From 53f14908efdebcf7881ce39a638faa375c4cd1b9 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 19 Jan 2022 23:33:47 +0000 Subject: [PATCH 1/2] Fix test_deserialize_* unit tests Fix: ``` def test_deserialize_xml_tool(tool_app): > tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL) test/unit/app/tools/test_tool_deserialization.py:59: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/unit/app/tools/test_tool_deserialization.py:54: in _deserialize return create_tool_from_source(app, tool_source=tool_source) lib/galaxy/tools/__init__.py:278: in create_tool_from_source tool = ToolClass(config_file, tool_source, app, **kwds) lib/galaxy/tools/__init__.py:606: in __init__ raise e lib/galaxy/tools/__init__.py:603: in __init__ self.parse(tool_source, guid=guid, dynamic=dynamic) if has_missing_data: biotools_reference = self.biotools_reference > metadata_source = self.app.biotools_metadata_source E AttributeError: 'ToolApp' object has no attribute 'biotools_metadata_source' lib/galaxy/tools/__init__.py:1032: AttributeError ``` introduced merging forward https://github.com/galaxyproject/galaxy/pull/13202 . --- test/unit/app/tools/test_tool_deserialization.py | 1 + 1 file changed, 1 insertion(+) diff --git a/test/unit/app/tools/test_tool_deserialization.py b/test/unit/app/tools/test_tool_deserialization.py index 91ddca5ddc5..3c0577bf81d 100644 --- a/test/unit/app/tools/test_tool_deserialization.py +++ b/test/unit/app/tools/test_tool_deserialization.py @@ -40,6 +40,7 @@ outputs: class ToolApp(GalaxyDataTestApp): name = 'galaxy' + biotools_metadata_source = None job_search = None From 15d4d2952d42f1d453a816dca18fa6dea583c41d Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 20 Jan 2022 08:39:20 +0100 Subject: [PATCH 2/2] Fix ToolApp --- lib/galaxy/tools/remote_tool_eval.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py index f6984818753..8ffef968398 100644 --- a/lib/galaxy/tools/remote_tool_eval.py +++ b/lib/galaxy/tools/remote_tool_eval.py @@ -63,6 +63,7 @@ class ToolApp(MinimalToolApp): self.genome_builds = GenomeBuilds(self) self.tool_data_tables = tool_data_table_manager self.file_sources = file_sources + self.biotools_metadata_source = None def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):