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Fix bugs in tool shed tool API. #18558

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merged 1 commit into from
Jul 17, 2024
Merged

Fix bugs in tool shed tool API. #18558

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9 changes: 8 additions & 1 deletion lib/tool_shed/managers/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from galaxy.exceptions import (
InternalServerError,
ObjectNotFound,
RequestParameterInvalidException,
)
from galaxy.tool_shed.metadata.metadata_generator import RepositoryMetadataToolDict
from galaxy.tool_shed.util.basic_util import remove_dir
Expand All @@ -28,6 +29,7 @@
ToolSource,
)
from galaxy.tools.stock import stock_tool_sources
from galaxy.util import relpath
from tool_shed.context import (
ProvidesRepositoriesContext,
SessionRequestContext,
Expand Down Expand Up @@ -82,6 +84,9 @@ def search(trans: SessionRequestContext, q: str, page: int = 1, page_size: int =
def get_repository_metadata_tool_dict(
trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str
) -> Tuple[RepositoryMetadata, RepositoryMetadataToolDict]:
if trs_tool_id.count("~") < 2:
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RequestParameterInvalidException(f"Invalid TRS tool id ({trs_tool_id})")

name, owner, tool_id = trs_tool_id.split("~", 3)
repository, metadata_by_version = trs_tool_id_to_repository_metadata(trans, trs_tool_id)
if tool_version not in metadata_by_version:
Expand Down Expand Up @@ -143,7 +148,9 @@ def _shed_tool_source_for(
cloned_ok, error_message = clone_repository(repository_clone_url, work_dir, str(ctx.rev()))
if error_message:
raise InternalServerError("Failed to materialize target repository revision")
path_to_tool = os.path.join(work_dir, tool_config)
repo_files_dir = repository_metadata.repository.repo_path(trans.app)
repo_rel_tool_path = relpath(tool_config, repo_files_dir)
path_to_tool = os.path.join(work_dir, repo_rel_tool_path)
tool_source = get_tool_source(path_to_tool)
return tool_source
finally:
Expand Down
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