mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 22:08:00 +08:00
a593e95ab3
* 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
114 lines
3.5 KiB
Python
114 lines
3.5 KiB
Python
from abc import ABCMeta, abstractmethod
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"""
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Sort order for methods
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1. Initialize
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2. Helper
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3. Filter
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4. Data & Metadata
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5. Computation
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"""
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class CXGDriver(metaclass=ABCMeta):
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def __init__(self, data_locator=None, args={}):
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self.config = self._get_default_config()
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self.config.update(args)
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if data_locator:
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self._load_data(data_locator)
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self.data_locator = data_locator
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else:
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self.data = None
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def update(self, data_locator=None, args={}):
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self.config.update(args)
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if data_locator:
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self._load_data(data_locator)
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self.data_locator = data_locator
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@staticmethod
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def _get_default_config():
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return {
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"layout": None,
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"max_category_items": None,
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"diffexp_lfc_cutoff": None,
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"disable_diffexp": False,
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"diffexp_may_be_slow": False
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}
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@abstractmethod
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def get_config_parameters(self, uid=None):
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"""
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return a dict of properties that will be used to set the engine-specific
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"parameters" info for client-side configuration.
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See rest.py /config route for use
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"""
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pass
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@property
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def features(self):
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features = {
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"cluster": {"available": False},
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"layout": {"obs": {"available": False}, "var": {"available": False}},
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"diffexp": {"available": True, "interactiveLimit": 50000}
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}
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# TODO - Interactive limit should be generated from the actual available methods see GH issue #94
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if self.config["layout"]:
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# TODO handle "var" when gene layout becomes available
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features["layout"]["obs"] = {"available": True, "interactiveLimit": 50000}
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return features
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@abstractmethod
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def get_schema(self):
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"""
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Return current schema
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"""
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pass
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@abstractmethod
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def _load_data(self, data_locator):
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pass
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@abstractmethod
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def annotation_to_fbs_matrix(self, axis, field=None, uid=None):
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"""
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Gets annotation value for each observation
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:param axis: string obs or var
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:param fields: list of keys for annotation to return, returns all annotation values if not set.
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:return: flatbuffer: in fbs/matrix.fbs encoding
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"""
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pass
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@abstractmethod
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def annotation_put_fbs(self, axis, fbs, uid=None):
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"""
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Put/save FBS as user-defined labels
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"""
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pass
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@abstractmethod
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def data_frame_to_fbs_matrix(self, filter, axis):
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pass
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@abstractmethod
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def diffexp_topN(self, obsFilter1, obsFilter2, top_n=None, interactive_limit=None):
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"""
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Computes the top N differentially expressed variables between two observation sets. If mode
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is "TOP_N", then stats for the top N
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dataframes
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contain a subset of variables, then statistics for all variables will be returned, otherwise
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only the top N vars will be returned.
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:param obsFilter1: filter: dictionary with filter params for first set of observations
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:param obsFilter2: filter: dictionary with filter params for second set of observations
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:param top_n: Limit results to top N (Top var mode only)
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:param interactive_limit: -- don't compute if total # genes in dataframes are larger than this
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:return: top N genes and corresponding stats
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"""
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pass
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@abstractmethod
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def layout_to_fbs_matrix(self, filter):
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""" same as layout, except returns a flatbuffer """
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pass
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