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TS migration. #2288. (#2328)

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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
2021-07-26 20:18:17 +00:00
committed by GitHub
co-authored by ts-migrate Timmy Huang
parent 7328cbdbd5
commit 934cc5c69b
206 changed files with 4719 additions and 2085 deletions
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client/src/actions/geneset.js
-148
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@@ -1,148 +0,0 @@
import { postUserErrorToast } from "../components/framework/toasters";
/*
Action creators for gene sets
Primarily used to keep the crossfilter and underlying data in sync with the UI.
The behavior manifest in these action creators:
Delete a gene set, will
* drop index & clear selection state on the gene set summary
* drop index & clear selection state of each gene in the geneset
Delete a gene from a gene set, will:
* drop index & clear selection state on the gene set summary
* drop index & clear selection state on the gene
Add a gene to a gene set, will:
* drop index & clear selection state on the gene set summary
* will NOT touch the selection state for the gene
Note that crossfilter indices are lazy created, as needed.
*/
export const genesetDelete = (genesetName) => (dispatch, getState) => {
const state = getState();
const { genesets } = state;
const gs = genesets?.genesets?.get(genesetName) ?? {};
const geneSymbols = Array.from(gs.genes.keys());
const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
if (genesetName === state.colors.colorAccessor) {
dispatch({
type: "reset colorscale",
});
}
dispatch({
type: "geneset: delete",
genesetName,
obsCrossfilter,
annoMatrix: obsCrossfilter.annoMatrix,
});
};
export const genesetAddGenes = (genesetName, genes) => async (
dispatch,
getState
) => {
const state = getState();
const { obsCrossfilter: prevObsCrossfilter, annoMatrix } = state;
const { schema } = annoMatrix;
const varIndex = schema.annotations.var.index;
const df = await annoMatrix.fetch("var", varIndex);
const geneNames = df.col(varIndex).asArray();
genes = genes.reduce((acc, gene) => {
if (geneNames.indexOf(gene.geneSymbol) === -1) {
postUserErrorToast(
`${gene.geneSymbol} doesn't appear to be a valid gene name.`
);
} else acc.push(gene);
return acc;
}, []);
const obsCrossfilter = dropGenesetSummaryDimension(
prevObsCrossfilter,
state,
genesetName
);
dispatch({
type: "continuous metadata histogram cancel",
continuousNamespace: { isGeneSetSummary: true },
selection: genesetName,
});
return dispatch({
type: "geneset: add genes",
genesetName,
genes,
obsCrossfilter,
annoMatrix: obsCrossfilter.annoMatrix,
});
};
export const genesetDeleteGenes = (genesetName, geneSymbols) => (
dispatch,
getState
) => {
const state = getState();
const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
return dispatch({
type: "geneset: delete genes",
genesetName,
geneSymbols,
obsCrossfilter,
annoMatrix: obsCrossfilter.annoMatrix,
});
};
/*
Private
*/
function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
const { annoMatrix, genesets } = state;
const varIndex = annoMatrix.schema.annotations?.var?.index;
const gs = genesets?.genesets?.get(genesetName) ?? {};
const genes = Array.from(gs.genes.keys());
const query = {
summarize: {
method: "mean",
field: "var",
column: varIndex,
values: genes,
},
};
return obsCrossfilter.dropDimension("X", query);
}
function dropGeneDimension(obsCrossfilter, state, gene) {
const { annoMatrix } = state;
const varIndex = annoMatrix.schema.annotations?.var?.index;
const query = {
where: {
field: "var",
column: varIndex,
value: gene,
},
};
return obsCrossfilter.dropDimension("X", query);
}
function dropGeneset(dispatch, state, genesetName, geneSymbols) {
const { obsCrossfilter: prevObsCrossfilter } = state;
const obsCrossfilter = geneSymbols.reduce(
(crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
);
dispatch({
type: "continuous metadata histogram cancel",
continuousNamespace: { isGeneSetSummary: true },
selection: genesetName,
});
geneSymbols.forEach((g) =>
dispatch({
type: "continuous metadata histogram cancel",
continuousNamespace: { isUserDefined: true },
selection: g,
})
);
return obsCrossfilter;
}