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Code Issues Packages Projects Releases Wiki Activity

do not hard-wire column names in annotations (#785)

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* enforce column name uniqueness for obs and var

* parameterize the column name containing obs and var user-readable names

* use the new annotation index value from schema

* update f/e unit tests

* PR review suggestions

* lint
This commit is contained in:
Bruce Martin
2019-05-24 21:00:54 -07:00
committed by GitHub
parent a8c2e408d1
commit 3dc45d6330
16 changed files with 246 additions and 155 deletions
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client/src/actions/index.js
+31 -20
View File
@@ -21,24 +21,32 @@ const doInitialDataLoad = () =>
dispatch({ type: "initial data load start" });
try {
const requestJson = _(["config", "schema"])
/*
Step 1 - config & schema, all JSON
*/
const requestJson = ["config", "schema"]
.map(r => `${globals.API.prefix}${globals.API.version}${r}`)
.map(url => doJsonRequest(url))
.value();
const requestBinary = _([
"annotations/obs",
"annotations/var?annotation-name=name",
"layout/obs"
])
.map(r => `${globals.API.prefix}${globals.API.version}${r}`)
.map(url => doBinaryRequest(url))
.value();
const results = await Promise.all(_.concat(requestJson, requestBinary));
.map(url => doJsonRequest(url));
const stepOneResults = await Promise.all(requestJson);
/* set config defaults */
const config = { ...globals.configDefaults, ...results[0].config };
const [, schema, obsAnno, varAnno, obsLayout] = [...results];
const config = { ...globals.configDefaults, ...stepOneResults[0].config };
const schema = stepOneResults[1];
/*
Step 2 - dataframes, all binary. NOTE: uses results of step 1.
*/
/* only load names for var annotations, if possible*/
const varIndexName = schema?.schema?.annotations?.var?.index;
const varAnnotationsQuery = varIndexName
? `?annotation-name=${varIndexName}`
: "";
const varAnnotationsURL = `annotations/var${varAnnotationsQuery}`;
const requestBinary = ["annotations/obs", varAnnotationsURL, "layout/obs"]
.map(r => `${globals.API.prefix}${globals.API.version}${r}`)
.map(url => doBinaryRequest(url));
const stepTwoResults = await Promise.all(requestBinary);
const [obsAnno, varAnno, obsLayout] = [...stepTwoResults];
const universe = Universe.createUniverseFromResponse(
config,
schema,
@@ -91,6 +99,10 @@ needs expression data.
Transparently utilizes cached data if it is already present.
*/
async function _doRequestExpressionData(dispatch, getState, genes) {
const state = getState();
const { universe } = state;
const varIndexName = universe.schema.annotations.var.index;
/* helper for this function only */
const fetchData = async geneNames => {
const res = await fetch(
@@ -100,7 +112,7 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
body: JSON.stringify({
filter: {
var: {
annotation_value: [{ name: "name", values: geneNames }]
annotation_value: [{ name: varIndexName, values: geneNames }]
}
}
}),
@@ -123,8 +135,6 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
return Universe.convertDataFBStoObject(universe, data);
};
const state = getState();
const { universe } = state;
/* preload data already in cache */
let expressionData = _.transform(
genes,
@@ -241,6 +251,7 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
*/
const state = getState();
const { universe } = state;
const varIndexName = universe.schema.annotations.var.index;
// Legal values are null, Array or TypedArray. Null is initial state.
if (!set1) set1 = [];
@@ -277,7 +288,7 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
const data = await res.json();
// result is [ [varIdx, ...], ... ]
const topNGenes = _.map(data, r =>
universe.varAnnotations.at(r[0], "name")
universe.varAnnotations.at(r[0], varIndexName)
);
/*