chore: cleanup stale files, unused code (msk-mind#385)

Co-authored-by: kohlia <[email protected]>

src/luna/common/utils.py

@@ -159,31 +159,6 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-def to_sql_field(s):
-    filter1 = s.replace(".", "_").replace(" ", "_")
-    filter2 = "".join(e for e in filter1 if e.isalnum() or e == "_")
-    return filter2
-
-
-def to_sql_value(s):
-    if isinstance(s, str):
-        return f"'{s}'"
-    if not s == s:
-        return "Null"
-    if s is None:
-        return "Null"
-    else:
-        return f"{s}"
-
-
-def clean_nested_colname(s):
-    """
-    Removes map name for MapType columns.
-    e.g. metadata.SeriesInstanceUID -> SeriesInstanceUID
-    """
-    return s[s.find(".") + 1 :]
-
-
 def generate_uuid(urlpath: str, prefix, storage_options={}):
     """
     Returns hash of the file given path, preceded by the prefix.
@@ -199,39 +174,6 @@ def generate_uuid(urlpath: str, prefix, storage_options={}):
     return "-".join(prefix)
 
 
-def rebase_schema_numeric(df):
-    """
-    Tries to convert all columns in a dataframe to numeric types, if possible, with integer types taking precident
-
-    Note: this is an in-place operation
-
-    Args:
-        df (pd.DataFrame): dataframe to convert columns
-    """
-    for col in df.columns:
-        if df[col].dtype != object:
-            continue
-
-        df[col] = df[col].astype(float, errors="ignore")
-
-
-def rebase_schema_mixed(df):
-    """
-    Tries to convert all columns with mixed types to strings.
-
-    Note: this is an in-place operation
-
-    Args:
-        df (pd.DataFrame): dataframe to convert columns
-    """
-    for col in df.columns:
-        mixed = (df[[col]].applymap(type) != df[[col]].iloc[0].apply(type)).any(axis=1)
-        if len(df[mixed]) > 0:
-            df[col] = df[col].astype(str)
-        if df[col].dtype == list:
-            df[col] = df[col].astype(str)
-
-
 def generate_uuid_binary(content, prefix):
     """
     Returns hash of the binary, preceded by the prefix.
@@ -267,68 +209,6 @@ def generate_uuid_dict(json_str, prefix):
     return "-".join(prefix)
 
 
-def does_not_contain(token, value):
-    """
-    Validate that `token` is not a substring of `value`
-
-    :param: token: string e.g. : | .
-    :param: value: dictionary, list, or str
-    """
-    if isinstance(value, str):
-        if token in value:
-            raise ValueError(f"{value} cannot contain {token}")
-
-    if isinstance(value, list):
-        if any([token in v for v in value]):
-            raise ValueError(str(value) + f" cannot contain {token}")
-
-    if isinstance(value, dict):
-        if any(
-            [
-                isinstance(key, str)
-                and token in key
-                or isinstance(val, str)
-                and token in val
-                for key, val in value.items()
-            ]
-        ):
-            raise ValueError(str(value) + f" cannot contain {token}")
-
-    return True
-
-
-def replace_token(token, token_replacement, value):
-    """
-    Replace `token` with `token_replacement` in `value`
-
-    :param: token: string e.g. : | .
-    :param: token_replacement: string e.g. _ -
-    :param: value: dictionary, list, or str
-    """
-    if isinstance(value, str):
-        return value.replace(token, token_replacement)
-
-    if isinstance(value, list):
-        new_value = []
-        for v in value:
-            new_value.append(v.replace(token, token_replacement))
-        return new_value
-
-    if isinstance(value, dict):
-        new_value = {}
-        for key, val in value.items():
-            new_key, new_val = key, val
-            if isinstance(key, str):
-                new_key = key.replace(token, token_replacement)
-            if isinstance(val, str):
-                new_val = val.replace(token, token_replacement)
-            new_value[new_key] = new_val
-
-        return new_value
-
-    return value
-
-
 def grouper(iterable, n):
     """Turn an iterable into an iterable of iterables
 
@@ -349,20 +229,6 @@ def grouper(iterable, n):
     ]
 
 
-def get_method_data(cohort_id, method_id):
-    """
-    Return method dict
-
-    :param: cohort_id: string
-    :param: method_id: string
-    """
-
-    method_dir = os.path.join(os.environ["MIND_GPFS_DIR"], "data", cohort_id, "methods")
-    with open(os.path.join(method_dir, f"{method_id}.json")) as json_file:
-        method_config = json.load(json_file)["params"]
-    return method_config
-
-
 def get_absolute_path(module_path, relative_path):
     """Given the path to a module file and the path, relative to the module file, of another file
     that needs to be referenced in the module, this method returns the absolute path of the file