Merge branch 'release_23.2' into dev

lib/galaxy/files/sources/__init__.py

@@ -1,6 +1,10 @@
 import abc
 import os
 import time
+from dataclasses import (
+    dataclass,
+    field,
+)
 from enum import Enum
 from typing import (
     Any,
@@ -88,19 +92,20 @@ class FilesSourceProperties(TypedDict):
     browsable: NotRequired[bool]
 
 
+@dataclass
 class FilesSourceOptions:
     """Options to control behavior of file source operations, such as realize_to, write_from and list."""
 
     # Indicates access to the FS operation with intent to write.
     # Even if a file source is "writeable" some directories (or elements) may be restricted or read-only
     # so those should be skipped while browsing with writeable=True.
-    writeable: Optional[bool]
+    writeable: Optional[bool] = False
 
     # Property overrides for values initially configured through the constructor. For example
     # the HTTPFilesSource passes in additional http_headers through these properties, which
     # are merged with constructor defined http_headers. The interpretation of these properties
     # are filesystem specific.
-    extra_props: Optional[FilesSourceProperties]
+    extra_props: Optional[FilesSourceProperties] = field(default_factory=lambda: FilesSourceProperties())
 
 
 class EntryData(TypedDict):

lib/galaxy/jobs/__init__.py

@@ -1244,15 +1244,13 @@ class MinimalJobWrapper(HasResourceParameters):
 
         tool_evaluator = self._get_tool_evaluator(job)
         compute_environment = compute_environment or self.default_compute_environment(job)
-        if hasattr(self.app, "interactivetool_manager"):
-            self.interactivetools = tool_evaluator.populate_interactivetools()
-            self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)
         tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
         (
             self.command_line,
             self.version_command_line,
             self.extra_filenames,
             self.environment_variables,
+            self.interactivetools,
         ) = tool_evaluator.build()
         job.command_line = self.command_line
 
@@ -2616,6 +2614,7 @@ class TaskWrapper(JobWrapper):
                 self.version_command_line,
                 extra_filenames,
                 self.environment_variables,
+                *_,
             ) = tool_evaluator.build()
             self.extra_filenames.extend(extra_filenames)
 

lib/galaxy/tools/evaluation.py

@@ -121,6 +121,7 @@ class ToolEvaluator:
         self.environment_variables: List[Dict[str, str]] = []
         self.version_command_line: Optional[str] = None
         self.command_line: Optional[str] = None
+        self.interactivetools: List[Dict[str, Any]] = []
 
     def set_compute_environment(self, compute_environment: ComputeEnvironment, get_special: Optional[Callable] = None):
         """
@@ -514,7 +515,12 @@ class ToolEvaluator:
             # the paths rewritten.
             self.__walk_inputs(self.tool.inputs, param_dict, rewrite_unstructured_paths)
 
-    def populate_interactivetools(self):
+    def _create_interactivetools_entry_points(self):
+        if hasattr(self.app, "interactivetool_manager"):
+            self.interactivetools = self._populate_interactivetools_template()
+            self.app.interactivetool_manager.create_interactivetool(self.job, self.tool, self.interactivetools)
+
+    def _populate_interactivetools_template(self):
         """
         Populate InteractiveTools templated values.
         """
@@ -571,12 +577,21 @@ class ToolEvaluator:
         compute environment.
         """
         config_file = self.tool.config_file
+        global_tool_logs(
+            self._create_interactivetools_entry_points, config_file, "Building Interactive Tool Entry Points"
+        )
         global_tool_logs(self._build_config_files, config_file, "Building Config Files")
         global_tool_logs(self._build_param_file, config_file, "Building Param File")
         global_tool_logs(self._build_command_line, config_file, "Building Command Line")
         global_tool_logs(self._build_version_command, config_file, "Building Version Command Line")
         global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
-        return self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables
+        return (
+            self.command_line,
+            self.version_command_line,
+            self.extra_filenames,
+            self.environment_variables,
+            self.interactivetools,
+        )
 
     def _build_command_line(self):
         """
@@ -819,7 +834,13 @@ class PartialToolEvaluator(ToolEvaluator):
     def build(self):
         config_file = self.tool.config_file
         global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
-        return self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables
+        return (
+            self.command_line,
+            self.version_command_line,
+            self.extra_filenames,
+            self.environment_variables,
+            self.interactivetools,
+        )
 
 
 class RemoteToolEvaluator(ToolEvaluator):
@@ -837,4 +858,10 @@ class RemoteToolEvaluator(ToolEvaluator):
         global_tool_logs(self._build_param_file, config_file, "Building Param File")
         global_tool_logs(self._build_command_line, config_file, "Building Command Line")
         global_tool_logs(self._build_version_command, config_file, "Building Version Command Line")
-        return self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables
+        return (
+            self.command_line,
+            self.version_command_line,
+            self.extra_filenames,
+            self.environment_variables,
+            self.interactivetools,
+        )

lib/galaxy/tools/remote_tool_eval.py

@@ -114,7 +114,7 @@ def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):
     )
     tool_evaluator.set_compute_environment(compute_environment=SharedComputeEnvironment(job_io=job_io, job=job_io.job))
     with open(os.path.join(WORKING_DIRECTORY, "tool_script.sh"), "a") as out:
-        command_line, version_command_line, extra_filenames, environment_variables = tool_evaluator.build()
+        command_line, version_command_line, extra_filenames, environment_variables, *_ = tool_evaluator.build()
         out.write(f'{version_command_line or ""}{command_line}')
 
 

lib/galaxy/webapps/galaxy/services/dataset_collections.py

@@ -247,7 +247,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
             raise exceptions.RequestParameterInvalidException(
                 "Parameter instance_type not being 'history' is not yet implemented."
             )
-        hdca: HistoryDatasetCollectionAssociation = self.collection_manager.get_dataset_collection_instance(
+        hdca: "HistoryDatasetCollectionAssociation" = self.collection_manager.get_dataset_collection_instance(
             trans, "history", hdca_id
         )