Fix/rename priv params

em_workflows/brt/flow.py

@@ -515,20 +515,20 @@ def brt_flow(
     # end user facing adoc params
     file_share: str,
     input_dir: str,
-    file_name: Optional[str] = None,
+    x_file_name: Optional[str] = None,
     callback_url: Optional[str] = None,
     token: Optional[str] = None,
-    no_api: bool = False,
-    keep_workdir: bool = False,
+    x_no_api: bool = False,
+    x_keep_workdir: bool = False,
     adoc_template: str = "plastic_brt",
 ):
-    utils.notify_api_running(no_api, token, callback_url)
+    utils.notify_api_running(x_no_api, token, callback_url)
 
     # a single input_dir will have n tomograms
     input_dir_fp = utils.get_input_dir(share_name=file_share, input_dir=input_dir)
     # input_dir_fp = utils.get_input_dir(input_dir=input_dir)
     input_fps = utils.list_files(
-        input_dir=input_dir_fp, exts=["MRC", "ST", "mrc", "st"], single_file=file_name
+        input_dir=input_dir_fp, exts=["MRC", "ST", "mrc", "st"], single_file=x_file_name
     )
 
     fps = utils.gen_fps(share_name=file_share, input_dir=input_dir_fp, fps_in=input_fps)
@@ -640,10 +640,10 @@ def brt_flow(
     utils.callback_with_cleanup(
         fps=fps,
         callback_result=callback_with_tilt_mov,
-        no_api=no_api,
+        x_no_api=x_no_api,
         callback_url=callback_url,
         token=token,
-        keep_workdir=keep_workdir,
+        x_keep_workdir=x_keep_workdir,
     )
 
     """

em_workflows/czi/flow.py

@@ -215,18 +215,18 @@ def update_file_metadata(file_path: FilePath, callback_with_zarr: Dict) -> Dict:
 async def czi_flow(
     file_share: str,
     input_dir: str,
-    file_name: Optional[str] = None,
+    x_file_name: Optional[str] = None,
     callback_url: Optional[str] = None,
     token: Optional[str] = None,
-    no_api: bool = False,
-    keep_workdir: bool = False,
+    x_no_api: bool = False,
+    x_keep_workdir: bool = False,
 ):
     input_dir_fp = utils.get_input_dir(share_name=file_share, input_dir=input_dir)
 
     input_fps = utils.list_files(
         input_dir_fp,
         VALID_CZI_INPUTS,
-        single_file=file_name,
+        single_file=x_file_name,
     )
     fps = utils.gen_fps(share_name=file_share, input_dir=input_dir_fp, fps_in=input_fps)
     prim_fps = utils.gen_prim_fps.map(fp_in=fps)
@@ -242,8 +242,8 @@ async def czi_flow(
     utils.callback_with_cleanup(
         fps=fps,
         callback_result=callback_with_zarrs,
-        no_api=no_api,
+        x_no_api=x_no_api,
         callback_url=callback_url,
         token=token,
-        keep_workdir=keep_workdir,
+        x_keep_workdir=x_keep_workdir,
     )

em_workflows/dm_conversion/flow.py

@@ -211,11 +211,11 @@ def convert_intermediate_files(fps):
 def dm_flow(
     file_share: str,
     input_dir: str,
-    file_name: Optional[str] = None,
+    x_file_name: Optional[str] = None,
     callback_url: Optional[str] = None,
     token: Optional[str] = None,
-    no_api: bool = False,
-    keep_workdir: bool = False,
+    x_no_api: bool = False,
+    x_keep_workdir: bool = False,
 ):
     # run_config=LocalRun(labels=[utils.get_environment()]),
     """
@@ -232,7 +232,7 @@ def dm_flow(
     input_fps = utils.list_files(
         input_dir_fp,
         VALID_2D_INPUT_EXTS,
-        single_file=file_name,
+        single_file=x_file_name,
     )
     fps = utils.gen_fps(share_name=file_share, input_dir=input_dir_fp, fps_in=input_fps)
     # logs = utils.init_log.map(file_path=fps)
@@ -253,8 +253,8 @@ def dm_flow(
     utils.callback_with_cleanup(
         fps=fps,
         callback_result=callback_with_keyimgs,
-        no_api=no_api,
+        x_no_api=x_no_api,
         callback_url=callback_url,
         token=token,
-        keep_workdir=keep_workdir,
+        x_keep_workdir=x_keep_workdir,
     )

em_workflows/lrg_2d_rgb/flow.py

@@ -146,19 +146,19 @@ def gen_thumb(file_path: FilePath):
 def lrg_2d_flow(
     file_share: str,
     input_dir: str,
-    file_name: Optional[str] = None,
+    x_file_name: Optional[str] = None,
     callback_url: Optional[str] = None,
     token: Optional[str] = None,
-    no_api: bool = False,
-    keep_workdir: bool = False,
+    x_no_api: bool = False,
+    x_keep_workdir: bool = False,
 ):
     """
     -list all png inputs (assumes all are "large")
     -create tmp dir for each.
     -convert to tiff -> zarr -> jpegs (thumb)
     """
-    if no_api:
-        utils.notify_api_running(no_api=no_api)
+    if x_no_api:
+        utils.notify_api_running(x_no_api=x_no_api)
     else:
         utils.notify_api_running(token=token, callback_url=callback_url)
 
@@ -167,7 +167,7 @@ def lrg_2d_flow(
     input_fps = utils.list_files(
         input_dir_fp,
         VALID_LRG_2D_RGB_INPUTS,
-        single_file=file_name,
+        single_file=x_file_name,
     )
     fps = utils.gen_fps(share_name=file_share, input_dir=input_dir_fp, fps_in=input_fps)
     tiffs = convert_png_to_tiff.map(file_path=fps)
@@ -185,10 +185,10 @@ def lrg_2d_flow(
     utils.callback_with_cleanup(
         fps=fps,
         callback_result=callback_with_pyramids,
-        no_api=no_api,
+        x_no_api=x_no_api,
         callback_url=callback_url,
         token=token,
-        keep_workdir=keep_workdir,
+        x_keep_workdir=x_keep_workdir,
     )
 
     """

em_workflows/sem_tomo/flow.py

@@ -309,11 +309,11 @@ def gen_ng_metadata(fp_in: FilePath) -> Dict:
 def sem_tomo_flow(
     file_share: str,
     input_dir: str,
-    file_name: Optional[str] = None,
+    x_file_name: Optional[str] = None,
     callback_url: Optional[str] = None,
     token: Optional[str] = None,
-    no_api: bool = False,
-    keep_workdir: bool = False,
+    x_no_api: bool = False,
+    x_keep_workdir: bool = False,
     tilt_angle: float = 0,
 ):
     input_dir_fp = utils.get_input_dir(share_name=file_share, input_dir=input_dir)
@@ -376,8 +376,8 @@ def sem_tomo_flow(
     utils.callback_with_cleanup(
         fps=fps,
         callback_result=callback_with_corr_movies,
-        no_api=no_api,
+        x_no_api=x_no_api,
         callback_url=callback_url,
         token=token,
-        keep_workdir=keep_workdir,
+        x_keep_workdir=x_keep_workdir,
     )

em_workflows/utils/utils.py

@@ -173,16 +173,16 @@ def add_asset(prim_fp: dict, asset: dict, image_idx: int = None) -> dict:
 
 # triggers like "always_run" are managed when calling the task itself
 @task(retries=3, retry_delay_seconds=10)
-def cleanup_workdir(fps: List[FilePath], keep_workdir: bool):
+def cleanup_workdir(fps: List[FilePath], x_keep_workdir: bool):
     """
     :param fp: a FilePath which has a working_dir to be removed
 
-    | working_dir isn't needed after run, so remove unless "keep_workdir" is True.
+    | working_dir isn't needed after run, so remove unless "x_keep_workdir" is True.
     | task wrapper on the FilePath rm_workdir method.
 
     """
-    if keep_workdir is True:
-        log("keep_workdir is set to True, skipping removal.")
+    if x_keep_workdir is True:
+        log("x_keep_workdir is set to True, skipping removal.")
     else:
         for fp in fps:
             log(f"Trying to remove {fp.working_dir}")
@@ -449,13 +449,13 @@ def list_dirs(input_dir_fp: Path) -> List[Path]:
 
 @task(retries=1, retry_delay_seconds=10)
 def notify_api_running(
-    no_api: bool = None, token: str = None, callback_url: str = None
+    x_no_api: bool = None, token: str = None, callback_url: str = None
 ):
     """
     tells API the workflow has started to run.
     """
-    if no_api:
-        log("no_api flag used, not interacting with API")
+    if x_no_api:
+        log("x_no_api flag used, not interacting with API")
         return
     elif not callback_url or not token:
         raise RuntimeError("impossible args for notify_api_running")
@@ -496,8 +496,8 @@ def notify_api_running(
 #     else:
 #         message = "error"
 #         ns = state
-#     if prefect.context.parameters.get("no_api"):
-#         log(f"no_api flag used, terminal: success is {message}")
+#     if prefect.context.parameters.get("x_no_api"):
+#         log(f"x_no_api flag used, terminal: success is {message}")
 #     else:
 #         callback_url = prefect.context.parameters.get("callback_url")
 #         token = prefect.context.parameters.get("token")
@@ -523,12 +523,12 @@ def notify_api_completion(flow: Flow, flow_run: FlowRun, state: State):
     https://docs.prefect.io/core/concepts/notifications.html#state-handlers
     """
     status = "Completed" if state.is_completed else "Failed"
-    no_api = flow_run.parameters.get("no_api", True)
+    x_no_api = flow_run.parameters.get("x_no_api", True)
     token = flow_run.parameters.get("token", "")
     callback_url = flow_run.parameters.get("callback_url", "")
 
-    if no_api:
-        log(f"no_api flag used\nCompletion status: {status}")
+    if x_no_api:
+        log(f"x_no_api flag used\nCompletion status: {status}")
         return
 
     headers = {
@@ -603,7 +603,7 @@ def gen_fps(share_name: str, input_dir: Path, fps_in: List[Path]) -> List[FilePa
 # TODO handle "trigger=any_successful"
 @task(retries=3, retry_delay_seconds=60)
 def send_callback_body(
-    no_api: bool,
+    x_no_api: bool,
     files_elts: List[Dict],
     token: str = None,
     callback_url: str = None,
@@ -617,8 +617,8 @@ def send_callback_body(
         Refer to docs/demo_callback.json for expected
     """
     data = {"files": files_elts}
-    if no_api is True:
-        log("no_api flag used, not interacting with API")
+    if x_no_api is True:
+        log("x_no_api flag used, not interacting with API")
         log(json.dumps(data))
         return
 
@@ -639,29 +639,29 @@ def send_callback_body(
             raise RuntimeError(msg)
     else:
         raise RuntimeError(
-            "Invalid state - need callback_url and token, OR set no_api to True."
+            "Invalid state - need callback_url and token, OR set x_no_api to True."
         )
 
 
 def callback_with_cleanup(
     fps: List[FilePath],
     callback_result: List,
-    no_api: bool = False,
+    x_no_api: bool = False,
     callback_url: str = None,
     token: str = None,
-    keep_workdir: bool = False,
+    x_keep_workdir: bool = False,
 ):
     cp_wd_logs_to_assets = copy_workdir_logs.map(fps, wait_for=[callback_result])
 
     cb = send_callback_body(
-        no_api=no_api,
+        x_no_api=x_no_api,
         token=token,
         callback_url=callback_url,
         files_elts=callback_result,
     )
     cleanup_workdir(
         fps,
-        keep_workdir,
+        x_keep_workdir,
         wait_for=[allow_failure(cb), allow_failure(cp_wd_logs_to_assets)],
     )
 

test/test_brt.py

@@ -31,8 +31,8 @@ def test_brt(mock_nfs_mount):
         THICKNESS=30,
         file_share="test",
         input_dir=input_dir,
-        no_api=True,
-        keep_workdir=True,
+        x_no_api=True,
+        x_keep_workdir=True,
         return_state=True,
     )
     assert result.is_completed(), "`result` is not successful!"
@@ -60,8 +60,8 @@ def test_brt_callback(mock_nfs_mount, caplog, mock_callback_data):
         THICKNESS=30,
         file_share="test",
         input_dir=input_dir,
-        no_api=True,
-        keep_workdir=True,
+        x_no_api=True,
+        x_keep_workdir=True,
         return_state=True,
     )
     assert result.is_completed(), "`result` is not successful!"

test/test_czi.py

@@ -13,7 +13,7 @@ async def test_input_fname(mock_nfs_mount, caplog, mock_reuse_zarr):
     state = await czi_flow(
         file_share="test",
         input_dir="test/input_files/IF_czi/Projects/Cropped_Image/",
-        no_api=True,
+        x_no_api=True,
         return_state=True,
     )
     assert state.is_completed()
@@ -35,7 +35,7 @@ async def test_no_mount_point_flow_fails(mock_binaries, monkeypatch, caplog):
         await czi_flow(
             file_share=share_name,
             input_dir="test/input_files/IF_czi/Projects/Cropped_Image/",
-            no_api=True,
+            x_no_api=True,
         )
     assert f"{share_name} doesn't exist. Failing!" in caplog.text, caplog.text
 
@@ -56,7 +56,7 @@ async def test_czi_workflow_callback_structure(
     state = await czi_flow(
         file_share="test",
         input_dir=input_dir,
-        no_api=True,
+        x_no_api=True,
         return_state=True,
     )
     assert state.is_completed()