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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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Handle failure to find files by URI 
Signed-off-by: Hersh Bhargava <hershkbhargava@gmail.com>
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@hbhargava7
hbhargava7 committed Sep 4, 2023
commit 3d00e290129b05695accc978f29db3cee8345564
12 changes: 8 additions & 4 deletions flowkit/_models/workspace.py
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Expand Up @@ -100,12 +100,16 @@ def uri_to_path(uri):
path = uri_to_path(sample_uri)

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

# Update the ID of the loaded data (otherwise analysis breaks)
sample_filedata.id = sample_name
# Update the ID of the loaded data (otherwise analysis breaks)
sample_filedata.id = sample_name

tmp_sample_lut[sample_name] = sample_filedata
tmp_sample_lut[sample_name] = sample_filedata

except FileNotFoundError:
warnings.warn("Sample file not found at path: {}".format(path))

# save group sample membership, we'll filter by loaded samples next
group_lut = wsp_data['groups']
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