Add type annotations - PR to dev

lib/galaxy/tool_util/parser/interface.py

@@ -363,7 +363,7 @@ def parse_python_template_version(self) -> Optional[packaging.version.Version]:
         Return minimum python version that the tool template has been developed against.
         """
 
-    def parse_cores_min(self):
+    def parse_cores_min(self) -> Union[float, int, str]:
         """Return minimum number of cores required to run this tool."""
         return 1
 

lib/galaxy/tools/__init__.py

@@ -803,11 +803,11 @@ def __init__(
         config_file,
         tool_source: ToolSource,
         app: "UniverseApplication",
-        guid=None,
+        guid: Optional[str] = None,
         repository_id=None,
         tool_shed_repository=None,
         allow_code_files=True,
-        dynamic=False,
+        dynamic: bool = False,
         tool_dir=None,
     ):
         """Load a tool from the config named by `config_file`"""
@@ -1057,7 +1057,7 @@ def allow_user_access(self, user, attempting_access=True):
             return False
         return True
 
-    def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
+    def parse(self, tool_source: ToolSource, guid: Optional[str] = None, dynamic: bool = False) -> None:
         """
         Read tool configuration from the element `root` and fill in `self`.
         """

lib/galaxy/tools/execute.py

@@ -285,7 +285,7 @@ def __init__(
         self.collection_info = collection_info
         self.completed_jobs = completed_jobs
 
-        self._on_text = None
+        self._on_text: Optional[str] = None
 
         # Populated as we go...
         self.failed_jobs = 0
@@ -322,7 +322,7 @@ def record_error(self, error):
         self.execution_errors.append(error)
 
     @property
-    def on_text(self):
+    def on_text(self) -> Optional[str]:
         collection_info = self.collection_info
         if self._on_text is None and collection_info is not None:
             if not collection_info.uses_ephemeral_collections:

lib/galaxy/tools/execution_helpers.py

@@ -5,6 +5,7 @@
 """
 
 import logging
+from typing import Collection
 
 log = logging.getLogger(__name__)
 
@@ -47,7 +48,7 @@ def filter_output(tool, output, incoming):
     return False
 
 
-def on_text_for_names(input_names):
+def on_text_for_names(input_names: Collection[str]) -> str:
     # input_names may contain duplicates... this is because the first value in
     # multiple input dataset parameters will appear twice once as param_name
     # and once as param_name1.

lib/galaxy/tools/parameters/basic.py

@@ -211,7 +211,7 @@ def get_label(self):
         """Return user friendly name for the parameter"""
         return self.label if self.label else self.name
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         """
         Convert a value from an HTML POST into the parameters preferred value
         format.
@@ -472,7 +472,7 @@ def __init__(self, tool, input_source):
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
         try:
             return int(value)
@@ -545,7 +545,7 @@ def __init__(self, tool, input_source):
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
         try:
             return float(value)
@@ -591,11 +591,11 @@ class BooleanToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
-    >>> print(p.from_json('true'))
+    >>> print(p.from_json('true', trans))
     True
     >>> print(p.to_param_dict_string(True))
     _truevalue
-    >>> print(p.from_json('false'))
+    >>> print(p.from_json('false', trans))
     False
     >>> print(p.to_param_dict_string(False))
     _falsevalue
@@ -619,7 +619,7 @@ def __init__(self, tool, input_source):
         self.optional = input_source.get_bool("optional", False)
         self.checked = boolean_is_checked(input_source)
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self.to_python(value)
 
     def to_python(self, value, app=None):
@@ -670,7 +670,7 @@ class FileToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         # Middleware or proxies may encode files in special ways (TODO: this
         # should be pluggable)
         if isinstance(value, FilesPayload):
@@ -769,7 +769,7 @@ def to_param_dict_string(self, value, other_values=None):
         else:
             return lst[0]
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self.to_python(value, trans.app, validate=True)
 
     def to_json(self, value, app, use_security):
@@ -889,7 +889,7 @@ def __init__(self, tool, input_source):
     def get_initial_value(self, trans, other_values):
         return self._get_value(trans)
 
-    def from_json(self, value=None, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self._get_value(trans)
 
     def _get_value(self, trans):
@@ -1008,7 +1008,7 @@ def get_legal_names(self, trans, other_values):
         """
         return {n: v for n, v, _ in self.get_options(trans, other_values)}
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self._select_from_json(value, trans, other_values=other_values, require_legal_value=True)
 
     def _select_from_json(self, value, trans, other_values=None, require_legal_value=True):
@@ -1288,7 +1288,7 @@ def __init__(self, tool, input_source):
             self.default_value = input_source.get("value", None)
         self.is_dynamic = True
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
         if self.multiple:
             tag_list = []
@@ -1416,7 +1416,7 @@ def to_json(self, value, app, use_security):
             return value.strip()
         return value
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         """
         Label convention prepends column number with a 'c', but tool uses the integer. This
         removes the 'c' when entered into a workflow.
@@ -1704,7 +1704,7 @@ def recurse_options(legal_values, options):
         recurse_options(legal_values, self.get_options(trans=trans, other_values=other_values))
         return legal_values
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
         legal_values = self.get_legal_values(trans, other_values, value)
         if not legal_values and trans.workflow_building_mode:
@@ -2111,7 +2111,7 @@ def __init__(self, tool, input_source, trans=None):
                     )
                 self.conversions.append((name, conv_extension, [conv_type]))
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         session = trans.sa_session
 
         other_values = other_values or {}
@@ -2468,7 +2468,7 @@ def match_multirun_collections(self, trans, history, dataset_collection_matcher)
             if match:
                 yield history_dataset_collection, match.implicit_conversion
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         session = trans.sa_session
 
         other_values = other_values or {}