✨ Add mypy support (redcap-tools#258)

angus-lherrou · Mar 28, 2023 · 23605e0 · 23605e0
1 parent c003da8
commit 23605e0
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Showing 25 changed files with 874 additions and 1,338 deletions.
diff --git a/mypy.ini b/mypy.ini
@@ -0,0 +1,8 @@
+[mypy]
+warn_unused_configs = True
+
+[mypy-tests/unit/callback_utils.*]
+ignore_errors = True
+
+[mypy-semantic_version]
+ignore_missing_imports = True
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -32,10 +32,14 @@ requests = "^2.20"
 semantic-version = "^2.8.5"
 pandas = {version = "^1.3.4", optional = true}
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.extras]
+data_science = ["pandas"]
+
+[tool.poetry.group.dev.dependencies]
 pytest = "^6.2.5"
 pytest-cov = "^3.0.0"
-pytest-black = {version = "^0.3.12", allow-prereleases = true}
+pytest-black = "^0.3.12"
+pytest-mypy = "^0.10.3"
 pytest-pylint = "^0.18.0"
 responses = "^0.14.0"
 pytest-mock = "^3.6.1"
@@ -47,9 +51,6 @@ mkdocstrings = "^0.17.0"
 pytest-doctestplus = "^0.11.2"
 Jinja2 = "~3.0.0"
 
-[tool.poetry.extras]
-data_science = ["pandas"]
-
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
diff --git a/pytest.ini b/pytest.ini
@@ -1,6 +1,6 @@
 [pytest]
 doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS FAIL_FAST REPORT_NDIFF
-addopts = -rsxX -l --tb=short --strict --pylint --black --cov=redcap --cov-report=xml
+addopts = -rsxX -l --tb=short --strict --pylint --black --cov=redcap --cov-report=xml --mypy
 markers =
     integration: test connects to redcapdemo.vanderbilt.edu server
 # Keep current format for future version of pytest

diff --git a/redcap/methods/base.py b/redcap/methods/base.py
@@ -9,6 +9,7 @@
     List,
     Literal,
     Optional,
+    cast,
     overload,
     Tuple,
     TYPE_CHECKING,
@@ -23,7 +24,6 @@
     RedcapError,
     FileUpload,
     Json,
-    EmptyJson,
 )
 
 if TYPE_CHECKING:
@@ -56,11 +56,11 @@ def __init__(
         self._request_kwargs = request_kwargs
 
         # attributes which require API calls
-        self._metadata = None
-        self._forms = None
-        self._field_names = None
-        self._def_field = None
-        self._is_longitudinal = None
+        self._metadata: Optional[Json] = None
+        self._forms: Optional[List[str]] = None
+        self._field_names: Optional[List[str]] = None
+        self._def_field: Optional[str] = None
+        self._is_longitudinal: Optional[bool] = None
 
     @property
     def url(self) -> str:
@@ -73,11 +73,11 @@ def token(self) -> str:
         return self._token
 
     @property
-    def metadata(self) -> List[Dict[str, Any]]:
+    def metadata(self) -> Json:
         """Project metadata in JSON format"""
         if self._metadata is None:
             payload = self._initialize_payload("metadata", format_type="json")
-            self._metadata = self._call_api(payload, return_type="json")
+            self._metadata = cast(Json, self._call_api(payload, return_type="json"))
 
         return self._metadata
 
@@ -236,6 +236,8 @@ def _filter_metadata(self, key: str, field_name: str) -> str:
 
     def _filter_metadata(self, key: str, field_name: Optional[str] = None):
         """Safely filter project metadata based off requested column and field_name"""
+        res: Union[list, str]
+
         if field_name:
             try:
                 res = str(
@@ -312,6 +314,8 @@ def _initialize_import_payload(
             content=content, return_format_type=return_format_type
         )
         if import_format == "df":
+            to_import = cast("pd.DataFrame", to_import)
+
             buf = StringIO()
             has_named_index = to_import.index.name is not None
             to_import.to_csv(buf, index=has_named_index)
@@ -322,83 +326,30 @@ def _initialize_import_payload(
             payload["data"] = json.dumps(to_import, separators=(",", ":"))
         else:
             # don't do anything to csv/xml
+            to_import = cast("str", to_import)
             payload["data"] = to_import
 
         payload["format"] = import_format
         return payload
 
-    @overload
-    def _return_data(
-        self,
-        response: Json,
-        content: Literal[
-            "exportFieldNames",
-            "formEventMapping",
-            "metadata",
-            "participantList",
-            "project",
-            "record",
-            "report",
-            "user",
-        ],
-        format_type: Literal["json"],
-        df_kwargs: None,
-        record_type: Literal["flat", "eav"] = "flat",
-    ) -> Json:
-        ...
-
-    @overload
-    def _return_data(
-        self,
-        response: str,
-        content: Literal[
-            "exportFieldNames",
-            "formEventMapping",
-            "metadata",
-            "participantList",
-            "project",
-            "record",
-            "report",
-            "user",
-        ],
-        format_type: Literal["csv", "xml"],
-        df_kwargs: None,
-        record_type: Literal["flat", "eav"] = "flat",
-    ) -> str:
-        ...
-
-    @overload
-    def _return_data(
-        self,
-        response: str,
-        content: Literal[
-            "exportFieldNames",
-            "formEventMapping",
-            "metadata",
-            "participantList",
-            "project",
-            "record",
-            "report",
-            "user",
-        ],
-        format_type: Literal["df"],
-        df_kwargs: Optional[Dict[str, Any]],
-        record_type: Literal["flat", "eav"] = "flat",
-    ) -> "pd.DataFrame":
-        ...
-
     def _return_data(
         self,
         response: Union[Json, str],
         content: Literal[
+            "dag",
             "exportFieldNames",
             "formEventMapping",
+            "log",
             "metadata",
             "participantList",
             "project",
             "record",
             "report",
             "user",
+            "userDagMapping",
+            "userRole",
+            "userRoleMapping",
+            "repeatingFormsEvents",
         ],
         format_type: Literal["json", "csv", "xml", "df"],
         df_kwargs: Optional[Dict[str, Any]] = None,
@@ -445,83 +396,24 @@ def _return_data(
             else:
                 df_kwargs = {}
 
+        response = cast(str, response)
+
         buf = StringIO(response)
         dataframe = self._read_csv(buf, **df_kwargs)
         buf.close()
 
         return dataframe
 
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["file_map"],
-        file: None,
-    ) -> FileMap:
-        ...
-
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["json"],
-        file: None = None,
-    ) -> Json:
-        ...
-
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["empty_json"],
-        file: FileUpload,
-    ) -> EmptyJson:
-        ...
-
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["count_dict"],
-        file: None = None,
-    ) -> Dict[str, int]:
-        ...
-
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["ids_list"],
-        file: None = None,
-    ) -> List[str]:
-        ...
-
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["int"],
-        file: None = None,
-    ) -> int:
-        ...
-
-    @overload
-    def _call_api(
-        self,
-        payload: Dict[str, Any],
-        return_type: Literal["str"],
-        file: None = None,
-    ) -> str:
-        ...
-
     def _call_api(
         self,
         payload: Dict[str, Any],
         return_type: Literal[
             "file_map", "json", "empty_json", "count_dict", "ids_list", "str", "int"
         ],
         file: Optional[FileUpload] = None,
-    ) -> Union[FileMap, Json, Dict[str, int], List[dict], List[str], int, str]:
+    ) -> Union[
+        FileMap, Json, Dict[str, int], List[dict], List[str], int, str, Literal["1"]
+    ]:
         """Make a POST Requst to the REDCap API
 
         Args: