From 59f74e3d1a741670f681b1201caf5b1d5d4e2ff2 Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Wed, 28 Aug 2019 14:07:03 -0400 Subject: [PATCH 1/4] Reverse previous edit Addresses this: https://github.com/galaxyproject/galaxy/pull/8475#discussion_r315966257 (None is the default) --- lib/galaxy/util/watcher.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py index 5882139db10..5ae9e41f6bb 100644 --- a/lib/galaxy/util/watcher.py +++ b/lib/galaxy/util/watcher.py @@ -143,7 +143,7 @@ class EventHandler(FileSystemEventHandler): # look at dest if it exists else use src. path = getattr(event, 'dest_path', None) or event.src_path path = os.path.abspath(path) - callback = self.watcher.file_callbacks.get(path, None) + callback = self.watcher.file_callbacks.get(path) if os.path.basename(path).startswith('.'): return if callback: From 1b08bcf5f44bcef61b9f6b47dfa551c71b8432ae Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Wed, 28 Aug 2019 14:13:34 -0400 Subject: [PATCH 2/4] Move config_manage unit tests to config/ config_manage.py was moved from webapps/ to config/. This edit makes the unit tests location consistent with the module they test. --- .../config_manage/1607_root_filters/config/galaxy.ini | 0 .../config_manage/1607_root_filters/config/tool_shed.ini | 0 .../config_manage/1607_root_samples/config/galaxy.ini | 0 .../config_manage/1607_root_samples/config/reports.ini | 0 .../config_manage/1607_root_samples/config/tool_shed.ini | 0 .../config_manage/1705_allow_path_paste/config/galaxy.ini | 0 test/unit/{webapps => config}/config_manage/__init__.py | 0 test/unit/{webapps => config}/config_manage/test_appschema.py | 0 test/unit/{webapps => config}/config_manage/test_config_manage.py | 0 9 files changed, 0 insertions(+), 0 deletions(-) rename test/unit/{webapps => config}/config_manage/1607_root_filters/config/galaxy.ini (100%) rename test/unit/{webapps => config}/config_manage/1607_root_filters/config/tool_shed.ini (100%) rename test/unit/{webapps => config}/config_manage/1607_root_samples/config/galaxy.ini (100%) rename test/unit/{webapps => config}/config_manage/1607_root_samples/config/reports.ini (100%) rename test/unit/{webapps => config}/config_manage/1607_root_samples/config/tool_shed.ini (100%) rename test/unit/{webapps => config}/config_manage/1705_allow_path_paste/config/galaxy.ini (100%) rename test/unit/{webapps => config}/config_manage/__init__.py (100%) rename test/unit/{webapps => config}/config_manage/test_appschema.py (100%) rename test/unit/{webapps => config}/config_manage/test_config_manage.py (100%) diff --git a/test/unit/webapps/config_manage/1607_root_filters/config/galaxy.ini b/test/unit/config/config_manage/1607_root_filters/config/galaxy.ini similarity index 100% rename from test/unit/webapps/config_manage/1607_root_filters/config/galaxy.ini rename to test/unit/config/config_manage/1607_root_filters/config/galaxy.ini diff --git a/test/unit/webapps/config_manage/1607_root_filters/config/tool_shed.ini b/test/unit/config/config_manage/1607_root_filters/config/tool_shed.ini similarity index 100% rename from test/unit/webapps/config_manage/1607_root_filters/config/tool_shed.ini rename to test/unit/config/config_manage/1607_root_filters/config/tool_shed.ini diff --git a/test/unit/webapps/config_manage/1607_root_samples/config/galaxy.ini b/test/unit/config/config_manage/1607_root_samples/config/galaxy.ini similarity index 100% rename from test/unit/webapps/config_manage/1607_root_samples/config/galaxy.ini rename to test/unit/config/config_manage/1607_root_samples/config/galaxy.ini diff --git a/test/unit/webapps/config_manage/1607_root_samples/config/reports.ini b/test/unit/config/config_manage/1607_root_samples/config/reports.ini similarity index 100% rename from test/unit/webapps/config_manage/1607_root_samples/config/reports.ini rename to test/unit/config/config_manage/1607_root_samples/config/reports.ini diff --git a/test/unit/webapps/config_manage/1607_root_samples/config/tool_shed.ini b/test/unit/config/config_manage/1607_root_samples/config/tool_shed.ini similarity index 100% rename from test/unit/webapps/config_manage/1607_root_samples/config/tool_shed.ini rename to test/unit/config/config_manage/1607_root_samples/config/tool_shed.ini diff --git a/test/unit/webapps/config_manage/1705_allow_path_paste/config/galaxy.ini b/test/unit/config/config_manage/1705_allow_path_paste/config/galaxy.ini similarity index 100% rename from test/unit/webapps/config_manage/1705_allow_path_paste/config/galaxy.ini rename to test/unit/config/config_manage/1705_allow_path_paste/config/galaxy.ini diff --git a/test/unit/webapps/config_manage/__init__.py b/test/unit/config/config_manage/__init__.py similarity index 100% rename from test/unit/webapps/config_manage/__init__.py rename to test/unit/config/config_manage/__init__.py diff --git a/test/unit/webapps/config_manage/test_appschema.py b/test/unit/config/config_manage/test_appschema.py similarity index 100% rename from test/unit/webapps/config_manage/test_appschema.py rename to test/unit/config/config_manage/test_appschema.py diff --git a/test/unit/webapps/config_manage/test_config_manage.py b/test/unit/config/config_manage/test_config_manage.py similarity index 100% rename from test/unit/webapps/config_manage/test_config_manage.py rename to test/unit/config/config_manage/test_config_manage.py From b451974d1bc0054a0276b44f7361c588cc4b72a5 Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Wed, 28 Aug 2019 15:01:03 -0400 Subject: [PATCH 3/4] Surround true/false default str values w/quotes To make consistent across file + not to confuse w/boolean values. --- lib/galaxy/webapps/galaxy/config_schema.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 7672a7c977d..d1e4f96dab8 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -28,7 +28,7 @@ mapping: config_dir: type: str - default: false + default: 'false' required: false desc: | The directory that will be prepended to relative paths in options specifying @@ -37,7 +37,7 @@ mapping: data_dir: type: str - default: false + default: 'false' required: false desc: | The directory that will be prepended to relative paths in options specifying From 2270dace269eb05796c3e10ec5b96883b5021d04 Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Wed, 28 Aug 2019 15:49:09 -0400 Subject: [PATCH 4/4] Run make config-rebuild to reflect latest edits --- doc/source/admin/galaxy_options.rst | 6 +++--- lib/galaxy/config/sample/galaxy.yml.sample | 10 +++++----- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 1aa7d153459..33140dc3a58 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -1248,12 +1248,12 @@ :Type: bool -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``interactivetools_enable`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Set this to true to enable InteractiveTools. + Enable InteractiveTools. :Default: ``false`` :Type: bool diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index b84c1be6194..712c62fd348 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -101,13 +101,13 @@ galaxy: # The directory that will be prepended to relative paths in options # specifying other Galaxy config files (e.g. datatypes_config_file). # Defaults to the directory in which galaxy.yml is located. - #config_dir: false + #config_dir: 'false' # The directory that will be prepended to relative paths in options # specifying Galaxy data/cache directories and files (such as the # default SQLite database, file_path, etc.). Defaults to `database/` # if running Galaxy from source or `/data` otherwise. - #data_dir: false + #data_dir: 'false' # By default, Galaxy uses a SQLite database at # 'database/universe.sqlite'. You may use a SQLAlchemy connection @@ -428,9 +428,6 @@ galaxy: # scenarios than the watchdog default. #watch_tool_data_dir: 'false' - # Enable InteractiveTools by setting to true - #interactivetools_enable: false - # File containing old-style genome builds #builds_file_path: tool-data/shared/ucsc/builds.txt @@ -676,6 +673,9 @@ galaxy: # third-party server, tricking a Galaxy user to access said site. #enable_old_display_applications: true + # Enable InteractiveTools. + #interactivetools_enable: false + # Show visualization tab and list in masthead. #visualizations_visible: true