@sjcrh/proteinpaint-server 2.30.4 → 2.31.0

package/cards/lollipop.json

@@ -1,327 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "label": "GDC API (GENCODE)",
-            "message": "To view a different gene from the GDC dataset: <ul><li>Scroll to the top of the page. Select 'human hg38' from the dropdown menu in the header.</li><li>Start typing the gene into the search bar. A vertical menu of gene options will appear. Click the appropriate option or hit enter.</li><li>The protein view of the gene will appear. Click on <div class='sja_opaque8' style='display: inline-block; color: black; padding: 1px 2px; border: solid 1px #545454; font-size: .9em;'>GDC</div> in the toolbar.</li></ul>",
-            "urlparam": "?genome=hg38&gene=ENST00000407796&mds3=GDC",
-            "runargs": {
-                "gene":"ENST00000407796",
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg38",
-                "tracks":[
-                    {
-                        "type": "mds3",
-                        "dslabel":"GDC"
-                    }
-                ]
-            },
-            "testSpec": {
-                "expected": { "circle": 10 }
-            }
-        },
-        {
-            "label": "GDC API (RefSeq)",
-            "message": "To view a different gene from the GDC dataset: <ul><li>Scroll to the top of the page. Select 'human hg38' from the dropdown menu in the header.</li><li>Start typing the gene into the search bar. A vertical menu of gene options will appear. Click the appropriate option or hit enter.</li><li>The protein view of the gene will appear. Click on <div class='sja_opaque8' style='display: inline-block; color: black; padding: 1px 2px; border: solid 1px #545454; font-size: .9em;'>GDC</div> in the toolbar.</li></ul>",
-            "urlparam": "?genome=hg38&gene=NM_005163&mds3=GDC",
-            "runargs": {
-                "gene":"NM_005163",
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg38",
-                "tracks":[
-                    {
-                        "type": "mds3",
-                        "dslabel":"GDC"
-                    }
-                ]
-            },
-            "testSpec": {
-                "expected": { "circle": 10 }
-            }
-        },
-        {
-            "label": "Custom Variants",
-            "runargs": {
-                "parseurl": true,
-                "noheader": true,
-                "nobox": true,
-                "genome": "hg19",
-                "gene": "NM_016734",
-                "tracks":[{
-                    "type":"mds3",
-                    "name":"custom snvindel and fusion",
-                    "custom_variants":[
-                        {"chr":"chr9","pos":37015165,"mname":"P80R","class":"M","dt":1,"ref":"G","alt":"C"},
-                        {
-                            "gene1":"PAX5", "chr1":"chr9", "pos1":37002646, "strand1":"-",
-                            "gene2":"JAK2", "chr2":"chr9", "pos2":5081726, "strand2":"+",
-                            "dt":2, "class":"Fuserna", "sample": "Fusion Sample ID"
-                        },
-                        {
-                            "gene1":"ZCCHC7", "chr1":"chr9", "pos1":37257786, "strand1":"-",
-                            "gene2":"PAX5", "chr2":"chr9", "pos2":37024824, "strand2":"-",
-                            "dt":5, "class":"SV", "sample": "SV Sample ID"
-                        }
-                    ]
-                }]
-            },
-            "testSpec": {
-                "expected": { "circle": 2 }
-            },
-            "buttons":[
-                {
-                    "name": "Custom Data Documentation",
-                    "link": "https://docs.google.com/document/d/1k50EWReR3jmJ1-Y1_jACaPkHTA65k6vLe5b-UbMgK1A/edit#heading=h.wi6hqrtn3tuq"
-                }
-            ]
-        },
-        {
-            "label": "Custom Data (Differential Phosphorylation)",
-            "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.",
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg38",
-                "gene": "NM_001203252",
-                "tracks": [
-                    {
-                        "type": "mds3",
-                        "skewerModes":[
-                            {"type":"numeric", "byAttribute":"logValue", "label":"Log2FC AD vs Control", "inuse":true, "axisheight":100}
-                        ],
-                        "name":"Tau Phosphosites",
-                        "custom_variants":[
-                            {"chr":"chr17","pos":45962452,"mname":"T39","class":"M","dt":1, "logValue": 1.32, "value2": 1},
-                            {"chr":"chr17","pos":45971861,"mname":"S46","class":"I","dt":1, "logValue": -0.06},
-                            {"chr":"chr17","pos":45971873,"mname":"T50","class":"M","dt":1, "logValue": -0.21},
-                            {"chr":"chr17","pos":45971879,"mname":"T52","class":"M","dt":1, "logValue": -0.14},
-                            {"chr":"chr17","pos":45971891,"mname":"S56","class":"I","dt":1, "logValue": 0.16, "value2": 3},
-                            {"chr":"chr17","pos":45971906,"mname":"S61","class":"I","dt":1, "logValue": -0.03},
-                            {"chr":"chr17","pos":45971912,"mname":"T63","class":"M","dt":1, "logValue": -0.05},
-                            {"chr":"chr17","pos":45971915,"mname":"S64","class":"I","dt":1, "logValue": -0.02},
-                            {"chr":"chr17","pos":45971927,"mname":"S68","class":"I","dt":1, "logValue": -0.03},
-                            {"chr":"chr17","pos":45971930,"mname":"T69","class":"M","dt":1, "logValue": -0.07},
-                            {"chr":"chr17","pos":45971936,"mname":"T71","class":"M","dt":1, "logValue": 0.08},
-                            {"chr":"chr17","pos":45974390,"mname":"T76","class":"M","dt":1, "logValue": -0.12},
-                            {"chr":"chr17","pos":45978398,"mname":"T111","class":"M","dt":1, "logValue": 0.65},
-                            {"chr":"chr17","pos":45978404,"mname":"S113","class":"I","dt":1, "logValue": 0.56},
-                            {"chr":"chr17","pos":45991553,"mname":"T175","class":"M","dt":1, "logValue": 1.74},
-                            {"chr":"chr17","pos":45991571,"mname":"T181","class":"M","dt":1, "logValue": 0.82, "value2": 4},
-                            {"chr":"chr17","pos":45991580,"mname":"S184","class":"I","dt":1, "logValue": 1.44},
-                            {"chr":"chr17","pos":45991583,"mname":"S185","class":"I","dt":1, "logValue": 0.49},
-                            {"chr":"chr17","pos":45996413,"mname":"S191","class":"I","dt":1, "logValue": 0.73},
-                            {"chr":"chr17","pos":45996425,"mname":"S195","class":"I","dt":1, "logValue": -0.21},
-                            {"chr":"chr17","pos":45996431,"mname":"Y197","class":"F","dt":1, "logValue": 0.44},
-                            {"chr":"chr17","pos":45996434,"mname":"S198","class":"I","dt":1, "logValue": 1.01},
-                            {"chr":"chr17","pos":45996437,"mname":"S199","class":"I","dt":1, "logValue": 1.59},
-                            {"chr":"chr17","pos":45996446,"mname":"S202","class":"I","dt":1, "logValue": 1.69},
-                            {"chr":"chr17","pos":45996455,"mname":"T205","class":"M","dt":1, "logValue": 1.53},
-                            {"chr":"chr17","pos":45996464,"mname":"S208","class":"I","dt":1, "logValue": -0.14},
-                            {"chr":"chr17","pos":45996470,"mname":"S210","class":"I","dt":1, "logValue": 0.04},
-                            {"chr":"chr17","pos":45996476,"mname":"S212","class":"I","dt":1, "logValue": 1.94},
-                            {"chr":"chr17","pos":45996482,"mname":"S214","class":"I","dt":1, "logValue": 0.01},
-                            {"chr":"chr17","pos":45996492,"mname":"T217","class":"M","dt":1, "logValue": 2.35},
-                            {"chr":"chr17","pos":45996502,"mname":"T220","class":"M","dt":1, "logValue": 1.82},
-                            {"chr":"chr17","pos":45996533,"mname":"T231","class":"M","dt":1, "logValue": 4.07},
-                            {"chr":"chr17","pos":45996545,"mname":"S235","class":"I","dt":1, "logValue": 4.31},
-                            {"chr":"chr17","pos":45996551,"mname":"S237","class":"I","dt":1, "logValue": 2.77},
-                            {"chr":"chr17","pos":45996554,"mname":"S238","class":"I","dt":1, "logValue": 4.36},
-                            {"chr":"chr17","pos":45996563,"mname":"S241","class":"I","dt":1, "logValue": 1.52},
-                            {"chr":"chr17","pos":45996626,"mname":"S262","class":"I","dt":1, "logValue": 2.43},
-                            {"chr":"chr17","pos":45996629,"mname":"T263","class":"M","dt":1, "logValue": 2.43},
-                            {"chr":"chr17","pos":46010340,"mname":"S285","class":"I","dt":1, "logValue": 3.22},
-                            {"chr":"chr17","pos":46010352,"mname":"S289","class":"I","dt":1, "logValue": 2.83},
-                            {"chr":"chr17","pos":46010400,"mname":"S305","class":"I","dt":1, "logValue": 5.07},
-                            {"chr":"chr17","pos":46014297,"mname":"S324","class":"I","dt":1, "logValue": 2.20},
-                            {"chr":"chr17","pos":46018686,"mname":"S356","class":"I","dt":1, "logValue": 0.65},
-                            {"chr":"chr17","pos":46018701,"mname":"T361","class":"M","dt":1, "logValue": 0.85},
-                            {"chr":"chr17","pos":46024001,"mname":"T386","class":"M","dt":1, "logValue": 1.76},
-                            {"chr":"chr17","pos":46024025,"mname":"Y394","class":"F","dt":1, "logValue": 1.43},
-                            {"chr":"chr17","pos":46024031,"mname":"S396","class":"I","dt":1, "logValue": 2.02},
-                            {"chr":"chr17","pos":46024043,"mname":"S400","class":"I","dt":1, "logValue": 2.06},
-                            {"chr":"chr17","pos":46024052,"mname":"T403","class":"M","dt":1, "logValue": 1.72},
-                            {"chr":"chr17","pos":46024055,"mname":"S404","class":"I","dt":1, "logValue": 0.61},
-                            {"chr":"chr17","pos":46024070,"mname":"S409","class":"I","dt":1, "logValue": 0.95},
-                            {"chr":"chr17","pos":46024085,"mname":"T414","class":"M","dt":1, "logValue": -0.21},
-                            {"chr":"chr17","pos":46024091,"mname":"S416","class":"I","dt":1, "logValue": 0.14},
-                            {"chr":"chr17","pos":46024109,"mname":"S422","class":"I","dt":1, "logValue": 0.53},
-                            {"chr":"chr17","pos":46024143,"mname":"S433","class":"I","dt":1, "logValue": 0.32},
-                            {"chr":"chr17","pos":46024149,"mname":"S435","class":"I","dt":1, "logValue": 0.51}
-
-                        ]
-                    }
-                ],
-                "mclassOverride": {
-                    "className": "Amino Acid Phosphosite",
-                    "classes":{
-                        "M": {
-                            "label": "Threonine",
-                            "color": "#2874A6",
-                            "desc": "phosphorylated amino acid"
-                        },
-                        "I": {
-                            "label": "Serine",
-                            "color": "#E74C3C",
-                            "desc": "phosphorylated amino acid"
-                        }, 
-                        "F": {
-                            "label": "Tyrosine",
-                            "color": "#00A86B",
-                            "desc": "phosphorylated amino acid"
-                        }
-                    }
-                }
-            },
-            "testSpec": {
-                "expected": { "circle": 10 }
-            },
-            "buttons":[
-                {
-                    "name": "Custom Data Documentation",
-                    "link": "https://docs.google.com/document/d/1k50EWReR3jmJ1-Y1_jACaPkHTA65k6vLe5b-UbMgK1A/edit#heading=h.wi6hqrtn3tuq"
-                }
-            ]
-        },
-        {
-            "label": "Data Point Shapes (Differential Phosphorylation)",
-            "message": "Add additional detail to lollipops by specifying the data point shape. Available shapes are: a solid dot (default), solid triangle, and circle. With the <span style='font-family: Courier; opacity: 0.6;'>variantShapeName</span> object, the count and additional details appears in the legend for each shape. ",
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg38",
-                "gene": "NM_001203252",
-                "tracks": [
-                    {
-                        "type": "mds3",
-                        "skewerModes":[
-                            {"type":"numeric", "byAttribute":"logValue", "label":"Log2FC AD vs Control", "inuse":true, "axisheight":100}
-                        ],
-                        "name":"Tau Phosphosites",
-                        "custom_variants":[
-                            {"chr":"chr17","pos":45962452,"mname":"T39","class":"M","dt":1, "logValue": 1.32, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45971861,"mname":"S46","class":"I","dt":1, "logValue": -0.06},
-                            {"chr":"chr17","pos":45971873,"mname":"T50","class":"M","dt":1, "logValue": -0.21, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45971879,"mname":"T52","class":"M","dt":1, "logValue": -0.14, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45971891,"mname":"S56","class":"I","dt":1, "logValue": 0.16},
-                            {"chr":"chr17","pos":45971906,"mname":"S61","class":"I","dt":1, "logValue": -0.03},
-                            {"chr":"chr17","pos":45971912,"mname":"T63","class":"M","dt":1, "logValue": -0.05, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45971915,"mname":"S64","class":"I","dt":1, "logValue": -0.02},
-                            {"chr":"chr17","pos":45971927,"mname":"S68","class":"I","dt":1, "logValue": -0.03},
-                            {"chr":"chr17","pos":45971930,"mname":"T69","class":"M","dt":1, "logValue": -0.07, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45971936,"mname":"T71","class":"M","dt":1, "logValue": 0.08, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45974390,"mname":"T76","class":"M","dt":1, "logValue": -0.12, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45978398,"mname":"T111","class":"M","dt":1, "logValue": 0.65, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45978404,"mname":"S113","class":"I","dt":1, "logValue": 0.56},
-                            {"chr":"chr17","pos":45991553,"mname":"T175","class":"M","dt":1, "logValue": 1.74, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45991571,"mname":"T181","class":"M","dt":1, "logValue": 0.82, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45991580,"mname":"S184","class":"I","dt":1, "logValue": 1.44},
-                            {"chr":"chr17","pos":45991583,"mname":"S185","class":"I","dt":1, "logValue": 0.49},
-                            {"chr":"chr17","pos":45996413,"mname":"S191","class":"I","dt":1, "logValue": 0.73},
-                            {"chr":"chr17","pos":45996425,"mname":"S195","class":"I","dt":1, "logValue": -0.21},
-                            {"chr":"chr17","pos":45996431,"mname":"Y197","class":"F","dt":1, "logValue": 0.44, "shapeCircle": true},
-                            {"chr":"chr17","pos":45996434,"mname":"S198","class":"I","dt":1, "logValue": 1.01},
-                            {"chr":"chr17","pos":45996437,"mname":"S199","class":"I","dt":1, "logValue": 1.59},
-                            {"chr":"chr17","pos":45996446,"mname":"S202","class":"I","dt":1, "logValue": 1.69},
-                            {"chr":"chr17","pos":45996455,"mname":"T205","class":"M","dt":1, "logValue": 1.53, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45996464,"mname":"S208","class":"I","dt":1, "logValue": -0.14},
-                            {"chr":"chr17","pos":45996470,"mname":"S210","class":"I","dt":1, "logValue": 0.04},
-                            {"chr":"chr17","pos":45996476,"mname":"S212","class":"I","dt":1, "logValue": 1.94},
-                            {"chr":"chr17","pos":45996482,"mname":"S214","class":"I","dt":1, "logValue": 0.01},
-                            {"chr":"chr17","pos":45996492,"mname":"T217","class":"M","dt":1, "logValue": 2.35, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45996502,"mname":"T220","class":"M","dt":1, "logValue": 1.82, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45996533,"mname":"T231","class":"M","dt":1, "logValue": 4.07, "shapeTriangle": true},
-                            {"chr":"chr17","pos":45996545,"mname":"S235","class":"I","dt":1, "logValue": 4.31},
-                            {"chr":"chr17","pos":45996551,"mname":"S237","class":"I","dt":1, "logValue": 2.77},
-                            {"chr":"chr17","pos":45996554,"mname":"S238","class":"I","dt":1, "logValue": 4.36},
-                            {"chr":"chr17","pos":45996563,"mname":"S241","class":"I","dt":1, "logValue": 1.52},
-                            {"chr":"chr17","pos":45996626,"mname":"S262","class":"I","dt":1, "logValue": 2.43},
-                            {"chr":"chr17","pos":45996629,"mname":"T263","class":"M","dt":1, "logValue": 2.43, "shapeTriangle": true},
-                            {"chr":"chr17","pos":46010340,"mname":"S285","class":"I","dt":1, "logValue": 3.22},
-                            {"chr":"chr17","pos":46010352,"mname":"S289","class":"I","dt":1, "logValue": 2.83},
-                            {"chr":"chr17","pos":46010400,"mname":"S305","class":"I","dt":1, "logValue": 5.07},
-                            {"chr":"chr17","pos":46014297,"mname":"S324","class":"I","dt":1, "logValue": 2.20},
-                            {"chr":"chr17","pos":46018686,"mname":"S356","class":"I","dt":1, "logValue": 0.65},
-                            {"chr":"chr17","pos":46018701,"mname":"T361","class":"M","dt":1, "logValue": 0.85, "shapeTriangle": true},
-                            {"chr":"chr17","pos":46024001,"mname":"T386","class":"M","dt":1, "logValue": 1.76, "shapeTriangle": true},
-                            {"chr":"chr17","pos":46024025,"mname":"Y394","class":"F","dt":1, "logValue": 1.43, "shapeCircle": true},
-                            {"chr":"chr17","pos":46024031,"mname":"S396","class":"I","dt":1, "logValue": 2.02},
-                            {"chr":"chr17","pos":46024043,"mname":"S400","class":"I","dt":1, "logValue": 2.06},
-                            {"chr":"chr17","pos":46024052,"mname":"T403","class":"M","dt":1, "logValue": 1.72, "shapeTriangle": true},
-                            {"chr":"chr17","pos":46024055,"mname":"S404","class":"I","dt":1, "logValue": 0.61},
-                            {"chr":"chr17","pos":46024070,"mname":"S409","class":"I","dt":1, "logValue": 0.95},
-                            {"chr":"chr17","pos":46024085,"mname":"T414","class":"M","dt":1, "logValue": -0.21, "shapeTriangle": true},
-                            {"chr":"chr17","pos":46024091,"mname":"S416","class":"I","dt":1, "logValue": 0.14},
-                            {"chr":"chr17","pos":46024109,"mname":"S422","class":"I","dt":1, "logValue": 0.53},
-                            {"chr":"chr17","pos":46024143,"mname":"S433","class":"I","dt":1, "logValue": 0.32},
-                            {"chr":"chr17","pos":46024149,"mname":"S435","class":"I","dt":1, "logValue": 0.51}
-
-                        ],
-                        "variantShapeName": {
-                            "dot": "Serine",
-                            "triangle": "Threonine",
-                            "circle": "Tyrosine"
-                        }
-                    }
-                ],
-                "mclassOverride": {
-                    "className": "Amino Acid Phosphosite",
-                    "classes":{
-                        "M": {
-                            "label": "Threonine",
-                            "color": "#2874A6",
-                            "desc": "phosphorylated amino acid"
-                        },
-                        "I": {
-                            "label": "Serine",
-                            "color": "#E74C3C",
-                            "desc": "phosphorylated amino acid"
-                        }, 
-                        "F": {
-                            "label": "Tyrosine",
-                            "color": "#00A86B",
-                            "desc": "phosphorylated amino acid"
-                        }
-                    }
-                }
-            },
-            "buttons":[
-                {
-                    "name":"Data Point Shape Documentation",
-                    "link": "https://docs.google.com/document/d/1k50EWReR3jmJ1-Y1_jACaPkHTA65k6vLe5b-UbMgK1A/edit#heading=h.40171yws7duw"
-                }
-            ],
-            "testSpec": {
-                "expected": { "circle": 10 }
-            }
-        },
-        {
-            "label": "Official dataset",
-            "urlparam": "?genome=hg19&gene=JAK2&dataset=Pediatric",
-            "runargs": {
-                "gene":"jak2",
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "dataset":"Pediatric"
-            },
-            "buttons":[
-                {
-                    "name":"Build an Official Dataset",
-                    "link": "https://docs.google.com/document/d/1iY7x9PzAzLKzdABam_Tfg8h-kQ0oh2UyyKC0cP-9YWA/edit"
-                }
-            ],
-            "testSpec": {
-                "expected": { "circle": 10 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1D78jKVaQrWBhAjnfmCqj0Cirf6s-CdcbfPkuZQMT8Co/edit#heading=h.tyjcwt"
-        }
-    ],
-    "ribbonMessage": "Please see the newest Custom Variant example!",
-    "citation_id": 1001
-} 

package/cards/maf.timeline.json

@@ -1,19 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true,
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "parseurl": false,
-                "maftimeline": { "uionly": true }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit"
-        }
-    ]
-}

package/cards/mavb.json

@@ -1,47 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true,
-            "runargs": {
-                "genome": "hg19",
-                "noheader": 1,
-                "parseurl": false,
-                "mavolcanoplot": {
-                "uionly": true
-                }
-            }
-        },
-        {
-            "download":"https://proteinpaint.stjude.org/ppdemo/hg19/mavb/mavbDemoData.tar.gz",
-            "runargs": {
-                "genome": "hg19",
-                "noheader": 1,
-                "mavolcanoplot": {
-                    "genome": "hg19",
-                    "noheader": 1,
-                    "file": "proteinpaint_demo/hg19/mavb/mavbDemoData.txt",
-                    "tracks": [{
-                        "name": "Demo RNA-seq coverage",
-                        "strand1": { 
-                            "file": "proteinpaint_demo/hg19/mavb/mavb_demo_sense.bw" 
-                        },
-                        "strand2": { 
-                            "file": "proteinpaint_demo/hg19/mavb/mavb_demo_antisense.bw", 
-                            "normalize": { "dividefactor": -1 } 
-                        },
-                        "type": "bigwigstranded"
-                    }]
-                }
-            },
-            "testSpec": {
-                "expected": { "rect": 2, "circle": 10 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit"
-        }
-    ]
-}

package/cards/nciGdcBtn.json

@@ -1,21 +0,0 @@
-{
-    "button": {
-        "name": "NCI GDC",
-        "intro": "The NCI's Genomic Data Commmons <a href='https://gdc.cancer.gov/about-gdc' target='GDC homepage'>(GDC)</a> coagulates data from NCI-supported programs, such as TCGA and TARGET.",
-        "searchBar": "gene",
-        "availableGenomes": ["hg38"],
-        "dsURLparam": "mds3=GDC",
-        "runargs": {
-            "nobox": true,
-            "parselurl": true,
-            "noheader": true,
-            "genome": "hg38",
-            "tracks": [
-                {
-                    "type": "mds3",
-                    "dslabel": "GDC"
-                }
-            ]
-        }
-    }
-}

package/cards/pcmBtn.json

@@ -1,16 +0,0 @@
-{
-    "button": 
-        {
-            "name": "Pediatric Cancer Mutation",
-            "intro": "The Pediatric dataset consists of somatic variants and tumor RNA-seq data shown in the protein view. The dataset is comprised of the GRCh37/hg19 genome as well as data from the Pediatric Cancer Genome Project <a href='https://permalinks.stjude.cloud/permalinks/pcgp' target='_blank'>(PCGP)</a>, NCI Target cohort, the Pan-TARGET study <a href='https://pubmed.ncbi.nlm.nih.gov/29489755/' target='_blank'>(PMID: 29489755)</a>, and the Shanghai Children's Medical Center T-ALL cohort <a href='https://pubmed.ncbi.nlm.nih.gov/32632335/' target='_blank'>(PMID: 32632335)</a>. A liftover of genomic variants and gene internals created the GRCh/hg38 dataset.",
-            "searchBar": "gene",
-            "availableGenomes": ["hg19", "hg38"],
-            "dsURLparam": "dataset=Pediatric",
-            "runargs": {
-                "nobox": true,
-                "parselurl": true,
-                "noheader": true, 
-                "dataset": "Pediatric"
-            }
-        }
-}

package/cards/ped2Btn.json

@@ -1,16 +0,0 @@
-{
-    "button": {
-        "name": "Pediatric2 GenomePaint",
-        "intro": "The Pediatric2 dataset expanded the original Pediatric dataset with non-coding variants and expression data in GenomePaint. The additional data includes Genome for Kids <a href='https://pubmed.ncbi.nlm.nih.gov/34301788/' target='blank'>(PMID: 34301788)</a>, Shanghai Children's Medical Center relapsed ALL cohort <a href='https://pubmed.ncbi.nlm.nih.gov/32632335/' target='_blank'>(PMID: 32632335)</a>, St Jude's Clinical cancer genomic profiling by three-platform sequencing study<a href='https://pubmed.ncbi.nlm.nih.gov/30262806/' target='_blank'> (PMID: 30262806)</a>, and St Jude's Pan-neuroblastoma analysis data study<a href='https://pubmed.ncbi.nlm.nih.gov/33056981/' target='_blank'> (PMID: 33056981)</a>.",
-        "searchBar": "all",
-        "availableGenomes": ["hg19", "hg38"],
-        "dsURLparam": "block=1&mds=Pediatric2,svcnv",
-        "runargs": {
-            "nobox": true,
-            "parselurl": true,
-            "noheader": true,
-            "block": true,
-            "datasetqueries":[ {"dataset": "Pediatric2", "querykey": "svcnv"} ]
-        }
-    }
-}

package/cards/pgv.json

@@ -1,59 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/pgv/pgvDemoData.tar.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/pgv/sample1.gz",
-                    "message": "",
-                    "tabixQueryCoord": "chr14:24549316-24584223"
-                },
-                {
-                    "file": "proteinpaint_demo/hg19/pgv/pgvdemo.fpkm.gz",
-                    "message": "",
-                    "tabixQueryCoord": "chr14:24549316-24584223"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "nativetracks": "RefGene",
-                "position": "chr14:24549316-24584223",
-                "tracks": [{
-                    "type": "profilegenevalue",
-                    "genevaluetrack": {
-                        "file": "proteinpaint_demo/hg19/pgv/pgvdemo.fpkm.gz"
-                    },
-                    "genevaluetype": "FPKM",
-                    "legendimg": {
-                        "file": "proteinpaint_demo/hg19/pgv/HMM.png",
-                        "width": 400,
-                        "height": 400
-                    },
-                    "name": "Demo chromHMM",
-                    "genevaluematchname": "sampleID",
-                    "tracks": [
-                        { "type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample1.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 1", "sampleID": "101" },
-                        { "type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample2.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 2", "sampleID": "102" },
-                        { "type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample3.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 3", "sampleID": "103" },
-                        { "type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample4.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 4", "sampleID": "104" },
-                        { "type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample5.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 5", "sampleID": "105" },
-                        { "type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample6.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 6", "sampleID": "106" }
-                    ]
-                }]
-            },
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1yrRpDUZWSRGuCa0snGwRuo721WRHgdYTX7GWIsZ_fSY/edit"
-        }
-    ]
-}

package/cards/scatterplot.json

@@ -1,31 +0,0 @@
-{
-    "ribbonMessage": "See the improved scatter plot! The new scatter plot contains features like grouping samples, exporting the image, plot configuration options, and more!",
-    "ppcalls": [
-        {
-            "message": "<ul style='line-height:1.5;'><li><strong>Change the plot configuration</strong>: click on the burger button (three stacked lines) in the top left of the plot. The menu provides options to change the term, dot sizes, etc.</li><li><strong>Create groups</strong>: click on the paint brush, lasso the samples of interest, and use the pop-up menu for next steps.</li><li>Open other plots and analysis tools by clicking on the grey buttons above the scatter plot.</li></ul> ",
-            "runargs": {
-                "noheader": true,
-                "mass":{
-                    "state": {
-                        "vocab": {
-                            "dslabel": "PNET",
-                            "genome": "hg19"
-                        },
-                        "plots": [
-                            {
-                                "chartType": "sampleScatter",
-                                "colorTW": {
-                                    "id": "TSNE Category"
-                                },
-                                "name": "Methylome TSNE"
-                            }
-                        ]
-                    }
-                }
-            },
-            "testSpec": {
-                "expected": { "rect": 1, "svg": 1 }
-            }
-        }
-    ]
-}

package/cards/singlecell.json

@@ -1,25 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/singlecell/singlecellDemoData.tar.gz",
-            "urlparam": "?genome=hg19&singlecell=proteinpaint_demo/hg19/singlecell/singlecell.json",
-            "jsonpath": "proteinpaint_demo/hg19/singlecell/singlecell.json",
-            "runargs": {
-                "noheader": 1,
-                "singlecell": {
-                    "genome": "hg19",
-                    "jsonfile":"proteinpaint_demo/hg19/singlecell/singlecell.json"
-                }
-            },
-            "testSpec": {
-                "expected": {"canvas": 1 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1YVxw2aPru6bAlTzUfE9GAQAvzbiBiqJiBR1X-g5ZBLI/edit"
-        }
-    ]
-}

package/cards/study.json

@@ -1,34 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true,
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "parseurl": false,
-                "project": { "uionly": true }
-            }
-        },
-        {
-            "message": "A few tips on how to interact with the study view: <ul><li>Clicking on the gene tab opens the gene table with detailed information about mutation and sample counts.</li><li>Launch the genome browser by clicking on the heatmap gene labels.</li><li>Hover over the heatmap cells to reveal the mutation and sample information</li></ul>",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/heatmapDemoData.tar.gz",
-            "jsonpath": "proteinpaint_demo/hg19/heatmap/heatmapDemo.json",
-            "runargs":{
-                "noheader": true,
-                "nobox": 1,
-                "genome": "hg19",
-                "study": "proteinpaint_demo/hg19/heatmap/heatmapDemo.json"
-            },
-            "testSpec": {
-                "timeout": 7000,
-                "expected": { "rect": 20, "line": 20, "text": 5 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1bx3VRdTzJDYdmt4CaU4PfHCOz5JSfTyuSFIuGTx-X2g/edit"
-        }
-    ]
-}