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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
Download Patch File Download Diff File Expand all files Collapse all files
client/src/components/continuous/continuous.js
+2 -1
View File
@@ -66,7 +66,8 @@ class Continuous extends React.Component {
? _.map(obsAnnotations.colIndex.keys(), key => {
const isColorField =
key.includes("color") || key.includes("Color");
if (key === "name" || isColorField) return null;
if (key === schema.annotations.obs.index || isColorField)
return null;
const summary = obsAnnotations.col(key).summarize();
const nonFiniteExtent =
client/src/components/geneExpression/index.js
+13 -6
View File
@@ -85,7 +85,8 @@ class GeneExpression extends React.Component {
*/
const { world } = this.props;
const { varAnnotations } = world;
const geneNames = varAnnotations.col("name").asArray();
const varIndexName = world.schema.annotations.var.index;
const geneNames = varAnnotations.col(varIndexName).asArray();
if (geneNames.length > 0) {
const placeholder = [];
let len = geneNames.length;
@@ -107,6 +108,7 @@ class GeneExpression extends React.Component {
handleClick(g) {
const { world, dispatch, userDefinedGenes } = this.props;
const varIndexName = world.schema.annotations.var.index;
const gene = g.target;
if (userDefinedGenes.indexOf(gene) !== -1) {
postUserErrorToast("That gene already exists");
@@ -114,7 +116,9 @@ class GeneExpression extends React.Component {
postUserErrorToast(
"That's too many genes, you can have at most 15 user defined genes"
);
} else if (world.varAnnotations.col("name").indexOf(gene) === undefined) {
} else if (
world.varAnnotations.col(varIndexName).indexOf(gene) === undefined
) {
postUserErrorToast("That doesn't appear to be a valid gene name.");
} else {
dispatch({ type: "single user defined gene start" });
@@ -127,6 +131,7 @@ class GeneExpression extends React.Component {
handleBulkAddClick() {
const { world, dispatch, userDefinedGenes } = this.props;
const varIndexName = world.schema.annotations.var.index;
const { bulkAdd } = this.state;
/*
@@ -145,7 +150,9 @@ class GeneExpression extends React.Component {
if (userDefinedGenes.indexOf(gene) !== -1) {
return keepAroundErrorToast("That gene already exists");
}
if (world.varAnnotations.col("name").indexOf(gene) === undefined) {
if (
world.varAnnotations.col(varIndexName).indexOf(gene) === undefined
) {
return keepAroundErrorToast(
`${gene} doesn't appear to be a valid gene name.`
);
@@ -168,7 +175,7 @@ class GeneExpression extends React.Component {
userDefinedGenesLoading,
differential
} = this.props;
const varIndexName = world?.schema?.annotations?.var?.index;
const { tab, bulkAdd } = this.state;
return (
@@ -243,7 +250,7 @@ class GeneExpression extends React.Component {
itemRenderer={renderGene.bind(this)}
items={
world && world.varAnnotations
? world.varAnnotations.col("name").asArray()
? world.varAnnotations.col(varIndexName).asArray()
: ["No genes"]
}
popoverProps={{ minimal: true }}
@@ -322,7 +329,7 @@ class GeneExpression extends React.Component {
<ExpressionButtons />
{differential.diffExp
? _.map(differential.diffExp, (value, index) => {
const name = world.varAnnotations.at(value[0], "name");
const name = world.varAnnotations.at(value[0], varIndexName);
const values = world.varData.col(name);
if (!values) {
return null;