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stephen-riggsstephen-riggs
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Make the murfey client config file optional (#768)
The /home/.murfey file should no longer be needed, as it only records the server and instrument names. This PR removes the need for this file. - Adds a --server flag on instrument server startup to supply the backend url. - The need for the instrument name has been removed entirely. If the --server flag is not provided we fall back to the config file.
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18 files changed

+118
-41
lines changed

18 files changed

+118
-41
lines changed

‎src/murfey/client/context.py‎

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@@ -201,6 +201,7 @@ def ensure_dcg_exists(
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router_name="workflow.router",
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function_name="register_dc_group",
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token=token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data=dcg_data,

‎src/murfey/client/contexts/atlas.py‎

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@@ -55,6 +55,7 @@ def post_transfer_serialem(
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router_name="session_control.spa_router",
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function_name="register_atlas",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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data={
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"name": transferred_file.stem,
@@ -85,6 +86,7 @@ def post_transfer_epu(
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router_name="session_control.spa_router",
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function_name="make_atlas_jpg",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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data={"path": str(transferred_atlas_name).replace("//", "/")},
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)
@@ -138,6 +140,7 @@ def post_transfer_epu(
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router_name="workflow.router",
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function_name="register_dc_group",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data=dcg_data,

‎src/murfey/client/contexts/clem.py‎

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@@ -329,6 +329,7 @@ def process_lif_file(
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router_name="clem.router",
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function_name="process_raw_lifs",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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data={"lif_file": str(lif_file)},
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)
@@ -353,6 +354,7 @@ def process_tiff_series(
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router_name="clem.router",
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function_name="process_raw_tiffs",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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data=tiff_dataset,
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)

‎src/murfey/client/contexts/fib.py‎

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@@ -237,6 +237,7 @@ def post_transfer(
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router_name="workflow.correlative_router",
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function_name="make_gif",
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token=self._token,
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instrument_name=environment.instrument_name,
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year=datetime.now().year,
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visit_name=environment.visit,
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session_id=environment.murfey_session,

‎src/murfey/client/contexts/spa.py‎

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@@ -326,6 +326,7 @@ def _position_analysis(
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router_name="session_control.spa_router",
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function_name="register_grid_square",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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gsid=grid_square,
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data={
@@ -378,6 +379,7 @@ def _position_analysis(
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router_name="session_control.spa_router",
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function_name="register_foil_hole",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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gs_name=grid_square,
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data={
@@ -402,6 +404,7 @@ def _position_analysis(
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router_name="session_control.spa_router",
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function_name="register_foil_hole",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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gs_name=grid_square,
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data={
@@ -476,6 +479,7 @@ def post_transfer(
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router_name="file_io_instrument.router",
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function_name="write_eer_fractionation_file",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={
@@ -539,6 +543,7 @@ def post_transfer(
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router_name="workflow.spa_router",
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function_name="request_spa_preprocessing",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={

‎src/murfey/client/contexts/spa_metadata.py‎

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@@ -138,6 +138,7 @@ def post_transfer(
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router_name="session_control.spa_router",
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function_name="register_grid_square",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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gsid=int(gs),
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data={
@@ -213,6 +214,7 @@ def post_transfer(
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router_name="session_control.spa_router",
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function_name="register_grid_square",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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gsid=gs_name,
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data={
@@ -232,6 +234,7 @@ def post_transfer(
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router_name="session_control.spa_router",
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function_name="register_foil_hole",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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gs_name=gs_name,
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data={

‎src/murfey/client/contexts/sxt.py‎

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@@ -78,6 +78,7 @@ def register_sxt_data_collection(
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router_name="workflow.router",
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function_name="start_dc",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data=dc_data,
@@ -92,6 +93,7 @@ def register_sxt_data_collection(
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router_name="workflow.router",
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function_name="register_proc",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={
@@ -221,6 +223,7 @@ def post_transfer(
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router_name="workflow.sxt_router",
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function_name="process_sxt_tilt_series",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={

‎src/murfey/client/contexts/tomo.py‎

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@@ -157,6 +157,7 @@ def register_tomography_data_collections(
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router_name="workflow.router",
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function_name="start_dc",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data=dc_data,
@@ -174,6 +175,7 @@ def register_tomography_data_collections(
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router_name="workflow.router",
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function_name="register_proc",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={
@@ -290,6 +292,7 @@ def _add_tilt(
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router_name="workflow.tomo_router",
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function_name="register_tilt_series_for_rerun",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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data=rerun_data,
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)
@@ -310,6 +313,7 @@ def _add_tilt(
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router_name="workflow.tomo_router",
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function_name="register_tilt_series",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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data=ts_data,
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)
@@ -345,6 +349,7 @@ def _add_tilt(
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router_name="workflow.tomo_router",
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function_name="register_tilt",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data=tilt_data,
@@ -357,6 +362,7 @@ def _add_tilt(
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router_name="file_io_instrument.router",
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function_name="write_eer_fractionation_file",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={
@@ -393,6 +399,7 @@ def _add_tilt(
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router_name="workflow.tomo_router",
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function_name="request_tomography_preprocessing",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data=preproc_data,
@@ -498,6 +505,7 @@ def post_transfer(
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router_name="workflow.tomo_router",
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function_name="register_tilt_series_length",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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data={
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"tags": [tilt_series],
@@ -518,6 +526,7 @@ def post_transfer(
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router_name="workflow.tomo_router",
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function_name="register_completed_tilt_series",
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token=self._token,
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instrument_name=environment.instrument_name,
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visit_name=environment.visit,
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session_id=environment.murfey_session,
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data={

‎src/murfey/client/contexts/tomo_metadata.py‎

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@@ -155,6 +155,7 @@ def post_transfer(
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router_name="session_control.tomo_router",
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function_name="register_search_map",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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sm_name=transferred_file.parent.name,
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data={
@@ -213,6 +214,7 @@ def post_transfer(
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router_name="session_control.tomo_router",
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function_name="register_search_map",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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sm_name=transferred_file.parent.name,
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data={
@@ -266,6 +268,7 @@ def post_transfer(
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router_name="session_control.tomo_router",
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function_name="register_search_map",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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sm_name=search_map_name,
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data={
@@ -279,6 +282,7 @@ def post_transfer(
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router_name="session_control.tomo_router",
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function_name="register_batch_position",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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batch_name=batch_name,
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data={
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router_name="session_control.tomo_router",
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function_name="register_batch_position",
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token=self._token,
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instrument_name=environment.instrument_name,
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session_id=environment.murfey_session,
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batch_name=beamshift_name,
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data={

‎src/murfey/client/destinations.py‎

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@@ -78,6 +78,7 @@ def determine_default_destination(
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router_name="file_io_instrument.router",
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function_name="suggest_path",
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token=token,
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instrument_name=environment.instrument_name,
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visit_name=visit,
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session_id=environment.murfey_session,
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data={

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