update jira

decoimpact/business/application.py

@@ -84,23 +84,11 @@ def run(self, input_path: Path):
 
  # build model
  for dataset in model_data.datasets:
- input_files = self._da_layer.retrieve_partitioned_file_names(
- dataset.path
- )
+ input_files = self._da_layer.retrieve_file_names(dataset.path)
  output_path_base = Path(model_data.output_path)
  for key, file_name in input_files.items():
  dataset.path = file_name
- if "*" in output_path_base.stem:
- output_path = Path(str(output_path_base).replace("*", key))
- else:
- partition_part = ""
- if key:
- partition_part = f"_{key}"
- output_path = Path.joinpath(
- output_path_base.parent,
- f"{output_path_base.stem}{partition_part}"
- f"{output_path_base.suffix}",
- )
+ output_path = self._generate_output_path(output_path_base, key)
 
  model_data.partition = key
  model = self._model_builder.build_model(model_data)
@@ -121,3 +109,16 @@ def run(self, input_path: Path):
 
  except Exception as exc: # pylint: disable=broad-except
  self._logger.log_error(f"Exiting application after error: {exc}")
+
+ def _generate_output_path(self, output_path_base, key):
+ if "*" in output_path_base.stem:
+ output_path = Path(str(output_path_base).replace("*", key))
+ else:
+ partition_part = ""
+ if key:
+ partition_part = f"_{key}"
+ output_path = Path.joinpath(
+ output_path_base.parent,
+ f"{output_path_base.stem}{partition_part}" f"{output_path_base.suffix}",
+ )
+ return output_path

decoimpact/data/api/i_data_access_layer.py

@@ -26,7 +26,7 @@ class IDataAccessLayer(ABC):
  """Interface for the data layer"""
 
  @abstractmethod
- def retrieve_partitioned_file_names(self, path: Path) -> dict:
+ def retrieve_file_names(self, path: Path) -> dict:
  """
  Find all files according to the pattern in the path string
 

decoimpact/data/entities/data_access_layer.py

@@ -35,9 +35,12 @@ class DataAccessLayer(IDataAccessLayer):
  def __init__(self, logger: ILogger):
  self._logger = logger
 
- def retrieve_partitioned_file_names(self, path: Path) -> dict:
+ def retrieve_file_names(self, path: Path) -> dict:
  """
  Find all files according to the pattern in the path string
+ If the user gives one filename, one file is returned. The user
+ can give in a * in the filename and all files that correspond to
+ that pattern will be retrieved.
 
  Args:
  path (str): path to input file (with * for generic part)

tests/business/test_application.py

@@ -35,7 +35,7 @@ def test_running_application():
  model.partition = ""
  model_builder.build_model.return_value = model
  data_layer.read_input_file.return_value = model_data
- data_layer.retrieve_partitioned_file_names.return_value = {"": "Test.nc"}
+ data_layer.retrieve_file_names.return_value = {"": "Test.nc"}
  model_data.version = [0, 0, 0]
  model_data.datasets = [dataset]
  model_data.output_path = "Result_test.nc"

tests_acceptance/test_main.py

@@ -16,15 +16,16 @@
 import pytest
 import xarray as _xr
 import yaml
-import yaml_include
 
 
 class SafeLoaderIgnoreUnknown(yaml.SafeLoader):
  def ignore_unknown(self, node):
  return None
 
 
-SafeLoaderIgnoreUnknown.add_constructor(None, SafeLoaderIgnoreUnknown.ignore_unknown)
+SafeLoaderIgnoreUnknown.add_constructor(
+ "!include", SafeLoaderIgnoreUnknown.ignore_unknown
+)
 
 parent_path = Path(__file__).parent