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stephen-riggsstephen-riggs
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Adjust remaining contexts
1 parent 814a286 commit 47f03b9

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4 files changed

+128
-52
lines changed

4 files changed

+128
-52
lines changed

‎src/murfey/client/contexts/fib.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,6 @@
99

1010
from murfey.client.context import Context
1111
from murfey.client.instance_environment import MurfeyInstanceEnvironment
12-
from murfey.util.api import url_path_for
1312
from murfey.util.client import capture_post
1413

1514
logger = logging.getLogger("murfey.client.contexts.fib")
@@ -93,8 +92,13 @@ def post_transfer(
9392
).name
9493
# post gif list to gif making API call
9594
capture_post(
96-
url=f"{environment.url.geturl()}{url_path_for('workflow.correlative_router', 'make_gif', year=datetime.now().year, visit_name=environment.visit, session_id=environment.murfey_session)}",
97-
json={
95+
base_url=str(environment.url.geturl()),
96+
router_name="workflow.correlative_router",
97+
function_name="make_gif",
98+
year=datetime.now().year,
99+
visit_name=environment.visit,
100+
session_id=environment.murfey_session,
101+
data={
98102
"lamella_number": lamella_number,
99103
"images": gif_list,
100104
"raw_directory": raw_directory,

‎src/murfey/client/contexts/spa.py‎

Lines changed: 41 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,6 @@
1313
MurfeyID,
1414
MurfeyInstanceEnvironment,
1515
)
16-
from murfey.util.api import url_path_for
1716
from murfey.util.client import capture_get, capture_post, get_machine_config_client
1817
from murfey.util.spa_metadata import (
1918
foil_hole_data,
@@ -227,7 +226,10 @@ def gather_metadata(
227226
binning_factor = 1
228227
if environment:
229228
server_config_response = capture_get(
230-
f"{str(environment.url.geturl())}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=environment.instrument_name)}"
229+
base_url=str(environment.url.geturl()),
230+
router_name="session_control.router",
231+
function_name="machine_info_by_instrument",
232+
instrument_name=environment.instrument_name,
231233
)
232234
if server_config_response is None:
233235
return None
@@ -297,7 +299,10 @@ def _position_analysis(
297299
] = (None, None, None, None, None, None, None)
298300
data_collection_group = (
299301
capture_get(
300-
f"{environment.url.geturl()}{url_path_for('session_info.router', 'get_dc_groups', session_id=environment.murfey_session)}"
302+
base_url=str(environment.url.geturl()),
303+
router_name="session_info.router",
304+
function_name="get_dc_groups",
305+
session_id=environment.murfey_session,
301306
)
302307
.json()
303308
.get(str(source), {})
@@ -319,7 +324,6 @@ def _position_analysis(
319324
local_atlas_path,
320325
grid_square=str(grid_square),
321326
)[str(grid_square)]
322-
gs_url = f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_grid_square', session_id=environment.murfey_session, gsid=grid_square)}"
323327
gs = grid_square_data(
324328
grid_square_metadata_file,
325329
grid_square,
@@ -340,8 +344,12 @@ def _position_analysis(
340344
else ""
341345
)
342346
capture_post(
343-
gs_url,
344-
json={
347+
base_url=str(environment.url.geturl()),
348+
router_name="session_control.spa_router",
349+
function_name="register_grid_square",
350+
session_id=environment.murfey_session,
351+
gsid=grid_square,
352+
data={
345353
"tag": str(source),
346354
"readout_area_x": gs.readout_area_x,
347355
"readout_area_y": gs.readout_area_y,
@@ -360,7 +368,6 @@ def _position_analysis(
360368
)
361369
foil_hole = foil_hole_from_file(transferred_file)
362370
if foil_hole not in self._foil_holes[grid_square]:
363-
fh_url = f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_foil_hole', session_id=environment.murfey_session, gs_name=grid_square)}"
364371
if environment.murfey_session is not None:
365372
fh = foil_hole_data(
366373
grid_square_metadata_file,
@@ -383,8 +390,12 @@ def _position_analysis(
383390
else ""
384391
)
385392
capture_post(
386-
fh_url,
387-
json={
393+
base_url=str(environment.url.geturl()),
394+
router_name="session_control.spa_router",
395+
function_name="register_foil_hole",
396+
session_id=environment.murfey_session,
397+
gs_name=grid_square,
398+
data={
388399
"name": foil_hole,
389400
"x_location": fh.x_location,
390401
"y_location": fh.y_location,
@@ -402,8 +413,12 @@ def _position_analysis(
402413
)
403414
else:
404415
capture_post(
405-
fh_url,
406-
json={
416+
base_url=str(environment.url.geturl()),
417+
router_name="session_control.spa_router",
418+
function_name="register_foil_hole",
419+
session_id=environment.murfey_session,
420+
gs_name=grid_square,
421+
data={
407422
"name": foil_hole,
408423
"tag": str(source),
409424
},
@@ -459,7 +474,9 @@ def post_transfer(
459474
)
460475
if not environment.movie_counters.get(str(source)):
461476
movie_counts_get = capture_get(
462-
f"{environment.url.geturl()}{url_path_for('session_control.router', 'count_number_of_movies')}",
477+
base_url=str(environment.url.geturl()),
478+
router_name="session_control.router",
479+
function_name="count_number_of_movies",
463480
)
464481
if movie_counts_get is not None:
465482
environment.movie_counters[str(source)] = count(
@@ -473,8 +490,12 @@ def post_transfer(
473490
eer_fractionation_file = None
474491
if file_transferred_to.suffix == ".eer":
475492
response = capture_post(
476-
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)}",
477-
json={
493+
base_url=str(environment.url.geturl()),
494+
router_name="file_io_instrument.router",
495+
function_name="write_eer_fractionation_file",
496+
visit_name=environment.visit,
497+
session_id=environment.murfey_session,
498+
data={
478499
"eer_path": str(file_transferred_to),
479500
"fractionation": self.data_collection_parameters[
480501
"eer_fractionation"
@@ -503,7 +524,6 @@ def post_transfer(
503524
)
504525
foil_hole = None
505526

506-
preproc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.spa_router', 'request_spa_preprocessing', visit_name=environment.visit, session_id=environment.murfey_session)}"
507527
preproc_data = {
508528
"path": str(file_transferred_to),
509529
"description": "",
@@ -529,8 +549,12 @@ def post_transfer(
529549
"foil_hole_id": foil_hole,
530550
}
531551
capture_post(
532-
preproc_url,
533-
json={
552+
base_url=str(environment.url.geturl()),
553+
router_name="workflow.spa_router",
554+
function_name="request_spa_preprocessing",
555+
visit_name=environment.visit,
556+
session_id=environment.murfey_session,
557+
data={
534558
k: None if v == "None" else v
535559
for k, v in preproc_data.items()
536560
},

‎src/murfey/client/contexts/spa_metadata.py‎

Lines changed: 34 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,6 @@
77
from murfey.client.context import Context
88
from murfey.client.contexts.spa import _file_transferred_to, _get_source
99
from murfey.client.instance_environment import MurfeyInstanceEnvironment, SampleInfo
10-
from murfey.util.api import url_path_for
1110
from murfey.util.client import capture_post, get_machine_config_client
1211
from murfey.util.spa_metadata import (
1312
FoilHoleInfo,
@@ -160,7 +159,6 @@ def post_transfer(
160159
environment.samples[source] = SampleInfo(
161160
atlas=Path(partial_path), sample=sample
162161
)
163-
url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
164162
dcg_search_dir = "/".join(
165163
p for p in transferred_file.parent.parts if p != environment.visit
166164
)
@@ -189,15 +187,26 @@ def post_transfer(
189187
"sample": environment.samples[source].sample,
190188
"atlas_pixel_size": atlas_pixel_size,
191189
}
192-
capture_post(url, json=dcg_data)
190+
capture_post(
191+
base_url=str(environment.url.geturl()),
192+
router_name="workflow.router",
193+
function_name="register_dc_group",
194+
visit_name=environment.visit,
195+
session_id=environment.murfey_session,
196+
data=dcg_data,
197+
)
193198
gs_pix_positions = get_grid_square_atlas_positions(
194199
source_visit_dir / partial_path
195200
)
196201
for gs, pos_data in gs_pix_positions.items():
197202
if pos_data:
198203
capture_post(
199-
f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_grid_square', session_id=environment.murfey_session, gsid=int(gs))}",
200-
json={
204+
base_url=str(environment.url.geturl()),
205+
router_name="session_control.spa_router",
206+
function_name="register_grid_square",
207+
session_id=environment.murfey_session,
208+
gsid=int(gs),
209+
data={
201210
"tag": dcg_tag,
202211
"x_location": pos_data[0],
203212
"y_location": pos_data[1],
@@ -215,7 +224,6 @@ def post_transfer(
215224
and environment
216225
):
217226
# Make sure we have a data collection group before trying to register grid square
218-
url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
219227
dcg_search_dir = "/".join(
220228
p
221229
for p in transferred_file.parent.parent.parts
@@ -239,7 +247,14 @@ def post_transfer(
239247
"experiment_type_id": 37,
240248
"tag": dcg_tag,
241249
}
242-
capture_post(url, json=dcg_data)
250+
capture_post(
251+
base_url=str(environment.url.geturl()),
252+
router_name="workflow.router",
253+
function_name="register_dc_group",
254+
visit_name=environment.visit,
255+
session_id=environment.murfey_session,
256+
data=dcg_data,
257+
)
243258

244259
gs_name = int(transferred_file.stem.split("_")[1])
245260
logger.info(
@@ -264,7 +279,6 @@ def post_transfer(
264279
visitless_source = str(visitless_source_images_dirs[-1])
265280

266281
if fh_positions:
267-
gs_url = f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_grid_square', session_id=environment.murfey_session, gsid=gs_name)}"
268282
gs_info = grid_square_data(
269283
transferred_file,
270284
gs_name,
@@ -275,8 +289,12 @@ def post_transfer(
275289
else ""
276290
)
277291
capture_post(
278-
gs_url,
279-
json={
292+
base_url=str(environment.url.geturl()),
293+
router_name="session_control.spa_router",
294+
function_name="register_grid_square",
295+
session_id=environment.murfey_session,
296+
gsid=gs_name,
297+
data={
280298
"tag": visitless_source,
281299
"readout_area_x": gs_info.readout_area_x,
282300
"readout_area_y": gs_info.readout_area_y,
@@ -289,8 +307,12 @@ def post_transfer(
289307

290308
for fh, fh_data in fh_positions.items():
291309
capture_post(
292-
f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_foil_hole', session_id=environment.murfey_session, gs_name=gs_name)}",
293-
json={
310+
base_url=str(environment.url.geturl()),
311+
router_name="session_control.spa_router",
312+
function_name="register_foil_hole",
313+
session_id=environment.murfey_session,
314+
gs_name=gs_name,
315+
data={
294316
"name": fh,
295317
"x_location": fh_data.x_location,
296318
"y_location": fh_data.y_location,

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