More typing of test case parsing.

lib/galaxy/tool_util/parser/interface.py

@@ -45,12 +45,13 @@ class AssertionDict(TypedDict):
 
 ToolSourceTestInputs = Any
 ToolSourceTestOutputs = Any
+TestSourceTestOutputColllection = Any
 
 
 class ToolSourceTest(TypedDict):
     inputs: ToolSourceTestInputs
     outputs: ToolSourceTestOutputs
-    output_collections: List[Any]
+    output_collections: List[TestSourceTestOutputColllection]
     stdout: AssertionList
     stderr: AssertionList
     expect_exit_code: Optional[XmlInt]

lib/galaxy/tool_util/verify/_types.py

@@ -0,0 +1,14 @@
+"""Types used by interactor and test case processor."""
+
+from typing import (
+    Any,
+    Dict,
+    List,
+    Tuple,
+)
+
+ExtraFileInfoDictT = Dict[str, Any]
+RequiredFileTuple = Tuple[str, ExtraFileInfoDictT]
+RequiredFilesT = List[RequiredFileTuple]
+RequiredDataTablesT = List[str]
+RequiredLocFileT = List[str]

lib/galaxy/tool_util/verify/interactor.py

@@ -39,6 +39,7 @@
     AssertionList,
     TestCollectionDef,
     TestCollectionOutputDef,
+    TestSourceTestOutputColllection,
 )
 from galaxy.util import requests
 from galaxy.util.bunch import Bunch
@@ -47,6 +48,11 @@
     parse_checksum_hash,
 )
 from . import verify
+from ._types import (
+    RequiredDataTablesT,
+    RequiredFilesT,
+    RequiredLocFileT,
+)
 from .asserts import verify_assertions
 from .wait import wait_on
 
@@ -92,7 +98,7 @@ def __getitem__(self, item):
 class ValidToolTestDict(TypedDict):
     inputs: Any
     outputs: Any
-    output_collections: List[Dict[str, Any]]
+    output_collections: List[TestSourceTestOutputColllection]
     stdout: NotRequired[AssertionList]
     stderr: NotRequired[AssertionList]
     expect_exit_code: NotRequired[Optional[Union[str, int]]]
@@ -102,9 +108,9 @@ class ValidToolTestDict(TypedDict):
     num_outputs: NotRequired[Optional[Union[str, int]]]
     command_line: NotRequired[AssertionList]
     command_version: NotRequired[AssertionList]
-    required_files: NotRequired[List[Any]]
-    required_data_tables: NotRequired[List[Any]]
-    required_loc_files: NotRequired[List[str]]
+    required_files: NotRequired[RequiredFilesT]
+    required_data_tables: NotRequired[RequiredDataTablesT]
+    required_loc_files: NotRequired[RequiredLocFileT]
     error: Literal[False]
     tool_id: str
     tool_version: str
@@ -1661,7 +1667,7 @@ class ToolTestDescriptionDict(TypedDict):
     name: str
     inputs: Any
     outputs: Any
-    output_collections: List[Dict[str, Any]]
+    output_collections: List[TestSourceTestOutputColllection]
     stdout: Optional[AssertionList]
     stderr: Optional[AssertionList]
     expect_exit_code: Optional[int]
@@ -1693,13 +1699,14 @@ class ToolTestDescription:
     stderr: Optional[AssertionList]
     command_line: Optional[AssertionList]
     command_version: Optional[AssertionList]
-    required_files: List[Any]
-    required_data_tables: List[Any]
-    required_loc_files: List[str]
+    required_files: RequiredFilesT
+    required_data_tables: RequiredDataTablesT
+    required_loc_files: RequiredLocFileT
     expect_exit_code: Optional[int]
     expect_failure: bool
     expect_test_failure: bool
     exception: Optional[str]
+    output_collections: List[TestCollectionOutputDef]
 
     def __init__(self, processed_test_dict: ToolTestDict):
         assert (
@@ -1708,14 +1715,31 @@ def __init__(self, processed_test_dict: ToolTestDict):
         test_index = processed_test_dict["test_index"]
         name = cast(str, processed_test_dict.get("name", f"Test-{test_index + 1}"))
         error_in_test_definition = processed_test_dict["error"]
+        num_outputs: Optional[int] = None
         if not error_in_test_definition:
             processed_test_dict = cast(ValidToolTestDict, processed_test_dict)
             maxseconds = int(processed_test_dict.get("maxseconds") or DEFAULT_TOOL_TEST_WAIT or 86400)
             output_collections = processed_test_dict.get("output_collections", [])
+            if "num_outputs" in processed_test_dict and processed_test_dict["num_outputs"]:
+                num_outputs = int(processed_test_dict["num_outputs"])
+            self.required_files = processed_test_dict.get("required_files", [])
+            self.required_data_tables = processed_test_dict.get("required_data_tables", [])
+            self.required_loc_files = processed_test_dict.get("required_loc_files", [])
+            self.command_line = processed_test_dict.get("command_line", None)
+            self.command_version = processed_test_dict.get("command_version", None)
+            self.stdout = processed_test_dict.get("stdout", None)
+            self.stderr = processed_test_dict.get("stderr", None)
         else:
             processed_test_dict = cast(InvalidToolTestDict, processed_test_dict)
             maxseconds = DEFAULT_TOOL_TEST_WAIT
             output_collections = []
+            self.required_files = []
+            self.required_data_tables = []
+            self.required_loc_files = []
+            self.command_line = None
+            self.command_version = None
+            self.stdout = None
+            self.stderr = None
 
         self.test_index = test_index
         assert (
@@ -1725,9 +1749,6 @@ def __init__(self, processed_test_dict: ToolTestDict):
         self.tool_version = processed_test_dict.get("tool_version")
         self.name = name
         self.maxseconds = maxseconds
-        self.required_files = cast(List[Any], processed_test_dict.get("required_files", []))
-        self.required_data_tables = cast(List[Any], processed_test_dict.get("required_data_tables", []))
-        self.required_loc_files = cast(List[str], processed_test_dict.get("required_loc_files", []))
 
         inputs = processed_test_dict.get("inputs", {})
         loaded_inputs = {}
@@ -1739,16 +1760,12 @@ def __init__(self, processed_test_dict: ToolTestDict):
 
         self.inputs = loaded_inputs
         self.outputs = processed_test_dict.get("outputs", [])
-        self.num_outputs = cast(Optional[int], processed_test_dict.get("num_outputs", None))
+        self.num_outputs = num_outputs
 
         self.error = processed_test_dict.get("error", False)
         self.exception = cast(Optional[str], processed_test_dict.get("exception", None))
 
         self.output_collections = [TestCollectionOutputDef.from_dict(d) for d in output_collections]
-        self.command_line = cast(Optional[AssertionList], processed_test_dict.get("command_line", None))
-        self.command_version = cast(Optional[AssertionList], processed_test_dict.get("command_version", None))
-        self.stdout = cast(Optional[AssertionList], processed_test_dict.get("stdout", None))
-        self.stderr = cast(Optional[AssertionList], processed_test_dict.get("stderr", None))
         self.expect_exit_code = cast(Optional[int], processed_test_dict.get("expect_exit_code", None))
         self.expect_failure = cast(bool, processed_test_dict.get("expect_failure", False))
         self.expect_test_failure = cast(bool, processed_test_dict.get("expect_test_failure", False))

lib/galaxy/tool_util/verify/parse.py

@@ -2,6 +2,7 @@
 import os
 from typing import (
     Any,
+    Dict,
     Iterable,
     List,
     Optional,
@@ -31,12 +32,16 @@
     string_as_bool_or_none,
     unicodify,
 )
+from ._types import (
+    ExtraFileInfoDictT,
+    RequiredDataTablesT,
+    RequiredFilesT,
+    RequiredLocFileT,
+)
 
 log = logging.getLogger(__name__)
 
-RequiredFilesT = List[Tuple[str, dict]]
-RequiredDataTablesT = List[str]
-RequiredLocFileT = List[str]
+AnyParamContext = Union["ParamContext", "RootParamContext"]
 
 
 def parse_tool_test_descriptions(
@@ -127,7 +132,7 @@ def _process_raw_inputs(
     required_files: RequiredFilesT,
     required_data_tables: RequiredDataTablesT,
     required_loc_files: RequiredLocFileT,
-    parent_context: Optional[Union["ParamContext", "RootParamContext"]] = None,
+    parent_context: Optional[AnyParamContext] = None,
 ):
     """
     Recursively expand flat list of inputs into "tree" form of flat list
@@ -192,7 +197,7 @@ def _process_raw_inputs(
         elif input_type == "repeat":
             repeat_index = 0
             while True:
-                context = ParamContext(name=name, index=repeat_index, parent_context=parent_context)
+                context = ParamContext(name=name, parent_context=parent_context, index=repeat_index)
                 updated = False
                 page_source = input_source.parse_nested_inputs_source()
                 for r_value in page_source.parse_input_sources():
@@ -268,20 +273,20 @@ def input_sources(tool_source: ToolSource) -> List[InputSource]:
 
 
 class ParamContext:
-    def __init__(self, name, index=None, parent_context=None):
+    def __init__(self, name: str, parent_context: AnyParamContext, index: Optional[int] = None):
         self.parent_context = parent_context
         self.name = name
         self.index = None if index is None else int(index)
 
-    def for_state(self):
+    def for_state(self) -> str:
         name = self.name if self.index is None else "%s_%d" % (self.name, self.index)
         parent_for_state = self.parent_context.for_state()
         if parent_for_state:
             return f"{parent_for_state}|{name}"
         else:
             return name
 
-    def __str__(self):
+    def __str__(self) -> str:
         return f"Context[for_state={self.for_state()}]"
 
     def param_names(self):
@@ -295,14 +300,14 @@ def param_names(self):
         else:
             yield self.name
 
-    def extract_value(self, raw_inputs):
+    def extract_value(self, raw_inputs: ToolSourceTestInputs):
         for param_name in self.param_names():
             value = self.__raw_param_found(param_name, raw_inputs)
             if value:
                 return value
         return None
 
-    def __raw_param_found(self, param_name, raw_inputs):
+    def __raw_param_found(self, param_name: str, raw_inputs: ToolSourceTestInputs):
         index = None
         for i, raw_input_dict in enumerate(raw_inputs):
             if raw_input_dict["name"] == param_name:
@@ -442,20 +447,26 @@ def matches_declared_value(case_value):
     return None
 
 
-def _add_uploaded_dataset(name: str, value: Any, extra, input_parameter: InputSource, required_files: RequiredFilesT):
+def _add_uploaded_dataset(
+    name: str,
+    value: Optional[str],
+    extra: ExtraFileInfoDictT,
+    input_parameter: InputSource,
+    required_files: RequiredFilesT,
+) -> Optional[str]:
     if value is None:
         assert input_parameter.parse_optional(), f"{name} is not optional. You must provide a valid filename."
         return value
     return require_file(name, value, extra, required_files)
 
 
-def require_file(name, value, extra, required_files):
+def require_file(name: str, value: str, extra: ExtraFileInfoDictT, required_files: RequiredFilesT) -> str:
     if (value, extra) not in required_files:
         required_files.append((value, extra))  # these files will be uploaded
-    name_change = [att for att in extra.get("edit_attributes", []) if att.get("type") == "name"]
-    if name_change:
-        name_change = name_change[-1].get("value")  # only the last name change really matters
-        value = name_change  # change value for select to renamed uploaded file for e.g. composite dataset
+    name_changes = [att for att in extra.get("edit_attributes", []) if att.get("type") == "name"]
+    if name_changes:
+        name_change = name_changes[-1].get("value")  # only the last name change really matters
+        value = str(name_change)  # change value for select to renamed uploaded file for e.g. composite dataset
     else:
         for end in [".zip", ".gz"]:
             if value.endswith(end):