mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 05:47:58 +08:00
94f95d6565
* 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
63 lines
1.6 KiB
Python
63 lines
1.6 KiB
Python
import json
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from argparse import ArgumentTypeError
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from numpy import float32, integer
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class Float32JSONEncoder(json.JSONEncoder):
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def default(self, obj):
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if isinstance(obj, float32):
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return float(obj)
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elif isinstance(obj, integer):
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return int(obj)
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return json.JSONEncoder.default(self, obj)
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class MimeTypeError(Exception):
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def __init__(self, message):
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self.message = message
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class FilterError(Exception):
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def __init__(self, message):
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self.message = message
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class InteractiveError(Exception):
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def __init__(self, message):
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self.message = message
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class PrepareError(Exception):
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def __init__(self, message):
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self.message = message
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def get_mime_type(default="application/json", acceptable_types=["application/json", "text/csv"], query_param=None,
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header=None):
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mime_type = default
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if query_param:
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if query_param in acceptable_types:
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mime_type = query_param
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else:
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raise MimeTypeError(f"Unsupported mime type {query_param} specified in query parameter 'accept-type'")
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elif len(header):
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mime_type = header.best_match(acceptable_types)
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if not mime_type:
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raise MimeTypeError(f"Unsupported mime type(s) {header} in HTTP Accept header")
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return mime_type
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def whole_number(value):
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try:
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value = int(value)
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except ValueError as e:
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raise ArgumentTypeError(f"{value} is not type int") from e
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if value < 0:
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raise ArgumentTypeError(f"{value} is not >= 0")
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return value
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