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https://github.com/chanzuckerberg/cellxgene.git
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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
89 lines
2.3 KiB
JavaScript
89 lines
2.3 KiB
JavaScript
// jshint esversion: 6
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import _ from "lodash";
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/*
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Very simple key/value cache for use by World & Universe.
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* constructor(lowWatermark, minTTL):
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- lowWatermark defines the number of cache elements below which
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flushing will not occur.
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- minTTL defines minimum time in milliseconds that cache entries will live.
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A value of -1 disables automatic flushing (flush() can still
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be called by external user).
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* set() - add a key/val pair.
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* get() - get a value or undefined if not present.
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* flush(minAgeMs) - flush cache entries in excess of lowWatermark if those
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entries are older than minAgeMs.
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*/
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const cachePrivateKey = "__kvcachekey__";
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function create(lowWatermark = 32, minTTL = 1000) {
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return {
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[cachePrivateKey]: {
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lowWatermark,
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minTTL
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}
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};
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}
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function get(kvcache, key) {
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const val = kvcache[key];
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if (val) {
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val[cachePrivateKey] = Date.now();
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}
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return val;
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}
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function set(kvcache, key, val) {
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const newKvCache = { ...kvcache };
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newKvCache[key] = val;
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val[cachePrivateKey] = Date.now();
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flush(newKvCache, newKvCache[cachePrivateKey].minTTL);
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return newKvCache;
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}
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/*
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Flush elements from cache IF cache size is greater than lowWatermark, and
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those elements are older than minAgeMS
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*/
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function flush(kvcache, minAgeMs = 0) {
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if (minAgeMs < 0) return kvcache;
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const eol = Date.now() - minAgeMs;
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const { lowWatermark } = kvcache[cachePrivateKey];
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const keys = _(kvcache)
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.keys()
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.filter(k => k !== cachePrivateKey)
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.filter(k => kvcache[k][cachePrivateKey] < eol)
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.sortBy([k => kvcache[k][cachePrivateKey]])
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.value();
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if (keys.length > lowWatermark) {
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const numKeysToDelete = keys.length - lowWatermark;
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const keysToDelete = _.slice(keys, 0, numKeysToDelete);
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_.forEach(keysToDelete, k => delete kvcache[k]);
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}
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return kvcache;
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}
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/*
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use to create a cache that is a transformation of another cache.
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*/
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function map(srcKvCache, cb, createOptions) {
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const keysInSrcKvCache = _(srcKvCache)
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.keys()
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.filter(k => k !== cachePrivateKey)
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.value();
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const newKvCache = create(createOptions.lowWatermark, createOptions.minTTL);
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_.forEach(keysInSrcKvCache, key => {
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const val = cb(get(srcKvCache, key));
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newKvCache[key] = val;
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val[cachePrivateKey] = Date.now();
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});
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return newKvCache;
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}
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export { create, get, set, flush, map };
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