@sjcrh/proteinpaint-server 2.113.0 → 2.115.0

package/routes/gdc.topMutatedGenes.js

@@ -1,275 +0,0 @@
-import { gdcTopMutatedGenePayload } from "#types/checkers";
-import { mclasscnvgain, mclasscnvloss, dtsnvindel } from "#shared/common.js";
-import ky from "ky";
-const api = {
-  endpoint: "gdc/topMutatedGenes",
-  methods: {
-    get: {
-      init,
-      ...gdcTopMutatedGenePayload
-    },
-    post: {
-      init,
-      ...gdcTopMutatedGenePayload
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    const g = genomes.hg38;
-    if (!g)
-      throw "hg38 missing";
-    const ds = g.datasets.GDC;
-    if (!ds)
-      throw "hg38 GDC missing";
-    try {
-      const genes = await getGenesGraphql(q, ds);
-      const payload = { genes };
-      res.send(payload);
-    } catch (e) {
-      res.send({ status: "error", error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
-      else
-        console.trace(e);
-    }
-  };
-}
-const queryV2 = {
-  query: `
-          query GenesTable(
-            $caseFilters: FiltersArgument
-            $genesTable_filters: FiltersArgument
-            $genesTable_size: Int
-            $genesTable_offset: Int
-            $score: String
-            $ssmCase: FiltersArgument
-            $geneCaseFilter: FiltersArgument
-            $ssmTested: FiltersArgument
-            $cnvTested: FiltersArgument
-            $cnvGainFilters: FiltersArgument
-            $cnvLossFilters: FiltersArgument
-            $sort: [Sort]
-          ) {
-            genesTableViewer: viewer {
-              explore {
-                cases {
-                  hits(first: 0, case_filters: $ssmTested) {
-                    total
-                  }
-                }
-                filteredCases: cases {
-                  hits(first: 0, case_filters: $geneCaseFilter) {
-                    total
-                  }
-                }
-                cnvCases: cases {
-                  hits(first: 0, case_filters: $cnvTested) {
-                    total
-                  }
-                }
-                genes {
-                  hits(
-                    first: $genesTable_size
-                    offset: $genesTable_offset
-                    filters: $genesTable_filters
-                    case_filters: $caseFilters
-                    score: $score
-                    sort: $sort
-                  ) {
-                    total
-                    edges {
-                      node {
-                        id
-                        numCases: score
-                        symbol
-                        name
-                        cytoband
-                        biotype
-                        gene_id
-                        is_cancer_gene_census
-                        ssm_case: case {
-                          hits(first: 0, filters: $ssmCase) {
-                            total
-                          }
-                        }
-                        cnv_case: case {
-                          hits(first: 0, filters: $cnvTested) {
-                            total
-                          }
-                        }
-                        case_cnv_gain: case {
-                          hits(first: 0, filters: $cnvGainFilters) {
-                            total
-                          }
-                        }
-                        case_cnv_loss: case {
-                          hits(first: 0, filters: $cnvLossFilters) {
-                            total
-                          }
-                        }
-                      }
-                    }
-                  }
-                }
-              }
-            }
-          }`,
-  getVariables: (q) => {
-    const variables = {
-      caseFilters: { op: "and", content: [] },
-      genesTable_filters: { op: "and", content: [] },
-      genesTable_size: q.maxGenes || 50,
-      genesTable_offset: 0,
-      score: "case.project.project_id",
-      ssmCase: {
-        op: "and",
-        content: [
-          {
-            op: "in",
-            content: {
-              field: "cases.available_variation_data",
-              value: ["ssm"]
-            }
-          },
-          {
-            op: "NOT",
-            content: {
-              field: "genes.case.ssm.observation.observation_id",
-              value: "MISSING"
-            }
-          }
-        ]
-      },
-      geneCaseFilter: {
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["ssm"]
-            },
-            op: "in"
-          }
-        ],
-        op: "and"
-      },
-      ssmTested: {
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["ssm"]
-            },
-            op: "in"
-          }
-        ],
-        op: "and"
-      },
-      cnvTested: {
-        op: "and",
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["cnv"]
-            },
-            op: "in"
-          }
-        ]
-      },
-      cnvGainFilters: {
-        op: "and",
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["cnv"]
-            },
-            op: "in"
-          },
-          {
-            content: {
-              field: "cnvs.cnv_change",
-              value: ["Gain"]
-            },
-            op: "in"
-          }
-        ]
-      },
-      cnvLossFilters: {
-        op: "and",
-        content: [
-          {
-            content: {
-              field: "cases.available_variation_data",
-              value: ["cnv"]
-            },
-            op: "in"
-          },
-          {
-            content: {
-              field: "cnvs.cnv_change",
-              value: ["Loss"]
-            },
-            op: "in"
-          }
-        ]
-      }
-    };
-    if (q.filter0) {
-      variables.ssmCase.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.caseFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.cnvGainFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
-      variables.cnvTested.content.push(JSON.parse(JSON.stringify(q.filter0)));
-    }
-    if (q.geneFilter == "CGC") {
-      variables.genesTable_filters.content.push(geneCGC());
-      variables.cnvLossFilters.content.push(geneCGC());
-      variables.cnvGainFilters.content.push(geneCGC());
-    }
-    return variables;
-  }
-};
-async function getGenesGraphql(q, ds) {
-  const { host, headers } = ds.getHostHeaders(q);
-  const query = queryV2.query;
-  const variables = queryV2.getVariables(q);
-  const re = await ky.post(host.graphql, {
-    timeout: false,
-    // do not let ky timeout
-    headers,
-    json: { query, variables }
-  }).json();
-  const genes = [];
-  for (const g of re.data.genesTableViewer.explore.genes.hits.edges) {
-    if (typeof g.node != "object")
-      throw "node missing from re.data.genesTableViewer.explore.genes.hits.edges[]";
-    const mutationStat = [];
-    if (Number.isInteger(g.node.case_cnv_gain?.hits?.total) && g.node.case_cnv_gain.hits.total > 0)
-      mutationStat.push({ class: mclasscnvgain, count: g.node.case_cnv_gain.hits.total });
-    if (Number.isInteger(g.node.case_cnv_loss?.hits?.total) && g.node.case_cnv_loss.hits.total > 0)
-      mutationStat.push({ class: mclasscnvloss, count: g.node.case_cnv_loss.hits.total });
-    if (Number.isInteger(g.node.ssm_case?.hits?.total) && g.node.ssm_case.hits.total > 0)
-      mutationStat.push({ dt: dtsnvindel, count: g.node.ssm_case.hits.total });
-    genes.push({
-      gene: g.node.symbol,
-      mutationStat
-    });
-  }
-  return genes;
-}
-function geneCGC() {
-  return {
-    content: {
-      field: "genes.is_cancer_gene_census",
-      value: ["true"]
-    },
-    op: "in"
-  };
-}
-export {
-  api
-};