Unverified Commit a4bad06a authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_24.2' into dev

parents 36ea7dad 2156e2d9

lib/galaxy/managers/jobs.py

+1 −1
Original line number Diff line number Diff line
@@ -1189,7 +1189,7 @@ def summarize_job_parameters(trans: ProvidesUserContext, job: Job): 
                            raise Exception(

                                f"Unhandled data input parameter type encountered {element.__class__.__name__}"

                            )

                    rval.append(dict(text=input.label, depth=depth, value=value))

                    rval.append(dict(text=input.label or input.name, depth=depth, value=value))

                elif input.visible:

                    if hasattr(input, "label") and input.label:

                        label = input.label

lib/galaxy/model/mapping.py

+2 −2
Original line number Diff line number Diff line
@@ -7,7 +7,6 @@ from typing import ( 
)



from galaxy import model

from galaxy.config import GalaxyAppConfiguration

from galaxy.model import (

    mapper_registry,

    setup_global_object_store_for_models,
@@ -18,6 +17,7 @@ from galaxy.model.security import GalaxyRBACAgent 
from galaxy.model.triggers.update_audit_table import install as install_timestamp_triggers



if TYPE_CHECKING:

    from galaxy.config import GalaxyAppConfiguration

    from galaxy.model import User as GalaxyUser

    from galaxy.objectstore import BaseObjectStore
@@ -103,7 +103,7 @@ def _build_model_mapping(engine, map_install_models, thread_local_log) -> Galaxy 




def init_models_from_config(

    config: GalaxyAppConfiguration,

    config: "GalaxyAppConfiguration",

    map_install_models: bool = False,

    object_store: Optional["BaseObjectStore"] = None,

    trace_logger=None,

lib/galaxy/tool_util/fetcher.py

+4 −2
Original line number Diff line number Diff line 
import os

from typing import (

    Dict,

    Type,
@@ -8,6 +9,7 @@ from galaxy.util import plugin_config 


if TYPE_CHECKING:

    from galaxy.tool_util.locations import ToolLocationResolver

    from galaxy.util.path import StrPath





class ToolLocationFetcher:
@@ -19,8 +21,8 @@ class ToolLocationFetcher: 


        return plugin_config.plugins_dict(galaxy.tool_util.locations, "scheme")



    def to_tool_path(self, path_or_uri_like: str, **kwds) -> str:

        if "://" not in path_or_uri_like:

    def to_tool_path(self, path_or_uri_like: "StrPath", **kwds) -> "StrPath":

        if isinstance(path_or_uri_like, os.PathLike) or "://" not in path_or_uri_like:

            path = path_or_uri_like

        else:

            uri_like = path_or_uri_like

lib/galaxy/tool_util/parser/factory.py

+1 −2
Original line number Diff line number Diff line
@@ -87,9 +87,8 @@ def get_tool_source( 
        tool_location_fetcher = ToolLocationFetcher()



    assert config_file

    config_file = str(config_file)



    config_file = tool_location_fetcher.to_tool_path(config_file)

    config_file = str(tool_location_fetcher.to_tool_path(config_file))

    if not enable_beta_formats:

        tree, macro_paths = load_tool_with_refereces(config_file)

        return XmlToolSource(tree, source_path=config_file, macro_paths=macro_paths)

lib/galaxy/tool_util/parser/xml.py

+7 −1
Original line number Diff line number Diff line
@@ -723,7 +723,13 @@ class XmlToolSource(ToolSource): 
            return citations



        for citation_elem in citations_elem:

            try:

                citation = parse_citation_elem(citation_elem)

            except Exception:

                if Version(self.parse_profile()) < Version("24.2"):

                    continue

                else:

                    raise

            if citation:

                citations.append(citation)