@sjcrh/proteinpaint-server 2.30.3 → 2.30.5

package/cards/bedj.json

@@ -1,304 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "label": "JSON BED",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/bedjDemoData.tar.gz",
-            "urlparam": "?block=on&genome=hg19&bedjfile=JSON-BED,proteinpaint_demo/hg19/bedj/gencode.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/bedj/gencode.gz",
-                    "message": "",
-                    "tabixQueryCoord": "chr17:7568451-7591984"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "bedj",
-                    "name": "JSON BED gene track demo",
-                    "file": "proteinpaint_demo/hg19/bedj/gencode.gz",
-                    "stackheight": 16,
-                    "stackspace": 1,
-                    "color": "teal"
-                }]
-            },
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        },
-        {
-            "label": "bigBed",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/knownGene.bb",
-            "urlparam": "?block=on&genome=hg19&bedjfile=bigBed demo,proteinpaint_demo/hg19/bedj/knownGene.bb",
-            "runargs": {
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "nativetracks":"RefGene",
-                "tracks":[
-                    {
-                        "type":"bedj",
-                        "name":"bigBed demo",
-                        "file":"proteinpaint_demo/hg19/bedj/knownGene.bb",
-                        "stackheight": 16,
-                        "stackspace": 1
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "bigBed file format",
-                    "link": "https://genome.ucsc.edu/goldenpath/help/bigBed.html"
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 1 }
-            }
-        },
-        {
-            "label": "BED3",
-            "message": "The bare minimum for the JSON BED track is a three column tab-delimited file with the chromosome, start position, and stop position. Below is example of the barebone rendering of the data.",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/bedj3DemoData.tar.gz",
-            "urlparam": "?genome=hg19&block=1&bedjfile=BED3_Example,proteinpaint_demo/hg19/bedj/bed3.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/bedj/bed3.gz",
-                    "tabixQueryCoord": "chr17:7449122-7706842"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "bedj",
-                    "name": "BED3 demo",
-                    "file": "proteinpaint_demo/hg19/bedj/bed3.gz",
-                    "stackheight": 16,
-                    "stackspace": 1
-                }]
-            },
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        },
-        {
-            "label": "Numeric Filter",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/numericDenomData.tar.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/bedj/value.gz",
-                    "tabixQueryCoord": "chr17:7449122-7706842"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position":"chr17:7449122-7706842",
-                "tracks":[{
-                    "type": "bedj",
-                    "name": "Numeric value demo",
-                    "file": "proteinpaint_demo/hg19/bedj/value.gz",
-                    "usevalue":{
-                        "key": "value",
-                        "dropBelowCutoff":1000
-                    },
-                    "stackheight": 16,
-                    "stackspace": 1
-                }]
-            },
-            "testSpec": {
-                "expected": {"image": 1 }
-            }
-        },
-        {
-            "label": "URL Linkout",
-            "message": "Click on a SNP item to see details on the dbSNP website.",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/bedjLinkoutDemoData.tar.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/bedj/snp.gz",
-                    "tabixQueryCoord": "chr17:7579546-7579629"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position":"chr17:7579546-7579629",
-                "tracks":[
-                    {
-                        "type": "bedj",
-                        "name": "URL linkout demo",
-                        "file": "proteinpaint_demo/hg19/bedj/snp.gz",
-                        "itemurl_appendname": "https://www.ncbi.nlm.nih.gov/snp/",
-                        "stackheight": 16,
-                        "stackspace": 1
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "'URL Linkout' Documentation",
-                    "link": "https://docs.google.com/document/d/1GP81rer7YEb0RpIej2XXfx-k7SCAL1Od9At_oczf06A/edit#heading=h.eqwpaqaeo973"
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 1, "rect": 1}
-            }
-        },
-        {
-            "label": "Hide item names",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/bedjDemoData.tar.gz",
-            "message": "In this example, the gene name is removed. To add the gene name, navigate to the right-hand side of the track, and click on <span style='color:gray; text-decoration: none;'>CONFIG</span>. Uncheck 'Hide item names' and the gene symbol will reappear.", 
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/bedj/gencode.gz",
-                    "tabixQueryCoord": "chr17:7449122-7706842"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "tracks":[
-                    {
-                        "type":"bedj",
-                        "name":"Hide names demo",
-                        "file":"proteinpaint_demo/hg19/bedj/gencode.gz",
-                        "hideItemNames": true,
-                        "stackheight": 16,
-                        "stackspace": 1
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "'Hide item names' Documentation",
-                    "link": "https://docs.google.com/document/d/1GP81rer7YEb0RpIej2XXfx-k7SCAL1Od9At_oczf06A/edit#heading=h.eqwpaqaeo973"
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 1 }
-            }
-        },
-        {
-            "label": "Show item by name",
-            "message": "To single out genes of interest, click <span style='color:gray; text-decoration: none;'>CONFIG</span> on the right-hand side of the track. Enter the isoform name(s) under 'Show items by names' and click <button>Submit</button>.<br><br>In this example, only MYC and PVT1 are shown. Delete one of the names and uncheck 'Show items by names' to see the differences in the track display.",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bedj/bedjDemoData.tar.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/bedj/gencode.gz",
-                    "tabixQueryCoord": "chr8:128538507-129301994"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position":"chr8:128538507-129301994",
-                "tracks":[
-                    {
-                        "type":"bedj",
-                        "name":"Show item names demo",
-                        "file":"proteinpaint_demo/hg19/bedj/gencode.gz",
-                        "filterByName": "ENST00000377970\nENST00000667305",
-                        "stackheight": 16,
-                        "stackspace": 1
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "'Show item by name' Documentation",
-                    "link": "https://docs.google.com/document/d/1GP81rer7YEb0RpIej2XXfx-k7SCAL1Od9At_oczf06A/edit#heading=h.eqwpaqaeo973"
-                }
-            ],
-            "arrowButtons": [
-                {
-                    "name": "Run track from URL",
-                    "message": "<p style='line-height:1.5em'>Genes of interest may be filtered in either the JSON BED, RefGene, or both. Use ensembl IDs separated by a space to filter a JSON BED track. For RefGene, use NCBI ids. See the examples below of how to use the <span style='font-family: courier; display: inline-block; color:gray;font-size:16px;'>bedjfilterbyname</span> URL parameter in each case.</p>",
-                    "links": [
-                        {
-                            "name": "JSON BED only",
-                            "link": "https://proteinpaint.stjude.org/?genome=hg19&block=1&position=chr8:128538507-129301994&bedjfilterbyname=ENST00000377970%20ENST00000667305&bedjfile=demo,proteinpaint_demo/hg19/bedj/gencode.gz"
-                        },
-                        {
-                            "name": "RefGene only",
-                            "link": "https://proteinpaint.stjude.org/?genome=hg19&block=1&position=chr8:128538507-129301994&bedjfilterbyname=NM_001354870%20NR_003367"
-                        },
-                        {
-                            "name": "JSON BED & RefGene",
-                            "link": "https://proteinpaint.stjude.org/?genome=hg19&block=1&position=chr8:128538507-129301994&bedjfilterbyname=ENST00000377970%20ENST00000667305%20NM_001354870%20NR_003367&bedjfile=demo,proteinpaint_demo/hg19/bedj/gencode.gz"
-                        }
-                    ]
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 1 }
-            }
-        },
-        {
-            "label": "Color exons",
-            "message": "<p style='margin:5px'>In the bedj file JSON object, create an \"exon2color\" array with {\"color\": \"XX\", \"start\": ##, \"stop\": ##} objects. For instance, this array defines the exon colors for this example.</p><pre style='color:#656566'><code>\"exon2color\": [{\"color\": \"red\", \"start\": 129146958, \"stop\": 129147048},...]</code></pre></p>",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg38/bedj/bedjExonColorDemoData.tar.gz",
-            "urlparam": "?genome=hg38&block=1&position=chr6:128566421-129833285&bedjfile=Exon2Color_Example,proteinpaint_demo/hg38/bedj/bedjExonColorDemo.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg38/bedj/bedjExonColorDemo.gz",
-                    "tabixQueryCoord": "chr6:128843664-129561504"
-                }
-            ],
-            "runargs": {
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg38",
-                "position":"chr6:128843664-129561504",
-                "tracks":[
-                    {
-                        "type":"bedj",
-                        "name":"Color exons demo",
-                        "file":"proteinpaint_demo/hg38/bedj/bedjExonColorDemo.gz",
-                        "stackheight": 16,
-                        "stackspace": 1
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "\"exon2color\" Documentation",
-                    "link": "https://docs.google.com/document/d/1GP81rer7YEb0RpIej2XXfx-k7SCAL1Od9At_oczf06A/edit#heading=h.j87g4brufqhu"
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 1 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1GP81rer7YEb0RpIej2XXfx-k7SCAL1Od9At_oczf06A"
-        }
-    ],
-    "ribbonMessage": "Now use bigBed files in ProteinPaint! Click on the bigBed example for more information."
-}

package/cards/bigwig.json

@@ -1,70 +0,0 @@
-{
-    "ppcalls":[
-        {
-            "isUi": true, 
-            "runargs": {
-                "noheader": true,
-                "nobox": 1, 
-                "parseurl": false, 
-                "tkui": "bigwig"
-            }
-        },
-        {
-            "label": "BigWig",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bigwig/file.bw",
-            "urlparam": "?block=on&genome=hg19&bigwigfile=BigWig_Demo,proteinpaint_demo/hg19/bigwig/file.bw",
-            "runargs":{
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "bigwig",
-                    "file": "proteinpaint_demo/hg19/bigwig/file.bw",
-                    "name": "BigWig Demo",
-                    "height": 100
-                }]
-            },
-            "buttons": [
-                {
-                    "name": "Documentation",
-                    "link": "https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9"
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        },
-        {
-            "label": "Stranded BigWig",
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/strandedbigwig/strandedbigwigDemoData.tar.gz",
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position": "chr12:6643235-6647792",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "name": "Stranded RNA-seq Demo",
-                    "strand1": { "file": "proteinpaint_demo/hg19/strandedbigwig/sense.bw" },
-                    "strand2": { "file": "proteinpaint_demo/hg19/strandedbigwig/antisense.bw", "normalize": { "dividefactor": -1 } },
-                    "type": "bigwigstranded"
-                }]
-            },
-            "buttons": [
-                {
-                    "name": "Documentation",
-                    "link": "https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.5m3g10g8lvol"
-                }
-            ],
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        }
-    ],
-    "ribbonMessage": "<p style='display: inline-block;'>Create your own bigwig track! Use the new form on the <span style='color:#1575ad; font-weight:600;'>Add Your Data</span> tab to create your own bigwig track. Additional configuration options coming soon.</p>"
-}

package/cards/citations.json

@@ -1,39 +0,0 @@
-{
-    "publications": [
-        {
-            "id": 1001,
-            "title": "Exploring genomic alteration in pediatric cancer using ProteinPaint",
-            "year": "2016",
-            "journal": "Nature Genetics",
-            "pmid": "26711108",
-            "pmidURL": "https://pubmed.ncbi.nlm.nih.gov/26711108/",
-            "doi": "https://doi.org/10.1038/ng.3466"        },
-        {
-            "id": 1002,
-            "title": "Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint",
-            "year": "2021",
-            "journal": "Cancer Cell",
-            "pmid": "33434514",
-            "pmidURL": "https://pubmed.ncbi.nlm.nih.gov/33434514/",
-            "doi": "https://doi.org/10.1016/j.ccell.2020.12.011"
-        },
-        {
-            "id": 1003,
-            "title": "CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data",
-            "year": "2020",
-            "journal": "Genome Biology",
-            "pmid": "32466770",
-            "pmidURL": "https://pubmed.ncbi.nlm.nih.gov/32466770/",
-            "doi": "https://doi.org/10.1186/s13059-020-02043-x"
-        },
-        {
-            "id": 1004,
-            "title": "ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping",
-            "year": "2023",
-            "journal": "Bioinformatics",
-            "pmid": "37140547",
-            "pmidURL": "https://ncbi.nlm.nih.gov/pmc/articles/PMC10182850/",
-            "doi": "https://doi.org/10.1093/bioinformatics/btad300"
-        }
-    ]
-}

package/cards/civicBtn.json

@@ -1,15 +0,0 @@
-{
-    "button":{
-        "name": "CIViC",
-        "intro": "The <a href='https://civicdb.org' target='_blank'>Clinical Interpretation of Variants in Cancer</a> is \"an open-source platform for crowdsourced and expert-moderated cancer variant curation.\" Supported by the NIH, NHGRI, and NCI, CIViC is a richly curated oncology dataset <a href='https://pubmed.ncbi.nlm.nih.gov/28138153/' target='_blank'>(PMID: 28138153)</a>.", 
-        "searchBar": "gene",
-        "availableGenomes": ["hg19"],
-        "dsURLparam": "dataset=CIViC",
-        "runargs": {
-            "nobox": true,
-            "parselurl": true,
-            "noheader": true,
-            "dataset": "CIViC"
-        }
-    }
-}