Merge branch 'master' of https://github.com/broadinstitute/dig-diabetes-portal

Author: dkjang

grails-app/conf/Config.groovy

@@ -599,65 +599,66 @@ grails.plugin.springsecurity.authority.className = 'org.broadinstitute.mpg.peopl
 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.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]",

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" ],

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
 
@@ -3108,7 +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
 
@@ -3622,14 +3624,15 @@ 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
@@ -3698,6 +3701,7 @@ 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
@@ -3836,6 +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

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)