@sjcrh/proteinpaint-types 2.83.0 → 2.85.0

package/package.json

@@ -1,30 +1,36 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.83.0",
+  "version": "2.85.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
-  "main": "src/index.ts",
-  "module": "src/index.ts",
-  "exports": {
-    ".": "./src/index.ts",
-    "./updated": "./src/terms/updated-types.ts",
+  "main": "src/index.js",
+  "module": "src/index.js",
+  "expo.js": {
+    ".": "./src/index.js",
+    "./updated": "./src/terms/updated-types.js",
     "./*": "./src/*",
-    "./routes/*": "./src/routes/*"
+    "./routes/*": "./src/routes/*",
+    "./checkers/*": "./dist/checkers/*"
   },
-  "imports": {
+  "impo.js": {
     "#shared": "@sjcrh/proteinpaint-shared"
   },
-  "scripts": {
+  "scri.js": {
     "prepare": "ts-patch install",
-    "test": "tsc"
+    "test": "tsc",
+    "build": "./build.sh",
+    "prepack": "./build.sh && mv src src-raw && mv srcjs src && mv package.json package.json-0 && mv src/package.json .",
+    "postpack": "rm -rf src && mv src-raw src && mv package.json-0 package.json",
+    "doc": "./doc.sh"
   },
   "devDependencies": {
     "ts-node": "^10.9.2",
     "ts-patch": "^3.2.1",
-    "typescript": "^5.6.2",
+    "typescript": "^5.6.3",
     "typia": "^4.1.14"
   },
   "files": [
+    "dist",
     "src"
   ]
 }

package/src/checkers/routes.js

@@ -0,0 +1,167 @@
+import { createValidate } from "typia";
+const validBrainImagingRequest = createValidate();
+const validBrainImagingResponse = createValidate();
+const validBrainImagingSamplesRequest = createValidate();
+const validBrainImagingSamplesResponse = createValidate();
+const validBurdenRequest = createValidate();
+const validBurdenResponse = createValidate();
+const validDatasetRequest = createValidate();
+const validDatasetResponse = createValidate();
+const validDsDataRequest = createValidate();
+const validDsDataResponse = createValidate();
+const validDZImagesRequest = createValidate();
+const validDZImagesResponse = createValidate();
+const validGdcMafRequest = createValidate();
+const validGdcMafResponse = createValidate();
+const validGdcTopMutatedGeneRequest = createValidate();
+const validGdcTopMutatedGeneResponse = createValidate();
+const validGeneLookupRequest = createValidate();
+const validGeneLookupResponse = createValidate();
+const validGenesetEnrichmentRequest = createValidate();
+const validGenesetEnrichmentResponse = createValidate();
+const validGenesetOverrepresentationRequest = createValidate();
+const validGenesetOverrepresentationResponse = createValidate();
+const validHealthCheckRequest = createValidate();
+const validHealthCheckResponse = createValidate();
+const validHicdataRequest = createValidate();
+const validHicdataResponse = createValidate();
+const validHicGenomeRequest = createValidate();
+const validHicGenomeResponse = createValidate();
+const validHicstatRequest = createValidate();
+const validHicstatResponse = createValidate();
+const validIsoformLstRequest = createValidate();
+const validIsoformLstResponse = createValidate();
+const validNtseqRequest = createValidate();
+const validNtseqResponse = createValidate();
+const validPdomainRequest = createValidate();
+const validPdomainResponse = createValidate();
+const validSampleWSImagesRequest = createValidate();
+const validSampleWSImagesResponse = createValidate();
+const validDERequest = createValidate();
+const validDEResponse = createValidate();
+const validBoxPlotRequest = createValidate();
+const validBoxPlotResponse = createValidate();
+const validCategoriesRequest = createValidate();
+const validCategoriesResponse = createValidate();
+const validTermdbClusterRequest = createValidate();
+const validTermdbClusterResponse = createValidate();
+const validTermdbCohortSummaryRequest = createValidate();
+const validTermdbCohortSummaryResponse = createValidate();
+const validTermdbCohortsRequest = createValidate();
+const validTermdbCohortsResponse = createValidate();
+const validDescrStatsRequest = createValidate();
+const validDescrStatsResponse = createValidate();
+const validNumericCategoriesRequest = createValidate();
+const validNumericCategoriesResponse = createValidate();
+const validPercentileRequest = createValidate();
+const validPercentileResponse = createValidate();
+const validRootTermRequest = createValidate();
+const validRootTermResponse = createValidate();
+const validTermdbSampleImagesRequest = createValidate();
+const validTermdbSampleImagesResponse = createValidate();
+const validTermdbSingleSampleMutationRequest = createValidate();
+const validTermdbSingleSampleMutationResponse = createValidate();
+const validTermdbSingleCellDEgenesRequest = createValidate();
+const validTermdbSingleCellDEgenesResponse = createValidate();
+const validTermdbSingleCellDataRequest = createValidate();
+const validTermdbSingleCellDataResponse = createValidate();
+const validTermdbSingleCellSamplesRequest = createValidate();
+const validTermdbSingleCellSamplesResponse = createValidate();
+const validTermChildrenRequest = createValidate();
+const validTermChildrenResponse = createValidate();
+const validTermsByIdsRequest = createValidate();
+const validTermsByIdsResponse = createValidate();
+const validTermdbTopTermsByTypeRequest = createValidate();
+const validTermdbTopTermsByTypeResponse = createValidate();
+const validTermdbTopVariablyExpressedGenesRequest = createValidate();
+const validTermdbTopVariablyExpressedGenesResponse = createValidate();
+const validViolinRequest = createValidate();
+const validViolinResponse = createValidate();
+const validTileRequest = createValidate();
+const validTileResponse = createValidate();
+const validWSImagesRequest = createValidate();
+const validWSImagesResponse = createValidate();
+export {
+  validBoxPlotRequest,
+  validBoxPlotResponse,
+  validBrainImagingRequest,
+  validBrainImagingResponse,
+  validBrainImagingSamplesRequest,
+  validBrainImagingSamplesResponse,
+  validBurdenRequest,
+  validBurdenResponse,
+  validCategoriesRequest,
+  validCategoriesResponse,
+  validDERequest,
+  validDEResponse,
+  validDZImagesRequest,
+  validDZImagesResponse,
+  validDatasetRequest,
+  validDatasetResponse,
+  validDescrStatsRequest,
+  validDescrStatsResponse,
+  validDsDataRequest,
+  validDsDataResponse,
+  validGdcMafRequest,
+  validGdcMafResponse,
+  validGdcTopMutatedGeneRequest,
+  validGdcTopMutatedGeneResponse,
+  validGeneLookupRequest,
+  validGeneLookupResponse,
+  validGenesetEnrichmentRequest,
+  validGenesetEnrichmentResponse,
+  validGenesetOverrepresentationRequest,
+  validGenesetOverrepresentationResponse,
+  validHealthCheckRequest,
+  validHealthCheckResponse,
+  validHicGenomeRequest,
+  validHicGenomeResponse,
+  validHicdataRequest,
+  validHicdataResponse,
+  validHicstatRequest,
+  validHicstatResponse,
+  validIsoformLstRequest,
+  validIsoformLstResponse,
+  validNtseqRequest,
+  validNtseqResponse,
+  validNumericCategoriesRequest,
+  validNumericCategoriesResponse,
+  validPdomainRequest,
+  validPdomainResponse,
+  validPercentileRequest,
+  validPercentileResponse,
+  validRootTermRequest,
+  validRootTermResponse,
+  validSampleWSImagesRequest,
+  validSampleWSImagesResponse,
+  validTermChildrenRequest,
+  validTermChildrenResponse,
+  validTermdbClusterRequest,
+  validTermdbClusterResponse,
+  validTermdbCohortSummaryRequest,
+  validTermdbCohortSummaryResponse,
+  validTermdbCohortsRequest,
+  validTermdbCohortsResponse,
+  validTermdbSampleImagesRequest,
+  validTermdbSampleImagesResponse,
+  validTermdbSingleCellDEgenesRequest,
+  validTermdbSingleCellDEgenesResponse,
+  validTermdbSingleCellDataRequest,
+  validTermdbSingleCellDataResponse,
+  validTermdbSingleCellSamplesRequest,
+  validTermdbSingleCellSamplesResponse,
+  validTermdbSingleSampleMutationRequest,
+  validTermdbSingleSampleMutationResponse,
+  validTermdbTopTermsByTypeRequest,
+  validTermdbTopTermsByTypeResponse,
+  validTermdbTopVariablyExpressedGenesRequest,
+  validTermdbTopVariablyExpressedGenesResponse,
+  validTermsByIdsRequest,
+  validTermsByIdsResponse,
+  validTileRequest,
+  validTileResponse,
+  validViolinRequest,
+  validViolinResponse,
+  validWSImagesRequest,
+  validWSImagesResponse
+};

package/src/index.js

@@ -0,0 +1,66 @@
+export * from "./genome.js";
+export * from "./dataset.js";
+export * from "./termsetting.js";
+export * from "./filter.js";
+export * from "./routes/routeApi.js";
+export * from "./routes/brainImaging.js";
+export * from "./routes/brainImagingSamples.js";
+export * from "./routes/burden.js";
+export * from "./routes/dataset.js";
+export * from "./routes/dsdata.js";
+export * from "./routes/dzimages.js";
+export * from "./routes/errorResponse.js";
+export * from "./routes/filter.gdc.js";
+export * from "./routes/gdc.maf.js";
+export * from "./routes/gdc.mafBuild.js";
+export * from "./routes/gdc.topMutatedGenes.js";
+export * from "./routes/genelookup.js";
+export * from "./routes/genesetEnrichment.js";
+export * from "./routes/genesetOverrepresentation.js";
+export * from "./routes/healthcheck.js";
+export * from "./routes/hicdata.js";
+export * from "./routes/hicgenome.js";
+export * from "./routes/hicstat.js";
+export * from "./routes/isoformlst.js";
+export * from "./routes/ntseq.js";
+export * from "./routes/pdomain.js";
+export * from "./routes/samplewsimages.js";
+export * from "./routes/snp.js";
+export * from "./routes/termdb.boxplot.js";
+export * from "./routes/termdb.categories.js";
+export * from "./routes/termdb.cluster.js";
+export * from "./routes/termdb.cohort.summary.js";
+export * from "./routes/termdb.cohorts.js";
+export * from "./routes/termdb.DE.js";
+export * from "./routes/termdb.descrstats.js";
+export * from "./routes/termdb.numericcategories.js";
+export * from "./routes/termdb.percentile.js";
+export * from "./routes/termdb.rootterm.js";
+export * from "./routes/termdb.termchildren.js";
+export * from "./routes/termdb.sampleImages.js";
+export * from "./routes/termdb.singlecellData.js";
+export * from "./routes/termdb.singlecellDEgenes.js";
+export * from "./routes/termdb.singlecellSamples.js";
+export * from "./routes/termdb.singleSampleMutation.js";
+export * from "./routes/termdb.termsbyids.js";
+export * from "./routes/termdb.termchildren.js";
+export * from "./routes/termdb.topTermsByType.js";
+export * from "./routes/termdb.topVariablyExpressedGenes.js";
+export * from "./routes/termdb.violin.js";
+export * from "./routes/tileserver.js";
+export * from "./routes/wsimages.js";
+export * from "./terms/categorical.js";
+export * from "./terms/condition.js";
+export * from "./terms/numeric.js";
+export * from "./terms/geneVariant.js";
+export * from "./terms/geneExpression.js";
+export * from "./terms/metaboliteIntensity.js";
+export * from "./terms/singleCellCellType.js";
+export * from "./terms/singleCellGeneExpression.js";
+export * from "./terms/snp.js";
+export * from "./terms/snps.js";
+export * from "./terms/samplelst.js";
+export * from "./terms/q.js";
+export * from "./terms/term.js";
+export * from "./terms/tw.js";
+export * from "./vocab.js";

package/src/routes/brainImaging.js

@@ -0,0 +1,11 @@
+const brainImagingPayload = {
+  request: {
+    typeId: "BrainImagingRequest"
+  },
+  response: {
+    typeId: "BrainImagingResponse"
+  }
+};
+export {
+  brainImagingPayload
+};

package/src/routes/brainImagingSamples.js

@@ -0,0 +1,11 @@
+const brainImagingSamplesPayload = {
+  request: {
+    typeId: "BrainImagingSamplesRequest"
+  },
+  response: {
+    typeId: "BrainImagingSamplesResponse"
+  }
+};
+export {
+  brainImagingSamplesPayload
+};

package/src/routes/burden.js

@@ -0,0 +1,44 @@
+const burdenPayload = {
+  request: {
+    typeId: "BurdenRequest"
+  },
+  response: {
+    typeId: "BurdenResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38",
+          // TODO: !!! use hg38-test and TermdbTest !!!
+          dslabel: "SJLife",
+          diaggrp: 5,
+          sex: 1,
+          white: 1,
+          agedx: 1,
+          bleo: 0,
+          etop: 0,
+          cisp: 0,
+          carbo: 0,
+          steriod: 0,
+          vcr: 0,
+          hdmtx: 0,
+          itmt: 0,
+          ced: 0,
+          dox: 0,
+          heart: 0,
+          brain: 0,
+          abd: 0,
+          pelvis: 0,
+          chest: 0
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  burdenPayload
+};

package/src/routes/dataset.js

@@ -0,0 +1,12 @@
+const datasetPayload = {
+  request: {
+    typeId: "DatasetRequest"
+  },
+  response: {
+    typeId: "DatasetResponse"
+  }
+  // examples: []
+};
+export {
+  datasetPayload
+};

package/src/routes/dsdata.js

@@ -0,0 +1,12 @@
+const dsDataPayload = {
+  request: {
+    typeId: "DsDataRequest"
+  },
+  response: {
+    typeId: "DsDataResponse"
+  }
+  // examples: []
+};
+export {
+  dsDataPayload
+};

package/src/routes/dzimages.js

@@ -0,0 +1,12 @@
+const dzImagesPayload = {
+  request: {
+    typeId: "DZImagesRequest"
+  },
+  response: {
+    typeId: "DZImagesResponse"
+  }
+  // examples: []
+};
+export {
+  dzImagesPayload
+};

package/src/routes/gdc.maf.js

@@ -0,0 +1,17 @@
+var ExperimentalStrategy = /* @__PURE__ */ ((ExperimentalStrategy2) => {
+  ExperimentalStrategy2["targeted"] = "Targeted Sequencing";
+  ExperimentalStrategy2["wxs"] = "WXS";
+  return ExperimentalStrategy2;
+})(ExperimentalStrategy || {});
+const gdcMafPayload = {
+  request: {
+    typeId: "GdcMafRequest"
+  },
+  response: {
+    typeId: "GdcMafResponse"
+  }
+  //examples: []
+};
+export {
+  gdcMafPayload
+};

package/src/routes/gdc.mafBuild.js

@@ -0,0 +1,12 @@
+const GdcMafPayload = {
+  request: {
+    typeId: "GdcMafRequest"
+  },
+  response: {
+    typeId: "GdcMafResponse"
+  }
+  //examples: []
+};
+export {
+  GdcMafPayload
+};

package/src/routes/gdc.topMutatedGenes.js

@@ -0,0 +1,12 @@
+const gdcTopMutatedGenePayload = {
+  request: {
+    typeId: "GdcTopMutatedGeneRequest"
+  },
+  response: {
+    typeId: "GdcTopMutatedGeneResponse"
+  }
+  //examples: []
+};
+export {
+  gdcTopMutatedGenePayload
+};

package/src/routes/genelookup.js

@@ -0,0 +1,12 @@
+const geneLookupPayload = {
+  request: {
+    typeId: "GeneLookupRequest"
+  },
+  response: {
+    typeId: "GeneLookupResponse"
+  }
+  //examples: []
+};
+export {
+  geneLookupPayload
+};

package/src/routes/genesetEnrichment.js

@@ -0,0 +1,12 @@
+const genesetEnrichmentPayload = {
+  request: {
+    typeId: "GenesetEnrichmentRequest"
+  },
+  response: {
+    typeId: "GenesetEnrichmentResponse"
+  }
+  //examples: []
+};
+export {
+  genesetEnrichmentPayload
+};

package/src/routes/genesetOverrepresentation.js

@@ -0,0 +1,12 @@
+const genesetOverrepresentationPayload = {
+  request: {
+    typeId: "GenesetOverrepresentationRequest"
+  },
+  response: {
+    typeId: "GenesetOverrepresentationResponse"
+  }
+  // examples: []
+};
+export {
+  genesetOverrepresentationPayload
+};

package/src/routes/healthcheck.js

@@ -0,0 +1,23 @@
+const healthcheckPayload = {
+  request: {
+    typeId: "HealthCheckRequest"
+  },
+  response: {
+    typeId: "HealthCheckResponse"
+  },
+  examples: [
+    {
+      request: { body: {} }
+      //response: {}
+    },
+    {
+      request: {
+        body: { dsLabel: "TermdbTest" }
+      }
+      //response: {}
+    }
+  ]
+};
+export {
+  healthcheckPayload
+};

package/src/routes/hicdata.js

@@ -0,0 +1,12 @@
+const hicdataPayload = {
+  request: {
+    typeId: "HicdataRequest"
+  },
+  response: {
+    typeId: "HicdataResponse"
+  }
+  // examples: []
+};
+export {
+  hicdataPayload
+};

package/src/routes/hicgenome.js

@@ -0,0 +1,29 @@
+const hicGenomePayload = {
+  request: {
+    typeId: "HicGenomeRequest"
+  },
+  response: {
+    typeId: "HicGenomeResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          embedder: "localhost",
+          url: "https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic",
+          matrixType: "observed",
+          nmeth: "NONE",
+          pos1: "3",
+          pos2: "2",
+          resolution: 1e6
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  hicGenomePayload
+};

package/src/routes/hicstat.js

@@ -0,0 +1,12 @@
+const hicstatPayload = {
+  request: {
+    typeId: "HicstatRequest"
+  },
+  response: {
+    typeId: "HicstatResponse"
+  }
+  // examples: []
+};
+export {
+  hicstatPayload
+};

package/src/routes/isoformlst.js

@@ -0,0 +1,12 @@
+const isoformlstPayload = {
+  request: {
+    typeId: "IsoformLstRequest"
+  },
+  response: {
+    typeId: "IsoformLstResponse"
+  }
+  //examples: []
+};
+export {
+  isoformlstPayload
+};

package/src/routes/ntseq.js

@@ -0,0 +1,12 @@
+const ntseqPayload = {
+  request: {
+    typeId: "NtseqRequest"
+  },
+  response: {
+    typeId: "NtseqResponse"
+  }
+  //examples: []
+};
+export {
+  ntseqPayload
+};

package/src/routes/pdomain.js

@@ -0,0 +1,12 @@
+const pdomainPayload = {
+  request: {
+    typeId: "PdomainRequest"
+  },
+  response: {
+    typeId: "PdomainResponse"
+  }
+  //examples: []
+};
+export {
+  pdomainPayload
+};

package/src/routes/samplewsimages.js

@@ -0,0 +1,12 @@
+const sampleWSImagesPayload = {
+  request: {
+    typeId: "SampleWSImagesRequest"
+  },
+  response: {
+    typeId: "SampleWSImagesResponse"
+  }
+  // examples: []
+};
+export {
+  sampleWSImagesPayload
+};

package/src/routes/snp.js

@@ -0,0 +1,11 @@
+const snpPayload = {
+  request: {
+    typeId: "any"
+  },
+  response: {
+    typeId: "any"
+  }
+};
+export {
+  snpPayload
+};

package/src/routes/termdb.DE.js

@@ -0,0 +1,13 @@
+const diffExpPayload = {
+  request: {
+    typeId: "DERequest"
+  },
+  response: {
+    typeId: "DEResponse"
+    // will combine this with type checker
+    //valid: (t) => {}
+  }
+};
+export {
+  diffExpPayload
+};

package/src/routes/termdb.boxplot.js

@@ -0,0 +1,12 @@
+const boxplotPayload = {
+  request: {
+    typeId: "BoxPlotRequest"
+  },
+  response: {
+    typeId: "BoxPlotResponse"
+  }
+  //examples: []
+};
+export {
+  boxplotPayload
+};