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Filter in engine (#307)

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* Add empty filter case

* Filtering dataframes moved to engine instead of rest

* minor changes from PR review

* Minor fixes from PR review

Pass {} instead of none if no filter
chain exceptions
typos
This commit is contained in:
Charlotte Weaver
2018-10-11 15:23:31 -07:00
committed by GitHub
parent ee0b066eb6
commit 210787cb5d
5 changed files with 127 additions and 93 deletions
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server/app/driver/driver.py
+12 -10
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@@ -57,7 +57,7 @@ class CXGDriver(metaclass=ABCMeta):
Filter cells from data and return a subset of the data. They can operate on both obs and var dimension with
indexing and filtering by annotation value. Filters are combined with the and operator.
See REST specs for info on filter format:
https://docs.google.com/document/d/1Fxjp1SKtCk7l8QP9-7KAjGXL0eldi_qEnNT0NmlGzXI/edit#heading=h.8qc9q57amldx
https://github.com/chanzuckerberg/cellxgene/blob/master/docs/REST_API.md
:param filter: dictionary with filter params
:return: View into scanpy object with cells/genes filtered
@@ -65,10 +65,10 @@ class CXGDriver(metaclass=ABCMeta):
pass
@abstractmethod
def annotation(self, df, axis, fields=None):
def annotation(self, filter, axis, fields=None):
"""
Gets annotation value for each observation
:param df: from filter_cells, dataframe
:param filter: filter: dictionary with filter params
:param axis: string obs or var
:param fields: list of keys for annotation to return, returns all annotation values if not set.
:return: dict: names - list of fields in order, data - list of lists or metadata
@@ -77,10 +77,10 @@ class CXGDriver(metaclass=ABCMeta):
pass
@abstractmethod
def data_frame(self, df, axis):
def data_frame(self, filter, axis):
"""
Retrieves data for each variable for observations in data frame
:param df: from filter_cells, dataframe
:param filter: filter: dictionary with filter params
:param axis: string obs or var
:return: {
"var": list of variable ids,
@@ -90,23 +90,25 @@ class CXGDriver(metaclass=ABCMeta):
pass
@abstractmethod
def diffexp(self, df1, df2, top_n):
def diffexp(self, filter1, filter2, top_n=None, interactive_limit=None):
"""
Computes the top differentially expressed variables between two observation sets. If dataframes
contain a subset of variables, then statistics for all variables will be returned, otherwise
only the top N vars will be returned.
:param df1: from filter_cells, dataframe containing first set of observations
:param df2: from filter_cells, dataframe containing second set of observations
:param filter1: filter: dictionary with filter params for first set of observations
:param filter2: filter: dictionary with filter params for second set of observations
:param top_n: Limit results to top N (Top var mode only)
:param interactive_limit: -- don't compute if total # genes in dataframes are larger than this
:return: top genes, stats and expression values for variables
"""
pass
@abstractmethod
def layout(self, df):
def layout(self, filter, interactive_limit=None):
"""
Computes a n-d layout for cells through dimensionality reduction.
:param df: from filter_cells, dataframe
:param filter: filter: dictionary with filter params
:param interactive_limit: -- don't compute if total # genes in dataframes are larger than this
:return: [cellid, x, y, ...]
"""
pass