chore: add TES data models

docs/source/conf.py

@@ -12,43 +12,43 @@
 
 import tomli
 
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 def _get_project_meta():
-	_pyproject_path = Path(__file__).parents[2] / 'pyproject.toml'
-	with open(_pyproject_path, mode='rb') as pyproject:
-		return tomli.load(pyproject)['tool']['poetry']
+  _pyproject_path = Path(__file__).parents[2] / "pyproject.toml"
+  with open(_pyproject_path, mode="rb") as pyproject:
+    return tomli.load(pyproject)["tool"]["poetry"]
 
 
 pkg_meta = _get_project_meta()
 current_year = datetime.datetime.now().year
-project = str(pkg_meta['name'])
+project = str(pkg_meta["name"])
 project_copyright = f"{current_year}, {str(pkg_meta['authors'][0])}"
-author = str(pkg_meta['authors'][0])
+author = str(pkg_meta["authors"][0])
 
-version = str(pkg_meta['version'])
+version = str(pkg_meta["version"])
 release = version
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-	'sphinx.ext.autodoc',
-	'sphinx.ext.doctest',
-	'sphinx.ext.todo',
-	'sphinx.ext.coverage',
-	'sphinx.ext.viewcode',
-	'sphinx.ext.autosummary',
-	# Used to write beautiful docstrings:
-	'sphinx.ext.napoleon',
-	# Used to include .md files:
-	'm2r2',
-	# Used to insert typehints into the final docs:
-	'sphinx_autodoc_typehints',
-	# Used to embed values from the source code into the docs:
-	'added_value',
+  "sphinx.ext.autodoc",
+  "sphinx.ext.doctest",
+  "sphinx.ext.todo",
+  "sphinx.ext.coverage",
+  "sphinx.ext.viewcode",
+  "sphinx.ext.autosummary",
+  # Used to write beautiful docstrings:
+  "sphinx.ext.napoleon",
+  # Used to include .md files:
+  "m2r2",
+  # Used to insert typehints into the final docs:
+  "sphinx_autodoc_typehints",
+  # Used to embed values from the source code into the docs:
+  "added_value",
 ]
 
 # Set `typing.TYPE_CHECKING` to `True`:
@@ -57,39 +57,39 @@ def _get_project_meta():
 always_document_param_types = False
 
 # 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", ".md"]
 
 # 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.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # 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"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'furo'
+html_theme = "furo"
 
 # 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"]
 
 # -- Extension configuration -------------------------------------------------
 napoleon_numpy_docstring = False

pyproject.toml

@@ -70,9 +70,9 @@ types-urllib3 = "^1.26.25.14"
 types-werkzeug = "^1.0.9"
 
 [tool.poetry.scripts]
-api = 'tesk.app:main'
-filer = 'tesk.services.filer:main'
-taskmaster = 'tesk.services.taskmaster:main'
+api = "tesk.app:main"
+filer = "tesk.services.filer:main"
+taskmaster = "tesk.services.taskmaster:main"
 
 [tool.pytest_env]
 FTP_FIXTURE_SCOPE = "function"
@@ -83,17 +83,20 @@ FTP_USER = "user"
 TESK_FTP_PASSWORD = "pass"
 TESK_FTP_USERNAME = "user"
 
+[tool.ruff]
+exclude = [
+  "tesk/services/*",
+  "tests/test_unit/test_services/*",
+]
+indent-width = 2
+
 [tool.ruff.format]
 docstring-code-format = true
-indent-style = "tab"
-quote-style = "single"
+indent-style = "space"
+line-ending = "lf"
+quote-style = "double"
 
 [tool.ruff.lint]
-ignore = [
-  "D203", # conflicts with D202 as formatter removes black line before class docstring
-  "D206", # conflicts with E101, `format.indent-style="tab"`
-  "D213", # conflicts with D212, would have been ignored regardless
-]
 select = [
   "B", # flake8-bugbear
   "D", # pydocstyle
@@ -105,12 +108,8 @@ select = [
   "UP", # pyupgrade
 ]
 
-[tool.ruff.lint.per-file-ignores] # ignore all pydocstyle errors in test and services modules
-"tesk/services/**/*.py" = ["D"]
-"tests/test_unit/test_services/**/*.py" = ["D"]
-
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
 [tool.typos.default.extend-words]
-mke = 'mke'
+mke = "mke"

tesk/api/ga4gh/tes/controllers.py

@@ -12,60 +12,60 @@
 # POST /tasks/{id}:cancel
 @log_traffic
 def CancelTask(id, *args, **kwargs) -> dict:  # type: ignore
-	"""Cancel unfinished task.
+  """Cancel unfinished task.
 
-	Args:
-			id: Task identifier.
-			*args: Variable length argument list.
-			**kwargs: Arbitrary keyword arguments.
-	"""
-	pass
+  Args:
+                  id: Task identifier.
+                  *args: Variable length argument list.
+                  **kwargs: Arbitrary keyword arguments.
+  """
+  pass
 
 
 # POST /tasks
 @log_traffic
 def CreateTask(*args, **kwargs) -> dict:  # type: ignore
-	"""Create task.
+  """Create task.
 
-	Args:
-			*args: Variable length argument list.
-			**kwargs: Arbitrary keyword arguments.
-	"""
-	pass
+  Args:
+                  *args: Variable length argument list.
+                  **kwargs: Arbitrary keyword arguments.
+  """
+  pass
 
 
 # GET /tasks/service-info
 @log_traffic
 def GetServiceInfo(*args, **kwargs) -> dict:  # type: ignore
-	"""Get service info.
+  """Get service info.
 
-	Args:
-			*args: Variable length argument list.
-			**kwargs: Arbitrary keyword arguments.
-	"""
-	pass
+  Args:
+                  *args: Variable length argument list.
+                  **kwargs: Arbitrary keyword arguments.
+  """
+  pass
 
 
 # GET /tasks
 @log_traffic
 def ListTasks(*args, **kwargs) -> dict:  # type: ignore
-	"""List all available tasks.
+  """List all available tasks.
 
-	Args:
-			*args: Variable length argument list.
-			**kwargs: Arbitrary keyword arguments.
-	"""
-	pass
+  Args:
+                  *args: Variable length argument list.
+                  **kwargs: Arbitrary keyword arguments.
+  """
+  pass
 
 
 # GET /tasks
 @log_traffic
 def GetTask(*args, **kwargs) -> dict:  # type: ignore
-	"""Get info for individual task.
-
-	Args:
-			id: Task identifier.
-			*args: Variable length argument list.
-			**kwargs: Arbitrary keyword arguments.
-	"""
-	pass
+  """Get info for individual task.
+
+  Args:
+                  id: Task identifier.
+                  *args: Variable length argument list.
+                  **kwargs: Arbitrary keyword arguments.
+  """
+  pass