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Add user-defined category-label colors (#1402)

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* Add user-defined category-label colors

Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152

As described in https://github.com/chanzuckerberg/cellxgene/issues/1307

* Respond to feedback from @bkmartinjr in nodejs

* Respond to feedback from @bkmartinjr in python

* Add tests to the server module

* Autoformat python, run linter

* Make colors_get error handling specific

* Respond to feedback from @bkmartinjr

* Respond to feedback from @bkmartinjr

* Fix whitespace

* Fix python lint errrors

* Update documentation

* Add --disable-user-colors option to launch and cxgtool.py

* Fix python formatting

* Rename '--disable-user-colors' to '--disable-custom-colors'
This commit is contained in:
Matt Weiden
2020-04-26 22:52:57 -07:00
committed by GitHub
parent 3c191c3f93
commit 546e272a60
91 changed files with 801 additions and 271 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/actions/index.js
+60 -68
View File
@@ -9,12 +9,13 @@ import {
} from "../util/actionHelpers";
import { PromiseLimit } from "../util/promiseLimit";
import { requestReembed, reembedResetWorldToUniverse } from "./reembed";
import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
/*
return promise to fetch the OBS annotations we need to load. Omit anything
we don't need.
*/
function obsAnnotationFetchAndLoad(dispatch, schema) {
async function obsAnnotationFetchAndLoad(dispatch, schema) {
const obsAnnotations = schema?.schema?.annotations?.obs ?? {};
const index = obsAnnotations.index ?? false;
const columns = (obsAnnotations.columns ?? []).filter(
@@ -23,21 +24,18 @@ function obsAnnotationFetchAndLoad(dispatch, schema) {
const plimit = new PromiseLimit(5);
return Promise.all(
columns.map((col) =>
plimit.add(() => {
const path = `annotations/obs?annotation-name=${encodeURIComponent(
col.name
)}`;
const url = `${globals.API.prefix}${globals.API.version}${path}`;
return doBinaryRequest(url).then((buffer) => {
const df = Universe.matrixFBSToDataframe(buffer);
dispatch({
type: "universe: column load success",
dim: "obsAnnotations",
dataframe: df,
});
});
})
columns.map(col =>
plimit.add(() =>
fetchBinary(`annotations/obs?annotation-name=${encodeURIComponent(col.name)}`)
.then(buffer => Universe.matrixFBSToDataframe(buffer))
.then(df =>
dispatch({
type: "universe: column load success",
dim: "obsAnnotations",
dataframe: df
})
)
)
)
);
}
@@ -45,31 +43,22 @@ function obsAnnotationFetchAndLoad(dispatch, schema) {
/*
return promise fetching VAR annotations we need to load. Only index is currently used.
*/
function varAnnotationFetchAndLoad(dispatch, schema) {
async function varAnnotationFetchAndLoad(dispatch, schema) {
const varAnnotations = schema?.schema?.annotations?.var ?? {};
const index = varAnnotations.index ?? false;
const names = index ? [index] : [];
return Promise.all(
names
.map((name) => {
const path = `annotations/var?annotation-name=${encodeURIComponent(
name
)}`;
const url = `${globals.API.prefix}${globals.API.version}${path}`;
return doBinaryRequest(url);
})
.map((rqst) =>
rqst.then((buffer) => Universe.matrixFBSToDataframe(buffer))
)
.map((resp) =>
resp.then((df) =>
names.map(name =>
fetchBinary(`annotations/var?annotation-name=${encodeURIComponent(name)}`)
.then(buffer => Universe.matrixFBSToDataframe(buffer))
.then(df =>
dispatch({
type: "universe: column load success",
dim: "varAnnotations",
dataframe: df,
dataframe: df
})
)
)
)
);
}
@@ -79,26 +68,35 @@ return promise fetching layout we need
function layoutFetchAndLoad(dispatch, schema) {
const embeddings = schema?.schema?.layout?.obs ?? [];
const embNames = embeddings.map((e) => e.name);
const baseURL = `${globals.API.prefix}${globals.API.version}layout/obs`;
const plimit = new PromiseLimit(5);
return Promise.all(
embNames.map((e) =>
plimit.add(() => {
const url = `${baseURL}?layout-name=${encodeURIComponent(e)}`;
return doBinaryRequest(url).then((buffer) =>
Universe.matrixFBSToDataframe(buffer)
);
})
embNames.map(e =>
plimit.add(() =>
fetchBinary(`layout/obs?layout-name=${encodeURIComponent(e)}`)
.then(buffer => Universe.matrixFBSToDataframe(buffer))
)
)
).then((dfs) => {
const df = Dataframe.Dataframe.empty().withColsFromAll(dfs);
).then(dfs =>
dispatch({
type: "universe: column load success",
dim: "obsLayout",
dataframe: df,
});
});
dataframe: Dataframe.Dataframe.empty().withColsFromAll(dfs)
})
);
}
/*
return promise fetching user-configured colors
*/
async function userColorsFetchAndLoad(dispatch) {
return fetchJson("colors")
.then(response =>
dispatch({
type: "universe: user color load success",
userColors: loadUserColorConfig(response)
})
);
}
/*
@@ -116,13 +114,10 @@ const doInitialDataLoad = () =>
/*
Step 1 - config & schema, all JSON
*/
const requestJson = ["config", "schema"]
.map((r) => `${globals.API.prefix}${globals.API.version}${r}`)
.map((url) => doJsonRequest(url));
const stepOneResults = await Promise.all(requestJson);
const requestJson = ["config", "schema"].map(fetchJson);
const [responseConfig, schema] = await Promise.all(requestJson);
/* set config defaults */
const config = { ...globals.configDefaults, ...stepOneResults[0].config };
const schema = stepOneResults[1];
const config = { ...globals.configDefaults, ...responseConfig.config };
const universe = Universe.createUniverseFromResponse(config, schema);
dispatch({
type: "universe exists, but loading is still in progress",
@@ -137,6 +132,7 @@ const doInitialDataLoad = () =>
Step 2 - load the minimum stuff required to display.
*/
await Promise.all([
userColorsFetchAndLoad(dispatch),
layoutFetchAndLoad(dispatch, schema),
varAnnotationFetchAndLoad(dispatch, schema),
]);
@@ -169,13 +165,6 @@ const setWorldToSelection = () => (dispatch, getState) => {
});
};
// Throws
const dispatchExpressionErrors = (dispatch, res) => {
const msg = `Unexpected HTTP response while fetching expression data ${res.status}, ${res.statusText}`;
dispatchNetworkErrorMessageToUser(msg);
throw new Error(msg);
};
/* double URI encode - needed for query-param filters */
function dubEncURIComponent(s) {
return encodeURIComponent(encodeURIComponent(s));
@@ -196,16 +185,11 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
/* helper for this function only */
const fetchData = async (geneNames) => {
const query = geneNames
.map(
(g) =>
`var:${dubEncURIComponent(varIndexName)}=${dubEncURIComponent(g)}`
)
.map(g => `var:${dubEncURIComponent(varIndexName)}=${dubEncURIComponent(g)}`)
.join("&");
const url = `${globals.API.prefix}${globals.API.version}data/var?${query}`;
return doBinaryRequest(url).then((buffer) =>
// TODO: why convert to an Object and not a Dataframe?
Universe.convertDataFBStoObject(universe, buffer)
);
// TODO: why convert to an Object and not a Dataframe?
return fetchBinary(`data/var?${query}`)
.then(buffer => Universe.convertDataFBStoObject(universe, buffer));
};
/* preload data already in cache */
@@ -367,7 +351,7 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
*/
const plimit = new PromiseLimit(5);
await Promise.all(
topNGenes.map((gene) =>
topNGenes.map(gene =>
plimit.add(() => _doRequestExpressionData(dispatch, getState, [gene]))
)
);
@@ -447,6 +431,14 @@ const saveObsAnnotations = () => async (dispatch, getState) => {
}
};
function fetchJson(pathAndQuery) {
return doJsonRequest(`${globals.API.prefix}${globals.API.version}${pathAndQuery}`);
}
function fetchBinary(pathAndQuery) {
return doBinaryRequest(`${globals.API.prefix}${globals.API.version}${pathAndQuery}`);
}
export default {
doInitialDataLoad,
requestDifferentialExpression,