From ebd5bad6237396220a4445d96dbd1013c25950ed Mon Sep 17 00:00:00 2001 From: selten Date: Mon, 10 Mar 2025 16:47:56 +0100 Subject: [PATCH 1/3] Allow overriding datatypes for planemo lint Allow overriding the datatypes_conf.xml.sample that's added by default by the Python galaxy-tool-util package for non-standard datatype support --- lib/galaxy/tool_util/linters/datatypes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/linters/datatypes.py b/lib/galaxy/tool_util/linters/datatypes.py index cd35f0600fc..d63ba6bd89a 100644 --- a/lib/galaxy/tool_util/linters/datatypes.py +++ b/lib/galaxy/tool_util/linters/datatypes.py @@ -18,7 +18,7 @@ if TYPE_CHECKING: from galaxy.tool_util.parser import ToolSource from galaxy.util.resources import Traversable -DATATYPES_CONF = resource_path(__name__, "datatypes_conf.xml.sample") +DATATYPES_CONF = os.getenv('DATATYPES_CONF', resource_path(__package__, "datatypes_conf.xml.sample")) def _parse_datatypes(datatype_conf_path: Union[str, "Traversable"]) -> Set[str]: From 48432c9c431a68f82aec2bc2d170acf2f5d9bf8a Mon Sep 17 00:00:00 2001 From: selten Date: Mon, 10 Mar 2025 16:58:21 +0100 Subject: [PATCH 2/3] Fix import and lint for quotes --- lib/galaxy/tool_util/linters/datatypes.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/linters/datatypes.py b/lib/galaxy/tool_util/linters/datatypes.py index d63ba6bd89a..a4f4514d399 100644 --- a/lib/galaxy/tool_util/linters/datatypes.py +++ b/lib/galaxy/tool_util/linters/datatypes.py @@ -1,4 +1,5 @@ import os.path +from os import getenv from typing import ( Set, TYPE_CHECKING, @@ -18,7 +19,7 @@ if TYPE_CHECKING: from galaxy.tool_util.parser import ToolSource from galaxy.util.resources import Traversable -DATATYPES_CONF = os.getenv('DATATYPES_CONF', resource_path(__package__, "datatypes_conf.xml.sample")) +DATATYPES_CONF = getenv("DATATYPES_CONF", resource_path(__package__, "datatypes_conf.xml.sample")) def _parse_datatypes(datatype_conf_path: Union[str, "Traversable"]) -> Set[str]: From 1f35aa2d69b34979f4030baf2050ee945c9eb2e7 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Tue, 6 May 2025 18:42:09 +0200 Subject: [PATCH 3/3] Restore resource_path args --- lib/galaxy/tool_util/linters/datatypes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/linters/datatypes.py b/lib/galaxy/tool_util/linters/datatypes.py index a4f4514d399..6d7c72a8c6b 100644 --- a/lib/galaxy/tool_util/linters/datatypes.py +++ b/lib/galaxy/tool_util/linters/datatypes.py @@ -19,7 +19,7 @@ if TYPE_CHECKING: from galaxy.tool_util.parser import ToolSource from galaxy.util.resources import Traversable -DATATYPES_CONF = getenv("DATATYPES_CONF", resource_path(__package__, "datatypes_conf.xml.sample")) +DATATYPES_CONF = getenv("DATATYPES_CONF", resource_path(__name__, "datatypes_conf.xml.sample")) def _parse_datatypes(datatype_conf_path: Union[str, "Traversable"]) -> Set[str]: