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Merge branch 'provenance-button' into samplegeno-ui-2
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@Bianca-Morris
Bianca-Morris committed Oct 8, 2020
2 parents a739419 + 552ae18 commit a2ee8f1
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Showing 8 changed files with 242 additions and 755 deletions.
30 changes: 15 additions & 15 deletions package-lock.json
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4 changes: 2 additions & 2 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -110,11 +110,11 @@
"html-react-parser": "^0.4.7",
"higlass": "1.11.2",
"higlass-register": "^0.3.0",
"higlass-sequence": "0.2.0",
"higlass-sequence": "0.3.1",
"higlass-transcripts": "0.2.1",
"higlass-text": "0.1.0",
"higlass-orthologs": "0.2.1",
"higlass-clinvar": "0.1.0",
"higlass-clinvar": "0.2.1",
"markdown-to-jsx": "^6.11.4",
"memoize-one": "^5.1.1",
"moment": "^2.27.0",
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
[tool.poetry]
# Note: Various modules refer to this system as "encoded", not "cgap-portal".
name = "encoded"
version = "3.2.1"
version = "3.2.3"
description = "Clinical Genomics Analysis Platform"
authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
license = "MIT"
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599 changes: 1 addition & 598 deletions src/encoded/schemas/higlass_view_config.json
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18 changes: 11 additions & 7 deletions src/encoded/static/components/item-pages/CaseView/index.js
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Expand Up @@ -677,26 +677,30 @@ const BioinformaticsTab = React.memo(function BioinformaticsTab(props) {
display_title: caseDisplayTitle,
family = null,
sample_processing: sampleProcessing = null,
sample: caseSample = null
sample: caseSample = null,
vcf_file: vcf = null
} = context;
const { "@id": vcfAtId = null } = vcf || {};

const {
original_pedigree: { display_title: pedFileName } = {},
// original_pedigree: { display_title: pedFileName } = {},
display_title: familyDisplayTitle
} = family;
const onClick = useMemo(function(){
return function(evt){
navigate("#pedigree", { skipRequest: true, replace: true });
navigate(`${vcfAtId}#provenance`, { replace: true });
};
}, []);

const title = (
<h4 data-family-index={0} className="pb-0 p-2 mb-0 d-inline-block w-100">
<span className="font-italic text-500">{ familyDisplayTitle }</span>
{ pedFileName ? <span className="text-300">{ " (" + pedFileName + ")" }</span> : null }
<button type="button" className="btn btn-sm btn-primary pull-right" data-tip="Click to view this family in the Pedigree Visualization tab" onClick={onClick}>
<i className="icon icon-fw icon-sitemap fas mr-1 small" />
View Pedigree in Separate Tab
{/* { pedFileName ? <span className="text-300">{ " (" + pedFileName + ")" }</span> : null } */}
<button type="button" className="btn btn-sm btn-primary pull-right"
data-tip="Click to view the provenance graph for the most up-to-date annotated VCF"
onClick={onClick} disabled={(!vcfAtId)}>
<i className="icon icon-fw icon-sitemap icon-rotate-90 fas mr-1 small" />
View <span className="text-500">Provenance Graph</span>
</button>
</h4>
);
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162 changes: 99 additions & 63 deletions src/encoded/tests/data/demo_inserts/higlass_view_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +3,10 @@
"viewconfig":{
"editable":true,
"zoomFixed":false,
"trackSourceServers":[
"https://cgap-higlass.com/api/v1"
],
"exportViewUrl":"/api/v1/viewconfs",
"trackSourceServers": ["https://cgap-higlass.com/api/v1"],
"views":[
{
"uid":"aa",
"initialXDomain":[
594954043.6728096,
2673883060.323411
],
"autocompleteSource":"/api/v1/suggest/?d=OHJakQICQD6gTD7skx4EWA&",
"genomePositionSearchBox":{
"autocompleteServer":"https://cgap-higlass.com/api/v1",
Expand All @@ -23,6 +16,91 @@
"visible":true
},
"chromInfoPath":"//s3.amazonaws.com/pkerp/data/hg38/chromSizes.tsv",
"tracks": {
"top": [
{
"type": "combined",
"uid": "FkGY-Yv9T8avNXljXklukw",
"height": 55,
"width": 568,
"contents": [
{
"filetype": "beddb",
"server": "https://higlass.io/api/v1",
"tilesetUid": "P0PLbQMwTYGy-5uPIQid7A",
"uid": "FocNIVsfRVWMRzfmHfncsQ",
"type": "gene-annotations",
"options": {
"fontSize": 10,
"labelColor": "black",
"labelBackgroundColor": "#ffffff",
"labelPosition": "hidden",
"labelLeftMargin": 0,
"labelRightMargin": 0,
"labelTopMargin": 0,
"labelBottomMargin": 0,
"minHeight": 24,
"plusStrandColor": "#8a8ccf",
"minusStrandColor": "#e8727a",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"showMousePosition": false,
"mousePositionColor": "#000000",
"geneAnnotationHeight": 12,
"geneLabelPosition": "outside",
"geneStrandSpacing": 2,
"name": "Gene Annotations (hg38)"
},
"width": 568,
"height": 55
},
{
"uid": "d6KeVfkNSmq_YNj_rWJgBA",
"type": "viewport-projection-horizontal",
"fromViewUid": "ab",
"options": {
"projectionFillColor": "#777",
"projectionStrokeColor": "#777",
"projectionFillOpacity": 0.3,
"projectionStrokeOpacity": 0.7,
"strokeWidth": 1
},
"width": 568,
"height": 55
}
],
"options": {}
}
],
"left": [],
"center": [],
"right": [],
"bottom": [],
"whole": [],
"gallery": []
},
"initialXDomain": [
594954043.6728096,
2673883060.323411
],
"initialYDomain": [
-2681117714.2684245,
-2681117686.505896
],
"layout": {
"w": 12,
"h": 2,
"x": 0,
"y": 0
},
"uid": "aa"
},
{
"uid":"ab",
"initialXDomain":[
594954043.6728096,
2673883060.323411
],
"tracks":{
"top":[
{
Expand Down Expand Up @@ -66,30 +144,22 @@
"barBorderColor":"white",
"sortLargestOnTop":true,
"extendedPreloading":false,
"colorScale":[
"#007FFF",
"#e8e500",
"#008000",
"#FF0038",
"#800080",
"colorScale": [
"#2c7bb6",
"#abd9e9",
"#f2f2b1",
"#fdae61",
"#808080",
"#DCDCDC"
]
},
"width":768,
"height":25
},
{
"server": "https://cgap-higlass.com/api/v1",
"uid": "emptytrack_transcripts",
"type": "empty",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 14,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"options": {},
"width": 568,
"height": 10
},
Expand Down Expand Up @@ -143,17 +213,9 @@
"height": 134
},
{
"server": "https://cgap-higlass.com/api/v1",
"uid": "emptytrack_clinvar",
"type": "empty",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 14,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"options": {},
"width": 568,
"height": 10
},
Expand Down Expand Up @@ -185,17 +247,9 @@
}
},
{
"server": "https://cgap-higlass.com/api/v1",
"uid": "emptytrack_orthologs",
"type": "empty",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 14,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"options": {},
"width": 568,
"height": 10
},
Expand All @@ -217,17 +271,9 @@
"height": 20
},
{
"server": "https://cgap-higlass.com/api/v1",
"uid": "emptytrack_orthologs2",
"type": "empty",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 14,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"options": {},
"width": 568,
"height": 7
},
Expand Down Expand Up @@ -265,17 +311,9 @@
}
},
{
"server": "https://cgap-higlass.com/api/v1",
"uid": "emptytrack",
"type": "empty",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 14,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"options": {},
"width": 568,
"height": 20
}
Expand Down Expand Up @@ -322,9 +360,7 @@
"w":12,
"h":12,
"x":0,
"y":0,
"moved":false,
"static":false
"y":0
},
"initialYDomain":[
655540254.4718345,
Expand Down Expand Up @@ -357,7 +393,7 @@
}
}
},
"name": "higlass-default-vewconf",
"name": "higlass-default-viewconf",
"title": "Default CGAP hg38 viewconf",
"genome_assembly": "GRCh38",
"uuid": "00000000-1111-0000-1111-000000000000",
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