Merge pull request #15825 from bernt-matthias/validation_metadata

Add ability to assert metadata properties on input dataset parameters

lib/galaxy/tool_util/linters/inputs.py

@@ -37,6 +37,7 @@
     ],
     "filename": ["dataset_metadata_in_file"],
     "metadata_name": [
+        "dataset_metadata_equal",
         "dataset_metadata_in_data_table",
         "dataset_metadata_not_in_data_table",
         "dataset_metadata_in_file",
@@ -56,6 +57,8 @@
     "exclude_max": ["in_range", "dataset_metadata_in_range"],
     "split": ["dataset_metadata_in_file"],
     "skip": ["metadata"],
+    "value": ["dataset_metadata_equal"],
+    "value_json": ["dataset_metadata_equal"],
 }
 
 PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = {
@@ -66,6 +69,7 @@
         "no_options",
         "unspecified_build",
         "dataset_ok_validator",
+        "dataset_metadata_equal",
         "dataset_metadata_in_range",
         "dataset_metadata_in_file",
         "dataset_metadata_in_data_table",
@@ -77,6 +81,7 @@
         "no_options",
         "unspecified_build",
         "dataset_ok_validator",
+        "dataset_metadata_equal",
         "dataset_metadata_in_range",
         "dataset_metadata_in_file",
         "dataset_metadata_in_data_table",
@@ -415,6 +420,21 @@ def lint_inputs(tool_source: "ToolSource", lint_ctx: "LintContext"):
                     f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)",
                     node=validator,
                 )
+            if vtype in ["dataset_metadata_equal"]:
+                if (
+                    not ("value" in validator.attrib or "value_json" in validator.attrib)
+                    or "metadata_name" not in validator.attrib
+                ):
+                    lint_ctx.error(
+                        f"Parameter [{param_name}]: '{vtype}' validators need to define the 'value'/'value_json' and 'metadata_name' attributes",
+                        node=validator,
+                    )
+                if "value" in validator.attrib and "value_json" in validator.attrib:
+                    lint_ctx.error(
+                        f"Parameter [{param_name}]: '{vtype}' validators must not define the 'value' and the 'value_json' attributes",
+                        node=validator,
+                    )
+
             if vtype in ["metadata"] and ("check" not in validator.attrib and "skip" not in validator.attrib):
                 lint_ctx.error(
                     f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s)",

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -4413,6 +4413,7 @@ Note that each data parameter has automatically a metadata validator that checks
 if all non-optional metadata are set, i.e. ``<validator type="metadata/>``.
 - ``unspecified_build``: Check of a build is defined.
 - ``dataset_ok_validator``: Check if the data set is in state OK.
+- ``dataset_metadata_equal``: Check if metadata (given by ``metadata_name``) is equal to a given string value (given by ``value``) or JSON encoded value (given by ``value_json``). ``value_json`` needs to be used for all non string types (e.g. int, float, list, dict).
 - ``dataset_metadata_in_range``: Check if a numeric metadata value is within
 a given range.
 - ``dataset_metadata_in_data_table``: Check if a metadata value is contained in a column of a data table.
@@ -4501,7 +4502,7 @@ use in filenames may not contain ``..``.
           <xs:annotation>
             <xs:documentation xml:lang="en"><![CDATA[
 Valid values are: ``expression``, ``regex``, ``in_range``, ``length``,
-``metadata``, ``unspecified_build``, ``no_options``, ``empty_field``,
+``metadata``, ``metadata_eq`` ``unspecified_build``, ``no_options``, ``empty_field``,
 ``dataset_metadata_in_data_table``, ``dataset_metadata_not_in_data_table``,
 ``value_in_data_table``, ``value_not_in_data_table``,
 ``dataset_ok_validator``, ``dataset_metadata_in_range``.
@@ -4600,6 +4601,18 @@ fields to skip if type is ``metadata``. If not specified, all non-optional
 metadata fields will be checked unless ``check`` attribute is specified.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
+        <xs:attribute name="value" type="xs:string">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">Value to check the metadata against. Only
+applicable to ``dataset_metadata_equal``. Mutually exclusive with ``value_json``.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="value_json" type="xs:string">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">JSON encoded value to check the metadata against. Only
+applicable to ``dataset_metadata_equal``. Mutually exclusive with ``value``.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
         <xs:attribute name="line_startswith" type="xs:string">
           <xs:annotation>
             <xs:documentation xml:lang="en">Deprecated. Used to indicate lines in the file
@@ -7069,6 +7082,7 @@ and ``bibtex`` are the only supported options.</xs:documentation>
       <xs:enumeration value="in_range"/>
       <xs:enumeration value="length"/>
       <xs:enumeration value="metadata"/>
+      <xs:enumeration value="dataset_metadata_equal" gxdocs:added="23.1"/>
       <xs:enumeration value="unspecified_build"/>
       <xs:enumeration value="no_options"/>
       <xs:enumeration value="empty_field"/>

lib/galaxy/tools/parameters/validation.py

@@ -2,6 +2,7 @@
 Classes related to parameter validation.
 """
 import abc
+import json
 import logging
 import os.path
 import re
@@ -31,7 +32,7 @@ class Validator(abc.ABC):
     @classmethod
     def from_element(cls, param, elem):
         """
-        Initialize the appropiate Validator class
+        Initialize the appropriate Validator class
 
         example call `validation.Validator.from_element(ToolParameter_object, Validator_object)`
 
@@ -559,6 +560,42 @@ def validate(self, value, trans=None):
             super().validate(isinstance(value, model.DatasetInstance) and not missing, value_to_show=missing)
 
 
+class MetadataEqualsValidator(Validator):
+    """
+    Validator that checks for a metadata value for equality
+
+    metadata values that are lists are converted as comma separated string
+    everything else is converted to the string representation
+    """
+
+    requires_dataset_metadata = True
+
+    def __init__(self, metadata_name=None, value=None, message=None, negate="false"):
+        if not message:
+            if not util.asbool(negate):
+                message = f"Metadata value for '{metadata_name}' must be '{value}', but it is '%s'."
+            else:
+                message = f"Metadata value for '{metadata_name}' must not be '{value}' but it is."
+        super().__init__(message, negate)
+        self.metadata_name = metadata_name
+        self.value = value
+
+    @classmethod
+    def from_element(cls, param, elem):
+        value = elem.get("value", None) or json.loads(elem.get("value_json", "null"))
+        return cls(
+            metadata_name=elem.get("metadata_name", None),
+            value=value,
+            message=elem.get("message", None),
+            negate=elem.get("negate", "false"),
+        )
+
+    def validate(self, value, trans=None):
+        if value:
+            metadata_value = getattr(value.metadata, self.metadata_name)
+            super().validate(metadata_value == self.value, value_to_show=metadata_value)
+
+
 class UnspecifiedBuildValidator(Validator):
     """
     Validator that checks for dbkey not equal to '?'
@@ -949,6 +986,7 @@ def validate(self, value, trans=None):
     in_range=InRangeValidator,
     length=LengthValidator,
     metadata=MetadataValidator,
+    dataset_metadata_equal=MetadataEqualsValidator,
     unspecified_build=UnspecifiedBuildValidator,
     no_options=NoOptionsValidator,
     empty_field=EmptyTextfieldValidator,