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9bcafeb7c115cd6ee0c01acc18ddacf111d39784
5
Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
 Bruce Martin
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3660a6cc27 |
Experimental - manual annotations (#837)
* 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 |
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Bruce Martin
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3dc45d6330 |
do not hard-wire column names in annotations (#785)
* 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 |
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Bruce Martin
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2357d0c1b8 |
layout change UI (#776)
* add layout to schema * add layout choice action and reducer * multi layout UI * update unit tests * add missing file * update test schema * fix duplicate test id * fix tabs * PR lint * fix pytest |
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Bruce Martin
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b181751493 |
add --obs-names and --var-names CLI params (#371)
* add --obs-names and --var-names CLI params * fix lint * performance improvements in scanpy engine * fix lint * fix typo * correctly handle sparse formats in diffexp * fix diffexp and 1d slicing * diffexp uses t-stat, not pval; clean up arg handling * make _slice a static method * revise scanpy tests to match new API |
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Bruce Martin
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eeec842ad0 |
Restv2 feature branch merge to master (#284)
Move to new REST v0.2 communication between front and back-end. This is a first cut implementation which is functional, but will need follow-up enhancements for performance, error checking, etc. Protocol spec is in docs directory. * Add filtering via indexing * Using new filter specs Indexing working * Added filtering by annotation value * factor out common methods * Documentation * create enum for axis (obs/var) * Better description for filter's return * Add boolean to enumerated types * Augmented enum for scanpy axis * Create schema for annotations Based on datatype within scanpy/anndata + tests * remove obsolete schema parse script * Update rest api to remove old routes and add schema route * Separate development requirements * Warning for unsupported datatypes * include -r requirements.txt in dev * Merged downcast warnings * Fixed bug where names were NaNs Needed to include the index too when creating the series * Add config endpoint * Generate app features from CLI selections * Move features to driver * Add tests for schema * Clearer version wording * python3 version of super * version from engine to package level * move features to driver * Revise layout function to match the new spec * GET for layout/obs * PUT Layout (#211) * PUT Layout * Csweaver/annotations (#212) * Update scanpy engine to support the rest v0.2 annotation requests * GET endpoint for obs annotations + tests * Documentation * Test annotations in scanpy engine * Description for annotation-keys param * annotation->annotations * clarified return for annotations * Use URL query list for annotations fields * parse_filter parses v0.2 GET filters (#215) * parse_filter parses v0.2 GET filters * Don't allow index filters from query params * Better variable conversion * Parse filter improvements - uses default dict - renamed filter -> query_filter * Cleanup Tasks (#216) * Add test_api back into travis build * Do custom JSON encoding the correct way * Run cellxgene server in test setup * Cleanup new tests too * Option to bind to all interfaces (#225) app.run("0.0.0.0") instead of app.run("127.0.0.1") binds to all interfaces. Note: There are comments on the internet that says that the flask server is not up to the task of production serving. I don't think that such scalability concerns apply here, but I was able to get cellxgene working with twistd relatively easily, and we could switch to that if there are scalability concerns. Test plan: browsed to <ip>:5005/api/v0.2/config on a different host. * Add filtering via indexing * Using new filter specs Indexing working * Added filtering by annotation value * factor out common methods * Documentation * create enum for axis (obs/var) * Better description for filter's return * Add boolean to enumerated types * Augmented enum for scanpy axis * Create schema for annotations Based on datatype within scanpy/anndata + tests * remove obsolete schema parse script * Update rest api to remove old routes and add schema route * Separate development requirements * Warning for unsupported datatypes * include -r requirements.txt in dev * Merged downcast warnings * Fixed bug where names were NaNs Needed to include the index too when creating the series * Add config endpoint * Generate app features from CLI selections * Move features to driver * Add tests for schema * Clearer version wording * python3 version of super * version from engine to package level * move features to driver * Revise layout function to match the new spec * GET for layout/obs * PUT Layout (#211) * PUT Layout * Csweaver/annotations (#212) * Update scanpy engine to support the rest v0.2 annotation requests * GET endpoint for obs annotations + tests * Documentation * Test annotations in scanpy engine * Description for annotation-keys param * annotation->annotations * clarified return for annotations * Use URL query list for annotations fields * parse_filter parses v0.2 GET filters (#215) * parse_filter parses v0.2 GET filters * Don't allow index filters from query params * Better variable conversion * Parse filter improvements - uses default dict - renamed filter -> query_filter * Cleanup Tasks (#216) * Add test_api back into travis build * Do custom JSON encoding the correct way * Run cellxgene server in test setup * Cleanup new tests too * Option to bind to all interfaces (#225) app.run("0.0.0.0") instead of app.run("127.0.0.1") binds to all interfaces. Note: There are comments on the internet that says that the flask server is not up to the task of production serving. I don't think that such scalability concerns apply here, but I was able to get cellxgene working with twistd relatively easily, and we could switch to that if there are scalability concerns. Test plan: browsed to <ip>:5005/api/v0.2/config on a different host. * Fix merge errors - import warnings was improperly deleted - scanpy engine tests were totally wrong * Fix merge error with driver * PUT /annotations (#235) * Add query param for annotation name * fix descriptions, eliminate else clause * first cut at initial data load on rest 0.2 api * Annotation var (#248) * Fix bug strings are always objects in pandas * Add axis to annotation method * Add /annotation/var to REST api * Csweaver/expressiondata (#242) * Refactor expression method for REST v2 * Add message to QueryStringError * Fix range filters * Add GET route for /data * /data PUT route * rename expression to data_frame * clarification of error * Improve accept type handling * support all schema types for 0.2 REST API * remove REST 0.1 code; connect var annotations loading * config reducer; use config to set data set title; remove obsolete templating code for data set title * REST 0.2 expression conversion support * partial port of expression to REST 0.2 * diffexp (#273) * Add diffexp method to scanpy and test * Minor tweaks to diffexp Get a minimal working version to unblock FE development * Fixing things git deleted * cleanup print statements * Add index test * additional, partial REST 0.2 bring up of diffexp * Ignore unstructured annotations for data (#275) This is a temp hack, need to figure out how to include data.uns if there is only one gene * diffexp REST 0.2 port finish * ignore unstructured annotaitons on all routes except layout * correctly use varDataCache; maintain state during world rebuild * correct varDataCache use * temporarily disable all memoization * refinements to expression data caching * clear cell sets upon regraph/reset * update version of REST to 0.2 * Travis build fixes - comment out cache import - fix duplicate test name * Remove dependency from travis * clarify semantics of config variables * move generic action helpers into util |