Merge pull request galaxyproject#14955 from jmchilton/default_uris_2

Implement default locations for data and collection parameters.

lib/galaxy/managers/workflows.py

@@ -1005,7 +1005,7 @@ def _workflow_to_dict_run(self, trans, stored, workflow, history=None):
                     for pja in step.post_job_actions
                 ]
             else:
-                inputs = step.module.get_runtime_inputs(connections=step.output_connections)
+                inputs = step.module.get_runtime_inputs(step, connections=step.output_connections)
                 step_model = {"inputs": [input.to_dict(trans) for input in inputs.values()]}
             step_model["when"] = step.when_expression
             step_model["replacement_parameters"] = step.module.get_informal_replacement_parameters(step)
@@ -1157,7 +1157,7 @@ def do_inputs(inputs, values, prefix, step, other_values=None):
             else:
                 module = step.module
                 step_dict["label"] = module.name
-                step_dict["inputs"] = do_inputs(module.get_runtime_inputs(), step.state.inputs, "", step)
+                step_dict["inputs"] = do_inputs(module.get_runtime_inputs(step), step.state.inputs, "", step)
             step_dicts.append(step_dict)
         return {
             "name": workflow.name,
@@ -1806,6 +1806,11 @@ def __module_from_dict(
 
         if "in" in step_dict:
             for input_name, input_dict in step_dict["in"].items():
+                # This is just a bug in gxformat? I think the input
+                # defaults should be called input to match the input modules's
+                # input parameter name.
+                if input_name == "default":
+                    input_name = "input"
                 step_input = step.get_or_add_input(input_name)
                 NO_DEFAULT_DEFINED = object()
                 default = input_dict.get("default", NO_DEFAULT_DEFINED)

lib/galaxy/model/__init__.py

@@ -7625,10 +7625,20 @@ def input_type(self):
 
     @property
     def input_default_value(self):
-        tool_state = self.tool_inputs
-        default_value = tool_state.get("default")
-        if default_value:
-            default_value = json.loads(default_value)["value"]
+        self.get_input_default_value(None)
+
+    def get_input_default_value(self, default_default):
+        # parameter_input and the data parameters handle this slightly differently
+        # unfortunately.
+        if self.type == "parameter_input":
+            tool_state = self.tool_inputs
+            default_value = tool_state.get("default", default_default)
+        else:
+            default_value = default_default
+            for step_input in self.inputs:
+                if step_input.name == "input" and step_input.default_value_set:
+                    default_value = step_input.default_value
+                    break
         return default_value
 
     @property

lib/galaxy/tool_util/parser/interface.py

@@ -425,6 +425,9 @@ def parse_test_input_source(self) -> "InputSource":
     def parse_when_input_sources(self):
         raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
 
+    def parse_default(self) -> Optional[Dict[str, Any]]:
+        return None
+
 
 class PageSource(metaclass=ABCMeta):
     def parse_display(self):

lib/galaxy/tool_util/parser/xml.py

@@ -5,7 +5,9 @@
 import re
 import uuid
 from typing import (
+    Any,
     cast,
+    Dict,
     Iterable,
     List,
     Optional,
@@ -1274,6 +1276,56 @@ def parse_when_input_sources(self):
             sources.append((value, case_page_source))
         return sources
 
+    def parse_default(self) -> Optional[Dict[str, Any]]:
+        def file_default_from_elem(elem):
+            # TODO: hashes, created_from_basename, etc...
+            return {"class": "File", "location": elem.get("location")}
+
+        def read_elements(collection_elem):
+            element_dicts = []
+            elements = collection_elem.findall("element")
+            for element in elements:
+                identifier = element.get("name")
+                subcollection_elem = element.find("collection")
+                if subcollection_elem:
+                    collection_type = subcollection_elem.get("collection_type")
+                    element_dicts.append(
+                        {
+                            "class": "Collection",
+                            "identifier": identifier,
+                            "collection_type": collection_type,
+                            "elements": read_elements(subcollection_elem),
+                        }
+                    )
+                else:
+                    element_dict = file_default_from_elem(element)
+                    element_dict["identifier"] = identifier
+                    element_dicts.append(element_dict)
+            return element_dicts
+
+        elem = self.input_elem
+        element_type = self.input_elem.get("type")
+        if element_type == "data":
+            default_elem = elem.find("default")
+            if default_elem is not None:
+                return file_default_from_elem(default_elem)
+            else:
+                return None
+        else:
+            default_elem = elem.find("default")
+            if default_elem is not None:
+                default_elem = elem.find("default")
+                collection_type = default_elem.get("collection_type")
+                name = default_elem.get("name", elem.get("name"))
+                return {
+                    "class": "Collection",
+                    "name": name,
+                    "collection_type": collection_type,
+                    "elements": read_elements(default_elem),
+                }
+            else:
+                return None
+
 
 class ParallelismInfo:
     """

lib/galaxy/tool_util/parser/yaml.py

@@ -1,7 +1,9 @@
 import json
 from typing import (
+    Any,
     Dict,
     List,
+    Optional,
 )
 
 import packaging.version
@@ -358,6 +360,11 @@ def parse_static_options(self):
             static_options.append((label, value, selected))
         return static_options
 
+    def parse_default(self) -> Optional[Dict[str, Any]]:
+        input_dict = self.input_dict
+        default_def = input_dict.get("default", None)
+        return default_def
+
 
 def _ensure_has(dict, defaults):
     for key, value in defaults.items():

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -3731,6 +3731,7 @@ allow access to Python code to generate options for a select list. See
       <xs:element name="options" type="ParamOptions"/>
       <xs:element name="validator" type="Validator" />
       <xs:element name="sanitizer" type="Sanitizer"/>
+      <xs:element name="default" type="ParamDefault" />
       <xs:element name="help" type="xs:string">
         <xs:annotation>
           <xs:documentation xml:lang="en">Documentation for help</xs:documentation>
@@ -4115,6 +4116,73 @@ dataset for the contained input of the type specified using the ``type`` tag.
     </xs:attribute>
   </xs:complexType>
 
+  <xs:complexType name="ParamDefault">
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[
+]]>
+</xs:documentation>
+    </xs:annotation>
+    <xs:sequence>
+      <!-- can have zero or one collection elements -->
+      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded" />
+    </xs:sequence>
+    <xs:attribute name="collection_type" type="CollectionType" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
+Collection type for default collection (if param type is data_collection). Simple collection types are
+either ``list`` or ``paired``, nested collections are specified as colon separated list of simple
+collection types (the most common types are ``list``, ``paired``,
+``list:paired``, or ``list:list``).
+        ]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+
+    <xs:attribute name="location" type="xs:anyURI" gxdocs:added="23.2" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
+Galaxy-aware URI for the default file. This should only be used with parameters of type "data".
+        ]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+
+  </xs:complexType>
+
+  <xs:complexType name="ParamDefaultCollection">
+    <xs:sequence>
+      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded" />
+    </xs:sequence>
+
+    <xs:attribute name="collection_type" type="CollectionType" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
+Collection type for default collection (if param type is data_collection). Simple collection types are
+either ``list`` or ``paired``, nested collections are specified as colon separated list of simple
+collection types (the most common types are ``list``, ``paired``,
+``list:paired``, or ``list:list``).
+        ]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+
+  </xs:complexType>
+
+  <xs:complexType name="ParamDefaultElement">
+    <xs:sequence>
+      <xs:element name="collection" type="ParamDefaultCollection" minOccurs="0" maxOccurs="1" />
+    </xs:sequence>
+    <xs:attribute name="name" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Name (and element identifier) for this element</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="location" type="xs:anyURI" gxdocs:added="23.2" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
+Galaxy-aware URI for the default file for collection element.
+        ]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
+
   <xs:complexType name="ParamOptions">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[