Code formatting

.gitignore

@@ -17,3 +17,4 @@ settings.py
 README.pdf
 docs/_build/
 examples
+.pre-commit-config.yaml

README.rst

@@ -10,7 +10,7 @@ FHIRBUG
 
 .. image:: https://img.shields.io/badge/python-3.6%20%7C%203.7-blue.svg
     :alt: Python Versions
-    :target:
+    :target: https://github.com/zensoup/fhirbug
 
 Fhirbug intends to be a full-featured `FHIR`_ server for python >= **3.6**. It has been
 designed to be easy to set up and configure and be flexible when it comes to

docs/conf.py

@@ -19,16 +19,17 @@
 
 # -- Project information -----------------------------------------------------
 import sys
-sys.path.append('..')
 
-project = 'fhirbug'
-copyright = '2018, Vangelis Kostalas'
-author = 'Vangelis Kostalas'
+sys.path.append("..")
+
+project = "fhirbug"
+copyright = "2018, Vangelis Kostalas"
+author = "Vangelis Kostalas"
 
 # The short X.Y version
-version = ''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = ''
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
@@ -41,23 +42,23 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -69,7 +70,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
@@ -92,7 +93,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -108,7 +109,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'fhirbugdoc'
+htmlhelp_basename = "fhirbugdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -117,15 +118,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -135,19 +133,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'fhirbug.tex', 'fhirbug Documentation',
-     'Vangelis Kostalas', 'manual'),
+    (master_doc, "fhirbug.tex", "fhirbug Documentation", "Vangelis Kostalas", "manual")
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'fhirbug', 'fhirbug Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "fhirbug", "fhirbug Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -156,9 +150,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'fhirbug', 'fhirbug Documentation',
-     author, 'fhirbug', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "fhirbug",
+        "fhirbug Documentation",
+        author,
+        "fhirbug",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
 
 
@@ -177,7 +177,7 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------

fhirbug/config/__init__.py

@@ -5,34 +5,40 @@
 
 settings = LazySettings()
 
+
 def import_models():
     """
     Dynamic import of the models module based on the backend selected in the configuration
     """
     global settings
     if not settings:
-        raise ConfigurationError('Fhirbug settings have not been initialized. Use fhirbug.config.configure before using fhirbug.')
+        raise ConfigurationError(
+            "Fhirbug settings have not been initialized. Use fhirbug.config.configure before using fhirbug."
+        )
     try:
-        models_path = getattr(settings, 'MODELS_PATH')
+        models_path = getattr(settings, "MODELS_PATH")
     except AttributeError:
-        raise ConfigurationError('settings.MODELS_PATH has not been defined.')
+        raise ConfigurationError("settings.MODELS_PATH has not been defined.")
     return importlib.import_module(models_path)
 
+
 def import_searches():
     """
     Dynamic import of the searches module based on the backend selected in the configuration
     """
     global settings
     if not settings:
-        raise ConfigurationError('Fhirbug settings have not been initialized. Use fhirbug.config.configure before using fhirbug.')
+        raise ConfigurationError(
+            "Fhirbug settings have not been initialized. Use fhirbug.config.configure before using fhirbug."
+        )
     try:
-        db_backend = getattr(settings, 'DB_BACKEND')
+        db_backend = getattr(settings, "DB_BACKEND")
     except AttributeError:
-        raise ConfigurationError('settings.DB_BACKEND has not been defined.')
+        raise ConfigurationError("settings.DB_BACKEND has not been defined.")
 
-    if db_backend.lower() == 'sqlalchemy':
-          return importlib.import_module('fhirbug.db.backends.SQLAlchemy.searches')
-    elif db_backend.lower() == 'djangoorm':
-        return importlib.import_module('fhirbug.db.backends.DjangoORM.searches')
-    elif db_backend.lower() == 'pymodm':
-        return importlib.import_module('fhirbug.db.backends.pymodm.searches')
+    if db_backend.lower() == "sqlalchemy":
+        return importlib.import_module("fhirbug.db.backends.SQLAlchemy.searches")
+    elif db_backend.lower() == "djangoorm":
+        return importlib.import_module("fhirbug.db.backends.DjangoORM.searches")
+    elif db_backend.lower() == "pymodm":
+        return importlib.import_module("fhirbug.db.backends.pymodm.searches")

fhirbug/config/default_settings.py

@@ -9,8 +9,8 @@
 MAX_BUNDLE_SIZE = 100
 
 # Path to the models module
-MODELS_PATH = 'models'
+MODELS_PATH = "models"
 
 # Which DB backend should be used
 # SQLAlchemy | DjangoORM | PyMODM
-DB_BACKEND = 'SQLAlchemy'
+DB_BACKEND = "SQLAlchemy"

fhirbug/config/utils.py

@@ -31,9 +31,13 @@ def configure(self, config=None):
         if config is None:
             settings = self._configure_from_defaults()
             self._wrapped = settings
-            print(('WARNING: Settings have been configured from the default values.'
-                   ' If this is not intended, you are probably not configuring '
-                   'them before importing your mappings'))
+            print(
+                (
+                    "WARNING: Settings have been configured from the default values."
+                    " If this is not intended, you are probably not configuring "
+                    "them before importing your mappings"
+                )
+            )
             return settings
         if isinstance(config, str):
             return self._configure_from_path(config)
@@ -49,7 +53,7 @@ def __getattr__(self, name):
         return getattr(self._wrapped, name)
 
     def __setattr__(self, name, value):
-        if name == '_wrapped':
+        if name == "_wrapped":
             # Assign to __dict__ to avoid infinite __setattr__ loops.
             self.__dict__["_wrapped"] = value
             return

fhirbug/db/__init__.py

@@ -1,3 +1,3 @@
-'''
+"""
 This package wraps all db related modules.
-'''
+"""

fhirbug/db/backends/DjangoORM/models.py

@@ -4,47 +4,47 @@
 from fhirbug.exceptions import DoesNotExistError
 
 
-
 class AbstractBaseModel(models.Model, FhirAbstractBaseMixin):
-  """
+    """
   The base class to provide functionality to
   our models.
   """
-  class Meta:
-      abstract = True
 
-  @classmethod
-  def _get_orm_query(cls):
-    return cls.objects
+    class Meta:
+        abstract = True
+
+    @classmethod
+    def _get_orm_query(cls):
+        return cls.objects
 
-  @classmethod
-  def _get_item_from_pk(cls, pk):
-      try:
-          return cls.objects.get(pk=pk)
-      except cls.DoesNotExist:
-          raise DoesNotExistError(resource_type=cls.__name__, pk=pk)
+    @classmethod
+    def _get_item_from_pk(cls, pk):
+        try:
+            return cls.objects.get(pk=pk)
+        except cls.DoesNotExist:
+            raise DoesNotExistError(resource_type=cls.__name__, pk=pk)
 
 
 class FhirBaseModel(AbstractBaseModel, FhirBaseModelMixin):
-  class Meta:
-    abstract = True
-
-  @classmethod
-  def paginate(cls, *args, **kwargs):
-    return paginate(*args, **kwargs)
-
-  @classmethod
-  def _after_create(cls, instance):
-      try:
-          instance.save()
-      except Exception as e:
-          raise e
-      return instance
-
-  @classmethod
-  def _after_update(cls, instance):
-      try:
-          instance.save()
-      except Exception as e:
-          raise e
-      return instance
+    class Meta:
+        abstract = True
+
+    @classmethod
+    def paginate(cls, *args, **kwargs):
+        return paginate(*args, **kwargs)
+
+    @classmethod
+    def _after_create(cls, instance):
+        try:
+            instance.save()
+        except Exception as e:
+            raise e
+        return instance
+
+    @classmethod
+    def _after_update(cls, instance):
+        try:
+            instance.save()
+        except Exception as e:
+            raise e
+        return instance

fhirbug/db/backends/DjangoORM/pagination.py

@@ -3,13 +3,13 @@
 
 
 def paginate(query, page, page_size):
-    '''
+    """
     Implement pagination for Django ORM.
-    '''
+    """
     if page <= 0:
-        raise AttributeError('page needs to be >= 1')
+        raise AttributeError("page needs to be >= 1")
     if page_size <= 0:
-        raise AttributeError('page_size needs to be >= 1')
+        raise AttributeError("page_size needs to be >= 1")
     items = query.all()
     paginator = Paginator(items, page_size)
     items = paginator.get_page(page)