From 51b820a594dcf9ddc9909240a246b6ac9c0de3c3 Mon Sep 17 00:00:00 2001 From: Simon Bray Date: Tue, 9 Feb 2021 23:42:08 +0100 Subject: [PATCH 1/2] submit input_format to tools API in payload, not as a parameter --- lib/galaxy/webapps/galaxy/api/tools.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index 274903f4604..f4450819d65 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -486,8 +486,12 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin): POST /api/tools Execute tool with a given parameter payload - :param input_format: input format for the payload. Possible values are the default 'legacy' (where inputs nested inside conditionals or repeats are identified with e.g. '|') or '21.01' (where inputs inside conditionals or repeats are nested elements). - :type input_format: string + :param input_format: input format for the payload. Possible values are + the default 'legacy' (where inputs nested inside conditionals or + repeats are identified with e.g. '|') or + '21.01' (where inputs inside conditionals or repeats are nested + elements). + :type input_format: str """ tool_id = payload.get("tool_id") tool_uuid = payload.get("tool_uuid") @@ -559,7 +563,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin): # as a regular tool parameter we accept both. use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false')) - input_format = kwd.get('input_format', 'legacy') + input_format = payload.get('input_format', 'legacy') vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format) From 33035a022f85cd82be8656344efd4d90563c56af Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 10 Feb 2021 04:03:14 +0000 Subject: [PATCH 2/2] Cast `input_format` to str When passed in the payload, '21.01' get somewhere converted to a float. --- lib/galaxy/webapps/galaxy/api/tools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index f4450819d65..1416a864de1 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -563,7 +563,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin): # as a regular tool parameter we accept both. use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false')) - input_format = payload.get('input_format', 'legacy') + input_format = str(payload.get('input_format', 'legacy')) vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)