mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-03 22:58:12 +08:00
* 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
@@ -1,485 +0,0 @@
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/*
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Action creators for user annotation
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*/
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import difference from "lodash.difference";
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import pako from "pako";
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import * as globals from "../globals";
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import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
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const { isUserAnnotation } = AnnotationsHelpers;
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export const annotationCreateCategoryAction = (
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newCategoryName,
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categoryToDuplicate
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) => async (dispatch, getState) => {
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/*
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Add a new user-created category to the obs annotations.
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Arguments:
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newCategoryName - string name for the category.
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categoryToDuplicate - obs category to use for initial values, or null.
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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const { schema } = prevAnnoMatrix;
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/* name must be a string, non-zero length */
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if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
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throw new Error("user annotations require string name");
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/* ensure the name isn't already in use! */
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if (schema.annotations.obsByName[newCategoryName])
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throw new Error("name collision on annotation category create");
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let initialValue;
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let newSchema;
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let ctor;
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if (categoryToDuplicate) {
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/* if we are duplicating a category, retrieve it */
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const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
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const catDupType = catDupSchema?.type;
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if (catDupType !== "string" && catDupType !== "categorical")
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throw new Error("categoryToDuplicate does not exist or has invalid type");
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const catToDupDf = await prevAnnoMatrix
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.base()
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.fetch("obs", categoryToDuplicate);
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const col = catToDupDf.col(categoryToDuplicate);
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initialValue = col.asArray();
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const { categories } = col.summarizeCategorical();
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// all user-created annotations must have the unassigned category
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if (!categories.includes(globals.unassignedCategoryLabel)) {
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categories.push(globals.unassignedCategoryLabel);
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}
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ctor = initialValue.constructor;
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newSchema = {
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...catDupSchema,
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name: newCategoryName,
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categories,
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writable: true,
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};
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} else {
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/* else assign to the standard default value */
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initialValue = globals.unassignedCategoryLabel;
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ctor = Array;
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newSchema = {
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name: newCategoryName,
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type: "categorical",
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categories: [globals.unassignedCategoryLabel],
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writable: true,
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};
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}
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const obsCrossfilter = prevObsCrossfilter.addObsColumn(
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newSchema,
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ctor,
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initialValue
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);
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dispatch({
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type: "annotation: create category",
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data: newCategoryName,
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categoryToDuplicate,
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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});
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};
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export const annotationRenameCategoryAction = (
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oldCategoryName,
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newCategoryName
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) => (dispatch, getState) => {
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/*
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Rename a user-created annotation category
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, oldCategoryName))
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throw new Error("not a user annotation");
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/* name must be a string, non-zero length */
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if (typeof newCategoryName !== "string" || newCategoryName.length === 0)
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throw new Error("user annotations require string name");
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if (oldCategoryName === newCategoryName) return;
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const obsCrossfilter = prevObsCrossfilter.renameObsColumn(
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oldCategoryName,
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newCategoryName
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);
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dispatch({
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type: "annotation: category edited",
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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metadataField: oldCategoryName,
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newCategoryText: newCategoryName,
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data: newCategoryName,
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});
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};
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export const annotationDeleteCategoryAction = (categoryName) => (
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dispatch,
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getState
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) => {
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/*
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Delete a user-created category
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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const obsCrossfilter = prevObsCrossfilter.dropObsColumn(categoryName);
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dispatch({
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type: "annotation: delete category",
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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metadataField: categoryName,
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});
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};
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export const annotationCreateLabelInCategory = (
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categoryName,
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labelName,
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assignSelected
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) => async (dispatch, getState) => {
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/*
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Add a new label to a user-defined category. If assignSelected is true, assign
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the label to all currently selected cells.
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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let obsCrossfilter = prevObsCrossfilter.addObsAnnoCategory(
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categoryName,
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labelName
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);
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if (assignSelected) {
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obsCrossfilter = await obsCrossfilter.setObsColumnValues(
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categoryName,
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prevObsCrossfilter.allSelectedLabels(),
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labelName
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);
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}
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dispatch({
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type: "annotation: add new label to category",
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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metadataField: categoryName,
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newLabelText: labelName,
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assignSelectedCells: assignSelected,
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});
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};
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export const annotationDeleteLabelFromCategory = (
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categoryName,
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labelName
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) => async (dispatch, getState) => {
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/*
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delete a label from a user-defined category
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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const obsCrossfilter = await prevObsCrossfilter.removeObsAnnoCategory(
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categoryName,
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labelName,
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globals.unassignedCategoryLabel
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);
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dispatch({
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type: "annotation: delete label",
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metadataField: categoryName,
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label: labelName,
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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});
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};
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export const annotationRenameLabelInCategory = (
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categoryName,
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oldLabelName,
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newLabelName
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) => async (dispatch, getState) => {
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/*
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label name change
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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let obsCrossfilter = await prevObsCrossfilter.resetObsColumnValues(
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categoryName,
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oldLabelName,
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newLabelName
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);
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obsCrossfilter = await obsCrossfilter.removeObsAnnoCategory(
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categoryName,
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oldLabelName,
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globals.unassignedCategoryLabel
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);
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dispatch({
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type: "annotation: label edited",
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editedLabel: newLabelName,
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metadataField: categoryName,
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label: oldLabelName,
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annoMatrix: obsCrossfilter.annoMatrix,
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obsCrossfilter,
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});
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};
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export const annotationLabelCurrentSelection = (
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categoryName,
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labelName
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) => async (dispatch, getState) => {
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/*
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set the label on all currently selected
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*/
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const {
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annoMatrix: prevAnnoMatrix,
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obsCrossfilter: prevObsCrossfilter,
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} = getState();
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if (!prevAnnoMatrix || !prevObsCrossfilter) return;
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if (!isUserAnnotation(prevAnnoMatrix, categoryName))
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throw new Error("not a user annotation");
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const obsCrossfilter = await prevObsCrossfilter.setObsColumnValues(
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categoryName,
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prevObsCrossfilter.allSelectedLabels(),
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labelName
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);
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dispatch({
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type: "annotation: label current cell selection",
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metadataField: categoryName,
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label: labelName,
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obsCrossfilter,
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annoMatrix: obsCrossfilter.annoMatrix,
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});
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};
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function writableAnnotations(annoMatrix) {
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return annoMatrix.schema.annotations.obs.columns
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.filter((s) => s.writable)
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.map((s) => s.name);
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}
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export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => {
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/*
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Return true if there are LIKELY user-defined annotation modifications between the two
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annoMatrices. Technically not an action creator, but intimately intertwined
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with the save process.
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Two conditions will trigger a need to save:
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* the collection of user-defined columns have changed
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* the contents of the user-defined columns have change
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*/
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annoMatrix = annoMatrix.base();
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// if the annoMatrix hasn't changed, we are guaranteed no changes to the matrix schema or contents.
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if (annoMatrix === lastSavedAnnoMatrix) return false;
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// if the schema has changed, we need to save
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const currentWritable = writableAnnotations(annoMatrix);
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if (difference(currentWritable, writableAnnotations(lastSavedAnnoMatrix))) {
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return true;
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}
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// no schema changes; check for change in contents
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return currentWritable.some(
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(col) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
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);
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};
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export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
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/*
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Save the user-created obs annotations IF any have changed.
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*/
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const state = getState();
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const { annotations, autosave } = state;
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const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
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const { lastSavedAnnoMatrix, saveInProgress } = autosave;
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const annoMatrix = state.annoMatrix.base();
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if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
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if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
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dispatch({
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type: "writable obs annotations - save complete",
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lastSavedAnnoMatrix: annoMatrix,
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});
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return;
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}
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/*
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Else, we really do need to save
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*/
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dispatch({
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type: "writable obs annotations - save started",
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});
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const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
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const matrix = MatrixFBS.encodeMatrixFBS(df);
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const compressedMatrix = pako.deflate(matrix);
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try {
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const queryString =
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!dataCollectionNameIsReadOnly && !!dataCollectionName
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? `?annotation-collection-name=${encodeURIComponent(
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dataCollectionName
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)}`
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: "";
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
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{
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method: "PUT",
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body: compressedMatrix,
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headers: new Headers({
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"Content-Type": "application/octet-stream",
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}),
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credentials: "include",
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}
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);
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if (res.ok) {
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dispatch({
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type: "writable obs annotations - save complete",
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lastSavedAnnoMatrix: annoMatrix,
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});
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} else {
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dispatch({
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type: "writable obs annotations - save error",
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message: `HTTP error ${res.status} - ${res.statusText}`,
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res,
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});
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}
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} catch (error) {
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dispatch({
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type: "writable obs annotations - save error",
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message: error.toString(),
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error,
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});
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}
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};
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export const saveGenesetsAction = () => async (dispatch, getState) => {
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const state = getState();
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// bail if gene sets not available, or in readonly mode.
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const { config } = state;
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const { lastTid, genesets } = state.genesets;
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const genesetsAreAvailable =
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config?.parameters?.annotations_genesets ?? false;
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const genesetsReadonly =
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config?.parameters?.annotations_genesets_readonly ?? true;
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if (!genesetsAreAvailable || genesetsReadonly) {
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// our non-save was completed!
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return dispatch({
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type: "autosave: genesets complete",
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lastSavedGenesets: genesets,
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});
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}
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dispatch({
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type: "autosave: genesets started",
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});
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/* Create the JSON OTA data structure */
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const tid = (lastTid ?? 0) + 1;
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const genesetsOTA = [];
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for (const [name, gs] of genesets) {
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const genes = [];
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for (const g of gs.genes.values()) {
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genes.push({
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gene_symbol: g.geneSymbol,
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gene_description: g.geneDescription,
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});
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}
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genesetsOTA.push({
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geneset_name: name,
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geneset_description: gs.genesetDescription,
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genes,
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});
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}
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const ota = {
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tid,
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genesets: genesetsOTA,
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};
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/* Save to server */
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try {
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const {
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dataCollectionNameIsReadOnly,
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dataCollectionName,
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} = state.annotations;
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const queryString =
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!dataCollectionNameIsReadOnly && !!dataCollectionName
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? `?annotation-collection-name=${encodeURIComponent(
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dataCollectionName
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)}`
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: "";
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const res = await fetch(
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`${globals.API.prefix}${globals.API.version}genesets${queryString}`,
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{
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method: "PUT",
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headers: new Headers({
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Accept: "application/json",
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"Content-Type": "application/json",
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}),
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body: JSON.stringify(ota),
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credentials: "include",
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}
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);
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if (!res.ok) {
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return dispatch({
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type: "autosave: genesets error",
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message: `HTTP error ${res.status} - ${res.statusText}`,
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res,
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});
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}
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return Promise.all([
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dispatch({
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type: "autosave: genesets complete",
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lastSavedGenesets: genesets,
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}),
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dispatch({
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type: "geneset: set tid",
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tid,
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}),
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]);
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} catch (error) {
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return dispatch({
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type: "autosave: genesets error",
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message: error.toString(),
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error,
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});
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}
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};
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Block a user