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Merged
stephen-riggs merged 1 commit into from
Mar 13, 2026
Merged

Change job aliases to more informative names #247

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4 changes: 2 additions & 2 deletions src/cryoemservices/services/cryolo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ def cryolo(self, rw, header: dict, message: dict):
return

# Check job alias
job_alias = job_dir.parent / "Live_processing"
job_alias = job_dir.parent / "Live_cryolo"
if not job_alias.exists():
job_alias.symlink_to(job_dir)
elif not (job_alias.is_symlink() and job_alias.readlink() == job_dir):
Expand Down Expand Up @@ -276,7 +276,7 @@ def cryolo(self, rw, header: dict, message: dict):
"stdout": result.stdout.decode("utf8", "replace"),
"stderr": result.stderr.decode("utf8", "replace"),
"experiment_type": cryolo_params.experiment_type,
"alias": "Live_processing",
"alias": "Live_cryolo",
}
if (
result.returncode
Expand Down
4 changes: 2 additions & 2 deletions src/cryoemservices/services/ctffind.py
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ def ctf_find(self, rw, header: dict, message: dict):
job_alias = Path(
re.sub(
f"CtfFind/job{ctf_job_number:03}/.+",
"CtfFind/Live_processing/",
"CtfFind/Live_ctffind/",
ctf_params.output_image,
)
)
Expand Down Expand Up @@ -254,7 +254,7 @@ def ctf_find(self, rw, header: dict, message: dict):
),
"stdout": result.stdout.decode("utf8", "replace"),
"stderr": result.stderr.decode("utf8", "replace"),
"alias": "Live_processing",
"alias": "Live_ctffind",
}
if result.returncode:
node_creator_parameters["success"] = False
Expand Down
2 changes: 1 addition & 1 deletion src/cryoemservices/services/extract_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ def extract_class(self, rw, header: dict, message: dict):
rw.transport.nack(header)
return
original_dir = Path(extract_params.class3d_dir).parent.parent
ctf_micrographs_file = "CtfFind/Live_processing/micrographs_ctf.star"
ctf_micrographs_file = "CtfFind/Live_ctffind/micrographs_ctf.star"

# Link the required files and pull out necessary parameters
particles_data = (
Expand Down
14 changes: 7 additions & 7 deletions src/cryoemservices/services/motioncorr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -316,7 +316,7 @@ def motion_correction(self, rw, header: dict, message: dict):
job_alias = Path(
re.sub(
f"MotionCorr/job{job_number:03}/.+",
"MotionCorr/Live_processing/",
"MotionCorr/Live_motioncorr/",
mc_params.mrc_out,
)
)
Expand Down Expand Up @@ -526,7 +526,7 @@ def motion_correction(self, rw, header: dict, message: dict):
"stdout": result.stdout.decode("utf8", "replace"),
"stderr": result.stderr.decode("utf8", "replace"),
"success": False,
"alias": "Live_processing",
"alias": "Live_motioncorr",
}
rw.send_to("node_creator", node_creator_parameters)
rw.transport.nack(header)
Expand Down Expand Up @@ -677,8 +677,8 @@ def motion_correction(self, rw, header: dict, message: dict):
)
if not import_movie.parent.is_dir():
import_movie.parent.mkdir(parents=True)
if not (project_dir / "Import/Live_processing").exists():
(project_dir / "Import/Live_processing").symlink_to(
if not (project_dir / "Import/Live_import").exists():
(project_dir / "Import/Live_import").symlink_to(
project_dir / f"Import/job{job_number - 1:03}"
)
import_movie.unlink(missing_ok=True)
Expand All @@ -693,7 +693,7 @@ def motion_correction(self, rw, header: dict, message: dict):
"command": "",
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_import",
}
else:
import_parameters = {
Expand All @@ -705,7 +705,7 @@ def motion_correction(self, rw, header: dict, message: dict):
"command": "",
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_import",
}
rw.send_to("node_creator", import_parameters)

Expand All @@ -725,7 +725,7 @@ def motion_correction(self, rw, header: dict, message: dict):
"early_motion": early_motion,
"late_motion": late_motion,
},
"alias": "Live_processing",
"alias": "Live_motioncorr",
}
rw.send_to("node_creator", node_creator_parameters)
# Remove tmp file after requesting node creation
Expand Down
4 changes: 2 additions & 2 deletions src/cryoemservices/services/topaz_pick.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ def topaz(self, rw, header: dict, message: dict):
job_alias = Path(
re.sub(
f"AutoPick/job{job_number:03}/.+",
"AutoPick/Live_processing/",
"AutoPick/Live_topaz_picking/",
topaz_params.output_path,
)
)
Expand Down Expand Up @@ -207,7 +207,7 @@ def topaz(self, rw, header: dict, message: dict):
"command": " ".join(command),
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_topaz_picking",
"success": True,
}
if not job_is_rerun:
Expand Down
14 changes: 7 additions & 7 deletions tests/services/test_cryolo_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,8 +119,8 @@ def write_cbox_file(command, cwd, capture_output):
)

# Check symlinks
assert (tmp_path / "AutoPick/Live_processing").is_symlink()
assert (tmp_path / "AutoPick/Live_processing").readlink() == (
assert (tmp_path / "AutoPick/Live_cryolo").is_symlink()
assert (tmp_path / "AutoPick/Live_cryolo").readlink() == (
tmp_path / "AutoPick/job007"
)

Expand Down Expand Up @@ -205,7 +205,7 @@ def write_cbox_file(command, cwd, capture_output):
"stdout": "stdout",
"stderr": "stderr",
"experiment_type": "spa",
"alias": "Live_processing",
"alias": "Live_cryolo",
"success": True,
},
)
Expand Down Expand Up @@ -349,7 +349,7 @@ def test_cryolo_service_tomography(mock_subprocess, offline_transport, tmp_path)
"stdout": "stdout",
"stderr": "stderr",
"experiment_type": "tomography",
"alias": "Live_processing",
"alias": "Live_cryolo",
"success": True,
},
)
Expand Down Expand Up @@ -469,13 +469,13 @@ def write_cbox_file(command, cwd, capture_output):
offline_transport.ack.assert_called_once()

# Case 2: ok symlink
assert (tmp_path / "AutoPick/Live_processing").is_symlink()
assert (tmp_path / "AutoPick/Live_cryolo").is_symlink()
service.cryolo(None, header=header, message=cryolo_test_message)
assert offline_transport.ack.call_count == 2

# Case 3: bad symlink
(tmp_path / "AutoPick/Live_processing").unlink()
(tmp_path / "AutoPick/Live_processing").symlink_to(tmp_path / "AutoPick")
(tmp_path / "AutoPick/Live_cryolo").unlink()
(tmp_path / "AutoPick/Live_cryolo").symlink_to(tmp_path / "AutoPick")
service.cryolo(None, header=header, message=cryolo_test_message)
offline_transport.nack.assert_called_once()

Expand Down
16 changes: 8 additions & 8 deletions tests/services/test_ctffind_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,8 +106,8 @@ def test_ctffind4_service_spa(mock_subprocess, offline_transport, tmp_path):
)

# Check symlinks
assert (tmp_path / "CtfFind/Live_processing").is_symlink()
assert (tmp_path / "CtfFind/Live_processing").readlink() == (
assert (tmp_path / "CtfFind/Live_ctffind").is_symlink()
assert (tmp_path / "CtfFind/Live_ctffind").readlink() == (
tmp_path / "CtfFind/job006"
)

Expand Down Expand Up @@ -174,7 +174,7 @@ def test_ctffind4_service_spa(mock_subprocess, offline_transport, tmp_path):
"command": f"ctffind\n{' '.join(map(str, parameters_list))}",
"stdout": "stdout",
"stderr": "stderr",
"alias": "Live_processing",
"alias": "Live_ctffind",
"success": True,
},
)
Expand Down Expand Up @@ -280,7 +280,7 @@ def test_ctffind5_service_tomo(mock_subprocess, offline_transport, tmp_path):
"command": f"ctffind5\n{' '.join(map(str, parameters_list))}",
"stdout": "stdout",
"stderr": "stderr",
"alias": "Live_processing",
"alias": "Live_ctffind",
"success": True,
},
)
Expand Down Expand Up @@ -428,13 +428,13 @@ def test_ctffind5_service_check_symlinks(mock_subprocess, offline_transport, tmp
offline_transport.ack.assert_called_once()

# Case 2: ok symlink
assert (tmp_path / "CtfFind/Live_processing").is_symlink()
assert (tmp_path / "CtfFind/Live_ctffind").is_symlink()
service.ctf_find(None, header=header, message=ctffind_test_message)
assert offline_transport.ack.call_count == 2

# Case 3: bad symlink
(tmp_path / "CtfFind/Live_processing").unlink()
(tmp_path / "CtfFind/Live_processing").symlink_to(tmp_path / "CtfFind")
(tmp_path / "CtfFind/Live_ctffind").unlink()
(tmp_path / "CtfFind/Live_ctffind").symlink_to(tmp_path / "CtfFind")
service.ctf_find(None, header=header, message=ctffind_test_message)
offline_transport.nack.assert_called_once()

Expand Down Expand Up @@ -523,7 +523,7 @@ def test_ctffind5_service_fail_cases(mock_subprocess, offline_transport, tmp_pat
"command": mock.ANY,
"stdout": "stdout",
"stderr": "stderr",
"alias": "Live_processing",
"alias": "Live_ctffind",
"success": False,
},
)
Expand Down
2 changes: 1 addition & 1 deletion tests/services/test_extract_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,7 @@ def test_extract_class_service(mock_requests, offline_transport, tmp_path):
{
"job_type": "relion.extract",
"input_file": (
f"CtfFind/Live_processing/micrographs_ctf.star"
f"CtfFind/Live_ctffind/micrographs_ctf.star"
f"::{tmp_path}/Select/job011/particles.star"
),
"output_file": f"{tmp_path}/Extract/job012/particles.star",
Expand Down
36 changes: 17 additions & 19 deletions tests/services/test_motioncorr_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,14 +197,12 @@ def test_motioncor2_service_spa(mock_subprocess, offline_transport, tmp_path):
mock_subprocess.assert_called_with(mc_command, capture_output=True)

# Check symlinks
assert (tmp_path / "MotionCorr/Live_processing").is_symlink()
assert (tmp_path / "MotionCorr/Live_processing").readlink() == (
assert (tmp_path / "MotionCorr/Live_motioncorr").is_symlink()
assert (tmp_path / "MotionCorr/Live_motioncorr").readlink() == (
tmp_path / "MotionCorr/job002"
)
assert (tmp_path / "Import/Live_processing").is_symlink()
assert (tmp_path / "Import/Live_processing").readlink() == (
tmp_path / "Import/job001"
)
assert (tmp_path / "Import/Live_import").is_symlink()
assert (tmp_path / "Import/Live_import").readlink() == (tmp_path / "Import/job001")

# Check plotly file creation
assert (tmp_path / "MotionCorr/job002/Movies/sample_drift_plot.json").is_file()
Expand Down Expand Up @@ -294,7 +292,7 @@ def test_motioncor2_service_spa(mock_subprocess, offline_transport, tmp_path):
"command": "",
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_import",
},
)
offline_transport.send.assert_any_call(
Expand All @@ -313,7 +311,7 @@ def test_motioncor2_service_spa(mock_subprocess, offline_transport, tmp_path):
"early_motion": early_motion,
"late_motion": late_motion,
},
"alias": "Live_processing",
"alias": "Live_motioncorr",
},
)

Expand Down Expand Up @@ -554,7 +552,7 @@ def test_motioncor_relion_service_spa(mock_subprocess, offline_transport, tmp_pa
"command": "",
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_import",
},
)
offline_transport.send.assert_any_call(
Expand All @@ -573,7 +571,7 @@ def test_motioncor_relion_service_spa(mock_subprocess, offline_transport, tmp_pa
"early_motion": early_motion,
"late_motion": late_motion,
},
"alias": "Live_processing",
"alias": "Live_motioncorr",
},
)

Expand Down Expand Up @@ -754,7 +752,7 @@ def test_motioncor2_service_tomo(mock_subprocess, offline_transport, tmp_path):
"command": "",
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_import",
},
)
offline_transport.send.assert_any_call(
Expand All @@ -773,7 +771,7 @@ def test_motioncor2_service_tomo(mock_subprocess, offline_transport, tmp_path):
"early_motion": early_motion,
"late_motion": late_motion,
},
"alias": "Live_processing",
"alias": "Live_motioncorr",
},
)

Expand Down Expand Up @@ -969,7 +967,7 @@ def test_motioncor_relion_service_tomo(mock_subprocess, offline_transport, tmp_p
"command": "",
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_import",
},
)
offline_transport.send.assert_any_call(
Expand All @@ -988,7 +986,7 @@ def test_motioncor_relion_service_tomo(mock_subprocess, offline_transport, tmp_p
"early_motion": early_motion,
"late_motion": late_motion,
},
"alias": "Live_processing",
"alias": "Live_motioncorr",
},
)

Expand Down Expand Up @@ -1145,7 +1143,7 @@ def test_motioncor2_slurm_service_spa(mock_requests, offline_transport, tmp_path
"early_motion": early_motion,
"late_motion": late_motion,
},
"alias": "Live_processing",
"alias": "Live_motioncorr",
},
)

Expand Down Expand Up @@ -1286,7 +1284,7 @@ def test_motioncor_superres_does_slurm(mock_requests, offline_transport, tmp_pat
"command": " ".join(mc_command),
"stdout": "cluster job submission",
"stderr": "failed to submit job",
"alias": "Live_processing",
"alias": "Live_motioncorr",
"success": False,
},
)
Expand Down Expand Up @@ -1544,15 +1542,15 @@ def test_motioncor_check_symlink(mock_subprocess, offline_transport, tmp_path):
# Case 2: ok symlink
service.x_shift_list = [-3.0, 3.0]
service.y_shift_list = [4.0, -4.0]
assert (tmp_path / "MotionCorr/Live_processing").is_symlink()
assert (tmp_path / "MotionCorr/Live_motioncorr").is_symlink()
service.motion_correction(None, header=header, message=motioncorr_test_message)
assert offline_transport.ack.call_count == 2

# Case 3: bad symlink
service.x_shift_list = [-3.0, 3.0]
service.y_shift_list = [4.0, -4.0]
(tmp_path / "MotionCorr/Live_processing").unlink()
(tmp_path / "MotionCorr/Live_processing").symlink_to(tmp_path / "Movies")
(tmp_path / "MotionCorr/Live_motioncorr").unlink()
(tmp_path / "MotionCorr/Live_motioncorr").symlink_to(tmp_path / "Movies")
service.motion_correction(None, header=header, message=motioncorr_test_message)
offline_transport.nack.assert_called_once()

Expand Down
12 changes: 6 additions & 6 deletions tests/services/test_topaz_pick.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,8 @@ def test_topaz_with_diameter(
assert (written_coords["rlnAutopickFigureOfMerit"] == [1, 2, 3]).all()

# Check symlinks
assert (tmp_path / "AutoPick/Live_processing").is_symlink()
assert (tmp_path / "AutoPick/Live_processing").readlink() == (
assert (tmp_path / "AutoPick/Live_topaz_picking").is_symlink()
assert (tmp_path / "AutoPick/Live_topaz_picking").readlink() == (
tmp_path / "AutoPick/job007"
)

Expand Down Expand Up @@ -145,7 +145,7 @@ def test_topaz_with_diameter(
),
"stdout": "",
"stderr": "",
"alias": "Live_processing",
"alias": "Live_topaz_picking",
"success": True,
},
)
Expand Down Expand Up @@ -305,13 +305,13 @@ def test_topaz_check_symlinks(
offline_transport.ack.assert_called_once()

# Case 2: ok symlink
assert (tmp_path / "AutoPick/Live_processing").is_symlink()
assert (tmp_path / "AutoPick/Live_topaz_picking").is_symlink()
service.topaz(None, header=header, message=topaz_test_message)
assert offline_transport.ack.call_count == 2

# Case 3: bad symlink
(tmp_path / "AutoPick/Live_processing").unlink()
(tmp_path / "AutoPick/Live_processing").symlink_to(tmp_path / "AutoPick")
(tmp_path / "AutoPick/Live_topaz_picking").unlink()
(tmp_path / "AutoPick/Live_topaz_picking").symlink_to(tmp_path / "AutoPick")
service.topaz(None, header=header, message=topaz_test_message)
offline_transport.nack.assert_called_once()

Expand Down
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