Better Typing for Tool Execution Plumbing

lib/galaxy/managers/datasets.py

@@ -547,7 +547,7 @@ def set_metadata(self, trans, dataset_assoc, overwrite=False, validate=True):
         if overwrite:
             self.overwrite_metadata(data)
 
-        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
+        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute_via_trans(
             self.app.datatypes_registry.set_external_metadata_tool,
             trans,
             incoming={"input1": data, "validate": validate},
@@ -883,7 +883,7 @@ def deserialize_datatype(self, item, key, val, **context):
         assert (
             trans
         ), "Logic error in Galaxy, deserialize_datatype not send a transation object"  # TODO: restructure this for stronger typing
-        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
+        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute_via_trans(
             self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={"input1": item}, overwrite=False
         )  # overwrite is False as per existing behavior
         trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)

lib/galaxy/managers/histories.py

@@ -424,7 +424,7 @@ def queue_history_export(
 
         # Run job to do export.
         history_exp_tool = trans.app.toolbox.get_tool(export_tool_id)
-        job, *_ = history_exp_tool.execute(trans, incoming=params, history=history, set_output_hid=True)
+        job, *_ = history_exp_tool.execute(trans, incoming=params, history=history)
         trans.app.job_manager.enqueue(job, tool=history_exp_tool)
         return job
 

lib/galaxy/tools/__init__.py

@@ -51,6 +51,7 @@
     StoredWorkflow,
 )
 from galaxy.model.base import transaction
+from galaxy.model.dataset_collections.matching import MatchingCollections
 from galaxy.tool_shed.util.repository_util import get_installed_repository
 from galaxy.tool_shed.util.shed_util_common import set_image_paths
 from galaxy.tool_util.deps import (
@@ -113,6 +114,7 @@
 from galaxy.tools.actions.model_operations import ModelOperationToolAction
 from galaxy.tools.cache import ToolDocumentCache
 from galaxy.tools.evaluation import global_tool_errors
+from galaxy.tools.execution_helpers import ToolExecutionCache
 from galaxy.tools.imp_exp import JobImportHistoryArchiveWrapper
 from galaxy.tools.parameters import (
     check_param,
@@ -183,8 +185,18 @@
 from galaxy.version import VERSION_MAJOR
 from galaxy.work.context import proxy_work_context_for_history
 from .execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    DEFAULT_USE_CACHED_JOB,
     execute as execute_job,
+    ExecutionSlice,
+    JobCallbackT,
     MappingParameters,
+    ToolParameterRequestInstanceT,
+    ToolParameterRequestT,
 )
 
 if TYPE_CHECKING:
@@ -1862,11 +1874,11 @@ def expand_incoming(self, trans, incoming, request_context, input_format="legacy
     def handle_input(
         self,
         trans,
-        incoming,
-        history=None,
-        use_cached_job=False,
-        preferred_object_store_id: Optional[str] = None,
-        input_format="legacy",
+        incoming: ToolParameterRequestT,
+        history: Optional[model.History] = None,
+        use_cached_job: bool = DEFAULT_USE_CACHED_JOB,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        input_format: str = "legacy",
     ):
         """
         Process incoming parameters for this tool from the dict `incoming`,
@@ -1942,23 +1954,23 @@ def handle_incoming_errors(self, all_errors):
     def handle_single_execution(
         self,
         trans,
-        rerun_remap_job_id,
-        execution_slice,
-        history,
-        execution_cache=None,
-        completed_job=None,
-        collection_info=None,
-        job_callback=None,
-        preferred_object_store_id=None,
-        flush_job=True,
-        skip=False,
+        rerun_remap_job_id: Optional[int],
+        execution_slice: ExecutionSlice,
+        history: model.History,
+        execution_cache: ToolExecutionCache,
+        completed_job: Optional[model.Job],
+        collection_info: Optional[MatchingCollections],
+        job_callback: Optional[JobCallbackT],
+        preferred_object_store_id: Optional[str],
+        flush_job: bool,
+        skip: bool,
     ):
         """
         Return a pair with whether execution is successful as well as either
         resulting output data or an error message indicating the problem.
         """
         try:
-            rval = self.execute(
+            rval = self._execute(
                 trans,
                 incoming=execution_slice.param_combination,
                 history=history,
@@ -2045,18 +2057,67 @@ def get_static_param_values(self, trans):
                 args[key] = param.get_initial_value(trans, None)
         return args
 
-    def execute(self, trans, incoming=None, set_output_hid=True, history=None, **kwargs):
+    def execute(
+        self,
+        trans,
+        incoming: Optional[ToolParameterRequestInstanceT] = None,
+        history: Optional[model.History] = None,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+    ):
         """
         Execute the tool using parameter values in `incoming`. This just
         dispatches to the `ToolAction` instance specified by
         `self.tool_action`. In general this will create a `Job` that
         when run will build the tool's outputs, e.g. `DefaultToolAction`.
+
+        _execute has many more options but should be accessed through
+        handle_single_execution. The public interface to execute should be
+        rarely used and in more specific ways.
         """
+        return self._execute(
+            trans,
+            incoming=incoming,
+            history=history,
+            set_output_hid=set_output_hid,
+            flush_job=flush_job,
+        )
+
+    def _execute(
+        self,
+        trans,
+        incoming: Optional[ToolParameterRequestInstanceT] = None,
+        history: Optional[model.History] = None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = None,
+        completed_job: Optional[model.Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ):
         if incoming is None:
             incoming = {}
         try:
             return self.tool_action.execute(
-                self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs
+                self,
+                trans,
+                incoming=incoming,
+                history=history,
+                job_params=None,
+                rerun_remap_job_id=rerun_remap_job_id,
+                execution_cache=execution_cache,
+                dataset_collection_elements=dataset_collection_elements,
+                completed_job=completed_job,
+                collection_info=collection_info,
+                job_callback=job_callback,
+                preferred_object_store_id=preferred_object_store_id,
+                set_output_hid=set_output_hid,
+                flush_job=flush_job,
+                skip=skip,
             )
         except exceptions.ToolExecutionError as exc:
             job = exc.job
@@ -2988,7 +3049,9 @@ class SetMetadataTool(Tool):
     requires_setting_metadata = False
     tool_action: "SetMetadataToolAction"
 
-    def regenerate_imported_metadata_if_needed(self, hda, history, user, session_id):
+    def regenerate_imported_metadata_if_needed(
+        self, hda: model.HistoryDatasetAssociation, history: model.History, user: model.User, session_id: int
+    ):
         if hda.has_metadata_files:
             job, *_ = self.tool_action.execute_via_app(
                 self,

lib/galaxy/tools/actions/__init__.py

@@ -9,7 +9,9 @@
     cast,
     Dict,
     List,
+    Optional,
     Set,
+    Tuple,
     TYPE_CHECKING,
     Union,
 )
@@ -24,15 +26,32 @@
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model import (
+    History,
     HistoryDatasetAssociation,
     Job,
     LibraryDatasetDatasetAssociation,
     WorkflowRequestInputParameter,
 )
 from galaxy.model.base import transaction
 from galaxy.model.dataset_collections.builder import CollectionBuilder
+from galaxy.model.dataset_collections.matching import MatchingCollections
 from galaxy.model.none_like import NoneDataset
 from galaxy.objectstore import ObjectStorePopulator
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+    ToolParameterRequestInstanceT,
+)
+from galaxy.tools.execution_helpers import (
+    filter_output,
+    on_text_for_names,
+    ToolExecutionCache,
+)
 from galaxy.tools.parameters import update_dataset_ids
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
@@ -54,32 +73,8 @@
 log = logging.getLogger(__name__)
 
 
-class ToolExecutionCache:
-    """An object mean to cache calculation caused by repeatedly evaluting
-    the same tool by the same user with slightly different parameters.
-    """
-
-    def __init__(self, trans):
-        self.trans = trans
-        self.current_user_roles = trans.get_current_user_roles()
-        self.chrom_info = {}
-        self.cached_collection_elements = {}
-
-    def get_chrom_info(self, tool_id, input_dbkey):
-        genome_builds = self.trans.app.genome_builds
-        custom_build_hack_get_len_from_fasta_conversion = tool_id != "CONVERTER_fasta_to_len"
-        if custom_build_hack_get_len_from_fasta_conversion and input_dbkey in self.chrom_info:
-            return self.chrom_info[input_dbkey]
-
-        chrom_info_pair = genome_builds.get_chrom_info(
-            input_dbkey,
-            trans=self.trans,
-            custom_build_hack_get_len_from_fasta_conversion=custom_build_hack_get_len_from_fasta_conversion,
-        )
-        if custom_build_hack_get_len_from_fasta_conversion:
-            self.chrom_info[input_dbkey] = chrom_info_pair
-
-        return chrom_info_pair
+OutputDatasetsT = Dict[str, "DatasetInstance"]
+ToolActionExecuteResult = Union[Tuple[Job, OutputDatasetsT, Optional[History]], Tuple[Job, OutputDatasetsT]]
 
 
 class ToolAction:
@@ -89,14 +84,31 @@ class ToolAction:
     """
 
     @abstractmethod
-    def execute(self, tool, trans, incoming=None, set_output_hid=True, **kwargs):
-        pass
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolParameterRequestInstanceT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
+        """Perform target tool action."""
 
 
 class DefaultToolAction(ToolAction):
     """Default tool action is to run an external command"""
 
-    produces_real_jobs = True
+    produces_real_jobs: bool = True
 
     def _collect_input_datasets(
         self,
@@ -389,21 +401,20 @@ def execute(
         self,
         tool,
         trans,
-        incoming=None,
-        return_job=False,
-        set_output_hid=True,
-        history=None,
+        incoming: Optional[ToolParameterRequestInstanceT] = None,
+        history: Optional[History] = None,
         job_params=None,
-        rerun_remap_job_id=None,
-        execution_cache=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
         dataset_collection_elements=None,
-        completed_job=None,
-        collection_info=None,
-        job_callback=None,
-        preferred_object_store_id=None,
-        flush_job=True,
-        skip=False,
-    ):
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
         """
         Executes a tool, creating job and tool outputs, associating them, and
         submitting the job to the job queue. If history is not specified, use
@@ -424,6 +435,7 @@ def execute(
             preserved_hdca_tags,
             all_permissions,
         ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
+        assert history  # tell type system we've set history and it is no longer optional
         # Build name for output datasets based on tool name and input names
         on_text = self._get_on_text(inp_data)
 
@@ -846,7 +858,7 @@ def _get_on_text(self, inp_data):
 
         return on_text_for_names(input_names)
 
-    def _new_job_for_session(self, trans, tool, history):
+    def _new_job_for_session(self, trans, tool, history) -> Tuple[model.Job, Optional[model.GalaxySession]]:
         job = trans.app.model.Job()
         job.galaxy_version = trans.app.config.version_major
         galaxy_session = None
@@ -1097,40 +1109,6 @@ def check_elements(elements):
             self.out_collection_instances[name] = hdca
 
 
-def on_text_for_names(input_names):
-    # input_names may contain duplicates... this is because the first value in
-    # multiple input dataset parameters will appear twice once as param_name
-    # and once as param_name1.
-    unique_names = []
-    for name in input_names:
-        if name not in unique_names:
-            unique_names.append(name)
-    input_names = unique_names
-
-    # Build name for output datasets based on tool name and input names
-    if len(input_names) == 0:
-        on_text = ""
-    elif len(input_names) == 1:
-        on_text = input_names[0]
-    elif len(input_names) == 2:
-        on_text = "{} and {}".format(*input_names)
-    elif len(input_names) == 3:
-        on_text = "{}, {}, and {}".format(*input_names)
-    else:
-        on_text = "{}, {}, and others".format(*input_names[:2])
-    return on_text
-
-
-def filter_output(tool, output, incoming):
-    for filter in output.filters:
-        try:
-            if not eval(filter.text.strip(), globals(), incoming):
-                return True  # do not create this dataset
-        except Exception as e:
-            log.debug(f"Tool {tool.id} output {output.name}: dataset output filter ({filter.text}) failed: {e}")
-    return False
-
-
 def get_ext_or_implicit_ext(hda):
     if hda.implicitly_converted_parent_datasets:
         # implicitly_converted_parent_datasets is a list of ImplicitlyConvertedDatasetAssociation