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stephen-riggsstephen-riggs
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Catch failed hook, and add some tests
1 parent 2b9f478 commit f258c97

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3 files changed

+389
-229
lines changed

3 files changed

+389
-229
lines changed

‎src/murfey/client/context.py‎

Lines changed: 11 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ def ensure_dcg_exists(
4141
metadata_source: Path,
4242
environment: MurfeyInstanceEnvironment,
4343
token: str,
44-
):
44+
) -> str | None:
4545
"""Create a data collection group"""
4646
if collection_type == "tomo":
4747
experiment_type_id = 36
@@ -50,11 +50,14 @@ def ensure_dcg_exists(
5050
experiment_type_id = 37
5151
session_file = metadata_source / "EpuSession.dm"
5252
for h in entry_points(group="murfey.hooks"):
53-
if h.name == "get_epu_session":
54-
h.load()(session_file, environment=environment)
53+
try:
54+
if h.name == "get_epu_session":
55+
h.load()(session_file, environment=environment)
56+
except Exception as e:
57+
logger.warning(f"Get EPU session hook failed: {e}")
5558
else:
5659
logger.error(f"Unknown collection type {collection_type}")
57-
return
60+
return None
5861

5962
if not session_file.is_file():
6063
logger.warning(f"Cannot find session file {str(session_file)}")
@@ -79,7 +82,7 @@ def ensure_dcg_exists(
7982
logger.info(f"Windows path to atlas metadata found: {windows_path}")
8083
if not windows_path:
8184
logger.warning("No atlas metadata path found")
82-
return
85+
return None
8386
visit_index = windows_path.split("\\").index(environment.visit)
8487
partial_path = "/".join(windows_path.split("\\")[visit_index + 1 :])
8588
logger.info("Partial Linux path successfully constructed from Windows path")
@@ -109,7 +112,7 @@ def ensure_dcg_exists(
109112
break
110113
else:
111114
logger.warning(f"Sample could not be identified for {metadata_source}")
112-
return
115+
return None
113116
environment.samples[metadata_source] = SampleInfo(
114117
atlas=Path(partial_path), sample=sample
115118
)
@@ -126,7 +129,7 @@ def ensure_dcg_exists(
126129
)
127130
if not dcg_images_dirs:
128131
logger.warning(f"Cannot find Images-Disc* in {dcg_search_dir}")
129-
return
132+
return None
130133
dcg_tag = str(dcg_images_dirs[-1])
131134

132135
dcg_data = {
@@ -136,7 +139,7 @@ def ensure_dcg_exists(
136139
_atlas_destination(environment, metadata_source, token)
137140
/ environment.samples[metadata_source].atlas.parent
138141
/ atlas_xml_path.with_suffix(".jpg").name
139-
),
142+
).replace("//", "/"),
140143
"sample": environment.samples[metadata_source].sample,
141144
"atlas_pixel_size": atlas_pixel_size,
142145
}

‎tests/client/contexts/test_tomo.py‎

Lines changed: 267 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,267 @@
1+
from __future__ import annotations
2+
3+
from pathlib import Path
4+
from unittest.mock import patch
5+
from urllib.parse import urlparse
6+
7+
from murfey.client.contexts.tomo import TomographyContext
8+
from murfey.client.instance_environment import MurfeyInstanceEnvironment
9+
10+
11+
def test_tomography_context_initialisation_for_tomo(tmp_path):
12+
context = TomographyContext("tomo", tmp_path, "")
13+
assert not context._completed_tilt_series
14+
assert context._acquisition_software == "tomo"
15+
16+
17+
@patch("requests.get")
18+
@patch("requests.post")
19+
def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path):
20+
mock_post().status_code = 200
21+
22+
env = MurfeyInstanceEnvironment(
23+
url=urlparse("http://localhost:8000"),
24+
client_id=0,
25+
sources=[tmp_path],
26+
default_destinations={tmp_path: str(tmp_path)},
27+
instrument_name="",
28+
visit="test",
29+
murfey_session=1,
30+
)
31+
context = TomographyContext("tomo", tmp_path, "")
32+
(tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch()
33+
context.post_transfer(
34+
tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff",
35+
required_position_files=[],
36+
required_strings=["fractions"],
37+
environment=env,
38+
)
39+
assert context._tilt_series == {
40+
"Position_1": [tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"]
41+
}
42+
(tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch()
43+
context.post_transfer(
44+
tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff",
45+
required_position_files=[],
46+
required_strings=["fractions"],
47+
environment=env,
48+
)
49+
assert not context._completed_tilt_series
50+
51+
# Add Position_1.mdoc, which completes this position
52+
with open(tmp_path / "Position_1.mdoc", "w") as mdoc:
53+
mdoc.write("[ZValue = 0]\n[ZValue = 1]\n")
54+
context.post_transfer(
55+
tmp_path / "Position_1.mdoc",
56+
required_position_files=[],
57+
required_strings=["fractions"],
58+
environment=env,
59+
)
60+
assert context._completed_tilt_series == ["Position_1"]
61+
62+
# Start Position_2, this is not complete
63+
(tmp_path / "Position_2_002_[30.0]_date_time_fractions.tiff").touch()
64+
context.post_transfer(
65+
tmp_path / "Position_2_002_[30.0]_date_time_fractions.tiff",
66+
required_position_files=[],
67+
required_strings=["fractions"],
68+
environment=env,
69+
)
70+
assert len(context._tilt_series.values()) == 2
71+
assert context._completed_tilt_series == ["Position_1"]
72+
73+
74+
@patch("requests.get")
75+
@patch("requests.post")
76+
def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_path):
77+
mock_post().status_code = 200
78+
79+
env = MurfeyInstanceEnvironment(
80+
url=urlparse("http://localhost:8000"),
81+
client_id=0,
82+
sources=[tmp_path],
83+
default_destinations={tmp_path: str(tmp_path)},
84+
instrument_name="",
85+
visit="test",
86+
murfey_session=1,
87+
)
88+
context = TomographyContext("tomo", tmp_path, "")
89+
(tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch()
90+
context.post_transfer(
91+
tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff",
92+
required_position_files=[],
93+
required_strings=["fractions"],
94+
environment=env,
95+
)
96+
assert context._tilt_series == {
97+
"Position_1": [tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"]
98+
}
99+
(tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch()
100+
context.post_transfer(
101+
tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff",
102+
required_position_files=[],
103+
required_strings=["fractions"],
104+
environment=env,
105+
)
106+
assert not context._completed_tilt_series
107+
(tmp_path / "Position_2_002_[-30.0]_date_time_fractions.tiff").touch()
108+
context.post_transfer(
109+
tmp_path / "Position_2_002_[-30.0]_date_time_fractions.tiff",
110+
required_position_files=[],
111+
required_strings=["fractions"],
112+
environment=env,
113+
)
114+
assert len(context._tilt_series.values()) == 2
115+
assert not context._completed_tilt_series
116+
(tmp_path / "Position_2_001_[30.0]_date_time_fractions.tiff").touch()
117+
context.post_transfer(
118+
tmp_path / "Position_2_001_[30.0]_date_time_fractions.tiff",
119+
required_position_files=[],
120+
required_strings=["fractions"],
121+
environment=env,
122+
)
123+
assert len(context._tilt_series.values()) == 2
124+
assert not context._completed_tilt_series
125+
(tmp_path / "Position_3_001_[30.0]_date_time_fractions.tiff").touch()
126+
(tmp_path / "Position_3_002_[-30.0]_date_time_fractions.tiff").touch()
127+
context.post_transfer(
128+
tmp_path / "Position_3_002_[-30.0]_date_time_fractions.tiff",
129+
required_position_files=[],
130+
required_strings=["fractions"],
131+
environment=env,
132+
)
133+
assert len(context._tilt_series.values()) == 3
134+
assert not context._completed_tilt_series
135+
136+
# Add Position_1.mdoc, which completes this position
137+
with open(tmp_path / "Position_1.mdoc", "w") as mdoc:
138+
mdoc.write("[ZValue = 0]\n[ZValue = 1]\n")
139+
context.post_transfer(
140+
tmp_path / "Position_1.mdoc",
141+
required_position_files=[],
142+
required_strings=["fractions"],
143+
environment=env,
144+
)
145+
assert context._completed_tilt_series == ["Position_1"]
146+
147+
# Add Position_2.mdoc, which completes this position
148+
with open(tmp_path / "Position_2.mdoc", "w") as mdoc:
149+
mdoc.write("[ZValue = 0]\n[ZValue = 1]\n")
150+
context.post_transfer(
151+
tmp_path / "Position_2.mdoc",
152+
required_position_files=[],
153+
required_strings=["fractions"],
154+
environment=env,
155+
)
156+
assert context._completed_tilt_series == ["Position_1", "Position_2"]
157+
158+
159+
@patch("requests.get")
160+
@patch("requests.post")
161+
def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_path):
162+
mock_post().status_code = 200
163+
164+
env = MurfeyInstanceEnvironment(
165+
url=urlparse("http://localhost:8000"),
166+
client_id=0,
167+
sources=[tmp_path],
168+
default_destinations={tmp_path: str(tmp_path)},
169+
instrument_name="",
170+
visit="test",
171+
murfey_session=1,
172+
)
173+
context = TomographyContext("tomo", tmp_path, "")
174+
(tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch()
175+
context.post_transfer(
176+
tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff",
177+
required_position_files=[],
178+
required_strings=["fractions"],
179+
environment=env,
180+
)
181+
assert context._tilt_series == {
182+
"Position_1": [tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"]
183+
}
184+
(tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch()
185+
context.post_transfer(
186+
tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff",
187+
required_position_files=[],
188+
required_strings=["fractions"],
189+
environment=env,
190+
)
191+
assert not context._completed_tilt_series
192+
193+
# Add Position_1.mdoc, with more tilts than have been seen so far
194+
with open(tmp_path / "Position_1.mdoc", "w") as mdoc:
195+
mdoc.write("[ZValue = 0]\n[ZValue = 1]\n[ZValue = 2]\n")
196+
context.post_transfer(
197+
tmp_path / "Position_1.mdoc",
198+
required_position_files=[],
199+
required_strings=["fractions"],
200+
environment=env,
201+
)
202+
assert not context._completed_tilt_series
203+
204+
# Now add the tilt which completes the series
205+
(tmp_path / "Position_1_003_[60.0]_data_time_fractions.tiff").touch()
206+
new_series = context.post_transfer(
207+
tmp_path / "Position_1_003_[60.0]_data_time_fractions.tiff",
208+
required_position_files=[],
209+
required_strings=["fractions"],
210+
environment=env,
211+
)
212+
assert context._completed_tilt_series == ["Position_1"]
213+
assert new_series == ["Position_1"]
214+
215+
216+
def test_tomography_context_initialisation_for_serialem(tmp_path):
217+
context = TomographyContext("serialem", tmp_path, "")
218+
assert not context._completed_tilt_series
219+
assert context._acquisition_software == "serialem"
220+
221+
222+
@patch("requests.get")
223+
@patch("requests.post")
224+
def test_setting_tilt_series_size_and_completion_from_mdoc_parsing(
225+
mock_post, mock_get, tmp_path
226+
):
227+
mock_post().status_code = 200
228+
229+
env = MurfeyInstanceEnvironment(
230+
url=urlparse("http://localhost:8000"),
231+
client_id=0,
232+
sources=[tmp_path],
233+
default_destinations={tmp_path: str(tmp_path)},
234+
instrument_name="",
235+
visit="test",
236+
murfey_session=1,
237+
)
238+
context = TomographyContext("tomo", tmp_path, "")
239+
assert len(context._tilt_series_sizes) == 0
240+
context.post_transfer(
241+
Path(__file__).parent.parent / "util" / "test_1.mdoc",
242+
environment=env,
243+
required_strings=["fractions"],
244+
)
245+
assert len(context._tilt_series_sizes) == 1
246+
assert context._tilt_series_sizes == {"test_1": 11}
247+
(tmp_path / "test_1.mdoc").touch()
248+
tilt = -50
249+
(tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff").touch()
250+
context.post_transfer(
251+
tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff",
252+
environment=env,
253+
required_strings=["fractions"],
254+
)
255+
assert context._tilt_series == {
256+
"test_1": [tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff"]
257+
}
258+
for i, t in enumerate(range(-40, 60, 10)):
259+
assert not context._completed_tilt_series
260+
(tmp_path / f"test_1_{i:03}_[{t:.1f}]_data_time_fractions.tiff").touch()
261+
context.post_transfer(
262+
tmp_path / f"test_1_{i:03}_[{t:.1f}]_data_time_fractions.tiff",
263+
environment=env,
264+
required_strings=["fractions"],
265+
)
266+
assert len(context._tilt_series["test_1"]) == 11
267+
assert context._completed_tilt_series == ["test_1"]

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