* 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
This PR contains a refactoring to make adding new features easier.
The new features include supporting the tiledb format, and the multi dataset application.
The refactoring includes
Simplifying the directory structure and files.
a class structure to handle annotations (currently one type: AnnotationsLocalFile).
a class to handle application configuration
a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb.
Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface.
The multi dataset option is not fully supported yet, and so the option to use it is hidden.
Use "cli launch --dataroot ..."
To access this feature.
All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
* revert MatrixProxy; replace with correct use of adata slicing
* work around 0.6 adata slicing bug
* fix incorrect var slice
* simplify slicing of X
* add warning about performance impact of anndata<=0.7
* lint and remove unused code
* improve comment
* lint
* correctly parse versions
* temp files should preserve file suffix if possible - anndata 0.7 compat
* update anndata dependency to 0.6.20
* resolve PR review comments
* add sample ontologies file
* add ontologies reducer
* Move select category to own component
* Dialog and Input factored out
* refactoring categorical, partway
* validationn
* anno
* suggest populates input
* frontend for ontology working
* initial implementation of back-end support for ontologies
* edit is now dialog again
* autosuggest working on edit
* part way through create arbitrary label
* handle choice in function
* pass duplicate cat prop
* editing works
* update test to match new CLI params
* fix occupancy alignment
* edit category as dialogue
* secondary button
* remove stubbed out ontologies
* add label setting upon new label creation
* Update legal characters for labels (#1119)
* Allow any term in the ontology (bypass legal name check)
* Add hyphens and parens to legal characters in names
* improve performance for large ontologies
* correctly handle case where ontologies are disabled
* fix logic error in CLI
Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>
* PR cleanup 1
* lint
* validate user generated labels
* finish hooking up connected suggest component
* protect against undefined callbacks
* Fix illegal characters error message
* break out npm run commands
* fix error detection on label edit
Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>
Co-authored-by: Sidney Bell <sidneymbell@users.noreply.github.com>
* Fix Makefile whitespace and .PHONY use
* Fix Makefile filename
* Modularize Makefile into client and server Makefiles
Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.
This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.
* Add auto-formatting to client and server modules
One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.
* Add yapf for automatic code formatting
* Add a root test target that calls sub-tests
* Apply yapf to python files
* Do not duplicate npm commands, simply pass through
* Update documentation
* Do not shadow reserved word len
* Add general test target
* Fix make call in dev-env
* Use black instead of yapf
* Run flake8 from the root directory
* Revert "Apply yapf to python files"
This reverts commit cdca128a01.
* Apply black to python code
* Resolve lint errors resulting from black format
* Add explanation of server unit tests in dev guidelines
* rename config param label-file
* annotations rework - CLI params, file naming and backups
* lint
* improve cli option error checks
* enable session cookies
* enable session cookies
* add session id
* name annotations file in multi-dataset and multi-user safe manner
* pass data user hash to front-end
* add annotation collection name support to front-end
* add constant for annotation data collection name
* parameterize annotation collection name; make it sticky in the session
* clarify comments
* hard wire a temporary data collection name for testing
* prettier
* test comment
* package command
* set annotations filename dialog
* name and hash are visible
* wire up data collection capture
* add last mod time lookup to data locator
* store data locator in Driver
* save metadata header in labels csv
* lint
* fix tests
* change datetime format to second precision
* initial cut at backed mode
* make flask multithreading conditional on debug flag
* update X access to support backed mode
* lint
* improve help message for backed mode
* fix tests
* add MatrixProxy to normalize supported matrix types
* add FAQ entry for --backed
* remove use of matrix.T
* clean up
* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user
* fix tests
* do not print diffexp speed warning if diffexp is disabled
* tweak wording of diffexp speed messages
* add FAQ entry on --disable-diffexp
* revise heuristic for warning about slow diffexp
* use quick tooltip delay on diffexp button
* add about arg
* add simple url validator
* attach about link to config api
* add links to configDefaults
* add conditional link in top left and menu item
* whitespace
* change to lower case
* move --about arg before click.command()
if this fixes it I have no idea why
* change link>URL
* be more descriptive about URL
* Make error more explicit
* refactor attach_data to accept about
* format
* change icon
* add trailing parenthesis
* whitespace
* initial commit of URL support for launch
* lint
* modify tests to use new data locator
* add locator unit tests
* fix typo in faq
* more lint
* update faq per PR review
* 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
* improve column access speed for sparse matrices
* add FAQ entry about data format performance
* add note about using --sparse flag for prepare command
* clean up for PR review
* Update docs/faq.md
Co-Authored-By: bkmartinjr <bruce@chanzuckerberg.com>
* improvements to big data faq
* move app creation to function
* create engine without load
* flake 8 fixes
* cleanup original scanpy test
* add default config
* handle missing data
* test data changes
* unify update
* load data isn't static anymore
* make app a class
* dead code and route removal
* more dead code cleanup
* fix scanpy_engine tests
* lint
* add missing catch in filter parsing
* update scanpy NaN tests
* more fbs tests and dead test removal
* remove forced default for content type negotiation
* bit of cleanup
* more fbs test cleanup
* lint
* remove swagger
* swagger cleanup
* lint
* correctly handle lack of templates
* more dead code removal
* remove unused files
* fix dev build
* lint
* first flatbuffer schema
* do not lint auto-generated files
* add flatbuffers package
* add flatbuffer module
* wire up /data/X/T route
* use flatbuffers for matrix data fetc
* clarity and comments
* add flatbuffer layout route
* clean up obsolete code
* fix tests
* move flake8 config to setup.cfg
* add comments
* lint
* rework layout routes for fbs
* add more type support to fbs
* lint
* add flatbuffer support for annotations
* function name improvements
* fix botched merge with master
* remove unused import
* route cleanup for flatbuffers
* rename function for clarity
* add missing globals to Jest tests
* fix client JS tests
* fix routes for Python tests
* comments for clarity
* non-finite floating point hardening
* more non-finite number handling
* lint
* fix tests for summarizeAnnotations
* harden diffexp calculation against FP errors
* cleanup unused code
* lint
* add encoding tests for flatbuffers
* application type specified as strings
* fix spelling error
* improve variable names
* add note about documentation gap
* rename FBS DataFrame to Matrix
* only load annotation var names
* remove incorrect usage of var annotation data
* temporary workaround for issue #480
* lint
* issue warnings only once per item
Matt Weiden