removed errant use of metadata.json file instead of import (#338)

* removed errant use of metadata.json file instead of import
* bump version

pypet2bids/pypet2bids/helper_functions.py

@@ -51,18 +51,10 @@
 if "PET2BIDS" not in project_dir.parts:
     project_dir = parent_dir
 
-metadata_dir = os.path.join(project_dir, "metadata")
-
-# check to see where the schema is at
-pet_metadata_json = os.path.join(metadata_dir, "PET_metadata.json")
-permalink_pet_metadata_json = "https://github.com/openneuropet/PET2BIDS/blob/76d95cf65fa8a14f55a4405df3fdec705e2147cf/metadata/PET_metadata.json"
-pet_reconstruction_metadata_json = os.path.join(
-    metadata_dir, "PET_reconstruction_methods.json"
-)
 
 # load bids schema
 schema = metadata.schema
-
+pet_metadata = metadata.PET_metadata
 # putting these paths here as they are reused in dcm2niix4pet.py, update_json_pet_file.py, and ecat.py
 module_folder = Path(__file__).parent.resolve()
 python_folder = module_folder.parent
@@ -95,19 +87,6 @@ def logger(name):
         return logger
 
 
-def load_pet_bids_requirements_json(
-    pet_bids_req_json: Union[str, pathlib.Path] = pet_metadata_json
-) -> dict:
-    if type(pet_bids_req_json) is str:
-        pet_bids_req_json = pathlib.Path(pet_bids_req_json)
-    if pet_bids_req_json.is_file():
-        with open(pet_bids_req_json, "r") as infile:
-            reqs = json.load(infile)
-        return reqs
-    else:
-        raise FileNotFoundError(pet_bids_req_json)
-
-
 def flatten_series(series):
     """
     This function retrieves either a list or a single value from a pandas series object thus converting a complex
@@ -150,12 +129,13 @@ def collect_spreadsheets(folder_path: pathlib.Path):
 
 def single_spreadsheet_reader(
     path_to_spreadsheet: Union[str, pathlib.Path],
-    pet2bids_metadata_json: Union[str, pathlib.Path] = pet_metadata_json,
+    pet2bids_metadata: dict = metadata.PET_metadata,
     dicom_metadata={},
     **kwargs,
 ) -> dict:
 
-    metadata = {}
+    spreadsheet_metadata = {}
+    metadata_fields = pet2bids_metadata.PET_metadata
 
     if type(path_to_spreadsheet) is str:
         path_to_spreadsheet = pathlib.Path(path_to_spreadsheet)
@@ -165,24 +145,6 @@ def single_spreadsheet_reader(
     else:
         raise FileNotFoundError(f"{path_to_spreadsheet} does not exist.")
 
-    if pet2bids_metadata_json:
-        if type(pet_metadata_json) is str:
-            pet2bids_metadata_json = pathlib.Path(pet2bids_metadata_json)
-
-        if pet2bids_metadata_json.is_file():
-            with open(pet_metadata_json, "r") as infile:
-                metadata_fields = json.load(infile)
-        else:
-            raise FileNotFoundError(
-                f"Required metadata file not found at {pet_metadata_json}, check to see if this file exists;"
-                f"\nelse pass path to file formatted to this {permalink_pet_metadata_json} via "
-                f"pet2bids_metadata_json argument in simplest_spreadsheet_reader call."
-            )
-    else:
-        raise FileNotFoundError(
-            f"pet2bids_metadata_json input required for function call, you provided {pet2bids_metadata_json}"
-        )
-
     spreadsheet_dataframe = open_meta_data(path_to_spreadsheet)
 
     log = logging.getLogger("pypet2bids")
@@ -192,7 +154,7 @@ def single_spreadsheet_reader(
         for field in metadata_fields[field_level]:
             series = spreadsheet_dataframe.get(field, Series(dtype=numpy.float64))
             if not series.empty:
-                metadata[field] = flatten_series(series)
+                spreadsheet_metadata[field] = flatten_series(series)
             elif (
                 series.empty
                 and field_level == "mandatory"
@@ -204,10 +166,10 @@ def single_spreadsheet_reader(
                 )
 
     # lastly apply any kwargs to the metadata
-    metadata.update(**kwargs)
+    spreadsheet_metadata.update(**kwargs)
 
     # more lastly, check to see if values are of the correct datatype (e.g. string, number, boolean)
-    for field, value in metadata.items():
+    for field, value in spreadsheet_metadata.items():
         # check schema for field
         field_schema_properties = schema["objects"]["metadata"].get(field, None)
         if field_schema_properties:
@@ -220,7 +182,7 @@ def single_spreadsheet_reader(
                     try:
                         check_bool = int(value) / 1
                         if check_bool == 0 or check_bool == 1:
-                            metadata[field] = bool(value)
+                            spreadsheet_metadata[field] = bool(value)
                         else:
                             log.warning(
                                 f"{field} is not boolean, it's value is {value}"
@@ -232,7 +194,7 @@ def single_spreadsheet_reader(
                     log.warning(f"{field} is not string, it's value is {value}")
             else:
                 pass
-    return metadata
+    return spreadsheet_metadata
 
 
 def compress(file_like_object, output_path: str = None):

pypet2bids/pypet2bids/metadata_spreadsheet_example_reader.py

@@ -5,15 +5,14 @@
 
 try:
     import helper_functions
+    import metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
+    import pypet2bids.metadata as metadata
 
 
 parent_dir = pathlib.Path(__file__).parent.resolve()
 project_dir = parent_dir.parent
-metadata_dir = join(project_dir, "metadata")
-pet_metadata_json = join(metadata_dir, "PET_metadata.json")
-permalink_pet_metadata_json = "https://github.com/openneuropet/PET2BIDS/blob/76d95cf65fa8a14f55a4405df3fdec705e2147cf/metadata/PET_metadata.json"
 
 """
 

pypet2bids/pypet2bids/update_json_pet_file.py

@@ -51,7 +51,7 @@ def check_json(
     :type spreadsheet_metadata:
     :param path_to_json: path to a json file e.g. a BIDS sidecar file created after running dcm2niix
     :param items_to_check: a dictionary with items to check for within that json. If None is supplied defaults to the
-           PET_metadata.json contained in this repository
+           PET_metadata imported from metadata.PET_metadata
     :param silent: Raises warnings or errors to stdout if this flag is set to True
     :return: dictionary of items existence and value state, if key is True/False there exists/(does not exist) a
             corresponding entry in the json the same can be said of value

pypet2bids/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.4.0"
+version = "1.4.1"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"]
 license = "MIT"