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Renamed 'clem' backend server module to 'workflow_clem' #794

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Merged
tieneupin merged 1 commit into from
Apr 30, 2026
Merged

Renamed 'clem' backend server module to 'workflow_clem' #794

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2 changes: 1 addition & 1 deletion src/murfey/cli/repost_failed_calls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,6 @@ def handle_failed_posts(messages_path: list[Path], murfey_db: Session):
# These imports need to happen after transport object is configured
import murfey.server.api.auth
import murfey.server.api.bootstrap
import murfey.server.api.clem
import murfey.server.api.display
import murfey.server.api.file_io_frontend
import murfey.server.api.file_io_instrument
Expand All @@ -106,6 +105,7 @@ def handle_failed_posts(messages_path: list[Path], murfey_db: Session):
import murfey.server.api.session_info
import murfey.server.api.websocket
import murfey.server.api.workflow
import murfey.server.api.workflow_clem

for json_file in messages_path:
with open(json_file, "r") as json_data:
Expand Down
4 changes: 2 additions & 2 deletions src/murfey/client/contexts/clem.py
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Expand Up @@ -326,7 +326,7 @@ def process_lif_file(
try:
capture_post(
base_url=str(environment.url.geturl()),
router_name="clem.router",
router_name="workflow_clem.router",
function_name="process_raw_lifs",
token=self._token,
instrument_name=environment.instrument_name,
Expand All @@ -351,7 +351,7 @@ def process_tiff_series(
try:
capture_post(
base_url=str(environment.url.geturl()),
router_name="clem.router",
router_name="workflow_clem.router",
function_name="process_raw_tiffs",
token=self._token,
instrument_name=environment.instrument_name,
Expand Down
0 src/murfey/server/api/clem.py → src/murfey/server/api/workflow_clem.py
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4 changes: 2 additions & 2 deletions src/murfey/server/main.py
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Expand Up @@ -12,7 +12,6 @@
import murfey.server
import murfey.server.api.auth
import murfey.server.api.bootstrap
import murfey.server.api.clem
import murfey.server.api.display
import murfey.server.api.file_io_frontend
import murfey.server.api.file_io_instrument
Expand All @@ -26,6 +25,7 @@
import murfey.server.api.session_info
import murfey.server.api.websocket
import murfey.server.api.workflow
import murfey.server.api.workflow_clem
import murfey.server.api.workflow_fib
from murfey.server import template_files
from murfey.util.config import get_security_config
Expand Down Expand Up @@ -97,7 +97,7 @@ class Settings(BaseSettings):
app.include_router(murfey.server.api.workflow.correlative_router)
app.include_router(murfey.server.api.workflow.spa_router)
app.include_router(murfey.server.api.workflow.tomo_router)
app.include_router(murfey.server.api.clem.router)
app.include_router(murfey.server.api.workflow_clem.router)
app.include_router(murfey.server.api.workflow_fib.router)

app.include_router(murfey.server.api.prometheus.router)
Expand Down
44 changes: 22 additions & 22 deletions src/murfey/util/route_manifest.yaml
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Expand Up @@ -382,28 +382,6 @@ murfey.server.api.bootstrap.version:
path_params: []
methods:
- GET
murfey.server.api.clem.router:
- path: /workflow/clem/sessions/{session_id}/process_raw_lifs
function: process_raw_lifs
path_params:
- name: session_id
type: int
methods:
- POST
- path: /workflow/clem/sessions/{session_id}/process_raw_tiffs
function: process_raw_tiffs
path_params:
- name: session_id
type: int
methods:
- POST
- path: /workflow/clem/sessions/{session_id}/align_and_merge_stacks
function: align_and_merge_stacks
path_params:
- name: session_id
type: int
methods:
- POST
murfey.server.api.display.router:
- path: /display/instruments/{instrument_name}/instrument_name
function: get_instrument_display_name
Expand Down Expand Up @@ -1432,6 +1410,28 @@ murfey.server.api.workflow.tomo_router:
type: int
methods:
- POST
murfey.server.api.workflow_clem.router:
- path: /workflow/clem/sessions/{session_id}/process_raw_lifs
function: process_raw_lifs
path_params:
- name: session_id
type: int
methods:
- POST
- path: /workflow/clem/sessions/{session_id}/process_raw_tiffs
function: process_raw_tiffs
path_params:
- name: session_id
type: int
methods:
- POST
- path: /workflow/clem/sessions/{session_id}/align_and_merge_stacks
function: align_and_merge_stacks
path_params:
- name: session_id
type: int
methods:
- POST
murfey.server.api.workflow_fib.router:
- path: /workflow/fib/sessions/{session_id}/register_atlas
function: register_fib_atlas
Expand Down
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