@sjcrh/proteinpaint-front 2.191.4-0 → 2.192.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/bundles.tgz +0 -0
  2. package/package.json +2 -2
  3. package/public/cards/bam.json +6 -7
  4. package/public/cards/lollipop.json +56 -76
package/bundles.tgz CHANGED
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@sjcrh/proteinpaint-front",
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- "version": "2.191.4-0",
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+ "version": "2.192.0",
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  "browser": "src/app.js",
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  "main": "src/index.js",
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  "bin": "init.js",
@@ -13,7 +13,7 @@
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  "test:integration": "echo 'TODO: front integration tests'"
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  },
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  "devDependencies": {
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- "@sjcrh/proteinpaint-client": "2.191.4-0",
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+ "@sjcrh/proteinpaint-client": "2.192.0",
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  "node-polyfill-webpack-plugin": "^4.0.0",
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  "webpack": "^5.76.0",
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  "webpack-cli": "^4.9.2",
package/public/cards/bam.json CHANGED
@@ -1,28 +1,27 @@
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  {
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  "ppcalls": [
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  {
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- "label": "Whole Exome",
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- "urlparam": "?genome=hg19&block=1&position=chr4:55589607-55590007&bamfile=Test%20WES%20BAM,proteinpaint_demo/hg19/bam/kit.exon8.del.bam",
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+ "label": "Mutation",
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+ "urlparam": "?genome=hg19&block=1&position=chr17:7577039-7577195&bamfile=Test,proteinpaint_demo/hg19/bam/tp53snv.bam",
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  "runargs": {
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  "parseurl": true,
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  "block": true,
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  "nobox": 1,
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  "noheader": 1,
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  "genome": "hg19",
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- "position": "chr4:55589707-55589907",
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+ "position": "chr17:7577039-7577195",
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  "nativetracks": "RefGene",
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  "tracks": [
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  {
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  "type": "bedj",
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  "file": "anno/refGene.hg19.gz",
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  "color": "#1D591D",
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- "name": "RefGene",
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- "filterByName": "NM_000222"
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+ "name": "RefGene"
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  },
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  {
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  "type": "bam",
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- "file": "proteinpaint_demo/hg19/bam/kit.exon8.del.bam",
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- "name": "WES KIT exon mutation demo"
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+ "file": "proteinpaint_demo/hg19/bam/tp53snv.bam",
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+ "name": "Mutation demo"
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  }
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  ]
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  },
package/public/cards/lollipop.json CHANGED
@@ -12,7 +12,8 @@
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  "tracks": [
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  {
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  "type": "mds3",
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- "dslabel": "GDC"
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+ "dslabel": "GDC",
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+ "snvIndelOnly":1
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  }
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  ]
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  },
@@ -46,7 +47,8 @@
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  }
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  },
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  {
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- "label": "Custom Variants",
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+ "label": "Custom Genomic Alterations",
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+ "message":"This example display supported genomic alterations including mutation, CNV, SV, fusion, ITD.",
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  "runargs": {
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  "parseurl": true,
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  "noheader": true,
@@ -56,7 +58,7 @@
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  "tracks": [
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  {
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  "type": "mds3",
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- "name": "custom snvindel and fusion",
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+ "name": "custom alterations",
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  "custom_variants": [
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  {
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  "chr": "chr9",
@@ -66,6 +68,7 @@
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  "dt": 1,
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  "ref": "G",
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  "alt": "C",
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+ "sample":"Sample 1",
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  "info":{"Pathogenicity":"P"}
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  },
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  {
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  "dt": 1,
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  "ref": "G",
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  "alt": "C",
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+ "sample":"Sample 1",
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  "info":{"Pathogenicity":"LP"}
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  },
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  {
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  "dt": 5,
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  "class": "SV",
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  "sample": "SV Sample ID"
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- }
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- ]
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- }
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- ]
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- },
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- "testSpec": {
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- "expected": {
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- "circle": 2
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- }
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- },
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- "buttons": [
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- {
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- "name": "Custom Data Documentation",
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- "link": "https://github.com/stjude/proteinpaint/wiki/Lollipop-%E2%80%90-mds3#tkskewermodes"
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- }
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- ]
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- },
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- {
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- "label": "Custom CNV and SNV Data",
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- "runargs": {
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- "nobox": 1,
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- "noheader": 1,
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- "genome": "hg38",
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- "gene": "NM_000546",
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- "tracks": [
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- {
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- "type": "mds3",
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- "name": "Custom data",
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- "custom_variants": [
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+ },
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  {
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- "chr": "chr17",
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- "start": 7670699,
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- "stop": 7674000,
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+ "chr": "chr9",
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+ "start": 36923400,
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+ "stop": 37015000,
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  "dt": 4,
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  "class": "CNV_amp",
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+ "sample":"Sample 1",
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  "value": 1
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  },
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  {
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- "chr": "chr17",
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- "start": 7670699,
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- "stop": 7674000,
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+ "chr": "chr9",
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+ "start": 36923535,
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+ "stop": 37034010,
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  "dt": 4,
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  "class": "CNV_loss",
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+ "sample":"Sample 2",
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  "value": -1
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  },
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  {
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- "chr": "chr17",
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- "start": 7670699,
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- "stop": 7676000,
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+ "chr": "chr9",
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+ "start": 36923333,
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+ "stop": 36923456,
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  "dt": 4,
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  "class": "CNV_loss",
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- "value": -0.5
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- },
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- {
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- "chr": "chr17",
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- "pos": 7675993,
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- "mname": "Custom snv 1",
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- "class": "M",
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- "dt": 1
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+ "value": -0.5,
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+ "sample":"Sample 3"
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  },
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  {
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- "chr": "chr17",
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- "pos": 7676520,
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- "mname": "Custom snv 2",
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- "class": "M",
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- "dt": 1
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+ "chr": "chr9",
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+ "start": 37015191,
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+ "stop": 37020799,
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+ "dt": 6,
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+ "class": "ITD",
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+ "sample":"Sample 1"
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  },
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  {
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- "chr": "chr17",
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- "pos": 7676381,
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- "mname": "Custom snv 3",
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- "class": "M",
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- "dt": 1
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+ "chr": "chr9",
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+ "start": 37015191,
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+ "stop": 37020799,
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+ "dt": 6,
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+ "class": "ITD",
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+ "sample":"Sample 2"
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  }
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  ]
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  }
@@ -183,12 +157,18 @@
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  },
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  "testSpec": {
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  "expected": {
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- "rect": 3
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+ "circle": 2
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  }
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- }
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+ },
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+ "buttons": [
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+ {
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+ "name": "Custom Data Documentation",
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+ "link": "https://github.com/stjude/proteinpaint/wiki/Lollipop-%E2%80%90-mds3#tkcustom_variants"
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+ }
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+ ]
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  },
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  {
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- "label": "Custom Data (Differential Phosphorylation)",
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+ "label": "Differential Phosphorylation",
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  "message": "Create custom datasets with the <span style='font-family: Courier; opacity: 0.6;'>mds3</span> track. In this example, custom data points with a specified value and custom mutatiion classes are shown. See the <span style='font-family: Courier; opacity: 0.6;'>skewerModes</span> attributes applied to the custom variants. <br><br><em>Tip:</em> Clicking on a class label in the legend shows and hides the mutation data.",
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  "runargs": {
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  "nobox": 1,
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  ]
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  },
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  {
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- "label": "Data Point Shapes (Differential Phosphorylation)",
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+ "label": "Data Point Shapes",
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  "message": "Add additional detail to lollipops by specifying the data point shape. Available shapes are described in <a href='https://github.com/stjude/proteinpaint/wiki/Lollipop-%E2%80%90-mds3#mshape' target='__blank' >the lollipop wiki page</a>. With the <span style='font-family: Courier; opacity: 0.6;'>.legend.customShapeLabels</span> object, the count and additional details appears in the legend for each shape.",
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  "runargs": {
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  "nobox": 1,
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  }
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  },
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  {
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- "label": "Official dataset",
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- "urlparam": "?genome=hg19&gene=JAK2&dataset=Pediatric",
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+ "label": "Default zoom",
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+ "urlparam": "?genome=hg38&gene=ENST00000407796&mds3=GDC&aarange=4,50",
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  "runargs": {
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- "gene": "jak2",
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+ "gene": "ENST00000407796",
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  "nobox": 1,
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  "noheader": 1,
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- "genome": "hg19",
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- "dataset": "Pediatric"
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+ "genome": "hg38",
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+ "aarange":[4,50],
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+ "tracks": [
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+ {
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+ "type": "mds3",
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+ "dslabel": "GDC",
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+ "snvIndelOnly":1
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+ }
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+ ]
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  },
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- "buttons": [
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- {
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- "name": "Build an Official Dataset",
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- "link": "https://docs.google.com/document/d/1iY7x9PzAzLKzdABam_Tfg8h-kQ0oh2UyyKC0cP-9YWA/edit"
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- }
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- ],
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  "testSpec": {
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  "expected": {
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  "circle": 10
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  "buttons": [
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  {
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  "name": "Documentation",
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- "link": "https://docs.google.com/document/d/1D78jKVaQrWBhAjnfmCqj0Cirf6s-CdcbfPkuZQMT8Co/edit#heading=h.tyjcwt"
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+ "link": "https://github.com/stjude/proteinpaint/wiki/Lollipop-%E2%80%90-mds3"
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  }
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  ],
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- "ribbonMessage": "Please see our newest examples for displaying cnv data: GDC CNV and Custom CNV and SNV Data.",
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  "citation_id": 1001
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  }