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Code Issues Packages Projects Releases Wiki Activity

Reorganize order of methods in engine and rest (#305)

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This commit is contained in:
Charlotte Weaver
2018-10-10 16:44:05 -07:00
committed by GitHub
parent dce778f658
commit eb3b3fc59a
3 changed files with 287 additions and 258 deletions
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server/app/driver/driver.py
+45 -35
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@@ -1,5 +1,14 @@
from abc import ABCMeta, abstractmethod
"""
Sort order for methods
1. Initialize
2. Helper
3. Filter
4. Data & Metadata
5. Computation
"""
class CXGDriver(metaclass=ABCMeta):
@@ -45,12 +54,12 @@ class CXGDriver(metaclass=ABCMeta):
@abstractmethod
def filter_dataframe(self, filter):
"""
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
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
:param filter: dictionary with filter parames
:param filter: dictionary with filter params
:return: View into scanpy object with cells/genes filtered
"""
pass
@@ -58,12 +67,38 @@ class CXGDriver(metaclass=ABCMeta):
@abstractmethod
def annotation(self, df, axis, fields=None):
"""
Gets annotation value for each observation
:param axis:
Gets annotation value for each observation
:param df: from filter_cells, dataframe
: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 [idx, val1, val2...]
:return: dict: names - list of fields in order, data - list of lists or metadata
[observation ids, val1, val2...]
"""
pass
@abstractmethod
def data_frame(self, df, axis):
"""
Retrieves data for each variable for observations in data frame
:param df: from filter_cells, dataframe
:param axis: string obs or var
:return: {
"var": list of variable ids,
"obs": [cellid, var1 expression, var2 expression, ...],
}
"""
pass
@abstractmethod
def diffexp(self, df1, df2, top_n):
"""
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 top_n: Limit results to top N (Top var mode only)
:return: top genes, stats and expression values for variables
"""
pass
@@ -72,31 +107,6 @@ class CXGDriver(metaclass=ABCMeta):
"""
Computes a n-d layout for cells through dimensionality reduction.
:param df: from filter_cells, dataframe
:return: [cellid, x, y]
"""
pass
@abstractmethod
def diffexp(self, df1, df2, genes):
"""
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 topN: Limit results to top N (Top var mode only)
:return: top genes, stats and expression values for variables
"""
pass
@abstractmethod
def data_frame(self, df):
"""
Retrieves expression for each gene for cells in data frame
:param df: from filter_cells, dataframe
:return: {
"var": list of variable ids,
"obs": [cellid, var1 expression, var2 expression, ...],
}
:return: [cellid, x, y, ...]
"""
pass