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Experimental - manual annotations (#837)

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* icons, partway

* redux for values

* onChange

* cancel

* annotations lifecycle for category names

* copy categorical

* edit category

* add Dataframe.withColsFrom

* render user annotations; default add/delete annotation category

* add label name to actions

* category name edit

* error checking improvements

* change schema field isUserAnnotation to writable

* always have an unassigned label; implement delete label

* implement add new label and edit label name

* label current cell selection

* fix select exact bug in crossfilter

* clean up categorical reducer

* fix tests

* remove debugging printf

* implement subset/reset for user annotations

* undo redo support for user annotations

* remove duplicate button from categories

* add modal

* remove obsolete duplicate annotation reducers

* remove old debugging printf

* connect modal to annotation create and dup

* initial full-stack wiring

* finish up end-to-end wiring

* fix existing unit tests

* fix pytests to match new schema API

* remove debugging printfs

* add label file rotation

* remove obsolete comment

* add fbs encode/decode tests

* add tests for writable annotations

* simplify code

* fix hashing bug with FBS encoding

* lint

* fix smoke tests

* improve error checking in Dataframe.withColsFrom

* add unit test for Dataframe.withColsFrom

* add unit test for Dataframe.columns and Dataframe.renameCol

* fix bug in FBS encode, add better error checks, refactor

* add FBS encode/decode test

* add clarifying comment

* clean up action type names; fix state inconsistency in crossfilter update

* change autosave timer to 2.5sec

* sort categorical metadata render order so it remains consistent

* add temporary autogenerated label for add-new-label operation

* fix hover-over label menu interference with cell highlighting

* remove debugging code

* add missing reducer cases & fix typo

* make dataframe memoize more general purpose

* add dev mode for annos

* fix error on select duplicate

* handle zero occupancy categories

* correctly maintain unclipped AND clipped world

* correctly handle zero length FBS matrix and label files

* ensure all writable categorical schema contains an unassigned category

* handle case where building occupancy stack for category with no members

* dialog for creating label, disable button if duplicate or empty

* visually separate writeable

* edit category

* fix edit category name

* remove debugging code

* fix edit annotation label

* visually define unassigned, change options

* Pull in requirements.txt from `master`

* label currently selected cells

* duplicate label

* lint

* fix pytest merge issues

* rename --label-file to --experimental-label-file

* remove debugging console log

* spelling error fix; fix bug found in PR review.

* lint
This commit is contained in:
Bruce Martin
2019-09-18 07:33:41 -04:00
committed by Colin Megill
parent ab2c423006
commit 3660a6cc27
51 changed files with 2823 additions and 337 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/util/stateManager/schemaHelpers.js
+96
View File
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/*
Helpers for schema management
*/
import _ from "lodash";
import fromEntries from "../fromEntries";
/*
System wide schema assumptions:
- schema and data wil be consistent (eg, for user-created annotations)
- schema will be internally self-consistent (eg, index matches columns)
- world & universe schema are same - only data is subset
*/
export function indexEntireSchema(schema) {
/* Index schema for ease of use */
schema.annotations.obsByName = fromEntries(
schema.annotations.obs.columns.map(v => [v.name, v])
);
schema.annotations.varByName = fromEntries(
schema.annotations.var.columns.map(v => [v.name, v])
);
schema.layout.obsByName = fromEntries(
schema.layout.obs.map(v => [v.name, v])
);
schema.layout.varByName = fromEntries(
schema.layout.var.map(v => [v.name, v])
);
return schema;
}
function _copy(schema) {
/* redux copy conventions - WARNING, only for modifyign obs annotations */
return {
...schema,
annotations: {
...schema.annotations,
obs: _.cloneDeep(schema.annotations.obs)
}
};
}
function _reindex(schema) {
/* reindex obs annotations ONLY */
schema.annotations.obsByName = fromEntries(
schema.annotations.obs.columns.map(v => [v.name, v])
);
return schema;
}
export function removeObsAnnoColumn(schema, name) {
const newSchema = _copy(schema);
newSchema.annotations.obs.columns = schema.annotations.obs.columns.filter(
v => v.name !== name
);
return _reindex(newSchema);
}
export function addObsAnnoColumn(schema, name, defn) {
const newSchema = _copy(schema);
newSchema.annotations.obs.columns.push(defn);
return _reindex(newSchema);
}
export function removeObsAnnoCategory(schema, name, category) {
/* remove a category from a categorical annotation */
const categories = schema.annotations.obsByName[name]?.categories;
if (!categories)
throw new Error("column does not exist or is not categorical");
const idx = categories.indexOf(category);
if (idx === -1) throw new Error("category does not exist");
const newSchema = _reindex(_copy(schema));
/* remove category */
newSchema.annotations.obsByName[name].categories.splice(idx, 1);
return newSchema;
}
export function addObsAnnoCategory(schema, name, category) {
/* add a category to a categorical annotation */
const categories = schema.annotations.obsByName[name]?.categories;
if (!categories)
throw new Error("column does not exist or is not categorical");
const idx = categories.indexOf(category);
if (idx !== -1) throw new Error("category already exists");
const newSchema = _reindex(_copy(schema));
/* remove category */
newSchema.annotations.obsByName[name].categories.push(category);
return newSchema;
}