@sjcrh/proteinpaint-server 2.25.0 → 2.26.0

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 (11) hide show
  1. package/dataset/clinvar.hg19.js +3 -3
  2. package/dataset/clinvar.hg38.js +20 -3
  3. package/genome/cgc.js +7 -0
  4. package/genome/hg19.js +2 -0
  5. package/genome/hg38.js +9 -2
  6. package/package.json +8 -8
  7. package/routes/genelookup.ts +58 -0
  8. package/routes/healthcheck.ts +72 -0
  9. package/server.js +1 -1
  10. package/utils/fastclust.R +8 -6
  11. package/src/routes/healthcheck.ts +0 -92
package/dataset/clinvar.hg19.js CHANGED
@@ -6,15 +6,15 @@ exports.default = {
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  dsinfo: [
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  { k: 'Source', v: '<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>' },
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  { k: 'Data type', v: 'SNV/Indel' },
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- { k: 'Gene annotation', v: 'VEP version 107' },
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- { k: 'Download date', v: 'July 2022' }
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+ { k: 'Gene annotation', v: 'VEP version 100' },
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+ { k: 'Download date', v: 'May 2023' }
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  ],
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  genome: 'hg19',
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  queries: {
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  snvindel: {
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  forTrack: true,
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  byrange: {
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- bcffile: 'hg19/clinvar.hg19.hgvs_short.vep.bcf.gz',
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+ bcffile: 'hg19/clinvar.hg19.bcf.gz',
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  infoFields: [
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  {
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  name: 'Clinical Significance',
package/dataset/clinvar.hg38.js CHANGED
@@ -6,15 +6,24 @@ exports.default = {
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  dsinfo: [
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  { k: 'Source', v: '<a href=http://www.ncbi.nlm.nih.gov/clinvar/ target=_blank>NCBI ClinVar</a>' },
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  { k: 'Data type', v: 'SNV/Indel' },
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- { k: 'Gene annotation', v: 'VEP version 107' },
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- { k: 'Download date', v: 'July 2022' }
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+ { k: 'Gene annotation', v: 'VEP version 100' },
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+ { k: 'Download date', v: 'May 2023' }
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  ],
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  genome: 'hg38',
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+ viewModes: [
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+ {
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+ byInfo: 'gnomAD_AF',
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+ inuse: true
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+ },
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+ {
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+ byInfo: 'gnomAD_AF_afr'
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+ }
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+ ],
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  queries: {
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  snvindel: {
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  forTrack: true,
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  byrange: {
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- bcffile: 'hg38/clinvar.hg38.hgvs_short.vep.bcf.gz',
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+ bcffile: 'hg38/clinvar.hg38.bcf.gz',
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  // list of info fields with special configurations
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  infoFields: [
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  {
@@ -22,6 +31,14 @@ exports.default = {
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  key: 'CLNSIG',
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  categories: clinvar_js_1.clinsig,
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  separator: '|'
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+ },
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+ {
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+ name: 'gnomAD_AF',
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+ key: 'gnomAD_AF'
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+ },
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+ {
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+ name: 'gnomAD_AF_afr',
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+ key: 'gnomAD_AF_afr'
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  }
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  ]
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  },
package/genome/cgc.js ADDED
@@ -0,0 +1,7 @@
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+ "use strict";
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+ /*
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+ */
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.CancerGeneCensusLst = void 0;
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+ var text = "\nA1CF\nABI1\nABL1\nABL2\nACKR3\nACSL3\nACSL6\nACVR1\nACVR1B\nACVR2A\nAFDN\nAFF1\nAFF3\nAFF4\nAKAP9\nAKT1\nAKT2\nAKT3\nALDH2\nALK\nAMER1\nANK1\nAPC\nAPOBEC3B\nAR\nARAF\nARHGAP26\nARHGAP35\nARHGAP5\nARHGEF10\nARHGEF10L\nARHGEF12\nARID1A\nARID1B\nARID2\nARNT\nASPM\nASPSCR1\nASXL1\nASXL2\nATF1\nATIC\nATM\nATP1A1\nATP2B3\nATR\nATRX\nAXIN1\nAXIN2\nB2M\nBAP1\nBARD1\nBAX\nBAZ1A\nBCL10\nBCL11A\nBCL11B\nBCL2\nBCL2L12\nBCL3\nBCL6\nBCL7A\nBCL9\nBCL9L\nBCLAF1\nBCOR\nBCORL1\nBCR\nBIRC3\nBIRC6\nBLM\nBMP5\nBMPR1A\nBRAF\nBRCA1\nBRCA2\nBRD3\nBRD4\nBRIP1\nBTG1\nBTG2\nBTK\nBUB1B\nC15orf65\nCACNA1D\nCALR\nCAMTA1\nCANT1\nCARD11\nCARS\nCASP3\nCASP8\nCASP9\nCBFA2T3\nCBFB\nCBL\nCBLB\nCBLC\nCCDC6\nCCNB1IP1\nCCNC\nCCND1\nCCND2\nCCND3\nCCNE1\nCCR4\nCCR7\nCD209\nCD274\nCD28\nCD74\nCD79A\nCD79B\nCDC73\nCDH1\nCDH10\nCDH11\nCDH17\nCDK12\nCDK4\nCDK6\nCDKN1A\nCDKN1B\nCDKN2A\nCDKN2C\nCDX2\nCEBPA\nCEP89\nCHCHD7\nCHD2\nCHD4\nCHEK2\nCHIC2\nCHST11\nCIC\nCIITA\nCLIP1\nCLP1\nCLTC\nCLTCL1\nCNBD1\nCNBP\nCNOT3\nCNTNAP2\nCNTRL\nCOL1A1\nCOL2A1\nCOL3A1\nCOX6C\nCPEB3\nCREB1\nCREB3L1\nCREB3L2\nCREBBP\nCRLF2\nCRNKL1\nCRTC1\nCRTC3\nCSF1R\nCSF3R\nCSMD3\nCTCF\nCTNNA1\nCTNNA2\nCTNNB1\nCTNND1\nCTNND2\nCUL3\nCUX1\nCXCR4\nCYLD\nCYP2C8\nCYSLTR2\nDAXX\nDCAF12L2\nDCC\nDCTN1\nDDB2\nDDIT3\nDDR2\nDDX10\nDDX3X\nDDX5\nDDX6\nDEK\nDGCR8\nDICER1\nDNAJB1\nDNM2\nDNMT3A\nDROSHA\nDUX4L1\nEBF1\nECT2L\nEED\nEGFR\nEIF1AX\nEIF3E\nEIF4A2\nELF3\nELF4\nELK4\nELL\nELN\nEML4\nEP300\nEPAS1\nEPHA3\nEPHA7\nEPS15\nERBB2\nERBB3\nERBB4\nERC1\nERCC2\nERCC3\nERCC4\nERCC5\nERG\nESR1\nETNK1\nETV1\nETV4\nETV5\nETV6\nEWSR1\nEXT1\nEXT2\nEZH2\nEZR\nFADD\nFAM131B\nFAM135B\nFAM47C\nFANCA\nFANCC\nFANCD2\nFANCE\nFANCF\nFANCG\nFAS\nFAT1\nFAT3\nFAT4\nFBLN2\nFBXO11\nFBXW7\nFCGR2B\nFCRL4\nFEN1\nFES\nFEV\nFGFR1\nFGFR1OP\nFGFR2\nFGFR3\nFGFR4\nFH\nFHIT\nFIP1L1\nFKBP9\nFLCN\nFLI1\nFLNA\nFLT3\nFLT4\nFNBP1\nFOXA1\nFOXL2\nFOXO1\nFOXO3\nFOXO4\nFOXP1\nFOXR1\nFSTL3\nFUBP1\nFUS\nGAS7\nGATA1\nGATA2\nGATA3\nGLI1\nGMPS\nGNA11\nGNAQ\nGNAS\nGOLGA5\nGOLPH3\nGOPC\nGPC3\nGPC5\nGPHN\nGRIN2A\nGRM3\nH3F3A\nH3F3B\nHERPUD1\nHEY1\nHIF1A\nHIP1\nHIST1H3B\nHIST1H4I\nHLA-A\nHLF\nHMGA1\nHMGA2\nHMGN2P46\nHNF1A\nHNRNPA2B1\nHOOK3\nHOXA11\nHOXA13\nHOXA9\nHOXC11\nHOXC13\nHOXD11\nHOXD13\nHRAS\nHSP90AA1\nHSP90AB1\nID3\nIDH1\nIDH2\nIGF2BP2\nIGH\nIGK\nIGL\nIKBKB\nIKZF1\nIKZF3\nIL2\nIL21R\nIL6ST\nIL7R\nIRF4\nIRS4\nISX\nITGAV\nITK\nJAK1\nJAK2\nJAK3\nJAZF1\nJUN\nKAT6A\nKAT6B\nKAT7\nKCNJ5\nKDM5A\nKDM5C\nKDM6A\nKDR\nKDSR\nKEAP1\nKIAA1549\nKIF5B\nKIT\nKLF4\nKLF6\nKLK2\nKMT2A\nKMT2C\nKMT2D\nKNL1\nKNSTRN\nKRAS\nKTN1\nLARP4B\nLASP1\nLATS1\nLATS2\nLCK\nLCP1\nLEF1\nLEPROTL1\nLHFPL6\nLIFR\nLMNA\nLMO1\nLMO2\nLPP\nLRIG3\nLRP1B\nLSM14A\nLYL1\nLYN\nLZTR1\nMACC1\nMAF\nMAFB\nMALAT1\nMALT1\nMAML2\nMAP2K1\nMAP2K2\nMAP2K4\nMAP3K1\nMAP3K13\nMAPK1\nMAX\nMB21D2\nMDM2\nMDM4\nMDS2\nMECOM\nMED12\nMEN1\nMET\nMGMT\nMITF\nMLF1\nMLH1\nMLLT1\nMLLT10\nMLLT11\nMLLT3\nMLLT6\nMN1\nMNX1\nMPL\nMRTFA\nMSH2\nMSH6\nMSI2\nMSN\nMTCP1\nMTOR\nMUC1\nMUC16\nMUC4\nMUTYH\nMYB\nMYC\nMYCL\nMYCN\nMYD88\nMYH11\nMYH9\nMYO5A\nMYOD1\nN4BP2\nNAB2\nNACA\nNBEA\nNBN\nNCKIPSD\nNCOA1\nNCOA2\nNCOA4\nNCOR1\nNCOR2\nNDRG1\nNF1\nNF2\nNFATC2\nNFE2L2\nNFIB\nNFKB2\nNFKBIE\nNIN\nNKX2-1\nNONO\nNOTCH1\nNOTCH2\nNPM1\nNR4A3\nNRAS\nNRG1\nNSD1\nNSD2\nNSD3\nNT5C2\nNTHL1\nNTRK1\nNTRK2\nNTRK3\nNUMA1\nNUP214\nNUP98\nNUTM1\nNUTM2B\nNUTM2D\nOLIG2\nOMD\nP2RY8\nPABPC1\nPAFAH1B2\nPALB2\nPATZ1\nPAX3\nPAX5\nPAX7\nPAX8\nPBRM1\nPBX1\nPCBP1\nPCM1\nPDCD1LG2\nPDE4DIP\nPDGFB\nPDGFRA\nPDGFRB\nPER1\nPHF6\nPHOX2B\nPICALM\nPIK3CA\nPIK3CB\nPIK3R1\nPIM1\nPLAG1\nPLCG1\nPML\nPMS1\nPMS2\nPOLD1\nPOLE\nPOLG\nPOLQ\nPOLR2A\nPOT1\nPOU2AF1\nPOU5F1\nPPARG\nPPFIBP1\nPPM1D\nPPP2R1A\nPPP6C\nPRCC\nPRDM1\nPRDM16\nPRDM2\nPREX2\nPRF1\nPRKACA\nPRKAR1A\nPRKCB\nPRKD1\nPRPF40B\nPRRX1\nPSIP1\nPTCH1\nPTEN\nPTK6\nPTPN11\nPTPN13\nPTPN6\nPTPRB\nPTPRC\nPTPRD\nPTPRK\nPTPRT\nPWWP2A\nQKI\nRABEP1\nRAC1\nRAD17\nRAD21\nRAD51B\nRAF1\nRALGDS\nRANBP2\nRAP1GDS1\nRARA\nRB1\nRBM10\nRBM15\nRECQL4\nREL\nRET\nRFWD3\nRGPD3\nRGS7\nRHOA\nRHOH\nRMI2\nRNF213\nRNF43\nROBO2\nROS1\nRPL10\nRPL22\nRPL5\nRPN1\nRSPO2\nRSPO3\nRUNX1\nRUNX1T1\nS100A7\nSALL4\nSBDS\nSDC4\nSDHA\nSDHAF2\nSDHB\nSDHC\nSDHD\nSEPT5\nSEPT6\nSEPT9\nSET\nSETBP1\nSETD1B\nSETD2\nSETDB1\nSF3B1\nSFPQ\nSFRP4\nSGK1\nSH2B3\nSH3GL1\nSHTN1\nSIRPA\nSIX1\nSIX2\nSKI\nSLC34A2\nSLC45A3\nSMAD2\nSMAD3\nSMAD4\nSMARCA4\nSMARCB1\nSMARCD1\nSMARCE1\nSMC1A\nSMO\nSND1\nSNX29\nSOCS1\nSOX2\nSOX21\nSPECC1\nSPEN\nSPOP\nSRC\nSRGAP3\nSRSF2\nSRSF3\nSS18\nSS18L1\nSSX1\nSSX2\nSSX4\nSTAG1\nSTAG2\nSTAT3\nSTAT5B\nSTAT6\nSTIL\nSTK11\nSTRN\nSUB1\nSUFU\nSUZ12\nSYK\nTAF15\nTAL1\nTAL2\nTBL1XR1\nTBX3\nTCEA1\nTCF12\nTCF3\nTCF7L2\nTCL1A\nTEC\nTENT5C\nTERT\nTET1\nTET2\nTFE3\nTFEB\nTFG\nTFPT\nTFRC\nTGFBR2\nTHRAP3\nTLX1\nTLX3\nTMEM127\nTMPRSS2\nTMSB4X\nTNC\nTNFAIP3\nTNFRSF14\nTNFRSF17\nTOP1\nTP53\nTP63\nTPM3\nTPM4\nTPR\nTRA\nTRAF7\nTRB\nTRD\nTRIM24\nTRIM27\nTRIM33\nTRIP11\nTRRAP\nTSC1\nTSC2\nTSHR\nU2AF1\nUBR5\nUSP44\nUSP6\nUSP8\nUSP9X\nVAV1\nVHL\nVTI1A\nWAS\nWDCP\nWIF1\nWNK2\nWRN\nWT1\nWWTR1\nXPA\nXPC\nXPO1\nYWHAE\nZBTB16\nZCCHC8\nZEB1\nZFHX3\nZMYM2\nZMYM3\nZNF331\nZNF384\nZNF429\nZNF479\nZNF521\nZNRF3\nZRSR2";
7
+ exports.CancerGeneCensusLst = text.trim().split('\n');
package/genome/hg19.js CHANGED
@@ -75,6 +75,7 @@ exports.default = {
75
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  }
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  }
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  ],
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+ /*
78
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  geneset: [
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  {
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  name: 'Signaling',
@@ -127,6 +128,7 @@ exports.default = {
127
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  ]
128
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  }
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  ],
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+ */
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  defaultcoord: {
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  chr: 'chr17',
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  start: 7568451,
package/genome/hg38.js CHANGED
@@ -1,6 +1,7 @@
1
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  "use strict";
2
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  Object.defineProperty(exports, "__esModule", { value: true });
3
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  var clinvar_1 = require("../dataset/clinvar");
4
+ var cgc_js_1 = require("./cgc.js");
4
5
  exports.default = {
5
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  species: 'human',
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  genomefile: 'genomes/hg38.gz',
@@ -48,7 +49,8 @@ exports.default = {
48
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  },
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  {
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  __isgene: true,
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- file: 'anno/gencode.v41.hg38.gz',
52
+ name: 'GENCODE v43',
53
+ file: 'anno/gencode.v43.hg38.gz',
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  translatecoding: true,
53
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  categories: {
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  coding: { color: '#004D99', label: 'Coding gene' },
@@ -57,7 +59,6 @@ exports.default = {
57
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  pseudo: { color: '#FF00CC', label: 'Pseudogene' }
58
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  },
59
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  type: 'bedj',
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- name: 'GENCODE v41',
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  stackheight: 16,
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  stackspace: 1,
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  vpad: 4
@@ -105,6 +106,12 @@ exports.default = {
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  file: 'anno/hicFragment/hic.NcoI.hg38.gz'
106
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  }
107
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  ],
109
+ geneset: [
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+ {
111
+ name: 'Cancer Gene Census',
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+ lst: cgc_js_1.CancerGeneCensusLst
113
+ }
114
+ ],
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  majorchr: "chr1\t248956422\nchr2\t242193529\nchr3\t198295559\nchr4\t190214555\nchr5\t181538259\nchr6\t170805979\nchr7\t159345973\nchr8\t145138636\nchr9\t138394717\nchr10\t133797422\nchr11\t135086622\nchr12\t133275309\nchr13\t114364328\nchr14\t107043718\nchr15\t101991189\nchr16\t90338345\nchr17\t83257441\nchr18\t80373285\nchr19\t58617616\nchr20\t64444167\nchr21\t46709983\nchr22\t50818468\nchrX\t156040895\nchrY\t57227415\nchrM\t16569",
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  minorchr: "chr15_KI270905v1_alt\t5161414 chr6_GL000256v2_alt\t4929269 chr6_GL000254v2_alt\t4827813 chr6_GL000251v2_alt\t4795265 chr6_GL000253v2_alt\t4677643\n\tchr6_GL000250v2_alt\t4672374 chr6_GL000255v2_alt\t4606388 chr6_GL000252v2_alt\t4604811 chr17_KI270857v1_alt\t2877074 chr16_KI270853v1_alt\t2659700\n\tchr16_KI270728v1_random\t1872759 chr17_GL000258v2_alt\t1821992 chr5_GL339449v2_alt\t1612928 chr14_KI270847v1_alt\t1511111 chr17_KI270908v1_alt\t1423190\n\tchr14_KI270846v1_alt\t1351393 chr5_KI270897v1_alt\t1144418 chr7_KI270803v1_alt\t1111570 chr19_GL949749v2_alt\t1091841 chr19_KI270938v1_alt\t1066800\n\tchr19_GL949750v2_alt\t1066390 chr19_GL949748v2_alt\t1064304 chr19_GL949751v2_alt\t1002683 chr19_GL949746v1_alt\t987716 chr19_GL949752v1_alt\t987100\n\tchr8_KI270821v1_alt\t985506 chr1_KI270763v1_alt\t911658 chr6_KI270801v1_alt\t870480 chr19_GL949753v2_alt\t796479 chr19_GL949747v2_alt\t729520\n\tchr8_KI270822v1_alt\t624492 chr4_GL000257v2_alt\t586476 chr12_KI270904v1_alt\t572349 chr4_KI270925v1_alt\t555799 chr15_KI270852v1_alt\t478999\n\tchr15_KI270727v1_random\t448248 chr9_KI270823v1_alt\t439082 chr15_KI270850v1_alt\t430880 chr1_KI270759v1_alt\t425601 chr12_GL877876v1_alt\t408271\n\tchrUn_KI270442v1\t392061 chr17_KI270862v1_alt\t391357 chr15_GL383555v2_alt\t388773 chr19_GL383573v1_alt\t385657 chr4_KI270896v1_alt\t378547\n\tchr4_GL383528v1_alt\t376187 chr17_GL383563v3_alt\t375691 chr8_KI270810v1_alt\t374415 chr1_GL383520v2_alt\t366580 chr1_KI270762v1_alt\t354444\n\tchr15_KI270848v1_alt\t327382 chr17_KI270909v1_alt\t325800 chr14_KI270844v1_alt\t322166 chr8_KI270900v1_alt\t318687 chr10_GL383546v1_alt\t309802\n\tchr13_KI270838v1_alt\t306913 chr8_KI270816v1_alt\t305841 chr22_KI270879v1_alt\t304135 chr8_KI270813v1_alt\t300230 chr11_KI270831v1_alt\t296895\n\tchr15_GL383554v1_alt\t296527 chr8_KI270811v1_alt\t292436 chr18_GL383567v1_alt\t289831 chrX_KI270880v1_alt\t284869 chr8_KI270812v1_alt\t282736\n\tchr19_KI270921v1_alt\t282224 chr17_KI270729v1_random\t280839 chr17_JH159146v1_alt\t278131 chrX_KI270913v1_alt\t274009 chr6_KI270798v1_alt\t271782\n\tchr7_KI270808v1_alt\t271455 chr22_KI270876v1_alt\t263666 chr15_KI270851v1_alt\t263054 chr22_KI270875v1_alt\t259914 chr1_KI270766v1_alt\t256271\n\tchr19_KI270882v1_alt\t248807 chr3_KI270778v1_alt\t248252 chr15_KI270849v1_alt\t244917 chr4_KI270786v1_alt\t244096 chr12_KI270835v1_alt\t238139\n\tchr17_KI270858v1_alt\t235827 chr19_KI270867v1_alt\t233762 chr16_KI270855v1_alt\t232857 chr8_KI270926v1_alt\t229282 chr5_GL949742v1_alt\t226852\n\tchr3_KI270780v1_alt\t224108 chr17_GL383565v1_alt\t223995 chr2_KI270774v1_alt\t223625 chr4_KI270790v1_alt\t220246 chr11_KI270927v1_alt\t218612\n\tchr19_KI270932v1_alt\t215732 chr11_KI270903v1_alt\t214625 chr2_KI270894v1_alt\t214158 chr14_GL000225v1_random\t211173 chrUn_KI270743v1\t210658\n\tchr11_KI270832v1_alt\t210133 chr7_KI270805v1_alt\t209988 chr4_GL000008v2_random\t209709 chr7_KI270809v1_alt\t209586 chr19_KI270887v1_alt\t209512\n\tchr4_KI270789v1_alt\t205944 chr3_KI270779v1_alt\t205312 chr19_KI270914v1_alt\t205194 chr19_KI270886v1_alt\t204239 chr11_KI270829v1_alt\t204059\n\tchr14_GL000009v2_random\t201709 chr21_GL383579v2_alt\t201197 chr11_JH159136v1_alt\t200998 chr19_KI270930v1_alt\t200773 chrUn_KI270747v1\t198735\n\tchr18_GL383571v1_alt\t198278\n\tchr19_KI270920v1_alt\t198005\n\tchr6_KI270797v1_alt\t197536\n\tchr3_KI270935v1_alt\t197351\n\tchr17_KI270861v1_alt\t196688\n\tchr15_KI270906v1_alt\t196384\n\tchr5_KI270791v1_alt\t195710\n\tchr14_KI270722v1_random\t194050\n\tchr16_GL383556v1_alt\t192462\n\tchr13_KI270840v1_alt\t191684\n\tchr14_GL000194v1_random\t191469\n\tchr11_JH159137v1_alt\t191409\n\tchr19_KI270917v1_alt\t190932\n\tchr7_KI270899v1_alt\t190869\n\tchr19_KI270923v1_alt\t189352\n\tchr10_KI270825v1_alt\t188315\n\tchr19_GL383576v1_alt\t188024\n\tchr19_KI270922v1_alt\t187935\n\tchrUn_KI270742v1\t186739\n\tchr22_KI270878v1_alt\t186262\n\tchr19_KI270929v1_alt\t186203\n\tchr11_KI270826v1_alt\t186169\n\tchr6_KB021644v2_alt\t185823\n\tchr17_GL000205v2_random\t185591\n\tchr1_KI270765v1_alt\t185285\n\tchr19_KI270916v1_alt\t184516\n\tchr19_KI270890v1_alt\t184499\n\tchr3_KI270784v1_alt\t184404\n\tchr12_GL383551v1_alt\t184319\n\tchr20_KI270870v1_alt\t183433\n\tchrUn_GL000195v1\t182896\n\tchr1_GL383518v1_alt\t182439\n\tchr22_KI270736v1_random\t181920\n\tchr10_KI270824v1_alt\t181496\n\tchr14_KI270845v1_alt\t180703\n\tchr3_GL383526v1_alt\t180671\n\tchr13_KI270839v1_alt\t180306\n\tchr22_KI270733v1_random\t179772\n\tchrUn_GL000224v1\t179693\n\tchr10_GL383545v1_alt\t179254\n\tchrUn_GL000219v1\t179198\n\tchr5_KI270792v1_alt\t179043\n\tchr17_KI270860v1_alt\t178921\n\tchr19_GL000209v2_alt\t177381\n\tchr11_KI270830v1_alt\t177092\n\tchr9_KI270719v1_random\t176845\n\tchrUn_GL000216v2\t176608\n\tchr22_KI270928v1_alt\t176103\n\tchr1_KI270712v1_random\t176043\n\tchr6_KI270800v1_alt\t175808\n\tchr1_KI270706v1_random\t175055\n\tchr2_KI270776v1_alt\t174166\n\tchr18_KI270912v1_alt\t174061\n\tchr3_KI270777v1_alt\t173649\n\tchr5_GL383531v1_alt\t173459\n\tchr3_JH636055v2_alt\t173151\n\tchr14_KI270725v1_random\t172810\n\tchr5_KI270796v1_alt\t172708\n\tchr9_GL383541v1_alt\t171286\n\tchr19_KI270885v1_alt\t171027\n\tchr19_KI270919v1_alt\t170701\n\tchr19_KI270889v1_alt\t170698\n\tchr19_KI270891v1_alt\t170680\n\tchr19_KI270915v1_alt\t170665\n\tchr19_KI270933v1_alt\t170537\n\tchr19_KI270883v1_alt\t170399\n\tchr19_GL383575v2_alt\t170222\n\tchr19_KI270931v1_alt\t170148\n\tchr12_GL383550v2_alt\t169178\n\tchr13_KI270841v1_alt\t169134\n\tchrUn_KI270744v1\t168472\n\tchr18_KI270863v1_alt\t167999\n\tchr18_GL383569v1_alt\t167950\n\tchr12_GL877875v1_alt\t167313\n\tchr21_KI270874v1_alt\t166743\n\tchr3_KI270924v1_alt\t166540\n\tchr1_KI270761v1_alt\t165834\n\tchr3_KI270937v1_alt\t165607\n\tchr22_KI270734v1_random\t165050\n\tchr18_GL383570v1_alt\t164789\n\tchr5_KI270794v1_alt\t164558\n\tchr4_GL383527v1_alt\t164536\n\tchrUn_GL000213v1\t164239\n\tchr3_KI270936v1_alt\t164170\n\tchr3_KI270934v1_alt\t163458\n\tchr9_GL383539v1_alt\t162988\n\tchr3_KI270895v1_alt\t162896\n\tchr22_GL383582v2_alt\t162811\n\tchr3_KI270782v1_alt\t162429\n\tchr1_KI270892v1_alt\t162212\n\tchrUn_GL000220v1\t161802\n\tchr2_KI270767v1_alt\t161578\n\tchr2_KI270715v1_random\t161471\n\tchr2_KI270893v1_alt\t161218\n\tchrUn_GL000218v1\t161147\n\tchr18_GL383572v1_alt\t159547\n\tchr8_KI270817v1_alt\t158983\n\tchr4_KI270788v1_alt\t158965\n\tchrUn_KI270749v1\t158759\n\tchr7_KI270806v1_alt\t158166\n\tchr7_KI270804v1_alt\t157952\n\tchr18_KI270911v1_alt\t157710\n\tchrUn_KI270741v1\t157432\n\tchr17_KI270910v1_alt\t157099\n\tchr19_KI270884v1_alt\t157053\n\tchr19_GL383574v1_alt\t155864\n\tchr19_KI270888v1_alt\t155532\n\tchr3_GL000221v1_random\t155397\n\tchr11_GL383547v1_alt\t154407\n\tchr2_KI270716v1_random\t153799\n\tchr12_GL383553v2_alt\t152874\n\tchr6_KI270799v1_alt\t152148\n\tchr22_KI270731v1_random\t150754\n\tchrUn_KI270751v1\t150742\n\tchrUn_KI270750v1\t148850\n\tchr8_KI270818v1_alt\t145606\n\tchrX_KI270881v1_alt\t144206\n\tchr21_KI270873v1_alt\t143900\n\tchr2_GL383521v1_alt\t143390\n\tchr8_KI270814v1_alt\t141812\n\tchr12_GL383552v1_alt\t138655\n\tchrUn_KI270519v1\t138126\n\tchr2_KI270775v1_alt\t138019\n\tchr17_KI270907v1_alt\t137721\n\tchrUn_GL000214v1\t137718\n\tchr8_KI270901v1_alt\t136959\n\tchr2_KI270770v1_alt\t136240\n\tchr16_KI270854v1_alt\t134193\n\tchr8_KI270819v1_alt\t133535\n\tchr17_GL383564v2_alt\t133151\n\tchr2_KI270772v1_alt\t133041\n\tchr8_KI270815v1_alt\t132244\n\tchr5_KI270795v1_alt\t131892\n\tchr5_KI270898v1_alt\t130957\n\tchr20_GL383577v2_alt\t128386\n\tchr1_KI270708v1_random\t127682\n\tchr7_KI270807v1_alt\t126434\n\tchr5_KI270793v1_alt\t126136\n\tchr6_GL383533v1_alt\t124736\n\tchr2_GL383522v1_alt\t123821\n\tchr19_KI270918v1_alt\t123111\n\tchr12_GL383549v1_alt\t120804\n\tchr2_KI270769v1_alt\t120616\n\tchr4_KI270785v1_alt\t119912\n\tchr12_KI270834v1_alt\t119498\n\tchr7_GL383534v2_alt\t119183\n\tchr20_KI270869v1_alt\t118774\n\tchr21_GL383581v2_alt\t116689\n\tchr3_KI270781v1_alt\t113034\n\tchr17_KI270730v1_random\t112551\n\tchrUn_KI270438v1\t112505\n\tchr4_KI270787v1_alt\t111943\n\tchr18_KI270864v1_alt\t111737\n\tchr2_KI270771v1_alt\t110395\n\tchr1_GL383519v1_alt\t110268\n\tchr2_KI270768v1_alt\t110099\n\tchr1_KI270760v1_alt\t109528\n\tchr3_KI270783v1_alt\t109187\n\tchr17_KI270859v1_alt\t108763\n\tchr11_KI270902v1_alt\t106711\n\tchr18_GL383568v1_alt\t104552\n\tchr22_KI270737v1_random\t103838\n\tchr13_KI270843v1_alt\t103832\n\tchr22_KI270877v1_alt\t101331\n\tchr5_GL383530v1_alt\t101241\n\tchr11_KI270721v1_random\t100316\n\tchr22_KI270738v1_random\t99375\n\tchr22_GL383583v2_alt\t96924\n\tchr2_GL582966v2_alt\t96131\n\tchrUn_KI270748v1\t93321\n\tchrUn_KI270435v1\t92983\n\tchr5_GL000208v1_random\t92689\n\tchrUn_KI270538v1\t91309\n\tchr17_GL383566v1_alt\t90219\n\tchr16_GL383557v1_alt\t89672\n\tchr17_JH159148v1_alt\t88070\n\tchr5_GL383532v1_alt\t82728\n\tchr21_KI270872v1_alt\t82692\n\tchrUn_KI270756v1\t79590\n\tchr6_KI270758v1_alt\t76752\n\tchr12_KI270833v1_alt\t76061\n\tchr6_KI270802v1_alt\t75005\n\tchr21_GL383580v2_alt\t74653\n\tchr22_KB663609v1_alt\t74013\n\tchr22_KI270739v1_random\t73985\n\tchr9_GL383540v1_alt\t71551\n\tchrUn_KI270757v1\t71251\n\tchr2_KI270773v1_alt\t70887\n\tchr17_JH159147v1_alt\t70345\n\tchr11_KI270827v1_alt\t67707\n\tchr1_KI270709v1_random\t66860\n\tchrUn_KI270746v1\t66486\n\tchr16_KI270856v1_alt\t63982\n\tchr21_GL383578v2_alt\t63917\n\tchrUn_KI270753v1\t62944\n\tchr19_KI270868v1_alt\t61734\n\tchr9_GL383542v1_alt\t60032\n\tchr20_KI270871v1_alt\t58661\n\tchr12_KI270836v1_alt\t56134\n\tchr19_KI270865v1_alt\t52969\n\tchr1_KI270764v1_alt\t50258\n\tchrUn_KI270589v1\t44474\n\tchr14_KI270726v1_random\t43739\n\tchr19_KI270866v1_alt\t43156\n\tchr22_KI270735v1_random\t42811\n\tchr1_KI270711v1_random\t42210\n\tchrUn_KI270745v1\t41891\n\tchr1_KI270714v1_random\t41717\n\tchr22_KI270732v1_random\t41543\n\tchr1_KI270713v1_random\t40745\n\tchrUn_KI270754v1\t40191\n\tchr1_KI270710v1_random\t40176\n\tchr12_KI270837v1_alt\t40090\n\tchr9_KI270717v1_random\t40062\n\tchr14_KI270724v1_random\t39555\n\tchr9_KI270720v1_random\t39050\n\tchr14_KI270723v1_random\t38115\n\tchr9_KI270718v1_random\t38054\n\tchrUn_KI270317v1\t37690\n\tchr13_KI270842v1_alt\t37287\n\tchrY_KI270740v1_random\t37240\n\tchrUn_KI270755v1\t36723\n\tchr8_KI270820v1_alt\t36640\n\tchr1_KI270707v1_random\t32032\n\tchrUn_KI270579v1\t31033\n\tchrUn_KI270752v1\t27745\n\tchrUn_KI270512v1\t22689\n\tchrUn_KI270322v1\t21476\n\tchrUn_GL000226v1\t15008\n\tchrUn_KI270311v1\t12399\n\tchrUn_KI270366v1\t8320\n\tchrUn_KI270511v1\t8127\n\tchrUn_KI270448v1\t7992\n\tchrUn_KI270521v1\t7642\n\tchrUn_KI270581v1\t7046\n\tchrUn_KI270582v1\t6504\n\tchrUn_KI270515v1\t6361\n\tchrUn_KI270588v1\t6158\n\tchrUn_KI270591v1\t5796\n\tchrUn_KI270522v1\t5674\n\tchrUn_KI270507v1\t5353\n\tchrUn_KI270590v1\t4685\n\tchrUn_KI270584v1\t4513\n\tchrUn_KI270320v1\t4416\n\tchrUn_KI270382v1\t4215\n\tchrUn_KI270468v1\t4055\n\tchrUn_KI270467v1\t3920\n\tchrUn_KI270362v1\t3530\n\tchrUn_KI270517v1\t3253\n\tchrUn_KI270593v1\t3041\n\tchrUn_KI270528v1\t2983\n\tchrUn_KI270587v1\t2969\n\tchrUn_KI270364v1\t2855\n\tchrUn_KI270371v1\t2805\n\tchrUn_KI270333v1\t2699\n\tchrUn_KI270374v1\t2656\n\tchrUn_KI270411v1\t2646\n\tchrUn_KI270414v1\t2489\n\tchrUn_KI270510v1\t2415\n\tchrUn_KI270390v1\t2387\n\tchrUn_KI270375v1\t2378\n\tchrUn_KI270420v1\t2321\n\tchrUn_KI270509v1\t2318\n\tchrUn_KI270315v1\t2276\n\tchrUn_KI270302v1\t2274\n\tchrUn_KI270518v1\t2186\n\tchrUn_KI270530v1\t2168\n\tchrUn_KI270304v1\t2165\n\tchrUn_KI270418v1\t2145\n\tchrUn_KI270424v1\t2140\n\tchrUn_KI270417v1\t2043\n\tchrUn_KI270508v1\t1951\n\tchrUn_KI270303v1\t1942\n\tchrUn_KI270381v1\t1930\n\tchrUn_KI270529v1\t1899\n\tchrUn_KI270425v1\t1884\n\tchrUn_KI270396v1\t1880\n\tchrUn_KI270363v1\t1803\n\tchrUn_KI270386v1\t1788\n\tchrUn_KI270465v1\t1774\n\tchrUn_KI270383v1\t1750\n\tchrUn_KI270384v1\t1658\n\tchrUn_KI270330v1\t1652\n\tchrUn_KI270372v1\t1650\n\tchrUn_KI270548v1\t1599\n\tchrUn_KI270580v1\t1553\n\tchrUn_KI270387v1\t1537\n\tchrUn_KI270391v1\t1484\n\tchrUn_KI270305v1\t1472\n\tchrUn_KI270373v1\t1451\n\tchrUn_KI270422v1\t1445\n\tchrUn_KI270316v1\t1444\n\tchrUn_KI270338v1\t1428\n\tchrUn_KI270340v1\t1428\n\tchrUn_KI270583v1\t1400\n\tchrUn_KI270334v1\t1368\n\tchrUn_KI270429v1\t1361\n\tchrUn_KI270393v1\t1308\n\tchrUn_KI270516v1\t1300\n\tchrUn_KI270389v1\t1298\n\tchrUn_KI270466v1\t1233\n\tchrUn_KI270388v1\t1216\n\tchrUn_KI270544v1\t1202\n\tchrUn_KI270310v1\t1201\n\tchrUn_KI270412v1\t1179\n\tchrUn_KI270395v1\t1143\n\tchrUn_KI270376v1\t1136\n\tchrUn_KI270337v1\t1121\n\tchrUn_KI270335v1\t1048\n\tchrUn_KI270378v1\t1048\n\tchrUn_KI270379v1\t1045\n\tchrUn_KI270329v1\t1040\n\tchrUn_KI270419v1\t1029\n\tchrUn_KI270336v1\t1026\n\tchrUn_KI270312v1\t998\n\tchrUn_KI270539v1\t993\n\tchrUn_KI270385v1\t990\n\tchrUn_KI270423v1\t981\n\tchrUn_KI270392v1\t971\n\tchrUn_KI270394v1\t970"
110
117
  };
package/package.json CHANGED
@@ -1,13 +1,13 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-server",
3
- "version": "2.25.0",
3
+ "version": "2.26.0",
4
4
  "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
5
5
  "main": "server.js",
6
6
  "bin": "start.js",
7
7
  "imports": {
8
8
  "#shared/*": "./shared/*.js",
9
- "#src/*": "./src/*.js",
10
- "#routes/*": "./src/routes/*.ts"
9
+ "#src/*": "./src/*",
10
+ "#routes/*": "./routes/*"
11
11
  },
12
12
  "scripts": {
13
13
  "prepare": "ts-patch install",
@@ -15,7 +15,7 @@
15
15
  "start": "tsc --esModuleInterop genome/*.ts dataset/*.ts && nodemon --enable-source-maps server.js --watch ./server*.js* --watch dataset/*.ts --watch genome/*.ts",
16
16
  "pretest": "tsc --esModuleInterop genome/*.ts dataset/*.ts && ./test/pretest.js",
17
17
  "test": "webpack --env NODE_ENV=test exportsFilename=all-test-context.js && node --enable-source-maps test/serverTests.js",
18
- "pretest:unit": "npm run checkers",
18
+ "pretest:unit": "npm run checkers && tsc genome/hg38.test.ts",
19
19
  "test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && tsc --esModuleInterop dataset/*.ts && node --enable-source-maps test/serverTests.js",
20
20
  "pretest:integration": "tsc --esModuleInterop genome/*.ts dataset/*.ts",
21
21
  "test:integration": "echo 'TODO: server integration tests'",
@@ -24,8 +24,8 @@
24
24
  "getconf": "../build/getConfigProp.js",
25
25
  "predoc": "npm run checkers",
26
26
  "doc": "typedoc --json ../public/docs/server.json",
27
- "checkers": "typia generate --input shared/checkers/raw --output shared/checkers/transformed --project ./shared/checkers/tsconfig.json",
28
- "doctest": "npm run checkers && npm run test:unit"
27
+ "precheckers": "npx ts-node ./augen/cli.js typeCheckers $PWD/routes ../../../routes > shared/checkers/raw/index.ts",
28
+ "checkers": "typia generate --input shared/checkers/raw --output shared/checkers/transformed --project ./shared/checkers/tsconfig.json"
29
29
  },
30
30
  "author": "",
31
31
  "license": "SEE LICENSE IN ./LICENSE",
@@ -54,7 +54,7 @@
54
54
  "webpack-notifier": "^1.15.0"
55
55
  },
56
56
  "dependencies": {
57
- "@sjcrh/proteinpaint-rust": "2.25.0",
57
+ "@sjcrh/proteinpaint-rust": "2.26.0",
58
58
  "better-sqlite3": "^7.5.3",
59
59
  "body-parser": "^1.15.2",
60
60
  "canvas": "~2.9.3",
@@ -90,7 +90,7 @@
90
90
  "src/mds3.gdc.filter.js",
91
91
  "src/checkReadingFrame.js",
92
92
  "src/bedj.parseBed.js",
93
- "src/routes/*",
93
+ "routes/*",
94
94
  "cards/*",
95
95
  "server.js*",
96
96
  "start.js",
package/routes/genelookup.ts ADDED
@@ -0,0 +1,58 @@
1
+ import { getResult } from '#src/gene.js'
2
+
3
+ function init({ genomes }) {
4
+ return (req: any, res: any): void => {
5
+ try {
6
+ const g = genomes[req.query.genome]
7
+ if (!g) throw 'invalid genome name'
8
+ res.send(getResult(g, req.query))
9
+ } catch (e: any) {
10
+ res.send({ error: e.message || e })
11
+ if (e.stack) console.log(e.stack)
12
+ }
13
+ }
14
+ }
15
+
16
+ export const api: any = {
17
+ endpoint: 'genelookup',
18
+ methods: {
19
+ get: {
20
+ init,
21
+ request: {
22
+ typeId: 'GeneLookupRequest'
23
+ //valid: default to type checker
24
+ },
25
+ response: {
26
+ typeId: 'GeneLookupResponse'
27
+ // will combine this with type checker
28
+ //valid: (t) => {}
29
+ },
30
+ examples: [
31
+ {
32
+ request: {
33
+ body: { input: 'kr', genome: 'hg38-test' }
34
+ },
35
+ response: {
36
+ header: { status: 200 },
37
+ body: { hits: ['KRAS'] }
38
+ }
39
+ }
40
+ ]
41
+ },
42
+ post: {
43
+ alternativeFor: 'get',
44
+ init
45
+ }
46
+ }
47
+ }
48
+
49
+ export type GeneLookupRequest = {
50
+ input: string
51
+ genome: string
52
+ deep: boolean
53
+ }
54
+
55
+ export type GeneLookupResponse = {
56
+ error?: string
57
+ hits: string[]
58
+ }
package/routes/healthcheck.ts ADDED
@@ -0,0 +1,72 @@
1
+ import { getStat } from '#src/health.ts'
2
+
3
+ export const api = {
4
+ endpoint: 'healthcheck',
5
+ methods: {
6
+ get: {
7
+ init({ genomes }) {
8
+ return async (req: any, res: any): Promise<void> => {
9
+ try {
10
+ const health = await getStat(genomes)
11
+ res.send(health)
12
+ } catch (e: any) {
13
+ res.send({ status: 'error', error: e.message || e })
14
+ }
15
+ }
16
+ },
17
+ request: {
18
+ typeId: null
19
+ //valid: default to type checker
20
+ },
21
+ response: {
22
+ typeId: 'HealthCheckResponse'
23
+ // will combine this with type checker
24
+ //valid: (t) => {}
25
+ }
26
+ }
27
+ }
28
+ }
29
+
30
+ /**
31
+ * for documentation only, to signify integer: not type-checked statically
32
+ */
33
+ type int = number
34
+
35
+ /**
36
+ * Information aboute the server build version and dates,
37
+ * including the date when the server was last launched
38
+ */
39
+ export type VersionInfo = {
40
+ pkgver: string
41
+ codedate: string
42
+ launchdate: string
43
+ }
44
+
45
+ type BuildByGenome = {
46
+ [index: string]: GenomeBuildInfo
47
+ }
48
+
49
+ export type GenomeBuildInfo = {
50
+ genedb: DbInfo
51
+ termdbs?: {
52
+ [index: string]: DbInfo
53
+ }
54
+ }
55
+
56
+ type DbInfo = {
57
+ buildDate: string // "unknown" or a Date-convertible string
58
+ tables?: {
59
+ [index: string]: int
60
+ }
61
+ }
62
+
63
+ /**
64
+ * Server sttus and data related to it's health
65
+ */
66
+ export type HealthCheckResponse = {
67
+ status: 'ok' | 'error'
68
+ genomes: BuildByGenome
69
+ versionInfo: VersionInfo
70
+ w?: number[]
71
+ rs?: number
72
+ }