@sjcrh/proteinpaint-client 2.212.0 → 2.213.0

package/dist/chunk-CWWE77DH.js

@@ -0,0 +1,498 @@
+import {
+  deepFreeze
+} from "./chunk-HBNB5TRH.js";
+
+// test/testdata/termjson.ts
+var diaggrp = {
+  id: "diaggrp",
+  name: "Diagnosis Group",
+  type: "categorical",
+  isleaf: true,
+  values: {
+    "Acute lymphoblastic leukemia": { label: "Acute lymphoblastic leukemia" },
+    "Acute myeloid leukemia": { label: "Acute myeloid leukemia" },
+    "Blood disorder": { label: "Blood disorder" },
+    "Central nervous system (CNS)": { label: "Central nervous system (CNS)" },
+    "Chronic myeloid leukemia": { label: "Chronic myeloid leukemia" },
+    "Colon carcinoma": { label: "Colon carcinoma" },
+    "Ewing sarcoma family of tumors": { label: "Ewing sarcoma family of tumors" },
+    "Germ cell tumor": { label: "Germ cell tumor" },
+    Histiocytosis: { label: "Histiocytosis" },
+    "Hodgkin lymphoma": { label: "Hodgkin lymphoma" },
+    "Liver malignancies": { label: "Liver malignancies" },
+    "MDS/Acute myeloid leukemia": { label: "MDS/Acute myeloid leukemia" },
+    Melanoma: { label: "Melanoma" },
+    "Myelodysplastic syndrome": { label: "Myelodysplastic syndrome" },
+    "Nasopharyngeal carcinoma": { label: "Nasopharyngeal carcinoma" },
+    Nephroblastomatosis: { label: "Nephroblastomatosis" },
+    Neuroblastoma: { label: "Neuroblastoma" },
+    "Non-Hodgkin lymphoma": { label: "Non-Hodgkin lymphoma" },
+    "Non-malignancy": { label: "Non-malignancy" },
+    Osteosarcoma: { label: "Osteosarcoma" },
+    "Other carcinoma": { label: "Other carcinoma" },
+    "Other leukemia": { label: "Other leukemia" },
+    "Other malignancy": { label: "Other malignancy" },
+    Retinoblastoma: { label: "Retinoblastoma" },
+    Rhabdomyosarcoma: { label: "Rhabdomyosarcoma" },
+    "Soft tissue sarcoma": { label: "Soft tissue sarcoma" },
+    "Wilms tumor": { label: "Wilms tumor" }
+  },
+  groupsetting: { disabled: false }
+};
+var agedx = {
+  id: "agedx",
+  name: "Age at Cancer Diagnosis",
+  unit: "Years",
+  type: "float",
+  bins: {
+    label_offset: 1,
+    default: {
+      type: "regular-bin",
+      label_offset: 1,
+      bin_size: 3,
+      //startinclusive: true,
+      first_bin: {
+        startunbounded: true,
+        stop: 2
+      }
+    },
+    less: {
+      type: "regular-bin",
+      label_offset: 1,
+      bin_size: 5,
+      //startinclusive: true,
+      first_bin: {
+        startunbounded: true,
+        stop: 5
+      },
+      last_bin: {
+        stopunbounded: true,
+        start: 15
+      }
+    }
+  },
+  isleaf: true
+};
+var termjson = deepFreeze({
+  diaggrp,
+  agedx,
+  os: {
+    id: "os",
+    name: "Overall survival",
+    type: "survival",
+    unit: "years",
+    isleaf: true
+  },
+  Arrhythmias: {
+    id: "Arrhythmias",
+    name: "Arrhythmias",
+    type: "condition",
+    values: {
+      0: { label: "0: No condition" },
+      1: { label: "1: Mild" },
+      2: { label: "2: Moderate" },
+      3: { label: "3: Severe" },
+      4: { label: "4: Life-threatening" },
+      5: { label: "5: Death" },
+      9: { label: "Unknown status", uncomputable: true }
+    }
+  },
+  aaclassic_5: {
+    id: "aaclassic_5",
+    name: "Cumulative Alkylating Agent (Cyclophosphamide Equivalent Dose)",
+    unit: "mg/m\xB2",
+    type: "float",
+    bins: {
+      label_offset: 1,
+      default: {
+        type: "regular-bin",
+        bin_size: 1e3,
+        startinclusive: true,
+        first_bin: {
+          startunbounded: true,
+          stop: 2e3
+        },
+        last_bin: {
+          stopunbounded: true,
+          start: 16e3
+        }
+      }
+    },
+    values: {
+      "-1": { label: "not exposed", uncomputable: true },
+      "-8888": { label: "Exposed but dose unknown", uncomputable: true },
+      "-9999": { label: "Unknown treatment record", uncomputable: true }
+    },
+    isleaf: true
+  },
+  sex: {
+    id: "sex",
+    name: "Sex",
+    type: "categorical",
+    groupsetting: { disabled: true },
+    values: {
+      1: { label: "Female", color: "blue" },
+      2: { label: "Male", color: "#e75480" }
+    }
+  },
+  idarubicin_5: {
+    id: "idarubicin_5",
+    name: "Idarubicin (IV)",
+    unit: "mg/m\xB2",
+    type: "float",
+    bins: {
+      default: {
+        type: "regular-bin",
+        bin_size: 10,
+        stopinclusive: true,
+        first_bin: {
+          startunbounded: true,
+          stop: 10,
+          stopinclusive: true
+        },
+        last_bin: {
+          stopunbounded: true,
+          start: 40
+        }
+      }
+    },
+    values: {
+      0: { label: "Not exposed", uncomputable: true },
+      "-8888": { label: "Exposed but dose unknown", uncomputable: true },
+      "-9999": { label: "Unknown treatment record", uncomputable: true }
+    }
+  },
+  hrtavg: {
+    type: "float",
+    bins: {
+      default: {
+        type: "regular-bin",
+        startinclusive: true,
+        bin_size: 500,
+        first_bin: { stop: 500 },
+        last_bin: { start: 3500 }
+      }
+    },
+    values: {
+      "-8888": { label: "exposed, dose unknown", uncomputable: true },
+      "-9999": { label: "unknown exposure", uncomputable: true }
+    },
+    name: "Average dose to heart + TBI, cGy",
+    skip0forPercentile: true,
+    id: "hrtavg",
+    isleaf: true
+  },
+  "Cardiac dysrhythmia": {
+    id: "Cardiac dysrhythmia",
+    name: "Cardiac dysrhythmia",
+    parent_id: "Arrhythmias",
+    type: "condition",
+    values: {
+      0: { label: "0: No condition" },
+      1: { label: "1: Mild" },
+      2: { label: "2: Moderate" },
+      3: { label: "3: Severe" },
+      4: { label: "4: Life-threatening" },
+      5: { label: "5: Death" },
+      9: { label: "Unknown status", uncomputable: true }
+    }
+  },
+  Acountry: {
+    id: "Acountry",
+    term: {
+      id: "Acountry",
+      type: "categorical",
+      name: "Country name",
+      isleaf: true,
+      parentId: "A",
+      order: 1e3,
+      domainDetails: "",
+      values: {
+        Kenya: {
+          label: "Kenya",
+          color: "rgb(110, 64, 170)"
+        },
+        Nigeria: {
+          label: "Nigeria",
+          color: "rgb(140, 62, 178)"
+        },
+        Ghana: {
+          label: "Ghana",
+          color: "rgb(172, 60, 178)"
+        },
+        Uganda: {
+          label: "Uganda",
+          color: "rgb(203, 61, 171)"
+        },
+        Panama: {
+          label: "Panama",
+          color: "rgb(230, 65, 156)"
+        },
+        Honduras: {
+          label: "Honduras",
+          color: "rgb(251, 73, 135)"
+        },
+        Mexico: {
+          label: "Mexico",
+          color: "rgb(255, 86, 111)"
+        },
+        Cameroon: {
+          label: "Cameroon",
+          color: "rgb(255, 103, 88)"
+        },
+        Ethiopia: {
+          label: "Ethiopia",
+          color: "rgb(255, 124, 67)"
+        },
+        "South Africa": {
+          label: "South Africa",
+          color: "rgb(252, 148, 52)"
+        },
+        Tanzania: {
+          label: "Tanzania",
+          color: "rgb(234, 173, 46)"
+        },
+        Ukraine: {
+          label: "Ukraine",
+          color: "rgb(213, 198, 51)"
+        },
+        Mongolia: {
+          label: "Mongolia",
+          color: "rgb(192, 221, 66)"
+        },
+        Armenia: {
+          label: "Armenia",
+          color: "rgb(175, 240, 91)"
+        },
+        Poland: {
+          label: "Poland",
+          color: "rgb(138, 245, 87)"
+        },
+        Serbia: {
+          label: "Serbia",
+          color: "rgb(102, 247, 94)"
+        },
+        Belarus: {
+          label: "Belarus",
+          color: "rgb(70, 245, 110)"
+        },
+        Tajikistan: {
+          label: "Tajikistan",
+          color: "rgb(46, 238, 133)"
+        },
+        Kazakhstan: {
+          label: "Kazakhstan",
+          color: "rgb(31, 226, 158)"
+        },
+        Russia: {
+          label: "Russia",
+          color: "rgb(25, 209, 183)"
+        },
+        Kyrgyzstan: {
+          label: "Kyrgyzstan",
+          color: "rgb(28, 189, 204)"
+        },
+        Azerbaijan: {
+          label: "Azerbaijan",
+          color: "rgb(38, 166, 218)"
+        },
+        Palestine: {
+          label: "Palestine",
+          color: "rgb(52, 142, 225)"
+        },
+        Brazil: {
+          label: "Brazil",
+          color: "rgb(69, 119, 223)"
+        },
+        Chile: {
+          label: "Chile",
+          color: "rgb(86, 98, 212)"
+        },
+        Peru: {
+          label: "Peru",
+          color: "rgb(100, 79, 194)"
+        }
+      },
+      groupsetting: {
+        disabled: true
+      }
+    },
+    isAtomic: true,
+    q: {
+      isAtomic: true,
+      mode: "discrete",
+      type: "values",
+      hiddenValues: {}
+    },
+    type: "QualTWValues"
+  },
+  AWHO_region: {
+    id: "AWHO_region",
+    term: {
+      id: "AWHO_region",
+      type: "categorical",
+      name: "WHO Region",
+      isleaf: true,
+      parentId: "A",
+      order: 1e3,
+      domainDetails: "",
+      values: {
+        Africa: {
+          label: "Africa",
+          color: "#1b9e77"
+        },
+        Americas: {
+          label: "Americas",
+          color: "#d95f02"
+        },
+        Europe: {
+          label: "Europe",
+          color: "#7570b3"
+        },
+        "Western Pacific": {
+          label: "Western Pacific",
+          color: "#e7298a"
+        },
+        "Eastern Mediterranean": {
+          label: "Eastern Mediterranean",
+          color: "#66a61e"
+        }
+      },
+      groupsetting: {
+        disabled: true
+      }
+    },
+    isAtomic: true,
+    q: {
+      isAtomic: true,
+      mode: "discrete",
+      type: "values",
+      hiddenValues: {}
+    },
+    type: "QualTWValues"
+  },
+  AIncome_group: {
+    id: "AIncome_group",
+    term: {
+      id: "AIncome_group",
+      type: "categorical",
+      name: "World Bank Income Group",
+      isleaf: true,
+      parentId: "A",
+      order: 1e3,
+      domainDetails: "",
+      values: {
+        "Lower middle income": {
+          label: "Lower middle income",
+          color: "#1b9e77"
+        },
+        "Low income": {
+          label: "Low income",
+          color: "#d95f02"
+        },
+        "High income": {
+          label: "High income",
+          color: "#7570b3"
+        },
+        "Upper middle income": {
+          label: "Upper middle income",
+          color: "#e7298a"
+        }
+      },
+      groupsetting: {
+        disabled: true
+      }
+    },
+    isAtomic: true,
+    q: {
+      isAtomic: true,
+      mode: "discrete",
+      type: "values",
+      hiddenValues: {}
+    },
+    type: "QualTWValues"
+  },
+  AFC_TypeofFacility: {
+    id: "AFC_TypeofFacility",
+    term: {
+      id: "AFC_TypeofFacility",
+      type: "categorical",
+      name: "Type of Hospital",
+      isleaf: true,
+      parentId: "A",
+      order: 1e3,
+      domainDetails: "",
+      values: {
+        "Children's Hospital": {
+          label: "Children's Hospital",
+          color: "#1b9e77"
+        },
+        "General Hospital": {
+          label: "General Hospital",
+          color: "#d95f02"
+        },
+        "Cancer Hospital or Institute": {
+          label: "Cancer Hospital or Institute",
+          color: "#7570b3"
+        },
+        Other: {
+          label: "Other",
+          color: "#e7298a"
+        },
+        "Pediatric Hematology and/or Oncology Hospital": {
+          label: "Pediatric Hematology and/or Oncology Hospital",
+          color: "#66a61e"
+        }
+      },
+      groupsetting: {
+        disabled: true
+      }
+    },
+    isAtomic: true,
+    q: {
+      isAtomic: true,
+      mode: "discrete",
+      type: "values",
+      hiddenValues: {}
+    },
+    type: "QualTWValues"
+  },
+  AFC_TeachingFacility: {
+    id: "AFC_TeachingFacility",
+    term: {
+      id: "AFC_TeachingFacility",
+      type: "categorical",
+      name: "Government-designated Teaching Facility Status",
+      isleaf: true,
+      parentId: "A",
+      order: 1e3,
+      domainDetails: "",
+      values: {
+        Yes: {
+          label: "Yes",
+          color: "#e75480"
+        },
+        No: {
+          label: "No",
+          color: "blue"
+        }
+      },
+      groupsetting: {
+        disabled: true
+      }
+    },
+    isAtomic: true,
+    q: {
+      isAtomic: true,
+      mode: "discrete",
+      type: "values",
+      hiddenValues: {}
+    },
+    type: "QualTWValues"
+  }
+});
+
+export {
+  termjson
+};
+//# sourceMappingURL=chunk-CWWE77DH.js.map

package/dist/chunk-DCHHIXIP.js

@@ -0,0 +1,103 @@
+import {
+  SearchHandler,
+  fillTermWrapper,
+  table2col,
+  termsettingInit
+} from "./chunk-QI6X4V43.js";
+
+// plots/summarizeMutationDiagnosis.ts
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let dictTw;
+  {
+    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
+    if (!t) throw "defaultTw4correlationPlot missing";
+    dictTw = structuredClone(t);
+    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+  }
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "0px 10px 10px 10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Mutation Variable");
+    const searchDiv = td2.append("div");
+    const geneSearchInst = new SearchHandler();
+    geneSearchInst.init({
+      holder: searchDiv,
+      app: chartsInstance.app,
+      // required to supply "opts.app.vocabApi" for the search ui
+      genomeObj: chartsInstance.app.opts.genome,
+      msg: "Hit ENTER to launch plot.",
+      /* the geneTw below is used as it comes, so a grouping the user built for this gene
+      elsewhere can be offered here, see keepsQ in client/termdb/TermTypeSearch.ts */
+      keepsQ: true,
+      callback: async (geneTw) => {
+        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
+        launchPlot({
+          tw1: dictTw,
+          tw2: geneTw,
+          chartsInstance,
+          holder
+        });
+      }
+    });
+    searchDiv.style("padding", "0px 0px 5px 0px");
+  }
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Compare Mutations Against");
+    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
+    const pill = await termsettingInit({
+      menuOptions: "{edit,replace}",
+      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
+      target="filter" works for gdc since in gdc ds it is overriding filter to dict
+      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
+      maybe this is okay for non-gdc ds as the default dictTw is meaningful
+      */
+      usecase: { target: "filter" },
+      vocabApi: chartsInstance.app.vocabApi,
+      holder: pillDiv,
+      callback: async (tw) => {
+        waitDiv.text("LOADING ...");
+        try {
+          await pill.main(tw);
+          dictTw = tw;
+          waitDiv.text("Click to edit/replace the variable before searching gene.");
+        } catch (e) {
+          waitDiv.text("Error: " + (e.message || e));
+        }
+      }
+    });
+    try {
+      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+      await pill.main(dictTw);
+      waitDiv.text("Click to edit/replace the variable before searching gene.");
+    } catch (e) {
+      waitDiv.text("Error: " + (e.message || e));
+    }
+  }
+}
+function launchPlot({ tw1, tw2, chartsInstance, holder }) {
+  const chart = {
+    config: {
+      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
+      // TODO define sandbox header with gene+term name
+      term: tw1,
+      term2: tw2
+    }
+  };
+  chartsInstance.plotCreate(chart);
+  holder.selectAll("*").remove();
+  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
+  setTimeout(() => {
+    holder.style("display", "none");
+  }, 1e3);
+}
+
+export {
+  makeChartBtnMenu,
+  launchPlot
+};
+//# sourceMappingURL=chunk-DCHHIXIP.js.map