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stephen-riggsstephen-riggs
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Update tomo posts
1 parent b1231c5 commit 814a286

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+73
-25
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1 file changed

+73
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‎src/murfey/client/contexts/tomo.py‎

Lines changed: 73 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,6 @@
1515
MurfeyID,
1616
MurfeyInstanceEnvironment,
1717
)
18-
from murfey.util.api import url_path_for
1918
from murfey.util.client import capture_get, capture_post, get_machine_config_client
2019
from murfey.util.mdoc import get_block, get_global_data, get_num_blocks
2120

@@ -102,19 +101,24 @@ def register_tomography_data_collections(
102101
)
103102
return
104103
try:
105-
dcg_url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
106104
dcg_data = {
107105
"experiment_type": "tomo",
108106
"experiment_type_id": 36,
109107
"tag": str(self._basepath),
110108
"atlas": "",
111109
"sample": None,
112110
}
113-
capture_post(dcg_url, json=dcg_data)
111+
capture_post(
112+
base_url=str(environment.url.geturl()),
113+
router_name="workflow.router",
114+
function_name="register_dc_group",
115+
visit_name=environment.visit,
116+
session_id=environment.murfey_session,
117+
data=dcg_data,
118+
)
114119

115120
for tilt_series in self._tilt_series.keys():
116121
if tilt_series not in self._tilt_series_with_pjids:
117-
dc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'start_dc', visit_name=environment.visit, session_id=environment.murfey_session)}"
118122
dc_data = {
119123
"experiment_type": "tomography",
120124
"file_extension": file_extension,
@@ -146,13 +150,23 @@ def register_tomography_data_collections(
146150
],
147151
}
148152
)
149-
capture_post(dc_url, json=dc_data)
153+
capture_post(
154+
base_url=str(environment.url.geturl()),
155+
router_name="workflow.router",
156+
function_name="start_dc",
157+
visit_name=environment.visit,
158+
session_id=environment.murfey_session,
159+
data=dc_data,
160+
)
150161

151-
proc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_proc', visit_name=environment.visit, session_id=environment.murfey_session)}"
152162
for recipe in ("em-tomo-preprocess", "em-tomo-align"):
153163
capture_post(
154-
proc_url,
155-
json={
164+
base_url=str(environment.url.geturl()),
165+
router_name="workflow.router",
166+
function_name="register_proc",
167+
visit_name=environment.visit,
168+
session_id=environment.murfey_session,
169+
data={
156170
"tag": tilt_series,
157171
"source": str(self._basepath),
158172
"recipe": recipe,
@@ -253,27 +267,37 @@ def _add_tilt(
253267
f"Tilt series {tilt_series} was previously thought complete but now {file_path} has been seen"
254268
)
255269
self._completed_tilt_series.remove(tilt_series)
256-
rerun_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt_series_for_rerun', visit_name=environment.visit)}"
257270
rerun_data = {
258271
"session_id": environment.murfey_session,
259272
"tag": tilt_series,
260273
"source": str(file_path.parent),
261274
}
262-
capture_post(rerun_url, json=rerun_data)
275+
capture_post(
276+
base_url=str(environment.url.geturl()),
277+
router_name="workflow.tomo_router",
278+
function_name="register_tilt_series_for_rerun",
279+
visit_name=environment.visit,
280+
data=rerun_data,
281+
)
263282
if tilt_series in self._aligned_tilt_series:
264283
with self._lock:
265284
self._aligned_tilt_series.remove(tilt_series)
266285

267286
if not self._tilt_series.get(tilt_series):
268287
logger.info(f"New tilt series found: {tilt_series}")
269288
self._tilt_series[tilt_series] = [file_path]
270-
ts_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt_series', visit_name=environment.visit)}"
271289
ts_data = {
272290
"session_id": environment.murfey_session,
273291
"tag": tilt_series,
274292
"source": str(file_path.parent),
275293
}
276-
capture_post(ts_url, json=ts_data)
294+
capture_post(
295+
base_url=str(environment.url.geturl()),
296+
router_name="workflow.tomo_router",
297+
function_name="register_tilt_series",
298+
visit_name=environment.visit,
299+
data=ts_data,
300+
)
277301
if not self._tilt_series_sizes.get(tilt_series):
278302
self._tilt_series_sizes[tilt_series] = 0
279303

@@ -296,19 +320,29 @@ def _add_tilt(
296320
self._tilt_series[tilt_series].append(file_path)
297321

298322
if environment:
299-
tilt_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt', visit_name=environment.visit, session_id=environment.murfey_session)}"
300323
tilt_data = {
301324
"movie_path": str(file_transferred_to),
302325
"tilt_series_tag": tilt_series,
303326
"source": str(file_path.parent),
304327
}
305-
capture_post(tilt_url, json=tilt_data)
328+
capture_post(
329+
base_url=str(environment.url.geturl()),
330+
router_name="workflow.tomo_router",
331+
function_name="register_tilt",
332+
visit_name=environment.visit,
333+
session_id=environment.murfey_session,
334+
data=tilt_data,
335+
)
306336

307337
eer_fractionation_file = None
308338
if self.data_collection_parameters.get("num_eer_frames"):
309339
response = capture_post(
310-
url=f"{str(environment.url.geturl())}{url_path_for('file_io_instrument.router', 'write_eer_fractionation_file', visit_name=environment.visit, session_id=environment.murfey_session)}",
311-
json={
340+
base_url=str(environment.url.geturl()),
341+
router_name="file_io_instrument.router",
342+
function_name="write_eer_fractionation_file",
343+
visit_name=environment.visit,
344+
session_id=environment.murfey_session,
345+
data={
312346
"num_frames": self.data_collection_parameters["num_eer_frames"],
313347
"fractionation": self.data_collection_parameters[
314348
"eer_fractionation"
@@ -318,7 +352,6 @@ def _add_tilt(
318352
},
319353
)
320354
eer_fractionation_file = response.json()["eer_fractionation_file"]
321-
preproc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'request_tomography_preprocessing', visit_name=environment.visit, session_id=environment.murfey_session)}"
322355
preproc_data = {
323356
"path": str(file_transferred_to),
324357
"description": "",
@@ -338,7 +371,14 @@ def _add_tilt(
338371
"tag": tilt_series,
339372
"group_tag": str(self._basepath),
340373
}
341-
capture_post(preproc_url, json=preproc_data)
374+
capture_post(
375+
base_url=str(environment.url.geturl()),
376+
router_name="workflow.tomo_router",
377+
function_name="request_tomography_preprocessing",
378+
visit_name=environment.visit,
379+
session_id=environment.murfey_session,
380+
data=preproc_data,
381+
)
342382

343383
return self._check_tilt_series(tilt_series)
344384

@@ -443,10 +483,12 @@ def post_transfer(
443483

444484
# Always update the tilt series length in the database after an mdoc
445485
if environment.murfey_session is not None:
446-
length_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt_series_length', session_id=environment.murfey_session)}"
447486
capture_post(
448-
length_url,
449-
json={
487+
base_url=str(environment.url.geturl()),
488+
router_name="workflow.tomo_router",
489+
function_name="register_tilt_series_length",
490+
session_id=environment.murfey_session,
491+
data={
450492
"tags": [tilt_series],
451493
"source": str(transferred_file.parent),
452494
"tilt_series_lengths": [
@@ -460,10 +502,13 @@ def post_transfer(
460502
f"The following tilt series are considered complete: {completed_tilts} "
461503
f"after {transferred_file}"
462504
)
463-
complete_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_completed_tilt_series', visit_name=environment.visit, session_id=environment.murfey_session)}"
464505
capture_post(
465-
complete_url,
466-
json={
506+
base_url=str(environment.url.geturl()),
507+
router_name="workflow.tomo_router",
508+
function_name="register_completed_tilt_series",
509+
visit_name=environment.visit,
510+
session_id=environment.murfey_session,
511+
data={
467512
"tags": completed_tilts,
468513
"source": str(transferred_file.parent),
469514
"tilt_series_lengths": [
@@ -544,7 +589,10 @@ def gather_metadata(
544589
binning_factor = 1
545590
if environment:
546591
server_config = capture_get(
547-
url=f"{str(environment.url.geturl())}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=environment.instrument_name)}"
592+
base_url=str(environment.url.geturl()),
593+
router_name="session_control.router",
594+
function_name="machine_info_by_instrument",
595+
instrument_name=environment.instrument_name,
548596
).json()
549597
if (
550598
server_config.get("superres")

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