@sjcrh/proteinpaint-types 2.83.0 → 2.85.0

package/src/routes/termdb.categories.js

@@ -0,0 +1,48 @@
+const termdbCategoriesPayload = {
+  request: {
+    typeId: "CategoriesRequest"
+  },
+  response: {
+    typeId: "CategoriesResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38-test",
+          dslabel: "TermdbTest",
+          embedder: "localhost",
+          term: { id: "diaggrp" },
+          filter: {
+            type: "tvslst",
+            in: true,
+            join: "",
+            lst: [
+              {
+                tag: "cohortFilter",
+                type: "tvs",
+                tvs: {
+                  term: {
+                    name: "Cohort",
+                    type: "categorical",
+                    values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
+                    id: "subcohort",
+                    isleaf: false,
+                    groupsetting: { disabled: true }
+                  },
+                  values: [{ key: "ABC", label: "ABC" }]
+                }
+              }
+            ]
+          }
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  termdbCategoriesPayload
+};

package/src/routes/termdb.cluster.js

@@ -0,0 +1,12 @@
+const termdbClusterPayload = {
+  request: {
+    typeId: "TermdbClusterRequest"
+  },
+  response: {
+    typeId: "TermdbClusterResponse"
+  }
+  //examples: []
+};
+export {
+  termdbClusterPayload
+};

package/src/routes/termdb.cohort.summary.js

@@ -0,0 +1,12 @@
+const termdbCohortSummaryPayload = {
+  request: {
+    typeId: "TermdbCohortSummaryRequest"
+  },
+  response: {
+    typeId: "TermdbCohortSummaryResponse"
+  }
+  // examples: []
+};
+export {
+  termdbCohortSummaryPayload
+};

package/src/routes/termdb.cohorts.js

@@ -0,0 +1,12 @@
+const termdbCohortsPayload = {
+  request: {
+    typeId: "TermdbCohortsRequest"
+  },
+  response: {
+    typeId: "TermdbCohortsResponse"
+  }
+  //examples: []
+};
+export {
+  termdbCohortsPayload
+};

package/src/routes/termdb.descrstats.js

@@ -0,0 +1,48 @@
+const descrStatsPayload = {
+  request: {
+    typeId: "DescrStatsRequest"
+  },
+  response: {
+    typeId: "DescrStatsResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38-test",
+          dslabel: "TermdbTest",
+          embedder: "localhost",
+          tw: { term: { id: "hrtavg" }, q: { mode: "continuous" } },
+          filter: {
+            type: "tvslst",
+            in: true,
+            join: "",
+            lst: [
+              {
+                tag: "cohortFilter",
+                type: "tvs",
+                tvs: {
+                  term: {
+                    name: "Cohort",
+                    type: "categorical",
+                    values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
+                    id: "subcohort",
+                    isleaf: false,
+                    groupsetting: { disabled: true }
+                  },
+                  values: [{ key: "ABC", label: "ABC" }]
+                }
+              }
+            ]
+          }
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  descrStatsPayload
+};

package/src/routes/termdb.numericcategories.js

@@ -0,0 +1,12 @@
+const numericCategoriesPayload = {
+  request: {
+    typeId: "NumericCategoriesRequest"
+  },
+  response: {
+    typeId: "NumericCategoriesResponse"
+  }
+  // examples: []
+};
+export {
+  numericCategoriesPayload
+};

package/src/routes/termdb.percentile.js

@@ -0,0 +1,49 @@
+const percentilePayload = {
+  request: {
+    typeId: "PercentileRequest"
+  },
+  response: {
+    typeId: "PercentileResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38-test",
+          dslabel: "TermdbTest",
+          embedder: "localhost",
+          getpercentile: [50],
+          tid: "agedx",
+          filter: {
+            type: "tvslst",
+            in: true,
+            join: "",
+            lst: [
+              {
+                tag: "cohortFilter",
+                type: "tvs",
+                tvs: {
+                  term: {
+                    name: "Cohort",
+                    type: "categorical",
+                    values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
+                    id: "subcohort",
+                    isleaf: false,
+                    groupsetting: { disabled: true }
+                  },
+                  values: [{ key: "ABC", label: "ABC" }]
+                }
+              }
+            ]
+          }
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  percentilePayload
+};

package/src/routes/termdb.rootterm.js

@@ -0,0 +1,27 @@
+const rootTermPayload = {
+  request: {
+    typeId: "RootTermRequest"
+  },
+  response: {
+    typeId: "RootTermResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38-test",
+          dslabel: "TermdbTest",
+          embedder: "localhost",
+          default_rootterm: 1,
+          cohortValues: "ABC"
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  rootTermPayload
+};

package/src/routes/termdb.sampleImages.js

@@ -0,0 +1,12 @@
+const termdbSampleImagesPayload = {
+  request: {
+    typeId: "TermdbSampleImagesRequest"
+  },
+  response: {
+    typeId: "TermdbSampleImagesResponse"
+  }
+  //examples: []
+};
+export {
+  termdbSampleImagesPayload
+};

package/src/routes/termdb.singleSampleMutation.js

@@ -0,0 +1,12 @@
+const termdbSingleSampleMutationPayload = {
+  request: {
+    typeId: "TermdbSingleSampleMutationRequest"
+  },
+  response: {
+    typeId: "TermdbSingleSampleMutationResponse"
+  }
+  // examples: []
+};
+export {
+  termdbSingleSampleMutationPayload
+};

package/src/routes/termdb.singlecellDEgenes.js

@@ -0,0 +1,12 @@
+const termdbSingleCellDEgenesPayload = {
+  request: {
+    typeId: "TermdbSingleCellDEgenesRequest"
+  },
+  response: {
+    typeId: "TermdbSingleCellDEgenesResponse"
+  }
+  // examples: []
+};
+export {
+  termdbSingleCellDEgenesPayload
+};

package/src/routes/termdb.singlecellData.js

@@ -0,0 +1,12 @@
+const termdbSingleCellDataPayload = {
+  request: {
+    typeId: "TermdbSingleCellDataRequest"
+  },
+  response: {
+    typeId: "TermdbSingleCellDataResponse"
+  }
+  // examples: []
+};
+export {
+  termdbSingleCellDataPayload
+};

package/src/routes/termdb.singlecellSamples.js

@@ -0,0 +1,12 @@
+const termdbSingleCellSamplesPayload = {
+  request: {
+    typeId: "TermdbSingleCellSamplesRequest"
+  },
+  response: {
+    typeId: "TermdbSingleCellSamplesResponse"
+  }
+  // examples: []
+};
+export {
+  termdbSingleCellSamplesPayload
+};

package/src/routes/termdb.termchildren.js

@@ -0,0 +1,28 @@
+const termChildrenPayload = {
+  request: {
+    typeId: "TermChildrenRequest"
+  },
+  response: {
+    typeId: "TermChildrenResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38-test",
+          dslabel: "TermdbTest",
+          embedder: "localhost",
+          get_children: 1,
+          cohortValues: "ABC",
+          tid: "GO:0000001"
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  termChildrenPayload
+};

package/src/routes/termdb.termsbyids.js

@@ -0,0 +1,12 @@
+const termsByIdsPayload = {
+  request: {
+    typeId: "TermsByIdsRequest"
+  },
+  response: {
+    typeId: "TermsByIdsResponse"
+  }
+  // examples: []
+};
+export {
+  termsByIdsPayload
+};

package/src/routes/termdb.topTermsByType.js

@@ -0,0 +1,12 @@
+const termdbTopTermsByTypePayload = {
+  request: {
+    typeId: "TermdbTopTermsByTypeRequest"
+  },
+  response: {
+    typeId: "TermdbTopTermsByTypeResponse"
+  }
+  // examples: []
+};
+export {
+  termdbTopTermsByTypePayload
+};

package/src/routes/termdb.topVariablyExpressedGenes.js

@@ -0,0 +1,12 @@
+const termdbTopVariablyExpressedGenesPayload = {
+  request: {
+    typeId: "TermdbTopVariablyExpressedGenesRequest"
+  },
+  response: {
+    typeId: "TermdbTopVariablyExpressedGenesResponse"
+  }
+  // examples: []
+};
+export {
+  termdbTopVariablyExpressedGenesPayload
+};

package/src/routes/termdb.violin.js

@@ -0,0 +1,49 @@
+const violinPayload = {
+  request: {
+    typeId: "ViolinRequest"
+  },
+  response: {
+    typeId: "ViolinResponse"
+  },
+  examples: [
+    {
+      request: {
+        body: {
+          genome: "hg38-test",
+          dslabel: "TermdbTest",
+          embedder: "localhost",
+          devicePixelRatio: 2.200000047683716,
+          maxThickness: 150,
+          screenThickness: 1218,
+          filter: {
+            type: "tvslst",
+            in: true,
+            join: "",
+            lst: [
+              {
+                tag: "cohortFilter",
+                type: "tvs",
+                tvs: { term: { id: "subcohort", type: "categorical" }, values: [{ key: "ABC", label: "ABC" }] }
+              }
+            ]
+          },
+          svgw: 227.27272234672367,
+          orientation: "horizontal",
+          datasymbol: "bean",
+          radius: 5,
+          strokeWidth: 0.2,
+          axisHeight: 60,
+          rightMargin: 50,
+          unit: "abs",
+          termid: "agedx"
+        }
+      },
+      response: {
+        header: { status: 200 }
+      }
+    }
+  ]
+};
+export {
+  violinPayload
+};

package/src/routes/tileserver.js

@@ -0,0 +1,12 @@
+const tilePayload = {
+  request: {
+    typeId: "TileRequest"
+  },
+  response: {
+    typeId: "TileResponse"
+  }
+  // examples: []
+};
+export {
+  tilePayload
+};

package/src/routes/wsimages.js

@@ -0,0 +1,12 @@
+const wsImagesPayload = {
+  request: {
+    typeId: "WSImagesRequest"
+  },
+  response: {
+    typeId: "WSImagesResponse"
+  }
+  // examples: []
+};
+export {
+  wsImagesPayload
+};

package/src/test/numeric.type.spec.js

@@ -0,0 +1,117 @@
+{
+  const valid = {
+    type: "float",
+    id: "someid",
+    name: "Some Dosage",
+    bins: {
+      default: {
+        type: "regular-bin",
+        bin_size: 1,
+        first_bin: {
+          startunbounded: true,
+          stop: 1
+        }
+      },
+      less: {
+        type: "custom-bin",
+        lst: [{ start: 0, stop: 1 }]
+      }
+    }
+  };
+  const A = { name: "test", type: "categorical" };
+  const B = { type: "integer" };
+  const C = {
+    // @ts-expect-error, should be string
+    name: 7,
+    type: "integer",
+    bins: {
+      default: {
+        type: "regular-bin",
+        bin_size: 1,
+        // tsc can detect type errors for deeply nested property values
+        // @ts-expect-error, does not match either StartUnboundedBin | FullyBoundedBin
+        first_bin: {
+          stop: 1
+        }
+      },
+      less: {
+        type: "custom-bin",
+        // @ts-expect-error, empty lst array
+        lst: []
+      }
+    }
+  };
+}
+{
+  const A = {
+    startunbounded: true,
+    startinclusive: true,
+    start: 0,
+    stop: 1,
+    stopinclusive: true,
+    stopunbounded: true
+  };
+  const B = {};
+  B.extraProp = "test";
+}
+{
+  const A = {
+    startunbounded: true,
+    stop: 1
+  };
+  const B = { startunbounded: true, start: 0, stop: 1 };
+  const C = { startunbounded: true };
+  const D = { startunbounded: true, start: 0, stop: 1, stopunbounded: true };
+  const E = {};
+  E.extraProp = "test";
+}
+{
+  const A = {
+    stopunbounded: true,
+    start: 0
+  };
+  const B = { stopunbounded: true, start: 0, stop: 1 };
+  const C = { stopunbounded: true };
+  const D = { startunbounded: true, start: 0, stop: 1, stopunbounded: true };
+}
+{
+  const A = {
+    startinclusive: true,
+    start: 0,
+    stop: 1
+  };
+  const B = { stop: 1 };
+  const C = { start: 0 };
+}
+const handlers = {
+  startUnbounded(bin) {
+    console.log(bin);
+  },
+  fullyBounded(bin) {
+    console.log(bin);
+  },
+  stopUnbounded(bin) {
+    console.log(bin);
+  }
+};
+function correctlyTypedProcessBin(bin) {
+  if (bin.startunbounded)
+    handlers.startUnbounded(bin);
+  else if (bin.stopunbounded)
+    handlers.stopUnbounded(bin);
+  else
+    handlers.fullyBounded(bin);
+}
+function incorrectProcessBin(bin) {
+  if (bin.startunbounded)
+    handlers.startUnbounded(bin);
+  else if (bin.stopunbounded)
+    handlers.stopUnbounded(bin);
+  else {
+    handlers.startUnbounded(bin);
+    handlers.stopUnbounded(bin);
+    handlers.fullyBounded(bin);
+    handlers.fullyBounded(bin);
+    handlers.fullyBounded(bin);
+  }
+}

package/src/Mclass.ts

@@ -1,8 +0,0 @@
-export type Mclass = {
-	[mclskey: string]: {
-		label?: string
-		color?: string
-		dt?: number | string
-		desc?: string
-	}
-}