // show the pheWAS plot - 1, // show the forest pheWAS plot - 1, // should we show the variant Association section on the variant info page - 0, // expose the green boxes on the variant info page - 0, // expose a secondary table and the credible set page built around genes, not just variants - 0, // clicking on a variant can take you to the variant info page, or else to a range page (as in V2F) - 1, // utilize bi-allelic gate, as opposed to the version that depends on multi-allelic definitions - 0, // access UC San Diego data remotely? I'm not sure if this works anymore - 0, // LEDGE tab on the gene page - 0, // Hi-C tab on the gene page - 1, // expose dynamic UI - 0, // expose the data set hierarchy in the sunburst visualization on the data page - 0, // expose the old school variant and association table. Potentially useful for debugging - 0, // expose the IGV interface in its own accordion section - 0, // expose an accordion section with the burden test on the gene page - 0, // expose the 'genes in region' tab on the gene page - 0, // expose the region adjuster for the gene page - 0, // expose the gene table on the dynamic UI - 0, // expose the variant table on the dynamic UI - 1 // expose the effector gene table - ), + // ["islet of Langerhans","liver","adipocyte"], // tissues to display beneath a LocusZoom plot -- use these for UCSD + ["GLYCEMIC", "ANTHROPOMETRIC", "RENAL", "HEPATIC", "LIPIDS", "CARDIOVASCULAR", "BLOOD PRESSURE"], // most important phenotype group name + [], // any data sets that should be omitted from LZ display + "[3]", // the assays we should search + "ExSeq_13k_mdv23", + "images/t2d/front_T2DKP_logo_2019.svg", + "portal.header.tagline", + "portal.header.title.short", + ["English", "Spanish"], + ["SLC30A8"], + ["rs13266634"], + ["chr9:21,940,000-22,190,000"], + "images/t2d/T2DKP_bg_2019.png", + "pheno.help.text", + "images/t2d/header_T2DKP_logo.svg", + "images/menu_bg_2017_5.png", + "true", + "gene.genePage.warning", + "", + '5010306206573083521', + 'http://raremetal.type2diabeteskb.org/aggregation/covariance',//URL for UMich aggregation tests + 'http://raremetal.type2diabeteskb.org/aggregation/metadata',//URL for metadata needed by aggregation tests + 1, // expose the common variant tab have on the gene page + 1, // expose the high-impact variant tab on the gene page + 1, // do we have parent level associations to show + 1, // Do we have gene level associations to show? + 1, // add a link to the GRS module into the headers. Note that the GRS module is available whether or not the link is in place + 1, // no longer used? + 0, // if true then entering a gene takes you to a region page around that chain + 1, // show the pheWAS plot + 1, // show the forest pheWAS plot + 1, // should we show the variant Association section on the variant info page + 0, // expose the green boxes on the variant info page + 0, // expose a secondary table and the credible set page built around genes, not just variants + 0, // clicking on a variant can take you to the variant info page, or else to a range page (as in V2F) + 1, // utilize bi-allelic gate, as opposed to the version that depends on multi-allelic definitions + 0, // access UC San Diego data remotely? I'm not sure if this works anymore + 0, // LEDGE tab on the gene page + 0, // Hi-C tab on the gene page + 1, // expose dynamic UI + 0, // expose the data set hierarchy in the sunburst visualization on the data page + 0, // expose the old school variant and association table. Potentially useful for debugging + 0, // expose the IGV interface in its own accordion section + 0, // expose an accordion section with the burden test on the gene page + 0, // expose the 'genes in region' tab on the gene page + 0, // expose the region adjuster for the gene page + 0, // expose the gene table on the dynamic UI + 0, // expose the variant table on the dynamic UI + 1 // expose the effector gene table +), new PortalVersionBean("stroke", "Stroke", "mdv76", @@ -997,7 +998,7 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for "GWAS_UKBiobankGEFOS_eu_mdv140",// used to pick a default data set for a gene query ["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"], ["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"], - ["SkeletalMuscle", "HSMM", "hASC-t1", "hASC-t2", "hASC-t3", "hASC-t4"], + ["Osteoblast_DNase","Osteoblast_ATAC-seq"], ["MUSCULOSKELETAL", "ANTHROPOMETRIC"], // most important phenotype group name [], "[3]", diff --git a/grails-app/controllers/org/broadinstitute/mpg/RegionInfoController.groovy b/grails-app/controllers/org/broadinstitute/mpg/RegionInfoController.groovy index 373ad7f89..0918b3313 100755 --- a/grails-app/controllers/org/broadinstitute/mpg/RegionInfoController.groovy +++ b/grails-app/controllers/org/broadinstitute/mpg/RegionInfoController.groovy @@ -520,7 +520,9 @@ class RegionInfoController { [value: 28, name:"RectalSmoothMuscle",description:"rectal smooth muscle"], [value: 29, name:"SkeletalMuscle",description:"skeletal muscle"], [value: 30, name:"StomachSmoothMuscle",description:"stomach smooth muscle"], - [value: 31, name:"SubstantiaNigra",description:"brain substantia nigra"] + [value: 31, name:"SubstantiaNigra",description:"brain substantia nigra"], + [value: 31, name:"Osteoblast_DNase",description:"Osteoblast_DNase"], + [value: 32, name:"Osteoblast_ATAC-seq ",description:"Osteoblast_ATAC-seq "], ] ArrayList annotationInformation = [ [annotationID: 1, value: 'coding', name: "Coding", description: "coding", type: "BINARY", sort_order: 1, group: "annotation" ], diff --git a/grails-app/services/org/broadinstitute/mpg/WidgetService.groovy b/grails-app/services/org/broadinstitute/mpg/WidgetService.groovy index 737b8e34d..1e8595480 100755 --- a/grails-app/services/org/broadinstitute/mpg/WidgetService.groovy +++ b/grails-app/services/org/broadinstitute/mpg/WidgetService.groovy @@ -1850,6 +1850,8 @@ public Map convertParametersToUsableFormat(def params){ beanList << new PhenotypeBean(key:"SkeletalMuscle", name:"SkeletalMuscle",description:"skeletal muscle", dataType:"tissue", suitableForDefaultDisplay: true) beanList << new PhenotypeBean(key:"StomachSmoothMuscle", name:"StomachSmoothMuscle",description:"stomach smooth muscle", dataType:"tissue", suitableForDefaultDisplay: true) beanList << new PhenotypeBean(key:"SubstantiaNigra", name:"SubstantiaNigra",description:"brain substantia nigra", dataType:"tissue", suitableForDefaultDisplay: true) + beanList << new PhenotypeBean(key:"Osteoblast_DNase ", name:"Osteoblast_DNase ",description:"Osteoblast_DNase ", dataType:"tissue", suitableForDefaultDisplay: true) + beanList << new PhenotypeBean(key:"Osteoblast_ATAC-seq", name:"Osteoblast_ATAC-seq",description:"Osteoblast_ATAC-seq", dataType:"tissue", suitableForDefaultDisplay: true) // beanList << new PhenotypeBean(key:"Islet1", name:"Islet1",description:"pancreatic islets 1", dataType:"tissue", assayId:4, suitableForDefaultDisplay: true) // beanList << new PhenotypeBean(key:"Islet2", name:"Islet2",description:"pancreatic islets 2", dataType:"tissue", assayId:4, suitableForDefaultDisplay: true) // beanList << new PhenotypeBean(key:"SkeletalMuscle", name:"SkeletalMuscle",description:"skeletal muscle", dataType:"tissue", assayId:4, suitableForDefaultDisplay: true) From c620443019c0ce4173d041c677c6d973b8cc0400 Mon Sep 17 00:00:00 2001 From: mariacos Date: Thu, 27 Feb 2020 12:25:20 -0500 Subject: [PATCH 05/10] added translations for new tissue names --- grails-app/i18n/metadata.properties | 2 ++ 1 file changed, 2 insertions(+) diff --git a/grails-app/i18n/metadata.properties b/grails-app/i18n/metadata.properties index 1f40cc8cb..90a0f4aee 100755 --- a/grails-app/i18n/metadata.properties +++ b/grails-app/i18n/metadata.properties @@ -866,6 +866,8 @@ metadata.T2D_crd=T2D credible sets metadata.BEST_VARIANT=Best variant metadata.CADD_RAW=CADD score metadata.CADD_PHRED=Phred-scaled CADD score +metadata.Osteoblast_DNase=osteoblast DNase hypersensitivity +metadata.Osteoblast_ATAC-seq=osteoblast ATAC-seq #GTex tissues From a359b1fc6f17de2f88d14453f50c689589b47f30 Mon Sep 17 00:00:00 2001 From: mariacos Date: Thu, 27 Feb 2020 15:45:40 -0500 Subject: [PATCH 06/10] updating dataset and trait stats on home page --- grails-app/views/home/portalHome.gsp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/grails-app/views/home/portalHome.gsp b/grails-app/views/home/portalHome.gsp index 34e3e2fff..cf5a8aecf 100755 --- a/grails-app/views/home/portalHome.gsp +++ b/grails-app/views/home/portalHome.gsp @@ -419,7 +419,7 @@

-

29 datasets, 52 traits

+

30 datasets, 52 traits

@@ -444,7 +444,7 @@

-

25 datasets, 73 traits

+

23 datasets, 69 traits

From 644a533a139cadb59bcec02f1a44ebb4b1dd4ac4 Mon Sep 17 00:00:00 2001 From: mariacos Date: Fri, 28 Feb 2020 14:03:01 -0500 Subject: [PATCH 07/10] added dataset name translation --- grails-app/i18n/metadata.properties | 1 + 1 file changed, 1 insertion(+) diff --git a/grails-app/i18n/metadata.properties b/grails-app/i18n/metadata.properties index 90a0f4aee..f90683a89 100755 --- a/grails-app/i18n/metadata.properties +++ b/grails-app/i18n/metadata.properties @@ -3840,6 +3840,7 @@ metadata.GWAS_GIANT-PA_men_mdv140=GIANT GWAS: men, active + inactive individuals metadata.GWAS_GIANT-PA_men_eu_mdv140=GIANT GWAS: men, Europeans, active + inactive individuals metadata.GWAS_GIANT-PA_women_mdv140=GIANT GWAS: women, active + inactive individuals metadata.GWAS_GIANT-PA_women_eu_mdv140=GIANT GWAS: women, Europeans, active + inactive individuals +metadata.GWAS_GiantUKBB_eu_mdv140=GIANT UK Biobank GWAS metadata.GWAS_GLGC_mdv140=GLGC GWAS metadata.GWAS_MAGIC_Metabochip_mdv140=MAGIC Metabochip metadata.GWAS_PGC_mdv140=PGC GWAS From 47eab057ce00b8e36477ab82f5ee5a0db7adb0dc Mon Sep 17 00:00:00 2001 From: mariacos Date: Fri, 28 Feb 2020 14:18:11 -0500 Subject: [PATCH 08/10] changed default portal type to t2d --- grails-app/conf/Config.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grails-app/conf/Config.groovy b/grails-app/conf/Config.groovy index 39708c0a6..8273b0714 100755 --- a/grails-app/conf/Config.groovy +++ b/grails-app/conf/Config.groovy @@ -596,7 +596,7 @@ grails.plugin.springsecurity.userLookup.authorityJoinClassName = 'org.broadinsti grails.plugin.springsecurity.authority.className = 'org.broadinstitute.mpg.people.Role' -portal.type.override = "bone" // options are "t2d", "stroke", "mi", "ibd", "epilepsy", or "sleep". What is the portal type for all nonsystem users? +portal.type.override = "t2d" // options are "t2d", "stroke", "mi", "ibd", "epilepsy", or "sleep". What is the portal type for all nonsystem users? portal.data.versionDesignator = [ new PortalVersionBean From bc013e474437c91155eeebcf661c247c690ab41c Mon Sep 17 00:00:00 2001 From: mariacos Date: Mon, 2 Mar 2020 19:50:14 -0500 Subject: [PATCH 09/10] updating help email --- grails-app/views/home/portalHome.gsp | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/grails-app/views/home/portalHome.gsp b/grails-app/views/home/portalHome.gsp index cf5a8aecf..0a2b5ca50 100755 --- a/grails-app/views/home/portalHome.gsp +++ b/grails-app/views/home/portalHome.gsp @@ -728,7 +728,7 @@

- +

@@ -739,7 +739,7 @@

- +

@@ -750,7 +750,7 @@

- +

@@ -762,7 +762,19 @@

- + + + +

+

+
+ + + + +
+

+

From 6e0727284dcde25c5c948c1e13e2a6b875159475 Mon Sep 17 00:00:00 2001 From: mariacos Date: Tue, 3 Mar 2020 10:50:38 -0500 Subject: [PATCH 10/10] added translation --- grails-app/i18n/metadata.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grails-app/i18n/metadata.properties b/grails-app/i18n/metadata.properties index f90683a89..7e00f5fdb 100755 --- a/grails-app/i18n/metadata.properties +++ b/grails-app/i18n/metadata.properties @@ -3110,7 +3110,7 @@ metadata.GWAS_MAGIC-Metabochip_eu_mdv76=MAGIC Metabochip GWAS metadata.GWAS_MAGIC_eu_mdv76=MAGIC GWAS metadata.GWAS_MTAGICH_eu_mdv76=Cerebral Small Vessel Disease Multi-Trait Analysis of GWAS metadata.GWAS_ISGC_eu_mdv76=Cerebral WMHV GWAS 2019 - +metadata.GWAS_GiantUKBB_eu_mdv76=GIANT UK Biobank GWAS #mdv80