From 5b41e32a842a7d9c021e5e770608065725adbd7c Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 22 Oct 2021 17:34:17 +0200 Subject: [PATCH 1/4] let Galaxy use output_to_working dir most importantly this will set the galaxy dir and its files dir to read only. which allows planemo test to find cases of tools that write into galaxy's files dir. see also here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483 --- planemo/galaxy/config.py | 1 + 1 file changed, 1 insertion(+) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index c995d96b9..a0a2a4a98 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -493,6 +493,7 @@ def config_join(*args): migrated_tools_config=empty_tool_conf, test_data_dir=test_data_dir, # TODO: make gx respect this shed_data_manager_config_file=shed_data_manager_config_file, + outputs_to_working_directory = "True", )) _handle_container_resolution(ctx, kwds, properties) write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args)) From 13c4f21cd6c7a53a949fb3155224f657a97cfc15 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 22 Oct 2021 17:45:58 +0200 Subject: [PATCH 2/4] add comment and fix linting --- planemo/galaxy/config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index a0a2a4a98..4b94e704c 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -493,7 +493,7 @@ def config_join(*args): migrated_tools_config=empty_tool_conf, test_data_dir=test_data_dir, # TODO: make gx respect this shed_data_manager_config_file=shed_data_manager_config_file, - outputs_to_working_directory = "True", + outputs_to_working_directory = "True", # this makes Galaxy's files dir RO for dockerized testing )) _handle_container_resolution(ctx, kwds, properties) write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args)) From 9e156db620334c40d1a80ae22311552385c7b8c7 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 22 Oct 2021 17:51:46 +0200 Subject: [PATCH 3/4] remove TODO --- planemo/galaxy/config.py | 1 - 1 file changed, 1 deletion(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index 4b94e704c..1a7394a90 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -509,7 +509,6 @@ def config_join(*args): # sanitize_all_html = True # serve_xss_vulnerable_mimetypes = False # track_jobs_in_database = None - # outputs_to_working_directory = False # retry_job_output_collection = 0 env = _build_env_for_galaxy(properties, template_args) From 4b699cbd1f501608c52daf969bd68901159bb184 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 22 Oct 2021 19:30:09 +0200 Subject: [PATCH 4/4] fix lint error --- planemo/galaxy/config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index 1a7394a90..b7195ad89 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -493,7 +493,7 @@ def config_join(*args): migrated_tools_config=empty_tool_conf, test_data_dir=test_data_dir, # TODO: make gx respect this shed_data_manager_config_file=shed_data_manager_config_file, - outputs_to_working_directory = "True", # this makes Galaxy's files dir RO for dockerized testing + outputs_to_working_directory="True", # this makes Galaxy's files dir RO for dockerized testing )) _handle_container_resolution(ctx, kwds, properties) write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args))