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CLI Launch (#366)

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* Scanpy engine now required

Without the --engine param we need to error if scanpy engine cannot be imported rather than waiting for all engines

* CLI options and help matches proposal

(but not all options hooked up yet)

* Flesh out top level args

* Move computation args to engine

* CLI input file (#374)

* Fix test command

(tests still won't work)

* Input is file instead of directory
- also renamed example file

* Csweaver/debug (#376)

* Respect debug flag for logging flask calls

* Add loading messages

* max categories (#377)

* Add max categories

* Rename max_categories to category_selection_limit

* ensure whole numbers
This commit is contained in:
Charlotte Weaver
2018-10-24 19:28:59 -07:00
committed by GitHub
parent 02b2349807
commit 94f95d6565
9 changed files with 130 additions and 52 deletions
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server/app/scanpy_engine/scanpy_engine.py
+12 -13
View File
@@ -1,4 +1,3 @@
import os
import warnings
import numpy as np
@@ -23,12 +22,15 @@ Sort order for methods
class ScanpyEngine(CXGDriver):
def __init__(self, data, layout_method=None, diffexp_method=None):
super().__init__(data, layout_method=layout_method, diffexp_method=diffexp_method)
def __init__(self, data, layout_method=None, diffexp_method=None, category_selection_limit=100):
super().__init__(data, layout_method=layout_method, diffexp_method=diffexp_method,
category_selection_limit=category_selection_limit)
self._validatate_data_types()
self._add_mandatory_annotations()
self.cell_count = self.data.shape[0]
self.gene_count = self.data.shape[1]
self.layout_options = ["umap", "tsne"]
self.diffexp_options = ["ttest"]
self._create_schema()
def _create_schema(self):
@@ -64,16 +66,13 @@ class ScanpyEngine(CXGDriver):
self.schema["annotations"][ax].append(ann_schema)
@classmethod
def add_to_parser(cls, subparsers, invocation_function):
scanpy_group = subparsers.add_parser("scanpy", help="run cellxgene using the scanpy engine")
def add_to_parser(cls, subparser):
computation_group = subparser.add_argument_group('computational arguments')
# TODO these choices should be generated from the actual available methods see GH issue #94
scanpy_group.add_argument("-l", "--layout", choices=["umap", "tsne"], default="umap",
help="Algorithm to use for graph layout")
scanpy_group.add_argument("-d", "--diffexp", choices=["ttest"], default="ttest",
help="Algorithm to used to calculate differential expression")
scanpy_group.add_argument("data_directory", metavar="dir", help="Directory containing data and schema file")
scanpy_group.set_defaults(func=invocation_function)
return scanpy_group
computation_group.add_argument("-l", "--layout", choices=["umap", "tsne"], default="umap",
help="Algorithm to use for graph layout")
computation_group.add_argument("-d", "--diffexp", choices=["ttest"], default="ttest",
help="Algorithm to used to calculate differential expression")
@staticmethod
def _load_data(data):
@@ -81,7 +80,7 @@ class ScanpyEngine(CXGDriver):
# Based upon this advice, setting cache=True parameter
# Note: as of current scanpy/anndata release, setting backed='r' will
# result in an error.
return sc.read(os.path.join(data, "data.h5ad"), cache=True)
return sc.read(data, cache=True)
@staticmethod
def _top_sort(values, sort_order, top_n=None):