* warning on maxCount for diffexp
* cleanup logging
* clarification
* make the limits configurable
* make diff exp limit work
* danger!
* remove debugging code
* fix merge with master
* fix unit tests
Co-authored-by: Colin Megill <colinmegill@gmail.com>
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1349
For more information see https://github.com/d3/d3-format
Note that does not _fully_ fix the issue described in #1349, but rather
makes the formatting issue far less likely. It is _still_ possible for
this to occur if the difference between two ticks in axes happes in the
a significant digit cropped by the scientific notation format
* Fix for favicon with --dataroot
* fix static assets in hosted cxg
The web proxy at aws eb was not finding the static assets.
The solution here is very simple: just copy the directory
containing the static assets to the top level of the artifact.zip.
This is not really the ideal solution. According to the AWS
docs you can make a mapping to the correct location in an
an ebextentions config file. I tried this and many combinations but
was not able to get this to work following that pattern.
Since we control the construction of the zip file, the solution
here isn't bad, but it could probably be made better.
* Add color mapping to the bar chart.
* Change histogram color generation from Viridis to InterpolateCool.
* Coloring of Histrogram based up the x axis instead of y axis.
Coloring of Histrogram based up the x axis instead of y axis.
* Respond to feedback from @colinmegill
* Only color histograms that are selected for colorby
* Add some small refactors to BrushableHistogram's componentDidUpdate
* Fix histogram coloring and binning
* Reuse binning functions from util/dataframe/histogram.js; this fixes
an issue with there being near-zero width bins
* Fix color mapping so that it matches the scale in the legend
* Do not attempt to plot bins if the calculated binWidth is zero; this
can happen if all values are the same
* Refactor the function that draws the histogram a bit
* Respond to feedback from @bkmartinjr
Co-authored-by: Donald Paul Herman <Donaldpherman@hotmail.com>
* maybe truncate string
* add string formatting to test
* correct import
* destructuring
* add maxlength
* test
* Respond to feedback from @bkmartinjr
Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
* add test labels
* prettier + add clcik return to clickOn()
* prettier + begin test
* finish label counting test
* add util to get coordinates of element
* add test id to labels
* add test to check overlay transform
* remove logs
* rename to match master
* first cut at re-embedding route and back-end support
* update and expand config route tests
* add scanpy_umap
* add reembedding to config route parameters
* front-end support for reembedding fetch and UI
* remove unused imports
* add loading state
* save reembedding in reducer state
* improve withColsFrom
* transmit reembed schema to client; pick unique embedding names
* display embeddings
* format
* lint
* spaces, tab size 2
* lint
* test hack for smoke-test race
* back out hack sleep
* add check for backed mode
* add unit test for reembedding
* lint
* hide re-embedding CLI param from help
* Remove unused variables and imports
* Simplify conditional
* Fix typo
* Do not overprune var data cache
There is a bug in how the universe and world gene sets are constructed
and passed to `ControlsHelpers.pruneVarDataCache` that causes the var
data cache to be over-pruned. This commit fixes the issue.
Consider the following example from the node console:
```
❯ node
Welcome to Node.js v13.5.0.
Type ".help" for more information.
> new Set([1], [2], [3])
Set(1) { 1 }
```
What we really want is the set `Set(3) { 1, 2, 3 }`, which can be
constructed as:
```
> new Set([].concat([1], [2], [3]))
Set(3) { 1, 2, 3 }
```
* Disable ColorBy button for truncated categories
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1156
For categories that have more than 100 labels we truncate the labels in
the UI, but still allowed users to ColorBy these categories. Coloring by
these categories can cause browsers to get bogged down.
This commit disables ColorBy for truncated categories.
* Minor documentation spelling and typo fixes
* Respond to feedback from @liaprins-czi
* Respond to feedback from @colinmegill and @bkmartinjr
* Undo selection appends diffExp genes to user gene list
Fixes https://github.com/chanzuckerberg/cellxgene/issues/1171
Need: When a user performs a differential expression from within
a sub-selection (world) of the data and then resets the selection to all
cells (universe), the differential expression results are no longer
valid.
Approach:
* When the selection is reset, move the top (maxUserDefinedGenes
- len(userDefinedGenes) from the differential expression results to the
list of user defined genes
* Raise maxUserDefinedGenes to 25 to give users more room and
accommodate the extra genes transferred in from differential expression
Other commits:
* Choose different button icons
* Add diff exp genes to user defined genes on subset too
* Respond to feedback from @liaprins-czi and @bkmartinjr
* add simple error message helper
* port all label name pickers to use the new LabelInput component
* use pure components where possible
* cleanup
* more cleanup
* lint
* change new label prompt
* Add undo/redo tests for annotations
Fixes https://github.com/chanzuckerberg/cellxgene/issues/969
... also refactor the tests for DRY.
* Add done()
* Make e2e annotations tests safer to concurrency
* Add data-testclass for save state.
* Simplify tests and make them dependent on save state
* Add codecov to Push Test workflow
* Empty commit
* Clear reports and tag each with flags
* Tag code reports by test
* Fix codecov tags
* One more fix
* Add user-generated annotations tests to the server
Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969
* Auto-format python code
* @skip_if: passing lambdas > than property strings
* Respond to feedback from @bkmartinjr
* Add smoke test for annotations features
* Do not save during annotations tests
* Fix botched rebase in dev guidelines
* Revert "Do not save during annotations tests"
This reverts commit f0bd970bb2.
* Respond to feedback from @bkmartinjr
* Collect all env vars in one, easy-to-find place
Past state:
* Default environement variables were stored in both client/package.json
and client/__tests__/e2e/config.js
* Constants that should have been linked--like the cellxgene server port
during testing--were repeated.
With this commit:
* All environment variables are parameterized
* All environment variables are packaged in default env files
* Move npm scripts to client Makefile
* Respond to feedback from @seve and @bkmartinjr
* check to see if display state has changed
* add display state
* create onDisplayChange
* check to see if displaying anything and add opacity drop
* pass callback down to children
* add middle truncation to labels
* remove unused import
* add a bit of documentation
* make prop addition more clear
* rename onDisplayChange -> overlayToggled for readability
* load annotations individually
* fix type check to be more general
* update node CI version from 10 to 12
* node 11
* debug print node version
* travis node version to latest
* try nvm
* remove extraneous node_js statement
* remove node version debugging printf
* incrementally load all annotations and layout
* process annotations and layout as they are loaded
* fix tests
* sort categories incrementally
* incrementally build category view summary; add category loading spinner
* add spinner to continuous metadata
* configure undoable reducer
* incremental crossfilter creation
* improve busy layout
* more layout cleanup
* correctly reconcile categories in schema
* refine layout of lsb spinners
* more spinner layout work
* more spinner layout
* always load layout before obs annotations
