refactor: use pathlib.Path for file paths (#134)

docs/api/conf.py

@@ -12,12 +12,12 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
+from pathlib import Path
 import sys
 
 from sphinx.ext import apidoc
 
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, Path.cwd().resolve().parents[1])
 
 
 # -- Project information -----------------------------------------------------

foca/__init__.py

@@ -2,4 +2,4 @@
 
 from foca.foca import Foca  # noqa: F401
 
-__version__ = '0.8.0'
+__version__ = '0.9.0'

foca/config/config_parser.py

@@ -49,7 +49,7 @@ class ConfigParser():
 
     def __init__(
         self,
-        config_file: Optional[str] = None,
+        config_file: Optional[Path] = None,
         custom_config_model: Optional[str] = None,
         format_logs: bool = True
     ) -> None:
@@ -82,7 +82,7 @@ def _configure_logging(self) -> None:
             )
 
     @staticmethod
-    def parse_yaml(conf: str) -> Dict:
+    def parse_yaml(conf: Path) -> Dict:
         """Parse YAML file.
 
         Args:
@@ -109,7 +109,7 @@ def parse_yaml(conf: str) -> Dict:
             ) from exc
 
     @staticmethod
-    def merge_yaml(*args: str) -> Optional[Dict]:
+    def merge_yaml(*args: Path) -> Optional[Dict]:
         """Parse and merge a set of YAML files.
 
         Merging is done iteratively, from the first, second to the n-th

foca/foca.py

@@ -1,6 +1,7 @@
 """Class for setting up and initializing a FOCA-based microservice."""
 
 import logging
+from pathlib import Path
 from typing import Optional
 
 from connexion import App
@@ -21,7 +22,7 @@ class Foca:
 
     def __init__(
         self,
-        config_file: Optional[str] = None,
+        config_file: Optional[Path] = None,
         custom_config_model: Optional[str] = None,
     ) -> None:
         """Instantiate FOCA class.
@@ -58,8 +59,10 @@ def __init__(
                     parameters, so as to make it easier for others to
                     write/modify their app configuration.
         """
-        self.config_file = config_file
-        self.custom_config_model = custom_config_model
+        self.config_file: Optional[Path] = Path(
+            config_file
+        ) if config_file is not None else None
+        self.custom_config_model: Optional[str] = custom_config_model
 
     def create_app(self) -> App:
         """Set up and initialize FOCA-based microservice.

foca/models/config.py

@@ -6,7 +6,6 @@
 import importlib
 import operator
 from pathlib import Path
-import os
 from typing import (Any, Dict, List, Optional, Union)
 
 from pydantic import (BaseModel, Field, validator)  # pylint: disable=E0611
@@ -532,9 +531,9 @@ class SpecConfig(FOCABaseConfig):
     Example:
 
         >>> SpecConfig(path="/my/path.yaml")
-        SpecConfig(path=['/my/path.yaml'], path_out='/my/path.modified.yaml', \
-append=None, add_operation_fields=None, add_security_fields=None, disable_auth\
-=False, connexion=None)
+        SpecConfig(path=[PosixPath('/my/path.yaml')], path_out=PosixPath('/my/\
+path.modified.yaml'), append=None, add_operation_fields=None, add_security_fie\
+lds=None, disable_auth=False, connexion=None)
 
         >>> SpecConfig(
         ...     path=["/path/to/specs.yaml", "/path/to/add_specs.yaml"],
@@ -563,16 +562,17 @@ class SpecConfig(FOCABaseConfig):
         ...     },
         ...     disable_auth = False
         ... )
-        SpecConfig(path=['/path/to/specs.yaml', '/path/to/add_specs.yaml'], pa\
-th_out='/path/to/specs.modified.yaml', append=[{'security': {'jwt': {'type': '\
-apiKey', 'name': 'Authorization', 'in': 'header'}}}, {'my_other_root_field': '\
-some_value'}], add_operation_fields={'x-swagger-router-controller': 'controlle\
-rs.my_specs', 'x-some-other-custom-field': 'some_value'}, add_security_fields=\
-{'x-apikeyInfoFunc': 'security.auth.validate_token', 'x-some-other-custom-fiel\
-d': 'some_value'}, disable_auth=False, connexion=None)
+        SpecConfig(path=[PosixPath('/path/to/specs.yaml'), PosixPath('/path/to\
+/add_specs.yaml')], path_out=PosixPath('/path/to/specs.modified.yaml'), append\
+=[{'security': {'jwt': {'type': 'apiKey', 'name': 'Authorization', 'in': 'head\
+er'}}}, {'my_other_root_field': 'some_value'}], add_operation_fields={'x-swagg\
+er-router-controller': 'controllers.my_specs', 'x-some-other-custom-field': 's\
+ome_value'}, add_security_fields={'x-apikeyInfoFunc': 'security.auth.validate_\
+token', 'x-some-other-custom-field': 'some_value'}, disable_auth=False, connex\
+ion=None)
     """
-    path: Union[str, List[str]]
-    path_out: Optional[str] = None
+    path: Union[Path, List[Path]]
+    path_out: Optional[Path] = None
     append: Optional[List[Dict]] = None
     add_operation_fields: Optional[Dict] = None
     add_security_fields: Optional[Dict] = None
@@ -585,16 +585,16 @@ def set_abs_path(cls, v):  # pylint: disable=E0213
         """Resolve path relative to caller's current working directory if no
         absolute path provided.
         """
-        # if path is a str, convert it to list
-        if(isinstance(v, str)):
-            if not Path(v).is_absolute():
-                return [str(Path.cwd() / v)]
+        # if path is not a list, convert it to single-item list
+        if(isinstance(v, Path)):
+            if not v.is_absolute():
+                return [Path.cwd() / v]
             return [v]
         else:
-            # modify each relaive part of the list
+            # make each path absolute
             v = [
-                str(Path.cwd() / path)
-                if not Path(path).is_absolute()
+                Path.cwd() / path
+                if not path.is_absolute()
                 else path
                 for path in v
             ]
@@ -603,16 +603,13 @@ def set_abs_path(cls, v):  # pylint: disable=E0213
     # set default if no output file path provided
     @validator('path_out', always=True, allow_reuse=True)
     def set_default_out_path(cls, v, *, values):  # pylint: disable=E0213
-        """Set default output path for spec file if not supplied by user.
-        """
+        """Set default output path for spec file if not supplied by user."""
         if 'path' in values and values['path'] is not None:
             if not v:
-                return '.'.join([
-                    os.path.splitext(values['path'][0])[0],
-                    "modified.yaml"
-                ])
-            if not Path(v).is_absolute():
-                return str(Path.cwd() / v)
+                path = values['path'][0]
+                return path.parent / f"{path.stem}.modified.yaml"
+            if not v.is_absolute():
+                return Path.cwd() / v
         return v
 
 
@@ -636,9 +633,9 @@ class APIConfig(FOCABaseConfig):
         >>> APIConfig(
         ...     specs=[SpecConfig(path='/path/to/specs.yaml')],
         ... )
-        APIConfig(specs=[SpecConfig(path='/path/to/specs.yaml', path_out='/pat\
-h/to/specs.modified.yaml', append=None, add_operation_fields=None, connexion=N\
-one)])
+        APIConfig(specs=[SpecConfig(path=[PosixPath('/path/to/specs.yaml')], p\
+ath_out=PosixPath('/path/to/specs.modified.yaml'), append=None, add_operation_\
+fields=None, add_security_fields=None, disable_auth=False, connexion=None)])
     """
     specs: List[SpecConfig] = []
 

setup.py

@@ -1,19 +1,18 @@
-import os
+"""Package setup."""
+
+from pathlib import Path
 from setuptools import setup, find_packages
 
-root_dir = os.path.dirname(os.path.abspath(__file__))
+root_dir = Path(__file__).parent.resolve()
 
-# Read long description from file
-file_name = os.path.join(root_dir, "README.md")
-with open(file_name, "r") as fh:
-    long_description = fh.read()
+file_name = root_dir / "README.md"
+with open(file_name, "r") as _file:
+    long_description = _file.read()
 
-# Read requirements from file
 install_requires = []
-req = root_dir + '/requirements.txt'
-if os.path.isfile(req):
-    with open(req) as f:
-        install_requires = f.read().splitlines()
+req = root_dir / 'requirements.txt'
+with open(req, "r") as _file:
+    install_requires = _file.read().splitlines()
 
 setup(
     name="foca",

tests/api/test_register_openapi.py

@@ -14,16 +14,16 @@
 from foca.models.config import SpecConfig
 
 # Define mock data
-DIR = Path(__file__).parent.parent / "test_files"
-PATH_SPECS_2_YAML_ORIGINAL = str(DIR / "openapi_2_petstore.original.yaml")
-PATH_SPECS_2_YAML_MODIFIED = str(DIR / "openapi_2_petstore.modified.yaml")
-PATH_SPECS_2_JSON_ORIGINAL = str(DIR / "openapi_2_petstore.original.json")
-PATH_SPECS_2_YAML_ADDITION = str(DIR / "openapi_2_petstore.addition.yaml")
-PATH_SPECS_3_YAML_ORIGINAL = str(DIR / "openapi_3_petstore.original.yaml")
-PATH_SPECS_3_YAML_MODIFIED = str(DIR / "openapi_3_petstore.modified.yaml")
-PATH_SPECS_INVALID_JSON = str(DIR / "invalid.json")
-PATH_SPECS_INVALID_YAML = str(DIR / "invalid.openapi.yaml")
-PATH_NOT_FOUND = str(DIR / "does/not/exist.yaml")
+DIR = Path(__file__).parents[1].resolve() / "test_files"
+PATH_SPECS_2_YAML_ORIGINAL = DIR / "openapi_2_petstore.original.yaml"
+PATH_SPECS_2_YAML_MODIFIED = DIR / "openapi_2_petstore.modified.yaml"
+PATH_SPECS_2_JSON_ORIGINAL = DIR / "openapi_2_petstore.original.json"
+PATH_SPECS_2_YAML_ADDITION = DIR / "openapi_2_petstore.addition.yaml"
+PATH_SPECS_3_YAML_ORIGINAL = DIR / "openapi_3_petstore.original.yaml"
+PATH_SPECS_3_YAML_MODIFIED = DIR / "openapi_3_petstore.modified.yaml"
+PATH_SPECS_INVALID_JSON = DIR / "invalid.json"
+PATH_SPECS_INVALID_YAML = DIR / "invalid.openapi.yaml"
+PATH_NOT_FOUND = DIR / "does/not/exist.yaml"
 OPERATION_FIELDS_2 = {"x-swagger-router-controller": "controllers"}
 OPERATION_FIELDS_2_NO_RESOLVE = {"x-swagger-router-controller": YAMLError}
 OPERATION_FIELDS_3 = {"x-openapi-router-controller": "controllers"}

tests/models/test_config.py

@@ -366,19 +366,19 @@ def test_spec_config_list_no_out():
 def test_SpecConfig_full():
     """Test SpecConfig instantiation; full example"""
     res = SpecConfig(**SPEC_CONFIG)
-    assert res.path_out == SPEC_CONFIG['path_out']
+    assert str(res.path_out) == SPEC_CONFIG['path_out']
 
 
 def test_SpecConfig_minimal():
     """Test SpecConfig instantiation; minimal example"""
     res = SpecConfig(path=PATH)
-    assert res.path_out == PATH_MODIFIED
+    assert str(res.path_out) == PATH_MODIFIED
 
 
 def test_SpecConfig_merge():
     """Test SpecConfig instantiation; multiple config files"""
     res = SpecConfig(path=[PATH, PATH_ADDITION])
-    assert res.path_out == PATH_MODIFIED
+    assert str(res.path_out) == PATH_MODIFIED
 
 
 def test_SpecConfig_extra_arg():

tests/test_foca.py

@@ -3,7 +3,6 @@
 from pathlib import Path
 import pytest
 import shutil
-import os
 
 from connexion import App
 from pydantic import ValidationError
@@ -101,7 +100,6 @@ def test_foca_api(tmpdir):
     foca = Foca(config_file=temp_file)
     app = foca.create_app()
     assert isinstance(app, App)
-    os.remove(temp_file)
 
 
 def test_foca_db():