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Change CLEM series name (tag) format #897

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Merged
tieneupin merged 2 commits into from
Sep 23, 2026
Merged

Change CLEM series name (tag) format #897

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4b7e3ee
CLEM tags will have their parts separated by '/' instead of '--'
tieneupin Sep 22, 2026
4e6665c
Updated tests to use new CLEM series name/tag format
tieneupin Sep 22, 2026
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4 changes: 2 additions & 2 deletions src/murfey/client/contexts/clem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def post_transfer(
)

# Create a unique name for the series
series_name = "--".join(
series_name = "/".join(
[
*destination_file.parent.parts[
-2:
Expand Down Expand Up @@ -167,7 +167,7 @@ def post_transfer(
# Create series name for XLIF file
# XLIF files don't have the "--ZXX--CXX" additions in the file name
# But they have "/Metadata/" as the immediate parent
series_name = "--".join(
series_name = "/".join(
[
*destination_file.parent.parent.parts[-2:],
destination_file.stem.replace(" ", "_"),
Expand Down
4 changes: 1 addition & 3 deletions src/murfey/workflows/clem/register_preprocessing_results.py
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Expand Up @@ -257,9 +257,7 @@ def _register_dcg_and_atlas(
visit_number = visit_name.split("-")[-1]

# Generate name/tag for data colleciton group based on series name
dcg_name = imaging_site.site_name.split("--")[0]
if imaging_site.site_name.split("--")[1].isdigit():
dcg_name += f"--{imaging_site.site_name.split('--')[1]}"
dcg_name = imaging_site.site_name.split("/")[0]

# Determine values for atlas
if is_atlas := imaging_site.data_type == "atlas":
Expand Down
4 changes: 2 additions & 2 deletions tests/workflows/clem/test_register_align_and_merge_results.py
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Expand Up @@ -51,7 +51,7 @@ def test_run(
/ registered_position_name
/ "*.tiff"
)
registered_series_name = f"{project_name}--TileScan_1--{registered_position_name}"
registered_series_name = f"{project_name}/TileScan_1/{registered_position_name}"
site_name = registered_series_name.rstrip(registered_type)
get_or_create_db_entry(
murfey_db_session,
Expand All @@ -65,7 +65,7 @@ def test_run(

# Create the incoming message
incoming_position_name = "Position_1" + incoming_type
incoming_series_name = f"{project_name}--TileScan_1--{incoming_position_name}"
incoming_series_name = f"{project_name}/TileScan_1/{incoming_position_name}"
# The site names should match
assert site_name == incoming_series_name.rstrip(incoming_type)

Expand Down
6 changes: 1 addition & 5 deletions tests/workflows/clem/test_register_preprocessing_results.py
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Expand Up @@ -101,11 +101,7 @@ def generate_preprocessing_messages(
messages: list[dict[str, Any]] = []
for series_path, is_stack, is_montage, shape, pixel_size, extent in datasets:
# Unpack items from list of dataset parameters
series_name = (
str(series_path.relative_to(processed_dir))
.replace("/", "--")
.replace(" ", "_")
)
series_name = str(series_path.relative_to(processed_dir)).replace(" ", "_")
metadata = series_path / "metadata" / f"{series_path.stem}.xml"
metadata.parent.mkdir(parents=True, exist_ok=True)
metadata.touch(exist_ok=True)
Expand Down
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