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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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Bug fix in relative path handling for fcs file autofinding 
Signed-off-by: Hersh Bhargava <hershkbhargava@gmail.com>
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@hbhargava7
hbhargava7 committed Sep 4, 2023
commit b314cd65c44ea0b99daf4032446ec73b2c04abb6
6 changes: 5 additions & 1 deletion flowkit/_models/workspace.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from bokeh.models import Title
from urllib.parse import urlparse, unquote
from urllib.request import url2pathname
from pathlib import Path
from .._conf import debug
from .._models import gates, dimension
from .._utils import plot_utils, wsp_utils, sample_utils, gating_utils
Expand Down Expand Up @@ -81,10 +82,13 @@ def uri_to_path(uri):

path = unquote(parsed.path)

# if the path is relative, join it with the wsp file's directory
if os.path.isabs(path):
return path
else:
return os.path.join(os.getcwd(), path)
# The relative path is relative to the wsp file's directory, so prepend that.
base_path = os.path.dirname(os.path.abspath(Path(wsp_file_path)))
return os.path.join(base_path, path)

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