Merge pull request #22566 from jmchilton/wf_test_job_schema

Tighten the workflow test schema

Author: mvdbeek

client/src/api/schema/schema.ts

@@ -305,8 +305,7 @@ def replacement_directory(value: Dict[str, Any]) -> Dict[str, Any]:
         file_path = value.get("location", None) or value.get("path", None)
         if file_path is None:
             return value
-        if not os.path.isabs(file_path):
-            file_path = os.path.join(test_data_directory, file_path)
+        file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
 
         file_type = value.get("filetype", None) or value.get("format", None) or "directory"
 

lib/galaxy/tool_util/cwl/util.py

@@ -51,7 +51,7 @@ def assert_has_n_columns(
 
     For instance, ``<has_n_columns n="3"/>``. The assertion tests only the first line.
     Number of columns can optionally also be specified with ``delta``. Alternatively the
-    range of expected occurences can be specified by ``min`` and/or ``max``.
+    range of expected occurrences can be specified by ``min`` and/or ``max``.
 
     Optionally a column separator (``sep``, default is ``\t``) `and comment character(s)
     can be specified (``comment``, default is empty string). The first non-comment

lib/galaxy/tool_util/verify/asserts/tabular.py

@@ -46,8 +46,8 @@ def assert_has_text(
         lambda o, t: o.find(t) >= 0,
         lambda o, t: len(re.findall(re.escape(t), o)),
         "{expected} text '{text}' in output ('{output}')",
-        "{expected} {n}+-{delta} occurences of '{text}' in output ('{output}')",
-        "{expected} that the number of occurences of '{text}' in output is in [{min}:{max}] ('{output}')",
+        "{expected} {n}+-{delta} occurrences of '{text}' in output ('{output}')",
+        "{expected} that the number of occurrences of '{text}' in output is in [{min}:{max}] ('{output}')",
     )
 
 
@@ -123,8 +123,8 @@ def assert_has_text_matching(
 ) -> None:
     """Asserts the specified output contains text matching the
     regular expression specified by the argument expression.
-    If n is given the assertion checks for exacly n (nonoverlapping)
-    occurences.
+    If n is given the assertion checks for exactly n (nonoverlapping)
+    occurrences.
     """
     _assert_presence_number(
         output,
@@ -153,7 +153,7 @@ def assert_has_line_matching(
 ) -> None:
     """Asserts the specified output contains a line matching the
     regular expression specified by the argument expression. If n is given
-    the assertion checks for exactly n occurences."""
+    the assertion checks for exactly n occurrences."""
     _assert_presence_number(
         output,
         expression,

lib/galaxy/tool_util/verify/asserts/text.py

@@ -96,7 +96,7 @@ def assert_has_n_elements_with_path(
     ```
 
     Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
-    can be used to specify the range of the expected number of occurences.
+    can be used to specify the range of the expected number of occurrences.
     With ``negate`` the result of the assertion can be inverted.
     """
     assert_xml_element(output, path, n=n, delta=delta, min=min, max=max, negate=negate)
@@ -222,7 +222,7 @@ def assert_xml_element(
 ) -> None:
     """Assert if the XML file contains element(s) or tag(s) with the specified
     [XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``
-    or ``min`` and ``max`` are given also the number of occurences is checked.
+    or ``min`` and ``max`` are given also the number of occurrences is checked.
 
     ```xml
     <assert_contents>
@@ -232,7 +232,7 @@ def assert_xml_element(
     </assert_contents>
     ```
 
-    With ``negate="true"`` the outcome of the assertions wrt the precence and number
+    With ``negate="true"`` the outcome of the assertions wrt the presence and number
     of ``path`` can be negated. If there are any sub assertions then check them against
 
     - the content of the attribute ``attribute``
@@ -247,7 +247,7 @@ def assert_xml_element(
     ```
 
     Sub-assertions are not subject to the ``negate`` attribute of ``xml_element``.
-    If ``all`` is ``true`` then the sub assertions are checked for all occurences.
+    If ``all`` is ``true`` then the sub assertions are checked for all occurrences.
 
     Note that all other XML assertions can be expressed by this assertion (Galaxy
     also implements the other assertions by calling this one).
@@ -269,7 +269,7 @@ def assert_xml_element(
         lambda x, p: len(x.findall(p)),
         "{expected} path '{text}' in xml",
         "{expected} {n}+-{delta} occurrences of path '{text}' in xml",
-        "{expected} that the number of occurences of path '{text}' in xml is in [{min}:{max}]",
+        "{expected} that the number of occurrences of path '{text}' in xml is in [{min}:{max}]",
     )
 
     # check sub-assertions

lib/galaxy/tool_util/verify/asserts/xml.py

@@ -27,7 +27,7 @@
 from galaxy.tool_util.verify.asserts._types import AssertionParameter as AssertionParameterAnnotation
 from galaxy.util.commands import shell
 
-models_path = os.path.join(os.path.dirname(__file__), "assertion_models.py")
+models_path = os.path.join(os.path.dirname(__file__), "..", "..", "tool_util_models", "assertions.py")
 galaxy_xsd_path = os.path.join(os.path.dirname(__file__), "..", "xsd", "galaxy.xsd")
 
 Children = Literal["allowed", "required", "forbidden"]
@@ -114,17 +114,19 @@ def check_non_negative_if_int(v: typing.Any):
 
 class base_{{assertion.name}}_model(AssertionModel):
     '''base model for {{assertion.name}} describing attributes.'''
+    model_config = ConfigDict(extra="forbid", title="base_{{assertion.name}}_model")
 {% for parameter in assertion.parameters %}
 {% if not parameter.is_deprecated %}
     {{ parameter.name }}: {{ parameter.type_str }} = Field(
         {{ parameter.field_default_str }},
+        title="{{ parameter.title }}",
         description={{ assertion.name }}_{{ parameter.name }}_description,
     )
 {% endif %}
 {% endfor %}
 {% if assertion.children in ["required", "allowed"] %}
-    children: typing.Optional["assertion_list"] = None
-    asserts: typing.Optional["assertion_list"] = None
+    children: typing.Optional["assertion_list"] = Field(None, title="Children")
+    asserts: typing.Optional["assertion_list"] = Field(None, title="Asserts")
 
 {% if assertion.children == "required" %}
     @model_validator(mode='before')
@@ -139,17 +141,19 @@ def validate_children(self, data: typing.Any):
 
 class base_{{assertion.name}}_model_relaxed(AssertionModel):
     '''base model for {{assertion.name}} describing attributes.'''
+    model_config = ConfigDict(extra="forbid", title="base_{{assertion.name}}_model_relaxed")
 {% for parameter in assertion.parameters %}
 {% if not parameter.is_deprecated %}
     {{ parameter.name }}: {{ parameter.lax_type_str }} = Field(
         {{ parameter.field_default_str }},
+        title="{{ parameter.title }}",
         description={{ assertion.name }}_{{ parameter.name }}_description,
     )
 {% endif %}
 {% endfor %}
 {% if assertion.children in ["required", "allowed"] %}
-    children: typing.Optional["assertion_list"] = None
-    asserts: typing.Optional["assertion_list"] = None
+    children: typing.Optional["assertion_list"] = Field(None, title="Children")
+    asserts: typing.Optional["assertion_list"] = Field(None, title="Asserts")
 
 {% if assertion.children == "required" %}
     @model_validator(mode='before')
@@ -164,15 +168,18 @@ def validate_children(self, data: typing.Any):
 
 class {{assertion.name}}_model(base_{{assertion.name}}_model):
     r\"\"\"{{ assertion.docstring }}\"\"\"
-    that: Literal["{{assertion.name}}"] = "{{assertion.name}}"
+    model_config = ConfigDict(extra="forbid", title="{{ assertion.title }}")
+    that: Literal["{{assertion.name}}"] = Field("{{assertion.name}}", title="That")
 
 class {{assertion.name}}_model_nested(AssertionModel):
     r\"\"\"Nested version of this assertion model.\"\"\"
-    {{assertion.name}}: base_{{assertion.name}}_model
+    model_config = ConfigDict(extra="forbid", title="{{ assertion.title }} (Nested)")
+    {{assertion.name}}: base_{{assertion.name}}_model = Field(..., title="{{ assertion.title }}")
 
 class {{assertion.name}}_model_relaxed(base_{{assertion.name}}_model_relaxed):
     r\"\"\"{{ assertion.docstring }}\"\"\"
-    that: Literal["{{assertion.name}}"] = "{{assertion.name}}"
+    model_config = ConfigDict(extra="forbid", title="{{ assertion.title }} (Relaxed)")
+    that: Literal["{{assertion.name}}"] = Field("{{assertion.name}}", title="That")
 {% endfor %}
 
 any_assertion_model_flat = Annotated[typing.Union[
@@ -193,15 +200,19 @@ class {{assertion.name}}_model_relaxed(base_{{assertion.name}}_model_relaxed):
 {% endfor %}
 ], Field(discriminator="that")]
 
-assertion_list = RootModel[typing.List[typing.Union[any_assertion_model_flat, any_assertion_model_nested]]]
+class assertion_list(RootModel[typing.List[typing.Union[any_assertion_model_flat, any_assertion_model_nested]]]):
+    model_config = ConfigDict(title="assertion_list")
+
 
 # used to model what the XML conversion should look like - not meant to be consumed outside of
 # of Galaxy internals / linting.
-relaxed_assertion_list = RootModel[typing.List[any_assertion_model_flat_relaxed]]
+class relaxed_assertion_list(RootModel[typing.List[any_assertion_model_flat_relaxed]]):
+    model_config = ConfigDict(title="relaxed_assertion_list")
 
 class assertion_dict(AssertionModel):
+    model_config = ConfigDict(extra="forbid", title="assertion_dict")
 {% for assertion in assertions %}
-    {{assertion.name}}: typing.Optional[base_{{assertion.name}}_model] = None
+    {{assertion.name}}: typing.Optional[base_{{assertion.name}}_model] = Field(None, title="{{ assertion.title }}")
 {% endfor %}
 
 
@@ -338,6 +349,10 @@ def __init__(self, name: str, type: str, default_value):
         self.type = type
         self.default_value = default_value
 
+    @property
+    def title(self) -> str:
+        return " ".join(w.capitalize() for w in self.name.split("_"))
+
     @property
     def description(self) -> str:
         type = self.type
@@ -490,6 +505,10 @@ def __init__(
         self.children = children
         self.module_and_function = module_and_function
 
+    @property
+    def title(self) -> str:
+        return "Assert " + " ".join(w.capitalize() for w in self.name.split("_"))
+
 
 def arg_parser() -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(description=DESCRIPTION)

lib/galaxy/tool_util/verify/codegen.py

@@ -2532,7 +2532,7 @@ $attribute_list::5]]></xs:documentation>
         <xs:annotation>
           <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output contains a line matching the
 regular expression specified by the argument expression. If n is given
-the assertion checks for exactly n occurences.
+the assertion checks for exactly n occurrences.
 
 $attribute_list::5]]></xs:documentation>
         </xs:annotation>
@@ -2653,8 +2653,8 @@ $attribute_list::5]]></xs:documentation>
         <xs:annotation>
           <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output contains text matching the
 regular expression specified by the argument expression.
-If n is given the assertion checks for exacly n (nonoverlapping)
-occurences.
+If n is given the assertion checks for exactly n (nonoverlapping)
+occurrences.
 
 $attribute_list::5]]></xs:documentation>
         </xs:annotation>
@@ -2715,7 +2715,7 @@ number (``n``) of columns.
 
 For instance, ``<has_n_columns n="3"/>``. The assertion tests only the first line.
 Number of columns can optionally also be specified with ``delta``. Alternatively the
-range of expected occurences can be specified by ``min`` and/or ``max``.
+range of expected occurrences can be specified by ``min`` and/or ``max``.
 
 Optionally a column separator (``sep``, default is ``       ``) `and comment character(s)
 can be specified (``comment``, default is empty string). The first non-comment
@@ -2991,7 +2991,7 @@ For example:
 ```
 
 Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
-can be used to specify the range of the expected number of occurences.
+can be used to specify the range of the expected number of occurrences.
 With ``negate`` the result of the assertion can be inverted.
 
 $attribute_list::5]]></xs:documentation>
@@ -3043,7 +3043,7 @@ $attribute_list::5]]></xs:documentation>
         <xs:annotation>
           <xs:documentation xml:lang="en"><![CDATA[Assert if the XML file contains element(s) or tag(s) with the specified
 [XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``
-or ``min`` and ``max`` are given also the number of occurences is checked.
+or ``min`` and ``max`` are given also the number of occurrences is checked.
 
 ```xml
 <assert_contents>
@@ -3053,7 +3053,7 @@ or ``min`` and ``max`` are given also the number of occurences is checked.
 </assert_contents>
 ```
 
-With ``negate="true"`` the outcome of the assertions wrt the precence and number
+With ``negate="true"`` the outcome of the assertions wrt the presence and number
 of ``path`` can be negated. If there are any sub assertions then check them against
 
 - the content of the attribute ``attribute``
@@ -3068,7 +3068,7 @@ of ``path`` can be negated. If there are any sub assertions then check them agai
 ```
 
 Sub-assertions are not subject to the ``negate`` attribute of ``xml_element``.
-If ``all`` is ``true`` then the sub assertions are checked for all occurences.
+If ``all`` is ``true`` then the sub assertions are checked for all occurrences.
 
 Note that all other XML assertions can be expressed by this assertion (Galaxy
 also implements the other assertions by calling this one).