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Add automatic FCS file reading from FlowJo WSP files #168

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merged 6 commits into from
Sep 12, 2023
Merged

Add automatic FCS file reading from FlowJo WSP files #168

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ee631fc
Update `Workspace.__init__` and `_parse_wsp_samples` to find FCS file…
hbhargava7 Aug 31, 2023
194f713
Update the sample filedata id to match the FlowJo name
hbhargava7 Sep 1, 2023
964f59d
Update `find_fcs_files_from_wsp` to handle relative paths
hbhargava7 Sep 4, 2023
3d00e29
Handle failure to find files by URI
hbhargava7 Sep 4, 2023
c9be7fb
Bug fix in error handling
hbhargava7 Sep 4, 2023
b314cd6
Bug fix in relative path handling for fcs file autofinding
hbhargava7 Sep 4, 2023
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Update find_fcs_files_from_wsp to handle relative paths 
Signed-off-by: Hersh Bhargava <hershkbhargava@gmail.com>
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@hbhargava7
hbhargava7 committed Sep 4, 2023
commit 964f59dc8dfbd3f93acebd0323380d968c15eb5e
18 changes: 15 additions & 3 deletions flowkit/_models/workspace.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,20 @@ def __init__(self, wsp_file_path, fcs_samples=None, ignore_missing_files=False,

# find samples in wsp file. in wsp_data['samples'], each item is a dict which has a key `sample_uri`
if find_fcs_files_from_wsp:
def uri_to_path(uri):
"""Convert a URI to a file path, handling both relative and absolute paths."""
parsed = urlparse(uri)

if parsed.scheme not in ('file', ''):
raise ValueError("Unsupported URI scheme: {}".format(parsed.scheme))

path = unquote(parsed.path)

if os.path.isabs(path):
return path
else:
return os.path.join(os.getcwd(), path)

if fcs_samples is not None:
warnings.warn("When `find_fcs_files_from_wsp` is True, `fcs_samples` will be ignored.")

Expand All @@ -83,9 +97,7 @@ def __init__(self, wsp_file_path, fcs_samples=None, ignore_missing_files=False,
sample_uri = sample_data['sample_uri']

# Convert the URI to a path
parsed = urlparse(sample_uri)
host = "{0}{0}{mnt}{0}".format(os.path.sep, mnt=parsed.netloc)
path = os.path.normpath(os.path.join(host, url2pathname(unquote(parsed.path))))
path = uri_to_path(sample_uri)

# Read in the sample files
sample_filedata = sample_utils.load_samples(path)[0]
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