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* Added TS. Updated build and linting config. Added types. * [ts-migrate][.] Rename files from JS/JSX to TS/TSX Co-authored-by: ts-migrate <> * [ts-migrate][.] Run TS Migrate Co-authored-by: ts-migrate <> * Corrected files mangled by ts-migrate. * Updated lint config, minor linting. * Re-enabled Husky. * Updated tests and config. * Reverted webpack devtool config. * Removed obsolete snapshots. * Added annotations snap. * Updated tsconfig includes wrt linting. * Removed ts-migrate. Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>
This commit is contained in:
Mim Hastie
co-authored by
ts-migrate
Timmy Huang
ts-migrate
Timmy Huang
parent
7328cbdbd5
commit
934cc5c69b
@@ -0,0 +1,411 @@
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/**
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* Gene set state. Geneset UI state is in a different reducer.
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*
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* geneset reducer state is a Map object, where:
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* key: the geneset name, a string.
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* val: the geneset defined as an object ("geneset object")
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*
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* A geneset object is:
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* {
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* genesetName: <string> # same as the map key
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* genesetDescription: <string>
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* genes: Map<<string>, {
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* geneSymbol: <string>, # same as the map key
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* geneDescription: <string>
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* }>
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* }
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*
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* Geneset and genes Map order is significant, and will be preserved across
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* CRUD operations on either.
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*
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* This reducer does light error checking, but not as much as the backend
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* routes. Do not rely on it to enforce geneset integrity - eg, no duplicate
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* genes in a geneset.
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*/
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import { diffexpPopNamePrefix1, diffexpPopNamePrefix2 } from "../globals";
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const GeneSets = (
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state = {
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initialized: false,
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lastTid: undefined,
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genesets: new Map(),
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},
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action: any
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) => {
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switch (action.type) {
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/**
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* Initial, load-time bootstrap.
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* {
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* type: "geneset: initial load"
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* data: JSON response
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* }
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*/
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case "geneset: initial load": {
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const { data } = action;
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if (
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!data ||
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typeof data.tid !== "number" ||
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!Array.isArray(data.genesets)
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)
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throw new Error("missing or malformed JSON response");
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const lastTid = data.tid;
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const genesetsData = data.genesets;
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const genesets = new Map();
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for (const gsData of genesetsData) {
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const genes = new Map();
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for (const gene of gsData.genes) {
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genes.set(gene.gene_symbol, {
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geneSymbol: gene.gene_symbol,
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geneDescription: gene?.gene_description ?? "",
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});
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}
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const gs = {
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genesetName: gsData.geneset_name,
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genesetDescription: gsData?.geneset_description ?? "",
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genes,
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};
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genesets.set(gsData.geneset_name, gs);
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}
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return {
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...state,
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initialized: true,
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lastTid,
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genesets,
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};
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}
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/**
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* Creates a new & empty geneset with the given name and description.
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* {
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* type: "geneset: create",
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* genesetName: string, // gene set name
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* genesetDescription: string, // geneset description
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* }
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*
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*/
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case "geneset: create": {
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const { genesetName, genesetDescription } = action;
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if (
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typeof genesetName !== "string" ||
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!genesetName ||
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genesetDescription === undefined
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)
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throw new Error("geneset: create -- name or description unspecified.");
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if (state.genesets.has(genesetName))
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throw new Error("geneset: create -- name already defined.");
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const genesets = new Map([
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[
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genesetName,
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{
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genesetName,
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genesetDescription,
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genes: new Map(),
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},
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],
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...state.genesets,
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]); // clone and add new geneset to beginning
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return {
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...state,
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genesets,
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};
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}
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/**
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* Deletes the named geneset, if it exists. Throws if it does not.
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* {
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* type: "geneset: delete",
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* genesetName: string
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* }
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*/
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case "geneset: delete": {
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const { genesetName } = action;
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if (!state.genesets.has(genesetName))
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throw new Error("geneset: delete -- geneset name does not exist.");
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const genesets = new Map(state.genesets); // clone
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genesets.delete(genesetName);
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return {
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...state,
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genesets,
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};
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}
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/**
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* Update the named geneset with a new name and description. Preserves the existing
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* order of the geneset, even when the genesetName changes.
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* {
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* type: "geneset: update",
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* genesetName: string, current name of geneset to be updated
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* update: {
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* genesetName: string, new name
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* genesetDescription: string, new description
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* }
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* }
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*
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* For example, if you want to update JUST the description:
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* dispatch({
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* action: "geneset: update",
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* genesetName: "foo",
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* update: { genesetName: "foo", genesetDescription: "a new description"}
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* })
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*/
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case "geneset: update": {
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const { genesetName, update } = action;
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if (
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typeof genesetName !== "string" ||
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!genesetName ||
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!state.genesets.has(genesetName)
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)
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throw new Error(
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"geneset: update -- geneset name unspecified or does not exist."
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);
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/* now that we've confirmed the gene set exists, check for duplicates */
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const genesetNameIsDuplicate = state.genesets.has(update.genesetName);
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const descriptionIsDuplicate =
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state.genesets.get(update.genesetName) &&
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state.genesets.get(update.genesetName).genesetDescription ===
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update.genesetDescription;
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if (genesetNameIsDuplicate && descriptionIsDuplicate)
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throw new Error(
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"geneset: update -- update specified existing name and description."
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);
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const prevGs = state.genesets.get(genesetName);
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const newGs = {
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...update,
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genes: prevGs.genes,
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}; // clone
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// clone the map, preserving current insert order, but mapping name->newName.
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const genesets = new Map();
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for (const [name, gs] of state.genesets) {
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if (name === genesetName) genesets.set(newGs.genesetName, newGs);
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else genesets.set(name, gs);
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}
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return {
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...state,
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genesets,
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};
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}
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/**
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* Adds genes to the geneset. They are appended to the END of the geneset, in the
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* order provided. Duplicates or genes already in the geneset, will be ignored.
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* {
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* type: "geneset: add genes"
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* genesetName: <string>, // gene set name
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* genes: Array<{
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* geneSymbol: <string>,
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* geneDescription: <string>
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* }>
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* }
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*
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* Example:
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* dispatch({
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* type: "add genes",
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* genesetName: "foo",
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* genes: [ { geneSymbol: "FOXP", geneDescription: "test" }]
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* });
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*/
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case "geneset: add genes": {
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const { genesetName, genes } = action;
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if (!state.genesets.has(genesetName))
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throw new Error("geneset: add genes -- geneset name does not exist.");
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// clone
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const genesets = new Map(state.genesets);
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const gs = {
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...genesets.get(genesetName),
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genes: new Map(genesets.get(genesetName).genes),
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};
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genesets.set(genesetName, gs);
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// add
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const newGenes = gs.genes;
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for (const gene of genes) {
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const { geneSymbol } = gene;
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const geneDescription = gene?.geneDescription ?? "";
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// ignore genes already present
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if (!newGenes.has(geneSymbol))
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newGenes.set(geneSymbol, {
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geneSymbol,
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geneDescription,
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});
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}
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return {
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...state,
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genesets,
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};
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}
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/**
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* Delete genes from the named geneset. Will throw if the genesetName does
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* not exist. Will ignore geneSymbols that do not exist.
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* {
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* type: "geneset: delete genes",
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* genesetName: <string>, // the geneset from which to delete genes
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* geneSymbols: [<string>, ...], // the gene symbols to delete.
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* }
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*
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* Example:
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* dispatch({
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* type: "geneset: delete genes",
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* genesetName: "a geneset name",
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* geneSymbols: ["F5"]
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* })
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*/
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case "geneset: delete genes": {
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const { genesetName, geneSymbols } = action;
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if (!state.genesets.has(genesetName))
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throw new Error(
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"geneset: delete genes -- geneset name does not exist."
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);
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// clone
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const genesets = new Map(state.genesets);
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const gs = {
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...genesets.get(genesetName),
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genes: new Map(genesets.get(genesetName).genes),
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};
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genesets.set(genesetName, gs);
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// delete
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const { genes } = gs;
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for (const geneSymbol of geneSymbols) {
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genes.delete(geneSymbol);
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}
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return {
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...state,
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genesets,
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};
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}
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/**
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* Set/update the description of the gene. NOTE that this does not allow the name
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* of the gene to change - only "geneset: add" and "geneset: delete" can change
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* the genes in a geneset. Use this to update a gene description AFTER you add it
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* to the geneset.
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* {
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* type: "geneset: set gene description",
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* genesetName: <string>, // the geneset to update
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* update: {
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* geneSymbol: <string>, // the gene to update, MUST exist already in the geneset
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* geneDescription: <string>
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* }
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* }
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*
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* Example:
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* dispatch({
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* type: "geneset: set gene description",
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* genesetName: "my fav geneset",
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* update: {
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* geneSymbol: "F5",
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* geneDescription: "tada, moar description"
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* }
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* })
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*/
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case "geneset: set gene description": {
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const { genesetName, update } = action;
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if (!state.genesets.has(genesetName))
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throw new Error(
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"geneset: set gene description -- geneset name does not exist."
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);
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// clone
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const genesets = new Map(state.genesets);
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const gs = {
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...genesets.get(genesetName),
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genes: new Map(genesets.get(genesetName).genes),
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};
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genesets.set(genesetName, gs);
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const { geneSymbol, geneDescription } = update;
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const gene = gs.genes.get(geneSymbol);
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if (!gene)
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throw new Error("geneset: set gene description -- no such gene");
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gs.genes.set(geneSymbol, {
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geneSymbol,
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geneDescription,
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});
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return {
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...state,
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genesets,
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};
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}
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/**
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* Used by autosave to update the server synchronization TID
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*/
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case "geneset: set tid": {
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const { tid } = action;
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if (!Number.isInteger(tid) || tid < 0)
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throw new Error("TID must be a positive integer number");
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// @ts-expect-error ts-migrate(2532) FIXME: Object is possibly 'undefined'.
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if (state.lastTid !== undefined && tid < state.lastTid)
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throw new Error("TID may not be decremented.");
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return {
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...state,
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lastTid: tid,
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};
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}
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case "request differential expression success": {
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const { data } = action;
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const dateString = new Date().toLocaleString();
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const genesetNames = {
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positive: `${diffexpPopNamePrefix1} (${dateString})`,
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negative: `${diffexpPopNamePrefix2} (${dateString})`,
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};
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const diffExpGeneSets = [];
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for (const polarity of Object.keys(genesetNames)) {
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const genes = new Map(
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data[polarity].map((diffExpGene: any) => [
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diffExpGene[0],
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{
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geneSymbol: diffExpGene[0],
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},
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])
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);
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diffExpGeneSets.push([
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// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
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genesetNames[polarity],
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{
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// @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
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genesetName: genesetNames[polarity],
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genesetDescription: "",
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genes,
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},
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]);
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}
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// @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call.
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const genesets = new Map([...diffExpGeneSets, ...state.genesets]); // clone
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return {
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...state,
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genesets,
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};
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}
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default:
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return state;
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}
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};
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export default GeneSets;
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