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Add lamella tomography experiment type id #848

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Merged
stephen-riggs merged 2 commits into from
Jul 30, 2026
Merged

Add lamella tomography experiment type id #848

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e3bf903
Add lamella tomography experiment type id
stephen-riggs Jul 30, 2026
892d170
Add a test
stephen-riggs Jul 30, 2026
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8 changes: 8 additions & 0 deletions src/murfey/client/context.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,6 +124,14 @@ def ensure_dcg_exists(

if collection_type == "tomo":
windows_path = session_data["TomographySession"]["AtlasId"]
if (
session_data.get("TomographySession", {}).get("LamellaWorkflow", None)
== "true"
):
# Lamella tomography experiment type
experiment_type_id = 49
else:
logger.warning("Cannot find tomography Session.dm file")
else:
windows_path = session_data["EpuSessionXml"]["Samples"]["_items"][
"SampleXml"
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23 changes: 19 additions & 4 deletions tests/client/test_context.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,22 @@
from unittest.mock import patch
from urllib.parse import urlparse

import pytest

from murfey.client.context import ensure_dcg_exists
from murfey.client.instance_environment import MurfeyInstanceEnvironment

# Lamella experiment type options and experiment type ids
lamella_types: list[tuple[str | None, int]] = [
(None, 36),
("false", 36),
("true", 49),
]


@pytest.mark.parametrize("lamella", lamella_types)
@patch("murfey.client.context.capture_post")
def test_ensure_dcg_exists_tomo(mock_capture_post, tmp_path):
def test_ensure_dcg_exists_tomo(mock_capture_post, lamella, tmp_path):
env = MurfeyInstanceEnvironment(
url=urlparse("http://localhost:8000"),
client_id=0,
Expand All @@ -25,9 +35,14 @@ def test_ensure_dcg_exists_tomo(mock_capture_post, tmp_path):
with open(metadata_source / "Session.dm", "w") as dm_file:
dm_file.write(
"<TomographySession><AtlasId>"
r"X:\cm12345-6\atlas\atlas_metadata\Sample6\Atlas\Atlas.dm"
"</AtlasId></TomographySession>"
r"X:\cm12345-6\atlas\atlas_metadata\Sample6\Atlas\Atlas.dm</AtlasId>"
)
dm_file.write(
rf"<LamellaWorkflow>{lamella[0]}</LamellaWorkflow>"
if lamella[0] is not None
else ""
)
dm_file.write(r"</TomographySession>")

atlas_xml = tmp_path / "cm12345-6/atlas/atlas_metadata/Sample6/Atlas/Atlas_4.xml"
atlas_xml.parent.mkdir(parents=True)
Expand All @@ -46,7 +61,7 @@ def test_ensure_dcg_exists_tomo(mock_capture_post, tmp_path):
)

dcg_data = {
"experiment_type_id": 36,
"experiment_type_id": lamella[1],
"tag": f"{tmp_path}/metadata_folder",
"atlas": f"{tmp_path}/destination/{atlas_xml.relative_to(tmp_path).with_suffix('.jpg')}",
"sample": 6,
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