Commit 64cf8bfe authored by John Chilton's avatar John Chilton
Browse files

Remove can_eliminate_tool_dependency from tool shed code.

parent 84dfd954

lib/galaxy/tool_shed/util/shed_util_common.py

+0 −33
Original line number Diff line number Diff line
@@ -29,31 +29,6 @@ def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owne 
    return True





def can_eliminate_tool_dependency(metadata_dict, name, dependency_type, version):

    """

    Determine if the relationship between a tool_dependency record

    associated with a tool_shed_repository record on the Galaxy side

    can be eliminated.

    """

    td_dict = metadata_dict.get("tool_dependencies", {})

    for td_key, td_val in td_dict.items():

        if td_key == "set_environment":

            for td in td_val:

                n = td.get("name", None)

                t = td.get("type", None)

                if n == name and t == dependency_type:

                    # The tool dependency is current, so keep it.

                    return False

        else:

            n = td_val.get("name", None)

            t = td_val.get("type", None)

            v = td_val.get("version", None)

            if n == name and t == dependency_type and v == version:

                # The tool dependency is current, so keep it.

                return False

    return True





def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, tool_shed_url):

    """

    Repositories of type tool_dependency_definition allow for defining a
@@ -71,13 +46,6 @@ def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, t 
            log.debug(message % (r.name, r.owner, tool_shed_repository.name, tool_shed_repository.owner))

            trans.install_model.context.delete(rrda)

            trans.install_model.context.flush()

    for td in tool_shed_repository.tool_dependencies:

        if can_eliminate_tool_dependency(metadata_dict, td.name, td.type, td.version):

            message = "Tool dependency %s, version %s is not required by repository %s, owner %s, "

            message += "removing from list of tool dependencies."

            log.debug(message % (td.name, td.version, tool_shed_repository.name, tool_shed_repository.owner))

            trans.install_model.context.delete(td)

            trans.install_model.context.flush()





def generate_tool_guid(repository_clone_url, tool):
@@ -212,7 +180,6 @@ def tool_shed_is_this_tool_shed(toolshed_base_url): 


__all__ = (

    "can_eliminate_repository_dependency",

    "can_eliminate_tool_dependency",

    "clean_dependency_relationships",

    "DATATYPES_CONFIG_FILENAME",

    "generate_tool_guid",

lib/tool_shed/util/shed_util_common.py

+0 −2
Original line number Diff line number Diff line
@@ -15,7 +15,6 @@ import galaxy.tool_util.deps.requirements 
from galaxy import util

from galaxy.tool_shed.util.shed_util_common import (

    can_eliminate_repository_dependency,

    can_eliminate_tool_dependency,

    clean_dependency_relationships,

    generate_tool_guid,

    get_ctx_rev,
@@ -499,7 +498,6 @@ def open_repository_files_folder(app, folder_path, repository_id, is_admin=False 


__all__ = (

    "can_eliminate_repository_dependency",

    "can_eliminate_tool_dependency",

    "clean_dependency_relationships",

    "count_repositories_in_category",

    "generate_tool_guid",