From d53576fca927c706710bebbdfc27006d10b25f72 Mon Sep 17 00:00:00 2001 From: Alexander Veit <53857412+alexander-veit@users.noreply.github.com> Date: Fri, 28 Jul 2023 09:11:41 -0400 Subject: [PATCH 1/2] Fix SV viewconf --- pyproject.toml | 2 +- .../master-inserts/higlass_view_config.json | 1007 +++++++++-------- 2 files changed, 519 insertions(+), 490 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b4c271f950..41c6b13186 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "14.0.0" +version = "14.0.1" description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" diff --git a/src/encoded/tests/data/master-inserts/higlass_view_config.json b/src/encoded/tests/data/master-inserts/higlass_view_config.json index 4c9801a491..8cae2cfadb 100644 --- a/src/encoded/tests/data/master-inserts/higlass_view_config.json +++ b/src/encoded/tests/data/master-inserts/higlass_view_config.json @@ -317,501 +317,530 @@ "name": "higlass-sv-viewconf", "title": "Default CGAP SV viewconf", "viewconfig": { - "views": [ - { - "uid": "aa", - "layout": { - "h": 2, - "w": 12, - "x": 0, - "y": 0 + "views": [ + { + "uid": "aa", + "layout": { + "h": 2, + "w": 12, + "x": 0, + "y": 0 + }, + "tracks": { + "top": [ + { + "uid": "BrlJsUYFRzuJRZyYeKDX2A", + "type": "chromosome-labels", + "width": 811, + "height": 30, + "server": "https://cgap-higlass.com/api/v1", + "options": { + "color": "#808080", + "stroke": "#ffffff", + "fontSize": 12, + "fontIsLeftAligned": false, + "showMousePosition": false, + "mousePositionColor": "#000000" }, - "tracks": { - "top": [ - { - "uid": "BrlJsUYFRzuJRZyYeKDX2A", - "type": "chromosome-labels", - "width": 811, - "height": 30, - "server": "https://cgap-higlass.com/api/v1", - "options": { - "color": "#808080", - "stroke": "#ffffff", - "fontSize": 12, - "fontIsLeftAligned": false, - "showMousePosition": false, - "mousePositionColor": "#000000" - }, - "filetype": "chromsizes-tsv", - "tilesetUid": "chromsizes_hg38" - }, - { - "uid": "FkGY-Yv9T8avNXljXklukw", - "type": "combined", - "width": 568, - "height": 55, - "options": {}, - "contents": [ - { - "uid": "FocNIVsfRVWMRzfmHfncsQ", - "type": "gene-annotations", - "width": 568, - "height": 55, - "server": "https://cgap-higlass.com/api/v1", - "options": { - "name": "Gene Annotations (hg38)", - "fontSize": 10, - "minHeight": 24, - "labelColor": "black", - "labelPosition": "hidden", - "labelTopMargin": 0, - "labelLeftMargin": 0, - "plusStrandColor": "#8a8ccf", - "labelRightMargin": 0, - "minusStrandColor": "#e8727a", - "trackBorderColor": "black", - "trackBorderWidth": 0, - "geneLabelPosition": "outside", - "geneStrandSpacing": 2, - "labelBottomMargin": 0, - "showMousePosition": false, - "mousePositionColor": "#000000", - "geneAnnotationHeight": 12, - "labelBackgroundColor": "#ffffff" - }, - "filetype": "beddb", - "tilesetUid": "gene_annotation_hg38" - }, - { - "uid": "d6KeVfkNSmq_YNj_rWJgBA", - "type": "viewport-projection-horizontal", - "width": 568, - "height": 55, - "options": { - "strokeWidth": 1, - "projectionFillColor": "#777", - "projectionFillOpacity": 0.3, - "projectionStrokeColor": "#777", - "projectionStrokeOpacity": 0.7 - }, - "fromViewUid": "ab" - } - ] - }, - { - "uid": "texttrack_cyto", - "type": "text", - "width": 568, - "height": 25, - "server": "https://cgap-higlass.com/api/v1", - "options": { - "text": "Chromosome bands", - "align": "left", - "offsetY": 12, - "fontSize": 11, - "textColor": "#777777", - "fontFamily": "Arial", - "fontWeight": "normal", - "backgroundColor": "#ffffff" - } - }, - { - "uid": "cytoband", - "data": { - "type": "vcf", - "tbiUrl": "https://cgap-higlass.s3.amazonaws.com/vcf/cytoBandWithDelimiter.hg38.vcf.gz.tbi", - "vcfUrl": "https://cgap-higlass.s3.amazonaws.com/vcf/cytoBandWithDelimiter.hg38.vcf.gz", - "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes" - }, - "type": "vcf", - "width": 470, - "height": 30, - "options": { - "displayConfiguration": { - "mark": { - "size": 16, - "type": "nominal", - "field": "INFO:GIESTAIN", - "range": [ - "triangle-east", - "triangle-west" - ], - "domain": [ - "acen-east", - "acen-west" - ], - "default": "rect" - }, - "xEnd": { - "field": "INFO:END" - }, - "color": { - "type": "nominal", - "field": "INFO:GIESTAIN", - "range": [ - "#3ed0ed", - "#FF2323", - "#FF2323", - "#9F9F9F", - "#4F4F4F", - "#EEEEEE", - "#B9B9B9", - "#848484", - "#6A6A6A", - "#4F4F4F" - ], - "domain": [ - "delimiter", - "acen-east", - "acen-west", - "stalk", - "gvar", - "gneg", - "gpos25", - "gpos50", - "gpos75", - "gpos100" - ], - "default": "#000000" - }, - "label": { - "text": "$INFO:NAME$", - "type": "contained", - "align": "left", - "color": "automatic", - "excludes": { - "field": "INFO:GIESTAIN", - "values": [ - "acen-east", - "acen-west", - "delimiter" - ] - }, - "fontSize": 13 - }, - "xStart": { - "field": "POS" - }, - "tooltip": { - "type": "nominal", - "field": "INFO:GIESTAIN", - "range": [ - "
Chromosome:$CHROM$
Name:$INFO:NAME$
Stain:acen
", - "
Chromosome:$CHROM$
Name:$INFO:NAME$
Stain:acen
", - "Chromosome boundary" - ], - "domain": [ - "acen-east", - "acen-west", - "delimiter" - ], - "default": "
Chromosome:$CHROM$
Name:$INFO:NAME$
Stain:$INFO:GIESTAIN$
" - }, - "yAlignment": { - "type": "horizontal" - } - } - } - } - ], - "left": [], - "right": [], - "whole": [ - { - "x": 1558492997, - "uid": "vr01", - "type": "vertical-rule", - "width": 20, - "height": 20, - "options": { - "color": "#ffd280" - } - }, - { - "x": 1558492998, - "uid": "vr02", - "type": "vertical-rule", - "width": 20, - "height": 20, - "options": { - "color": "#ffd280" - } - } - ], - "bottom": [], - "center": [], - "gallery": [] + "filetype": "chromsizes-tsv", + "tilesetUid": "chromsizes_hg38" + }, + { + "uid": "FkGY-Yv9T8avNXljXklukw", + "type": "combined", + "width": 568, + "height": 55, + "options": {}, + "contents": [ + { + "uid": "FocNIVsfRVWMRzfmHfncsQ", + "type": "gene-annotations", + "width": 568, + "height": 55, + "server": "https://cgap-higlass.com/api/v1", + "options": { + "name": "Gene Annotations (hg38)", + "fontSize": 10, + "minHeight": 24, + "labelColor": "black", + "labelPosition": "hidden", + "labelTopMargin": 0, + "labelLeftMargin": 0, + "plusStrandColor": "#8a8ccf", + "labelRightMargin": 0, + "minusStrandColor": "#e8727a", + "trackBorderColor": "black", + "trackBorderWidth": 0, + "geneLabelPosition": "outside", + "geneStrandSpacing": 2, + "labelBottomMargin": 0, + "showMousePosition": false, + "mousePositionColor": "#000000", + "geneAnnotationHeight": 12, + "labelBackgroundColor": "#ffffff" + }, + "filetype": "beddb", + "tilesetUid": "gene_annotation_hg38" + }, + { + "uid": "d6KeVfkNSmq_YNj_rWJgBA", + "type": "viewport-projection-horizontal", + "width": 568, + "height": 55, + "options": { + "strokeWidth": 1, + "projectionFillColor": "#777", + "projectionFillOpacity": 0.3, + "projectionStrokeColor": "#777", + "projectionStrokeOpacity": 0.7 + }, + "fromViewUid": "ab" + } + ] + }, + { + "uid": "texttrack_cyto", + "type": "text", + "width": 568, + "height": 25, + "server": "https://cgap-higlass.com/api/v1", + "options": { + "text": "Chromosome bands", + "align": "left", + "offsetY": 12, + "fontSize": 11, + "textColor": "#777777", + "fontFamily": "Arial", + "fontWeight": "normal", + "backgroundColor": "#ffffff" + } + }, + { + "uid": "cytoband", + "data": { + "type": "vcf", + "tbiUrl": "https://cgap-higlass.s3.amazonaws.com/vcf/cytoBandWithDelimiter.hg38.vcf.gz.tbi", + "vcfUrl": "https://cgap-higlass.s3.amazonaws.com/vcf/cytoBandWithDelimiter.hg38.vcf.gz", + "chromSizesUrl": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes" }, - "chromInfoPath": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes", - "initialXDomain": [ - 594954043.6728096, - 2673883060.323411 - ], - "initialYDomain": [ - -2681117714.2684245, - -2681117686.505896 - ], - "autocompleteSource": "/api/v1/suggest/?d=gene_annotation_hg38&", - "genomePositionSearchBox": { - "visible": true, - "chromInfoId": "hg38", - "autocompleteId": "gene_annotation_hg38", - "chromInfoServer": "https://cgap-higlass.com/api/v1", - "autocompleteServer": "https://cgap-higlass.com/api/v1" + "type": "vcf", + "width": 470, + "height": 30, + "options": { + "displayConfiguration": { + "mark": { + "size": 16, + "type": "nominal", + "field": "INFO:GIESTAIN", + "range": ["triangle-east", "triangle-west"], + "domain": ["acen-east", "acen-west"], + "default": "rect" + }, + "xEnd": { + "field": "INFO:END" + }, + "color": { + "type": "nominal", + "field": "INFO:GIESTAIN", + "range": [ + "#3ed0ed", + "#FF2323", + "#FF2323", + "#9F9F9F", + "#4F4F4F", + "#EEEEEE", + "#B9B9B9", + "#848484", + "#6A6A6A", + "#4F4F4F" + ], + "domain": [ + "delimiter", + "acen-east", + "acen-west", + "stalk", + "gvar", + "gneg", + "gpos25", + "gpos50", + "gpos75", + "gpos100" + ], + "default": "#000000" + }, + "label": { + "text": "$INFO:NAME$", + "type": "contained", + "align": "left", + "color": "automatic", + "excludes": { + "field": "INFO:GIESTAIN", + "values": ["acen-east", "acen-west", "delimiter"] + }, + "fontSize": 13 + }, + "xStart": { + "field": "POS" + }, + "tooltip": { + "type": "nominal", + "field": "INFO:GIESTAIN", + "range": [ + "
Chromosome:$CHROM$
Name:$INFO:NAME$
Stain:acen
", + "
Chromosome:$CHROM$
Name:$INFO:NAME$
Stain:acen
", + "Chromosome boundary" + ], + "domain": ["acen-east", "acen-west", "delimiter"], + "default": "
Chromosome:$CHROM$
Name:$INFO:NAME$
Stain:$INFO:GIESTAIN$
" + }, + "yAlignment": { + "type": "horizontal" + } + } } - }, - { - "uid": "ab", - "layout": { - "h": 12, - "w": 12, - "x": 0, - "y": 0 + } + ], + "left": [], + "right": [], + "whole": [ + { + "x": 1558492997, + "uid": "vr01", + "type": "vertical-rule", + "width": 20, + "height": 20, + "options": { + "color": "#ffd280" + } + }, + { + "x": 1558492998, + "uid": "vr02", + "type": "vertical-rule", + "width": 20, + "height": 20, + "options": { + "color": "#ffd280" + } + } + ], + "bottom": [], + "center": [], + "gallery": [] + }, + "chromInfoPath": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes", + "initialXDomain": [594954043.6728096, 2673883060.323411], + "initialYDomain": [-2681117714.2684245, -2681117686.505896], + "autocompleteSource": "/api/v1/suggest/?d=gene_annotation_hg38&", + "genomePositionSearchBox": { + "visible": true, + "chromInfoId": "hg38", + "autocompleteId": "gene_annotation_hg38", + "chromInfoServer": "https://cgap-higlass.com/api/v1", + 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"chromSizesUrl": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes" + }, + "type": "sv", + "width": 470, + "height": 55, + "options": { + "dataSource": "cgap-sv" + } + }, + { + "uid": "vcf-cgap-cnv", + "data": { + "type": "vcf", + "vcfUrl": "VCF_URL", + "tbiUrl": "TBI_URL", + "chromSizesUrl": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes" + }, + "type": "sv", + "width": 470, + "height": 150, + "options": { + "dataSource": "cgap-cnv" + } + }, + { + "uid": "gnomad-sv-hg38", + "data": { + "type": "vcf", + "tbiUrl": "https://cgap-higlass.s3.amazonaws.com/gnomad/gnomad_sv_hg38.vcf.gz.tbi", + "vcfUrl": "https://cgap-higlass.s3.amazonaws.com/gnomad/gnomad_sv_hg38.vcf.gz", + "chromSizesUrl": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes" + }, + "type": "sv", + "width": 470, + "height": 250, + "options": { + "dataSource": "gnomad" + } + } + ], + "left": [], + "right": [], + "whole": [ + { + "x": 1558492997, + "uid": "vr11", + "type": "vertical-rule", + "width": 20, + "height": 20, + "options": { + "color": "#ffd280" + } + }, + { + "x": 1558492998, + "uid": "vr12", + "type": "vertical-rule", + "width": 20, + "height": 20, + "options": { + "color": "#ffd280" + } + } + ], + "bottom": [], + "center": [], + "gallery": [] + }, + "chromInfoPath": "https://cgap-higlass.s3.amazonaws.com/sequence/hg38.mod.chrom.sizes", + "initialXDomain": [1069795.099783097, 1070508.6726894341], + "initialYDomain": [1350225534.8565273, 1350225534.8565273], + "autocompleteSource": "/api/v1/suggest/?d=gene_annotation_hg38&", + "genomePositionSearchBox": { + "visible": true, + "chromInfoId": "hg38", + "autocompleteId": "gene_annotation_hg38", + "chromInfoServer": "https://cgap-higlass.com/api/v1", + "autocompleteServer": "https://cgap-higlass.com/api/v1" + } + } + ], + "editable": true, + "zoomFixed": false, + "zoomLocks": { + "locksDict": {}, + "locksByViewUid": {} + }, + "exportViewUrl": "/api/v1/viewconfs", + "locationLocks": { + "locksDict": {}, + "locksByViewUid": {} + }, + "valueScaleLocks": { + "locksDict": {}, + "locksByViewUid": {} + }, + "trackSourceServers": ["https://cgap-higlass.com/api/v1"] }, "genome_assembly": "GRCh38", "instance_height": 500, From 672a1bae72cdbc0ef991dcb87d23aca9cde288a9 Mon Sep 17 00:00:00 2001 From: Alexander Veit <53857412+alexander-veit@users.noreply.github.com> Date: Fri, 28 Jul 2023 09:16:31 -0400 Subject: [PATCH 2/2] Update CHANGELOG.rst --- CHANGELOG.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 01c2905597..1e9ac8652a 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,11 @@ cgap-portal Change Log ---------- +14.0.1 +====== +* Update Higlass SV view config + + 14.0.0 ====== * July 2023