Merge pull request galaxyproject#18560 from jmchilton/test_parsing_work

Improvements to Tool Test Parsing

lib/galaxy/app_unittest_utils/tools_support.py

@@ -106,9 +106,13 @@ def setup_app(self):
         self.app.config.tool_secret = "testsecret"
         self.app.config.track_jobs_in_database = False
 
-    def __setup_tool(self):
+    @property
+    def tool_source(self):
         tool_source = get_tool_source(self.tool_file)
-        self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)
+        return tool_source
+
+    def __setup_tool(self):
+        self.tool = create_tool_from_source(self.app, self.tool_source, config_file=self.tool_file)
         if getattr(self, "tool_action", None):
             self.tool.tool_action = self.tool_action
         return self.tool

lib/galaxy/tool_util/parameters/factory.py

@@ -130,7 +130,11 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
             # Function... example in devteam cummeRbund.
             optional = input_source.parse_optional()
             dynamic_options = input_source.get("dynamic_options", None)
-            dynamic_options_elem = input_source.parse_dynamic_options_elem()
+            dynamic_options_config = input_source.parse_dynamic_options()
+            if dynamic_options_config:
+                dynamic_options_elem = dynamic_options.elem()
+            else:
+                dynamic_options_elem = None
             multiple = input_source.get_bool("multiple", False)
             is_static = dynamic_options is None and dynamic_options_elem is None
             options: Optional[List[LabelValue]] = None

lib/galaxy/tool_util/parser/cwl.py

@@ -113,7 +113,7 @@ def parse_description(self):
     def parse_interactivetool(self):
         return []
 
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> PagesSource:
         page_source = CwlPageSource(self.tool_proxy)
         return PagesSource([page_source])
 

lib/galaxy/tool_util/parser/interface.py

@@ -20,6 +20,7 @@
 from pydantic import BaseModel
 from typing_extensions import TypedDict
 
+from galaxy.util import Element
 from galaxy.util.path import safe_walk
 from .util import _parse_name
 
@@ -42,11 +43,15 @@ class AssertionDict(TypedDict):
 AssertionList = Optional[List[AssertionDict]]
 XmlInt = Union[str, int]
 
+ToolSourceTestInputs = Any
+ToolSourceTestOutputs = Any
+TestSourceTestOutputColllection = Any
+
 
 class ToolSourceTest(TypedDict):
-    inputs: Any
-    outputs: Any
-    output_collections: List[Any]
+    inputs: ToolSourceTestInputs
+    outputs: ToolSourceTestOutputs
+    output_collections: List[TestSourceTestOutputColllection]
     stdout: AssertionList
     stderr: AssertionList
     expect_exit_code: Optional[XmlInt]
@@ -245,7 +250,7 @@ def parse_requirements_and_containers(
         """Return triple of ToolRequirement, ContainerDescription and ResourceRequirement lists."""
 
     @abstractmethod
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> "PagesSource":
         """Return a PagesSource representing inputs by page for tool."""
 
     def parse_provided_metadata_style(self):
@@ -359,6 +364,23 @@ def inputs_defined(self):
         return True
 
 
+class DynamicOptions(metaclass=ABCMeta):
+
+    def elem(self) -> Element:
+        # For things in transition that still depend on XML - provide a way
+        # to grab it and just throw an error if feature is attempted to be
+        # used with other tool sources.
+        raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
+
+    @abstractmethod
+    def get_data_table_name(self) -> Optional[str]:
+        """If dynamic options are loaded from a data table, return the name."""
+
+    @abstractmethod
+    def get_index_file_name(self) -> Optional[str]:
+        """If dynamic options are loaded from an index file, return the name."""
+
+
 class InputSource(metaclass=ABCMeta):
     default_optional = False
 
@@ -418,8 +440,12 @@ def parse_optional(self, default=None):
             default = self.default_optional
         return self.get_bool("optional", default)
 
-    def parse_dynamic_options_elem(self):
-        """Return an XML element describing dynamic options."""
+    def parse_dynamic_options(self) -> Optional[DynamicOptions]:
+        """Return an optional element describing dynamic options.
+
+        These options are still very XML based but as they are adapted to the infrastructure, the return
+        type here will evolve.
+        """
         return None
 
     def parse_static_options(self) -> List[Tuple[str, str, bool]]:

lib/galaxy/tool_util/parser/util.py

@@ -1,4 +1,18 @@
 from collections import OrderedDict
+from typing import (
+    Optional,
+    Tuple,
+    TYPE_CHECKING,
+    Union,
+)
+
+from packaging.version import Version
+
+if TYPE_CHECKING:
+    from .interface import (
+        InputSource,
+        ToolSource,
+    )
 
 DEFAULT_DELTA = 10000
 DEFAULT_DELTA_FRAC = None
@@ -23,3 +37,53 @@ def _parse_name(name, argument):
             raise ValueError("parameter must specify a 'name' or 'argument'.")
         name = argument.lstrip("-").replace("-", "_")
     return name
+
+
+def parse_profile_version(tool_source: "ToolSource") -> float:
+    return float(tool_source.parse_profile())
+
+
+def parse_tool_version_with_defaults(
+    id: Optional[str], tool_source: "ToolSource", profile: Optional[Version] = None
+) -> str:
+    if profile is None:
+        profile = Version(tool_source.parse_profile())
+
+    version = tool_source.parse_version()
+    if not version:
+        if profile < Version("16.04"):
+            # For backward compatibility, some tools may not have versions yet.
+            version = "1.0.0"
+        else:
+            raise Exception(f"Missing tool 'version' for tool with id '{id}' at '{tool_source}'")
+    return version
+
+
+def boolean_is_checked(input_source: "InputSource"):
+    nullable = input_source.get_bool("optional", False)
+    return input_source.get_bool("checked", None if nullable else False)
+
+
+def boolean_true_and_false_values(input_source, profile: Optional[Union[float, str]] = None) -> Tuple[str, str]:
+    truevalue = input_source.get("truevalue", "true")
+    falsevalue = input_source.get("falsevalue", "false")
+    if profile and Version(str(profile)) >= Version("23.1"):
+        if truevalue == falsevalue:
+            raise ParameterParseException("Cannot set true and false to the same value")
+        if truevalue.lower() == "false":
+            raise ParameterParseException(
+                f"Cannot set truevalue to [{truevalue}], Galaxy state may encounter issues distinguishing booleans and strings in this case."
+            )
+        if falsevalue.lower() == "true":
+            raise ParameterParseException(
+                f"Cannot set falsevalue to [{falsevalue}], Galaxy state may encounter issues distinguishing booleans and strings in this case."
+            )
+    return (truevalue, falsevalue)
+
+
+class ParameterParseException(Exception):
+    message: str
+
+    def __init__(self, message):
+        super().__init__(message)
+        self.message = message

lib/galaxy/tool_util/parser/xml.py

@@ -34,6 +34,7 @@
 from .interface import (
     AssertionList,
     Citation,
+    DynamicOptions,
     InputSource,
     PageSource,
     PagesSource,
@@ -391,7 +392,7 @@ def parse_include_exclude_list(tag_name):
     def parse_requirements_and_containers(self):
         return requirements.parse_requirements_from_xml(self.root, parse_resources=True)
 
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> "XmlPagesSource":
         return XmlPagesSource(self.root)
 
     def parse_provided_metadata_style(self):
@@ -1217,6 +1218,22 @@ def parse_input_sources(self):
         return list(map(XmlInputSource, self.parent_elem))
 
 
+class XmlDynamicOptions(DynamicOptions):
+
+    def __init__(self, options_elem: Element):
+        self._options_elem = options_elem
+
+    def elem(self) -> Element:
+        return self._options_elem
+
+    def get_data_table_name(self) -> Optional[str]:
+        """If dynamic options are loaded from a data table, return the name."""
+        return self._options_elem.get("from_data_table")
+
+    def get_index_file_name(self) -> Optional[str]:
+        return self._options_elem.get("from_file")
+
+
 class XmlInputSource(InputSource):
     def __init__(self, input_elem):
         self.input_elem = input_elem
@@ -1246,12 +1263,10 @@ def parse_sanitizer_elem(self):
     def parse_validator_elems(self):
         return self.input_elem.findall("validator")
 
-    def parse_dynamic_options_elem(self):
-        """Return a galaxy.tools.parameters.dynamic_options.DynamicOptions
-        if appropriate.
-        """
+    def parse_dynamic_options(self) -> Optional[XmlDynamicOptions]:
+        """Return a XmlDynamicOptions to describe dynamic options if options elem is available."""
         options_elem = self.input_elem.find("options")
-        return options_elem
+        return XmlDynamicOptions(options_elem) if options_elem is not None else None
 
     def parse_static_options(self) -> List[Tuple[str, str, bool]]:
         """

lib/galaxy/tool_util/parser/yaml.py

@@ -110,7 +110,7 @@ def parse_requirements_and_containers(self):
             resource_requirements=[r for r in mixed_requirements if r.get("type") == "resource"],
         )
 
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> PagesSource:
         # All YAML tools have only one page (feature is deprecated)
         page_source = YamlPageSource(self.root_dict.get("inputs", {}))
         return PagesSource([page_source])

lib/galaxy/tool_util/unittest_utils/__init__.py

@@ -1,3 +1,4 @@
+import os
 from typing import (
     Callable,
     Dict,
@@ -6,6 +7,8 @@
 )
 from unittest.mock import Mock
 
+from galaxy.util import galaxy_directory
+
 
 def mock_trans(has_user=True, is_admin=False):
     """A mock ``trans`` object for exposing user info to toolbox filter unit tests."""
@@ -26,3 +29,7 @@ def get_content(filename: Optional[str]) -> bytes:
             return content
 
     return get_content
+
+
+def functional_test_tool_path(test_path: str) -> str:
+    return os.path.join(galaxy_directory(), "test/functional/tools", test_path)

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]