diff --git a/src/murfey/cli/transfer.py b/src/murfey/cli/transfer.py index f8a8b7eb1..3c03c8e05 100644 --- a/src/murfey/cli/transfer.py +++ b/src/murfey/cli/transfer.py @@ -36,10 +36,8 @@ def run(): murfey_url = urlparse(args.server, allow_fragments=False) machine_data = requests.get(f"{murfey_url.geturl()}/machine").json() - if Path(args.source or ".").resolve() in machine_data.data_directories.keys(): - console.print( - f"[red]Source directory is the base directory for the {machine_data.data_directories[Path(args.source or '.').resolve()]}, exiting" - ) + if Path(args.source or ".").resolve() in machine_data.data_directories: + console.print("[red]Source directory is the base directory, exiting") return cmd = [ diff --git a/src/murfey/client/__init__.py b/src/murfey/client/__init__.py index b72b26078..4cc6b7108 100644 --- a/src/murfey/client/__init__.py +++ b/src/murfey/client/__init__.py @@ -215,12 +215,6 @@ def run(): default=False, help="Remove source files immediately after their transfer", ) - parser.add_argument( - "--relax", - action="store_true", - default=False, - help="Relax the condition that the source directory needs to be recognised from the configuration", - ) parser.add_argument( "--name", type=str, @@ -344,7 +338,6 @@ def run(): gain_ref=gain_ref, redirected_logger=rich_handler, force_mdoc_metadata=not args.ignore_mdoc_metadata, - strict=not args.relax, processing_enabled=machine_data.get("processing_enabled", True), skip_existing_processing=args.skip_existing_processing, ) diff --git a/src/murfey/client/analyser.py b/src/murfey/client/analyser.py index 5ae587a00..c18b06fe4 100644 --- a/src/murfey/client/analyser.py +++ b/src/murfey/client/analyser.py @@ -57,7 +57,6 @@ def __init__( self._limited = limited self._experiment_type = "" self._acquisition_software = "" - self._role = "" self._extension: str = "" self._unseen_xml: list = [] self._context: Context | None = None @@ -126,14 +125,12 @@ def _find_context(self, file_path: Path) -> bool: in the Context classes themselves. """ if "atlas" in file_path.parts: - self._role = "detector" self._context = SPAMetadataContext("epu", self._basepath) return True # CLEM workflow checks # Look for LIF and XLIF files if file_path.suffix in (".lif", ".xlif"): - self._role = "detector" self._context = CLEMContext("leica", self._basepath) return True # Look for TIFF files associated with CLEM workflow @@ -152,7 +149,6 @@ def _find_context(self, file_path: Path) -> bool: ).get("analyse_created_directories", []) ) if created_directories.intersection(set(file_path.parts)): - self._role = "detector" self._context = CLEMContext("leica", self._basepath) return True @@ -181,9 +177,6 @@ def _find_context(self, file_path: Path) -> bool: else SPAContext("epu", self._basepath) ) self.parameters_model = ProcessingParametersSPA - # Assign it the detector attribute if not already present - if not self._role: - self._role = "detector" return True # Files starting with "Position" belong to the standard tomography workflow @@ -198,23 +191,6 @@ def _find_context(self, file_path: Path) -> bool: logger.info("Acquisition software: tomo") self._context = TomographyContext("tomo", self._basepath) self.parameters_model = PreprocessingParametersTomo - # Assign role if not already present - if not self._role: - # Fractions files attributed to the detector - if ( - "Fractions" in split_file_name[-1] - or "fractions" in split_file_name[-1] - ): - self._role = "detector" - # MDOC files attributed to the microscope - elif ( - file_path.suffix == ".mdoc" - or file_path.with_suffix(".mdoc").is_file() - ): - self._role = "microscope" - # Attribute all other files to the detector - else: - self._role = "detector" return True # Files with these suffixes belong to the serial EM tomography workflow @@ -239,11 +215,6 @@ def _find_context(self, file_path: Path) -> bool: return False self._context = TomographyContext("serialem", self._basepath) self.parameters_model = PreprocessingParametersTomo - if not self._role: - if "Frames" in file_path.parts: - self._role = "detector" - else: - self._role = "microscope" return True return False @@ -251,7 +222,7 @@ def post_transfer(self, transferred_file: Path): try: if self._context: self._context.post_transfer( - transferred_file, role=self._role, environment=self._environment + transferred_file, environment=self._environment ) except Exception as e: logger.error(f"An exception was encountered post transfer: {e}") @@ -309,19 +280,17 @@ def _analyse(self): self.queue.task_done() continue elif self._extension: - logger.info(f"Context found successfully: {self._role}") + logger.info( + f"Context found successfully for {transferred_file}" + ) try: self._context.post_first_transfer( transferred_file, - role=self._role, environment=self._environment, ) except Exception as e: logger.error(f"Exception encountered: {e}") - if ( - self._role == "detector" - and "atlas" not in transferred_file.parts - ): + if "atlas" not in transferred_file.parts: if not dc_metadata: try: dc_metadata = self._context.gather_metadata( @@ -377,20 +346,16 @@ def _analyse(self): self._find_extension(transferred_file) if self._extension: logger.info( - f"Context found successfully: {self._role}, {transferred_file}" + f"Extension found successfully for {transferred_file}" ) try: self._context.post_first_transfer( transferred_file, - role=self._role, environment=self._environment, ) except Exception as e: logger.error(f"Exception encountered: {e}") - if ( - self._role == "detector" - and "atlas" not in transferred_file.parts - ): + if "atlas" not in transferred_file.parts: if not dc_metadata: try: dc_metadata = self._context.gather_metadata( @@ -443,8 +408,8 @@ def _xml_file(self, data_file: Path) -> Path: if not self._environment: return data_file.with_suffix(".xml") file_name = f"{'_'.join(p for p in data_file.stem.split('_')[:-1])}.xml" - data_directories = self._murfey_config.get("data_directories", {}) - for dd in data_directories.keys(): + data_directories = self._murfey_config.get("data_directories", []) + for dd in data_directories: if str(data_file).startswith(dd): base_dir = Path(dd) mid_dir = data_file.relative_to(dd).parent diff --git a/src/murfey/client/context.py b/src/murfey/client/context.py index 5230a89bb..7077ab861 100644 --- a/src/murfey/client/context.py +++ b/src/murfey/client/context.py @@ -40,14 +40,24 @@ def __init__(self, name: str, acquisition_software: str): self._acquisition_software = acquisition_software self.name = name - def post_transfer(self, transferred_file: Path, role: str = "", **kwargs): + def post_transfer( + self, + transferred_file: Path, + environment: MurfeyInstanceEnvironment | None = None, + **kwargs, + ): # Search external packages for additional hooks to include in Murfey for h in entry_points(group="murfey.post_transfer_hooks"): if h.name == self.name: - h.load()(transferred_file, role=role, **kwargs) + h.load()(transferred_file, environment=environment, **kwargs) - def post_first_transfer(self, transferred_file: Path, role: str = "", **kwargs): - self.post_transfer(transferred_file, role=role, **kwargs) + def post_first_transfer( + self, + transferred_file: Path, + environment: MurfeyInstanceEnvironment | None = None, + **kwargs, + ): + self.post_transfer(transferred_file, environment=environment, **kwargs) def gather_metadata( self, metadata_file: Path, environment: MurfeyInstanceEnvironment | None = None diff --git a/src/murfey/client/contexts/clem.py b/src/murfey/client/contexts/clem.py index 8cae42469..72f8f54b9 100644 --- a/src/murfey/client/contexts/clem.py +++ b/src/murfey/client/contexts/clem.py @@ -101,14 +101,11 @@ def __init__(self, acquisition_software: str, basepath: Path): def post_transfer( self, transferred_file: Path, - role: str = "", environment: Optional[MurfeyInstanceEnvironment] = None, **kwargs, ) -> bool: - super().post_transfer( - transferred_file, role=role, environment=environment, **kwargs - ) + super().post_transfer(transferred_file, environment=environment, **kwargs) # Process files generated by "auto-save" acquisition mode # These include TIF/TIFF and XLIF files diff --git a/src/murfey/client/contexts/fib.py b/src/murfey/client/contexts/fib.py index c0ea3723d..12afdb6a7 100644 --- a/src/murfey/client/contexts/fib.py +++ b/src/murfey/client/contexts/fib.py @@ -44,13 +44,10 @@ def __init__(self, acquisition_software: str, basepath: Path): def post_transfer( self, transferred_file: Path, - role: str = "", environment: MurfeyInstanceEnvironment | None = None, **kwargs, ): - super().post_transfer( - transferred_file, role=role, environment=environment, **kwargs - ) + super().post_transfer(transferred_file, environment=environment, **kwargs) if self._acquisition_software == "autotem": parts = transferred_file.parts if "DCImages" in parts and transferred_file.suffix == ".png": diff --git a/src/murfey/client/contexts/spa.py b/src/murfey/client/contexts/spa.py index 29e139497..7f3b00bd6 100644 --- a/src/murfey/client/contexts/spa.py +++ b/src/murfey/client/contexts/spa.py @@ -136,9 +136,9 @@ def _foil_hole_from_file(f: Path) -> int: def _grid_square_metadata_file( - f: Path, data_directories: Dict[Path, str], visit: str, grid_square: int + f: Path, data_directories: List[Path], visit: str, grid_square: int ) -> Path: - for dd in data_directories.keys(): + for dd in data_directories: if str(f).startswith(str(dd)): base_dir = dd mid_dir = f.relative_to(dd).parent @@ -542,7 +542,7 @@ def _position_analysis( grid_square = _grid_square_from_file(transferred_file) grid_square_metadata_file = _grid_square_metadata_file( transferred_file, - {Path(d): l for d, l in machine_config["data_directories"].items()}, + machine_config["data_directories"], environment.visit, grid_square, ) @@ -669,18 +669,16 @@ def _position_analysis( def post_transfer( self, transferred_file: Path, - role: str = "", environment: MurfeyInstanceEnvironment | None = None, **kwargs, ) -> bool: super().post_transfer( transferred_file=transferred_file, - role=role, environment=environment, **kwargs, ) data_suffixes = (".mrc", ".tiff", ".tif", ".eer") - if role == "detector" and "gain" not in transferred_file.name: + if "gain" not in transferred_file.name: if transferred_file.suffix in data_suffixes: if self._acquisition_software == "epu": if environment: @@ -856,7 +854,6 @@ def _register_data_collection( def post_transfer( self, transferred_file: Path, - role: str = "", environment: MurfeyInstanceEnvironment | None = None, **kwargs, ) -> bool: diff --git a/src/murfey/client/contexts/spa_metadata.py b/src/murfey/client/contexts/spa_metadata.py index 4588df86a..83766d30d 100644 --- a/src/murfey/client/contexts/spa_metadata.py +++ b/src/murfey/client/contexts/spa_metadata.py @@ -43,13 +43,11 @@ def __init__(self, acquisition_software: str, basepath: Path): def post_transfer( self, transferred_file: Path, - role: str = "", environment: Optional[MurfeyInstanceEnvironment] = None, **kwargs, ): super().post_transfer( transferred_file=transferred_file, - role=role, environment=environment, **kwargs, ) diff --git a/src/murfey/client/contexts/tomo.py b/src/murfey/client/contexts/tomo.py index 54b3f7b34..a17c81712 100644 --- a/src/murfey/client/contexts/tomo.py +++ b/src/murfey/client/contexts/tomo.py @@ -549,20 +549,19 @@ def _extract_tilt_series(p: Path) -> str: def post_transfer( self, transferred_file: Path, - role: str = "", environment: MurfeyInstanceEnvironment | None = None, **kwargs, ) -> List[str]: super().post_transfer( transferred_file=transferred_file, - role=role, environment=environment, **kwargs, ) data_suffixes = (".mrc", ".tiff", ".tif", ".eer") completed_tilts = [] - if role == "detector" and "gain" not in transferred_file.name: + + if "gain" not in transferred_file.name: if transferred_file.suffix in data_suffixes: if self._acquisition_software == "tomo": if environment: @@ -632,13 +631,10 @@ def post_transfer( def post_first_transfer( self, transferred_file: Path, - role: str = "", environment: MurfeyInstanceEnvironment | None = None, **kwargs, ): - self.post_transfer( - transferred_file, role=role, environment=environment, **kwargs - ) + self.post_transfer(transferred_file, environment=environment, **kwargs) def gather_metadata( self, metadata_file: Path, environment: MurfeyInstanceEnvironment | None = None diff --git a/src/murfey/client/multigrid_control.py b/src/murfey/client/multigrid_control.py index 4216f4d11..7affd38bc 100644 --- a/src/murfey/client/multigrid_control.py +++ b/src/murfey/client/multigrid_control.py @@ -257,13 +257,6 @@ def rsync_result(update: RSyncerUpdate): force_mdoc_metadata=self.force_mdoc_metadata, limited=limited, ) - for data_dir in self._machine_config["data_directories"].keys(): - if source.resolve().is_relative_to(Path(data_dir)): - self.analysers[source]._role = self._machine_config[ - "data_directories" - ][data_dir] - log.info(f"role found for {source}") - break if force_metadata: self.analysers[source].subscribe( partial(self._start_dc, from_form=True) diff --git a/src/murfey/client/tui/app.py b/src/murfey/client/tui/app.py index 505889f65..4a7195871 100644 --- a/src/murfey/client/tui/app.py +++ b/src/murfey/client/tui/app.py @@ -74,7 +74,6 @@ def __init__( gain_ref: Path | None = None, redirected_logger=None, force_mdoc_metadata: bool = False, - strict: bool = False, processing_enabled: bool = True, skip_existing_processing: bool = False, **kwargs, @@ -104,7 +103,6 @@ def __init__( self._processing_enabled = processing_enabled self._multigrid_watcher: MultigridDirWatcher | None = None self._force_mdoc_metadata = force_mdoc_metadata - self._strict = strict self._skip_existing_processing = skip_existing_processing self._machine_config = get_machine_config_client( str(self._environment.url.geturl()), @@ -120,12 +118,6 @@ def __init__( ] self.install_screen(MainScreen(), "main") - @property - def role(self) -> str: - if self.analyser: - return self.analyser._role - return "" - def _launch_multigrid_watcher( self, source: Path, destination_overrides: Dict[Path, str] | None = None ): @@ -291,16 +283,6 @@ def rsync_result(update: RSyncerUpdate): force_mdoc_metadata=self._force_mdoc_metadata, limited=limited, ) - machine_data = requests.get( - f"{self._environment.url.geturl()}/machine" - ).json() - for data_dir in machine_data["data_directories"].keys(): - if source.resolve().is_relative_to(Path(data_dir)): - self.analysers[source]._role = machine_data["data_directories"][ - data_dir - ] - log.info(f"role found for {source}") - break if force_metadata: self.analysers[source].subscribe( partial(self._start_dc, from_form=True) diff --git a/src/murfey/client/tui/screens.py b/src/murfey/client/tui/screens.py index 54d3b6e8e..2268014f5 100644 --- a/src/murfey/client/tui/screens.py +++ b/src/murfey/client/tui/screens.py @@ -89,19 +89,14 @@ def determine_default_destination( log.info(f"Processing only mode with sources {environment.sources}") _default = str(environment.sources[0].resolve()) or str(Path.cwd()) elif machine_data.get("data_directories"): - for data_dir in machine_data["data_directories"].keys(): + for data_dir in machine_data["data_directories"]: if source.resolve() == Path(data_dir): _default = destination + f"/{visit}" - if analysers.get(source): - analysers[source]._role = machine_data["data_directories"][data_dir] break else: try: mid_path = source.resolve().relative_to(data_dir) - if ( - machine_data["data_directories"][data_dir] == "detector" - and use_suggested_path - ): + if use_suggested_path: with global_env_lock: source_name = ( source.name @@ -127,10 +122,6 @@ def determine_default_destination( environment.destination_registry[source_name] = _default else: _default = f"{destination}/{visit}/{mid_path if include_mid_path else source.name}" - if analysers.get(source): - analysers[source]._role = machine_data["data_directories"][ - data_dir - ] break except (ValueError, KeyError): _default = "" @@ -209,10 +200,10 @@ def validate_form(form: dict, model: BaseModel) -> bool: class _DirectoryTree(DirectoryTree): valid_selection = reactive(False) - def __init__(self, *args, data_directories: dict | None = None, **kwargs): + def __init__(self, *args, data_directories: List[Path] | None = None, **kwargs): super().__init__(*args, **kwargs) self._selected_path = self.path - self._data_directories = data_directories or {} + self._data_directories = data_directories or [] def on_tree_node_selected(self, event: Tree.NodeSelected) -> None: event.stop() @@ -281,9 +272,7 @@ def compose(self): ).json() self._dir_tree = _DirectoryTree( str(self._selected_dir), - data_directories=( - machine_data.get("data_directories", {}) if self.app._strict else {} - ), + data_directories=machine_data.get("data_directories", []), id="dir-select", ) @@ -295,7 +284,7 @@ def compose(self): text_log.write("Selected directories:\n") btn_disabled = True - for d in machine_data.get("data_directories", {}).keys(): + for d in machine_data.get("data_directories", []): if ( Path(self._dir_tree._selected_path).resolve().is_relative_to(d) or self.app._environment.processing_only_mode @@ -724,11 +713,7 @@ def on_button_pressed(self, event: Button.Pressed): if self._switch_status: self.app.install_screen( DirectorySelection( - [ - p[0] - for p in machine_data.get("data_directories", {}).items() - if p[1] == "detector" and Path(p[0]).exists() - ] + [p for p in machine_data.get("data_directories", []) if p.exists()] ), "directory-select", ) @@ -790,11 +775,7 @@ def on_button_pressed(self, event: Button.Pressed): self.app.install_screen( DirectorySelection( - [ - p[0] - for p in machine_data.get("data_directories", {}).items() - if p[1] == "detector" and Path(p[0]).exists() - ] + [p for p in machine_data.get("data_directories", []) if p.exists()] ), "directory-select", ) diff --git a/src/murfey/server/api/instrument.py b/src/murfey/server/api/instrument.py index fb0fa37a5..4c32df65c 100644 --- a/src/murfey/server/api/instrument.py +++ b/src/murfey/server/api/instrument.py @@ -92,9 +92,7 @@ async def start_multigrid_watcher( _config = { "acquisition_software": machine_config.acquisition_software, "calibrations": machine_config.calibrations, - "data_directories": { - str(k): v for k, v in machine_config.data_directories.items() - }, + "data_directories": [str(k) for k in machine_config.data_directories], "rsync_basepath": str(machine_config.rsync_basepath), "visit": visit, "default_model": str(machine_config.default_model), diff --git a/src/murfey/util/config.py b/src/murfey/util/config.py index fc058cca8..9380e33f3 100644 --- a/src/murfey/util/config.py +++ b/src/murfey/util/config.py @@ -14,7 +14,7 @@ class MachineConfig(BaseModel, extra=Extra.allow): # type: ignore acquisition_software: List[str] calibrations: Dict[str, Dict[str, Union[dict, float]]] - data_directories: Dict[Path, str] + data_directories: List[Path] rsync_basepath: Path default_model: Path display_name: str = "" @@ -148,7 +148,7 @@ def get_machine_config(instrument_name: str = "") -> Dict[str, MachineConfig]: "": MachineConfig( acquisition_software=[], calibrations={}, - data_directories={}, + data_directories=[], rsync_basepath=Path("dls/tmp"), murfey_db_credentials="", default_model="/tmp/weights.h5", diff --git a/src/murfey/util/dummy_setup.py b/src/murfey/util/dummy_setup.py index c0ce4a12e..ca89645a6 100644 --- a/src/murfey/util/dummy_setup.py +++ b/src/murfey/util/dummy_setup.py @@ -17,10 +17,7 @@ def initialise(dummy_location: Path) -> Path: base = dummy_location / "murfey_dummy" base.mkdir() - microscope_dir = base / "M" detector_dir = base / "Data" - microscope_dir.mkdir() - (microscope_dir / "Supervisor").mkdir() detector_dir.mkdir() (detector_dir / "Supervisor").mkdir() with open(base / "config.yaml", "w") as yaml_out: @@ -28,10 +25,7 @@ def initialise(dummy_location: Path) -> Path: { "m12": { "acquisition_software": ["epu", "tomo", "serialem"], - "data_directories": { - str(detector_dir): "detector", - str(microscope_dir): "microscope", - }, + "data_directories": [str(detector_dir)], "rsync_basepath": str(dummy_location), "calibrations": {"dummy": 0}, } @@ -99,7 +93,7 @@ def generate_data(base_path: Path, timeout: int | None = None, pause: int = 10): base_path, "Supervisor", f"Position_{tilt}.mrc", - data_dir="M", + data_dir="Data", size=(128, 128), ) except ValueError: diff --git a/tests/client/test_context.py b/tests/client/test_context.py index d9cf4bf2b..c6431c72e 100644 --- a/tests/client/test_context.py +++ b/tests/client/test_context.py @@ -30,7 +30,6 @@ def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path): (tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -41,7 +40,6 @@ def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path): (tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -53,7 +51,6 @@ def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path): mdoc.write("[ZValue = 0]\n[ZValue = 1]\n") context.post_transfer( tmp_path / "Position_1.mdoc", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -64,7 +61,6 @@ def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path): (tmp_path / "Position_2_002_[30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_2_002_[30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -89,7 +85,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ (tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -100,7 +95,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ (tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -109,7 +103,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ (tmp_path / "Position_2_002_[-30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_2_002_[-30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -119,7 +112,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ (tmp_path / "Position_2_001_[30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_2_001_[30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -130,7 +122,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ (tmp_path / "Position_3_002_[-30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_3_002_[-30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -143,7 +134,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ mdoc.write("[ZValue = 0]\n[ZValue = 1]\n") context.post_transfer( tmp_path / "Position_1.mdoc", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -155,7 +145,6 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_ mdoc.write("[ZValue = 0]\n[ZValue = 1]\n") context.post_transfer( tmp_path / "Position_2.mdoc", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -179,7 +168,6 @@ def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_ (tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -190,7 +178,6 @@ def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_ (tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch() context.post_transfer( tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -202,7 +189,6 @@ def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_ mdoc.write("[ZValue = 0]\n[ZValue = 1]\n[ZValue = 2]\n") context.post_transfer( tmp_path / "Position_1.mdoc", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -213,7 +199,6 @@ def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_ (tmp_path / "Position_1_003_[60.0]_data_time_fractions.tiff").touch() new_series = context.post_transfer( tmp_path / "Position_1_003_[60.0]_data_time_fractions.tiff", - role="detector", required_position_files=[], required_strings=["fractions"], environment=env, @@ -246,7 +231,6 @@ def test_setting_tilt_series_size_and_completion_from_mdoc_parsing( assert len(context._tilt_series_sizes) == 0 context.post_transfer( Path(__file__).parent.parent / "util" / "test_1.mdoc", - role="detector", environment=env, required_strings=["fractions"], ) @@ -257,7 +241,6 @@ def test_setting_tilt_series_size_and_completion_from_mdoc_parsing( (tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff").touch() context.post_transfer( tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff", - role="detector", environment=env, required_strings=["fractions"], ) @@ -269,7 +252,6 @@ def test_setting_tilt_series_size_and_completion_from_mdoc_parsing( (tmp_path / f"test_1_{i:03}_[{t:.1f}]_data_time_fractions.tiff").touch() context.post_transfer( tmp_path / f"test_1_{i:03}_[{t:.1f}]_data_time_fractions.tiff", - role="detector", environment=env, required_strings=["fractions"], )