@sjcrh/proteinpaint-server 2.30.3 → 2.30.5

package/src/serverconfig.js

@@ -178,6 +178,17 @@ if (!serverconfig.features) {
 	// mdjsonform: true, healthcheck_keys: ["w", "rs"], etc.
 	serverconfig.features = {}
 }
+if (process.argv.find(a => a == 'validate')) {
+	// issues in the GDC API (like its servers being under maintenance) should not affect
+	// the ability of the PP server to launch itself, so skip GDC-caching during validation
+	// as the GDC API may come online later (and not require a PP server restart).
+	// This allows `npx @sjcrh/proteinpaint-server validate` to finish faster.
+	//
+	// NOTE: The server validation waits for the nodejs main thread to finish, so any unfinished
+	// async methods will still block the validation. Only other async methods are not blocked
+	// by each other while executing.
+	serverconfig.features.stopGdcCacheAliquot = true
+}
 
 if (!serverconfig.backend_only && fs.existsSync(path.join(process.cwd(), './public'))) {
 	const defaultTarget = path.join(serverconfig.binpath, 'cards')
@@ -187,25 +198,6 @@ if (!serverconfig.backend_only && fs.existsSync(path.join(process.cwd(), './publ
 			path: 'cards'
 		}
 	}
-	const cards = serverconfig.cards
-	const cardsPath = path.join(process.cwd(), './public/', cards.path)
-
-	let cardsSymlink
-	try {
-		cardsSymlink = fs.lstatSync(cardsPath)
-	} catch (e) {
-		cardsSymlink = false
-	}
-
-	// only set up the symlink if the user doesn't already have a custom public/${cards.path} directory
-	// a user may also not specify cards.path for other reasons, in that case no need for symlink
-	if (cards.path && !fs.existsSync(cardsPath) && !cardsSymlink) {
-		// a user may only wish to use a different public path for the cards
-		// and keep the defaulf of using server/cards
-		if (!cards.target) cards.target = defaultTarget
-
-		fs.symlink(serverconfig.cards.target, cardsPath, 'dir', console.error)
-	}
 }
 
 if (fs.existsSync('./public/rev.txt')) {

package/cards/2dmaf.json

@@ -1,37 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true,
-            "runargs": {
-                "genome": "hg19",
-                "nobox": 1,
-                "noheader": 1,
-                "parseurl": false,
-                "twodmaf": { "uionly": true }
-            }
-        },
-        {
-            "message": "Click on the sample label in the bar graph to display the 2DMAF plot. A new plot will appear for each clicked sample. Hide the plot by clicking on the bolded sample label.",
-            "runargs": {
-                "genome": "hg19",
-                "nobox": 1,
-                "noheader": 1,
-                "twodmaf": { 
-                    "genome": "hg19",
-                    "datasetname": "2DMAF Demo",
-                    "input": "source\tPatient\tType\tIndex\tMinD.D1_G1\tTinD.D1_G1\tdMAF\tMinN.D1_G1\tTinN.D1_G1\tMinD.R1_G1\tTinD.R1_G1\trMAF\tMinN.R1_G1\tTinN.R1_G1\tGENENAME\tCHR\tWU_HG19_POS\tCLASS\tAACHANGE\trefseq\tCALL_D1_G1\tPrimary_Purity.SNVIndel\tPrimary_Purity.CNVLOH\tnewComment.LOH\tCALL_R1_G1\tRelapse_Purity.SNVIndel\tRecurrent_purity.CNVLOH\tRelapse.CNV new comment\tlabelAs\tlabelIsVisible\tsymbol\tsymbollabel\nfiltered\tPABLDZ\tsnv\t3.140185548.C.T\t16\t41\t0.39\t0\t57\t0\t5\t0\t0\t5\tCLSTN2\t3\t140185548\tmissense\tA440V\tNM_022131\tsomatic\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\twildtype\t80%\t20%\tis low CNVLOH\tABCXYZ\t1\tstar\tXYZ-ABC\nfiltered\tPABLDZ\tsnv\t9.132630419.C.T\t14\t36\t0.39\t0\t80\t14\t36\t0.39\t0\t80\tUSP20\t9\t132630419\tmissense\tR276W\tNM_006676\tsomatic\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t11.32413565.C.G\t48\t52\t0.92\t0\t48\t20\t49\t0.41\t0\t48\tWT1\t11\t32413565\tmissense\tR445P\tNM_000378\tsomatic\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t14.102493608.A.G\t7\t30\t0.23\t1\t39\t0\t5\t0\t0\t5\tDYNC1H1\t14\t102493608\tmissense\tS2957G\tNM_001376\tsomatic\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t15.79587229.A.T\t10\t27\t0.37\t0\t43\t0\t5\t0\t0\t5\tANKRD34C\t15\t79587229\tmissense\tT535S\tNM_001146341\tsomatic\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t17.35988658.T.G\t4\t14\t0.29\t0\t22\t0\t5\t0\t0\t5\tDDX52\t17\t35988658\tmissense\tH269P\tNM_007010\tsomatic\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t2.102835470.G.A\t0\t5\t0\t0\t5\t6\t42\t0.14\t0\t42\tIL1RL2\t2\t102835470\tmissense\tR261Q\tNM_003854\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t2.224462734.C.T\t0\t5\t0\t0\t5\t15\t39\t0.38\t0\t55\tSCG2\t2\t224462734\tmissense\tG423R\tNM_003469\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t3.120998770.C.T\t0\t5\t0\t0\t5\t12\t26\t0.46\t0\t34\tSTXBP5L\t3\t120998770\tmissense\tR693W\tNM_014980\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t5.112178210.T.A\t0\t5\t0\t0\t5\t13\t45\t0.29\t0\t55\tAPC\t5\t112178210\tmissense\tS2307T\tNM_000038\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t5.167645836.G.A\t0\t5\t0\t0\t5\t5\t25\t0.2\t0\t22\tTENM2\t5\t167645836\tmissense\tR1638H\tNM_001122679\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t6.139266738.G.A\t0\t5\t0\t0\t5\t10\t33\t0.3\t0\t28\tREPS1\t6\t139266738\tmissense\tS125L\tNM_031922\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t8.131922042.C.T\t0\t5\t0\t0\t5\t9\t43\t0.21\t0\t26\tADCY8\t8\t131922042\tmissense\tG518S\tNM_001115\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPABLDZ\tsnv\t15.42985456.G.A\t0\t5\t0\t0\t5\t5\t37\t0.14\t0\t33\tSTARD9\t15\t42985456\tmissense\tV3894M\tNM_020759\twildtype\t90%\t90%, LOH 9p, 11p\tchr9p;chr11p\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tsnv\t1.202914204.A.G\t5\t43\t0.12\t0\t49\t0\t5\t0\t0\t5\tADIPOR1\t1\t202914204\tmissense\tM175T\tNM_015999\tsomatic\t80%\t20%\tis low CNVLOH\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tsnv\t2.100019386.A.G\t12\t31\t0.39\t0\t30\t15\t37\t0.41\t0\t30\tREV1\t2\t100019386\tmissense\tL1117P\tNM_016316\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tsnv\t2.168099251.A.G\t18\t36\t0.5\t0\t40\t13\t41\t0.32\t0\t40\tXIRP2\t2\t168099251\tmissense\tE450G\tNM_152381\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tsnv\t6.44248025.C.T\t25\t56\t0.45\t0\t49\t15\t43\t0.35\t0\t49\tTCTE1\t6\t44248025\tmissense\tG467S\tNM_182539\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tsnv\t6.131913557.C.T\t12\t32\t0.38\t0\t35\t16\t32\t0.5\t0\t35\tMED23\t6\t131913557\tmissense\tA1148T\tNM_004830\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tindel\t16.85682289.-.C\t13\t25\t0.52\t2\t25\t0\t5\t0\t0\t5\tGSE1\t16\t85682289\tframeshift\tT120fs\tNM_014615\tsomatic\t80%\t20%\tis low CNVLOH\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPADZCG\tsnv\t8.133090175.T.A\t0\t5\t0\t0\t5\t5\t39\t0.13\t0\t36\tHHLA1\t8\t133090175\tmissense\tR323S\tNM_001145095\twildtype\t80%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAECCE\tsnv\t2.27290381.G.A\t0\t5\t0\t0\t5\t7\t38\t0.18\t0\t29\tAGBL5\t2\t27290381\tmissense\tR703_R704>RG\tNM_021831\twildtype\t20%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAECCE\tsnv\t19.52448853.A.T\t0\t5\t0\t0\t5\t6\t35\t0.17\t0\t40\tZNF613\t19\t52448853\tmissense\tT573S\tNM_001031721\twildtype\t20%\t20%\tis low CNVLOH\tsomatic\t50%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAECCE\tsnv\tX.123182926.C.A\t0\t5\t0\t0\t5\t9\t16\t0.56\t0\t14\tSTAG2\tX\t123182926\tnonsense\tY297*\tNM_001042749\twildtype\t20%\t20%\tis low CNVLOH\tsomatic\t50%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tsnv\t1.43914293.T.C\t5\t45\t0.11\t0\t42\t0\t5\t0\t0\t5\tSZT2\t1\t43914293\tmissense\tL3270P\tNM_015284\tsomatic\t20%\t20%\tis low CNVLOH\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tsnv\t1.231556975.CT.TC\t5\t26\t0.19\t0\t30\t0\t5\t0\t0\t5\tEGLN1\t1\t231556975\tmissense\tQ220R\tNM_022051\tsomatic\t20%\t20%\tis low CNVLOH\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tindel\t1.231556978.-.C\t5\t31\t0.16\t0\t36\t0\t5\t0\t0\t5\tEGLN1\t1\t231556978\tframeshift\tG219fs\tNM_022051\tsomatic\t20%\t20%\tis low CNVLOH\twildtype\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tsnv\t8.104341924.A.G\t4\t34\t0.12\t1\t31\t9\t39\t0.23\t1\t31\tFZD6\t8\t104341924\tmissense\tE528G\tNM_003506\tsomatic\t20%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tsnv\t11.6648669.A.C\t0\t5\t0\t0\t5\t6\t26\t0.23\t0\t21\tDCHS1\t11\t6648669\tmissense\tD1867E\tNM_003737\twildtype\t20%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tsnv\t17.21117424.A.T\t0\t5\t0\t0\t5\t9\t22\t0.41\t0\t17\tTMEM11\t17\t21117424\tmissense\tS14R\tNM_003876\twildtype\t20%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEDKB\tsnv\t22.22057685.A.G\t0\t5\t0\t0\t5\t6\t39\t0.15\t0\t47\tYPEL1\t22\t22057685\tmissense\tN81_C82>HL\tNM_013313\twildtype\t20%\t20%\tis low CNVLOH\tsomatic\t80%\t20%\tis low CNVLOH\t\t\t\t\nfiltered\tPAEERJ\tsnv\t1.32207286.CA.AC\t7\t38\t0.18\t0\t23\t0\t5\t0\t0\t5\tBAI2\t1\t32207286\tmissense\tM542S\tNM_001294335\tsomatic\t80%\t20%\tis low CNVLOH\twildtype\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t2.230456366.G.A\t9\t30\t0.3\t0\t34\t9\t25\t0.36\t0\t34\tDNER\t2\t230456366\tmissense\tT172M\tNM_139072\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t5.95761588.G.T\t4\t35\t0.11\t0\t47\t0\t5\t0\t0\t5\tPCSK1\t5\t95761588\tnonsense\tS111*\tNM_000439\tsomatic\t80%\t20%\tis low CNVLOH\twildtype\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t6.31726618.G.A\t17\t41\t0.41\t0\t43\t19\t44\t0.43\t0\t43\tMSH5\t6\t31726618\tmissense\tR448H\tNM_025259\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t7.88963976.G.T\t23\t40\t0.58\t0\t38\t20\t38\t0.53\t0\t38\tZNF804B\t7\t88963976\tmissense\tE560D\tNM_181646\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t12.99093310.G.T\t6\t26\t0.23\t0\t15\t0\t5\t0\t0\t5\tAPAF1\t12\t99093310\tmissense\tG799V\tNM_013229\tsomatic\t80%\t20%\tis low CNVLOH\twildtype\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t15.42985912.G.A\t23\t37\t0.62\t0\t34\t21\t41\t0.51\t0\t34\tSTARD9\t15\t42985912\tmissense\tG4046S\tNM_020759\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t15.63929754.T.C\t13\t28\t0.46\t0\t25\t12\t25\t0.48\t0\t25\tHERC1\t15\t63929754\tmissense\tQ4061R\tNM_003922\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t15.89010548.T.A\t6\t31\t0.19\t0\t23\t0\t5\t0\t0\t5\tMRPL46\t15\t89010548\tmissense\tR21W\tNM_022163\tsomatic\t80%\t20%\tis low CNVLOH\twildtype\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tindel\t11.32417912.C.-\t10\t26\t0.38\t1\t35\t9\t34\t0.26\t1\t35\tWT1\t11\t32417912\tframeshift\tR363fs\tNM_000378\tsomatic\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t12.124337792.C.T\t0\t5\t0\t0\t5\t14\t31\t0.45\t0\t36\tDNAH10\t12\t124337792\tmissense\tR1993W\tNM_207437\twildtype\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t15.58357751.A.G\t0\t5\t0\t0\t5\t5\t31\t0.16\t0\t25\tALDH1A2\t15\t58357751\tmissense\tL33P\tNM_003888\twildtype\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tsnv\t16.2203366.C.T\t0\t5\t0\t0\t5\t7\t36\t0.19\t0\t31\tRAB26\t16\t2203366\tmissense\tR239W\tNM_014353\twildtype\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEERJ\tindel\t11.32417941.-.A\t0\t5\t0\t0\t5\t13\t36\t0.36\t1\t38\tWT1\t11\t32417941\tframeshift\tR353fs\tNM_000378\twildtype\t80%\t20%\tis low CNVLOH\tsomatic\t90%\t90%, LOH 13\tchr13\t\t\t\t\nfiltered\tPAEFGR\tsnv\t1.18808931.C.T\t11\t25\t0.44\t0\t14\t6\t21\t0.29\t0\t14\tKLHDC7A\t1\t18808931\tmissense\tR486C\tNM_152375\tsomatic\t60%\t60%\tchr16:15.5M-16.5M\tsomatic\t60%\t60%\tchr16:15.5M-16.5M\t\t\t\t\nfiltered\tPAEFGR\tsnv\t1.75097485.A.G\t4\t21\t0.19\t0\t25\t0\t5\t0\t0\t5\tERICH3\t1\t75097485\tmissense\tI244T\tNM_001002912\tsomatic\t60%\t60%\tchr16:15.5M-16.5M\twildtype\t60%\t60%\tchr16:15.5M-16.5M\t\t\t\t\nfiltered\tPAEFGR\tsnv\t1.184675840.A.C\t7\t49\t0.14\t0\t20\t0\t5\t0\t0\t5\tEDEM3\t1\t184675840\tmissense\tC714G\tNM_025191\tsomatic\t60%\t60%\tchr16:15.5M-16.5M\twildtype\t60%\t60%\tchr16:15.5M-16.5M\t\t\t\t\nfiltered\tPAEFGR\tsnv\t1.184675843.G.T\t7\t44\t0.16\t0\t21\t0\t5\t0\t0\t5\tEDEM3\t1\t184675843\tmissense\tQ713K\tNM_025191\tsomatic\t60%\t60%\tchr16:15.5M-16.5M\twildtype\t60%\t60%\tchr16:15.5M-16.5M\t\t\t\t\nfiltered\tPAEFGR\tsnv\t10.101120595.AC.TG\t11\t57\t0.19\t0\t31\t0\t5\t0\t0\t5\tCNNM1\t10\t101120595\tmissense\tD574V\tNM_020348\tsomatic\t60%\t60%\tchr16:15.5M-16.5M\twildtype\t60%\t60%\tchr16:15.5M-16.5M\t\t\t\t\t\t"
-                }
-            },
-            "testSpec": {
-                "timeout": 7000,
-                "expected": { "td": 1, "svg": 1 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1anyEDMcW1lTSf8399Li2G9r57V-Fqp2591WvoODY7n4/edit#heading=h.mne2ecmp9m13"
-        }
-    ]
-}

package/cards/README.md

@@ -1,15 +0,0 @@
-# App Drawer 
-
-JSON and .txt for the elements appearing on the app drawer
-
-## Documentation
-
-Documentation for index.json, sandbox JSONs, and other supporting files in ./server/cards is described in this [google document](https://docs.google.com/document/d/18sQH9KxG7wOUkx8kecptElEjwAuJl0xIJqDRbyhahA4/edit#heading=h.jwyqi1mhacps). 
-
-## Local Instances
-
-To run the app drawer, download demo files from hpc:~/tp/proteinpaint_demo to /local/path/data/tp. These files are also used for example htmls and http://localhost:3000/url.html links. 
-
-### Client code
-
-See `./client/appdrawer` for client side code

package/cards/ai.json

@@ -1,37 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/aicheck/aicheckDemoData.tar.gz",
-            "urlparam": "?block=on&genome=hg19&position=chr9:36816442-37058548&aicheckfile=Demo%20sample%20tumor%20allelic%20imbalance,proteinpaint_demo/hg19/aicheck/file.gz",
-            "datapreview": [
-                {
-                    "file": "proteinpaint_demo/hg19/aicheck/file.gz",
-                    "tabixQueryCoord": "chr9:36816442-37058548"
-                }
-            ],
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position": "chr9:36816442-37058548",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "aicheck",
-                    "file": "proteinpaint_demo/hg19/aicheck/file.gz",
-                    "name": "Demo sample tumor allelic imbalance"
-                }]
-            },
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1dZIOoLLbQE-kmZ31Ia_5cud30d9UeRodP4hRCSw3HII"
-        }
-    ]
-}

package/cards/arc.json

@@ -1,34 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "download":"https://proteinpaint.stjude.org/ppdemo/hg19/arc/arcDemoData.tar.gz",
-            "urlparam": "?genome=hg19&block=1&position=chr11:7839893-9165172&arcfile=Arc Track,proteinpaint_demo/hg19/arc/mango.gz",
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position": "chr11:7839893-9165172",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "hicstraw",
-                    "bedfile": "proteinpaint_demo/hg19/arc/mango.gz",
-                    "name": "Arc Track Demo",
-                    "percentile_max":99,
-                    "mode_arc": true,
-                    "mode_hm": false
-                }]
-            },
-            "testSpec": {
-                "expected": {"image": 2 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit#heading=h.8zct8j3cscak"
-        }
-    ]
-}

package/cards/ase.json

@@ -1,99 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "download":"https://proteinpaint.stjude.org/ppdemo/hg38/ase/aseDemoData.tar.gz",
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg38",
-                "position": "chr5:1252462-1297568",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "mdssvcnv",
-                    "name": "ASE Demo",
-                    "checkvcf": {
-                        "file": "proteinpaint_demo/hg38/ase/vcf.gz"
-                    },
-                    "checkrnabam": {
-                        "hetsnp_minbaf": 0.2,
-                        "hetsnp_maxbaf": 0.8,
-                        "samples": {
-                            "sample1": {
-                                "file": "proteinpaint_demo/hg38/ase/sample1.bam",
-                                "totalreads": 172048689,
-                                "pairedend": true
-                            },
-                            "sample2": {
-                                "file": "proteinpaint_demo/hg38/ase/sample2.bam",
-                                "totalreads": 151710239,
-                                "pairedend": true
-                            },
-                            "sample3": {
-                                "file": "proteinpaint_demo/hg38/ase/sample3.bam",
-                                "totalreads": 167864903,
-                                "pairedend": true
-                            },
-                            "sample4": {
-                                "file": "proteinpaint_demo/hg38/ase/sample4.bam",
-                                "totalreads": 153196442,
-                                "pairedend": true
-                            },
-                            "sample12": {
-                                "file": "proteinpaint_demo/hg38/ase/sample12.bam",
-                                "totalreads": 155650314,
-                                "pairedend": true
-                            },
-                            "sample5": {
-                                "file": "proteinpaint_demo/hg38/ase/sample5.bam",
-                                "totalreads": 144649042,
-                                "pairedend": true
-                            },
-                            "sample6": {
-                                "file": "proteinpaint_demo/hg38/ase/sample6.bam",
-                                "totalreads": 170516947,
-                                "pairedend": true
-                            },
-                            "sample7": {
-                                "file": "proteinpaint_demo/hg38/ase/sample7.bam",
-                                "totalreads": 167971047,
-                                "pairedend": true
-                            },
-                            "sample8": {
-                                "file": "proteinpaint_demo/hg38/ase/sample8.bam",
-                                "totalreads": 137990338,
-                                "pairedend": true
-                            },
-                            "sample9": {
-                                "file": "proteinpaint_demo/hg38/ase/sample9.bam",
-                                "totalreads": 150401722,
-                                "pairedend": true
-                            },
-                            "sample10": {
-                                "file": "proteinpaint_demo/hg38/ase/sample10.bam",
-                                "totalreads": 131681552,
-                                "pairedend": true
-                            },
-                            "sample11": {
-                                "file": "proteinpaint_demo/hg38/ase/sample11.bam",
-                                "totalreads": 150240544,
-                                "pairedend": true
-                            }
-                        }
-                    }
-                }]
-            },
-            "testSpec": {
-                "timeout": 7000,
-                "expected": { "rect": 5, "line": 10 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit#heading=h.ly3x0hngycmz"
-        }
-    ]
-}

package/cards/bam.json

@@ -1,264 +0,0 @@
-{
-	"ppcalls": [
-		{
-			"label": "Whole Exome",
-			"download": "https://proteinpaint.stjude.org/ppdemo/hg19/bam/bamDemoData.westkit.tar.gz",
-			"urlparam": "?genome=hg19&block=1&position=chr4:55589607-55590007&bamfile=Test%20WES%20BAM,proteinpaint_demo/hg19/bam/kit.exon8.del.bam",
-			"runargs": {
-				"parseurl": true,
-				"block": true,
-				"nobox": 1,
-				"noheader": 1,
-				"genome": "hg19",
-				"position": "chr4:55589707-55589907",
-				"nativetracks": "RefGene",
-				"tracks": [
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_000222"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/kit.exon8.del.bam",
-						"name": "WES KIT exon mutation demo"
-					}
-				]
-			},
-			"testSpec": {
-				"expected": { "image": 2 }
-			}
-		},
-		{
-			"label": "TP53 Deletion (deep sequencing)",
-			"message": "For specific variants, use the <span style='font-family: courier; display: inline-block; opacity: 0.7;font-size:16px;'>variants</span> key. Enter a number that is <em>zero based</em> for the position (i.e. <span style='font-family: courier; display: inline-block; opacity: 0.7; font-size:16px;'>pos</span> value).",
-			"urlparam": "?genome=hg19&block=1&bamfile=TP53_del,proteinpaint_demo/hg19/bam/TP53_del.bam&position=chr17:7578191-7578591&variant=chr17.7578383.AGCAGCGCTCATGGTGGGG.A&bedjfilterbyname=NM_000546",
-			"download": "https://proteinpaint.stjude.org/ppdemo/hg19/bam/bamTP53ExonDelDemo.tar.gz",
-			"runargs": {
-				"parseurl": true,
-				"block": true,
-				"nobox": 1,
-				"noheader": 1,
-				"genome": "hg19",
-				"position": "chr17:7578191-7578591",
-				"nativetracks": "RefGene",
-				"tracks": [
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_000546"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/TP53_del.bam",
-						"name": "TP53 deletion demo",
-						"variants": [
-							{
-								"chr": "chr17",
-								"pos": 7578382,
-								"ref": "AGCAGCGCTCATGGTGGGG",
-								"alt": "A"
-							}
-						]
-					}
-				]
-			},
-			"testSpec": {
-				"expected": { "image": 2 }
-			}
-		},
-		{
-			"label": "CBL Complex Mutation (exome-seq)",
-			"urlparam": "?genome=hg19&block=1&bamfile=SJAML040555_D2%20WES,proteinpaint_demo/hg19/bam/wrong_indel.bam&position=chr4:55589768-55589770&variant=chr4.55589768.CTTACGA.AGGG",
-			"download": "https://proteinpaint.stjude.org/ppdemo/hg19/bam/bamExonMutDemo.tar.gz",
-			"runargs": {
-				"parseurl": true,
-				"block": true,
-				"nobox": 1,
-				"noheader": 1,
-				"genome": "hg19",
-				"position": "chr4:55589768-55589770",
-				"nativetracks": "RefGene",
-				"tracks": [
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_000222"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/wrong_indel.bam",
-						"name": "CBL complex mutation",
-						"variants": [
-							{
-								"chr": "chr4",
-								"pos": 55589767,
-								"ref": "CTTACGA",
-								"alt": "AGGG"
-							}
-						]
-					}
-				]
-			},
-			"testSpec": {
-				"expected": { "image": 2 }
-			}
-		},
-		{
-			"label": "SETD2 Splice Site Insertion (RNA-seq)",
-			"urlparam": "?genome=hg19&block=1&position=chr3:47155260-47155500&hlregion=chr3:47155365-47155365&bamfile=splice_junction_variant,proteinpaint_demo/hg19/bam/splice_junction_variant.bam&variant=chr3.47155366.G.GGGGCT",
-			"download": "https://proteinpaint.stjude.org/ppdemo/hg19/bam/bamSpliceSiteDemo.tar.gz",
-			"runargs": {
-				"parseurl": true,
-				"block": true,
-				"nobox": 1,
-				"noheader": 1,
-				"genome": "hg19",
-				"position": "chr3:47155260-47155500",
-				"nativetracks": "RefGene",
-				"tracks": [
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_014159"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/splice_junction_variant.bam",
-						"name": "SETD2 splice site 5-bp insertion",
-						"variants": [
-							{
-								"chr": "chr3",
-								"pos": 47155365,
-								"ref": "G",
-								"alt": "GGGGCT"
-							}
-						]
-					}
-				]
-			},
-			"testSpec": {
-				"expected": { "image": 2 }
-			}
-		},
-		{
-			"label": "Multi-allelic Complex Mutations (RNA-seq)",
-			"message": "In this example, two alternate alleles, CTGACAGGCT and GTTTC, for multi-allelic KIT exonic complex mutations in one tumor are shown. Continue scrolling down to see the second BAM track for GTTTC",
-			"download": "https://proteinpaint.stjude.org/ppdemo/hg19/bam/bamMAMutDemo.tar.gz",
-			"runargs": {
-				"parseurl": true,
-				"block": true,
-				"nobox": 1,
-				"noheader": 1,
-				"genome": "hg19",
-				"position": "chr4:55589660-55589870",
-				"nativetracks": "RefGene",
-				"tracks": [
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_000222"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/multi_allele.bam",
-						"name": "CTGACAGGCT Alternate Allele",
-						"variants": [
-							{
-								"chr": "chr4",
-								"pos": 55589772,
-								"ref": "GACAGGC",
-								"alt": "CTGACAGGCT"
-							}
-						]
-					},
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_000222"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/multi_allele.bam",
-						"name": "GTTTC Alternate Allele",
-						"variants": [
-							{
-								"chr": "chr4",
-								"pos": 55589765,
-								"ref": "GACTTACGACA",
-								"alt": "GTTTC"
-							}
-						]
-					}
-				]
-			},
-			"testSpec": {
-				"expected": { "image": 2 }
-			},
-			"buttons": [
-				{
-					"name": "Run 1st Allele Track from URL",
-					"link": "https://proteinpaint.stjude.org/?genome=hg19&block=1&position=chr4:55589660-55589870&hlregion=chr4:55589768-55589768&bamfile=Alternate_allele1,proteinpaint_demo/hg19/bam/multi_allele.bam&variant=chr4.55589773.GACAGGC.CTGACAGGCT"
-				},
-				{
-					"name": "Run 2nd Allele Track from URL",
-					"link": "https://proteinpaint.stjude.org/?genome=hg19&block=1&position=chr4:55589660-55589870&hlregion=chr4:55589768-55589768&bamfile=Alternate_allele2,proteinpaint_demo/hg19/bam/multi_allele.bam&variant=chr4.55589766.GACTTACGACA.GTTTC"
-				}
-			]
-		},
-		{
-			"label": "CREBBP Focal Deletion",
-			"urlparam": "?genome=hg19&block=1&bamfile=Focal deletion demo,proteinpaint_demo/hg19/bam/crebbp.bam&position=chr16:3800245-3803429",
-			"download": "https://proteinpaint.stjude.org/ppdemo/hg19/bam/bamExonicDelDemo.tar.gz",
-			"runargs": {
-				"parseurl": true,
-				"block": true,
-				"nobox": 1,
-				"noheader": 1,
-				"genome": "hg19",
-				"position": "chr16:3800245-3803429",
-				"nativetracks": "RefGene",
-				"tracks": [
-					{
-						"type": "bedj",
-						"file": "anno/refGene.hg19.gz",
-						"color": "#1D591D",
-						"name": "RefGene",
-						"filterByName": "NM_004380"
-					},
-					{
-						"type": "bam",
-						"file": "proteinpaint_demo/hg19/bam/crebbp.bam",
-						"name": "CREBBP focal deletion"
-					}
-				]
-			},
-			"testSpec": {
-				"expected": { "image": 2 }
-			}
-		}
-	],
-	"buttons": [
-		{
-			"name": "Download BAM Slicing Script",
-			"download": "https://proteinpaint.stjude.org/ppdemo/scripts/slice_bam4pp.py.gz"
-		},
-		{
-			"name": "BAM track supporting information",
-			"link": "https://proteinpaint.stjude.org/bam"
-		}
-	],
-	"citation_id": 1004
-}

package/cards/bampile.json

@@ -1,22 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "download": "https://proteinpaint.stjude.org/ppdemo/hg19/bampile/bampileDemoData.tar.gz",
-            "urlparam": "?block=on&genome=hg19&position=chr12:25362480-25363264&bampilefile=Test%20Bampile,proteinpaint_demo/hg19/bampile/tk.gz",
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position": "chr12:25362480-25363264",
-                "nativetracks": "RefGene",
-                "tracks": [{
-                    "type": "bampile",
-                    "file": "proteinpaint_demo/hg19/bampile/tk.gz",
-                    "name": "Bampile Demo"
-                }]
-            }
-        }
-    ]
-}