From b6d5675f5da1e91aece2df4af5d037072e897185 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 15 Jan 2019 12:21:30 +0100 Subject: [PATCH 1/6] Update galaxy.yml.sample for prefix config --- config/galaxy.yml.sample | 13 +++++++++++-- config/reports.yml.sample | 8 ++++++++ config/tool_shed.yml.sample | 8 ++++++++ doc/source/admin/galaxy_options.rst | 5 +++-- lib/galaxy/webapps/config_manage.py | 10 ++++++++++ lib/galaxy/webapps/galaxy/config_schema.yml | 4 ++-- 6 files changed, 42 insertions(+), 6 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index f2f30ce7bee..593d6179faf 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -66,6 +66,14 @@ uwsgi: # Reports, etc.) that you are loading. module: galaxy.webapps.galaxy.buildapp:uwsgi_app() + # Mount the web application (e.g. Galaxy, Reports, etc.) at the given + # prefix. Cannot be used together with 'module:' above. + #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() + + # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount- + # points. Set this to true if a prefix is used. + manage-script-name: false + # It is usually a good idea to set this to ``true`` if processes is # greater than 1. thunder-lock: false @@ -91,8 +99,9 @@ uwsgi: galaxy: # If running behind a proxy server and Galaxy is served from a - # subdirectory, enable the proxy-prefix filter and set the prefix in - # the [filter:proxy-prefix] section above. + # subdirectory, enable the proxy-prefix filter, uncomment the 'mount: + # /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()' line and enable + # `manage-script-name` in the uwsgi config section. #filter-with: proxy-prefix # If proxy-prefix is enabled and you're running more than one Galaxy diff --git a/config/reports.yml.sample b/config/reports.yml.sample index aa6fc445e21..3f426e10135 100644 --- a/config/reports.yml.sample +++ b/config/reports.yml.sample @@ -48,6 +48,14 @@ uwsgi: # Reports, etc.) that you are loading. module: galaxy.webapps.reports.buildapp:uwsgi_app() + # Mount the web application (e.g. Galaxy, Reports, etc.) at the given + # prefix. Cannot be used together with 'module:' above. + #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() + + # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount- + # points. Set this to true if a prefix is used. + manage-script-name: false + # It is usually a good idea to set this to ``true`` if processes is # greater than 1. thunder-lock: false diff --git a/config/tool_shed.yml.sample b/config/tool_shed.yml.sample index ea86936c839..619729600f8 100644 --- a/config/tool_shed.yml.sample +++ b/config/tool_shed.yml.sample @@ -48,6 +48,14 @@ uwsgi: # Reports, etc.) that you are loading. module: galaxy.webapps.tool_shed.buildapp:uwsgi_app() + # Mount the web application (e.g. Galaxy, Reports, etc.) at the given + # prefix. Cannot be used together with 'module:' above. + #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() + + # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount- + # points. Set this to true if a prefix is used. + manage-script-name: false + # It is usually a good idea to set this to ``true`` if processes is # greater than 1. thunder-lock: false diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index c9a2b47dc69..45230831bbc 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -4,8 +4,9 @@ :Description: If running behind a proxy server and Galaxy is served from a - subdirectory, enable the proxy-prefix filter and set the prefix in - the [filter:proxy-prefix] section above. + subdirectory, enable the proxy-prefix filter, uncomment the + 'mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()' line + and enable `manage-script-name` in the uwsgi config section. :Default: ``proxy-prefix`` :Type: str diff --git a/lib/galaxy/webapps/config_manage.py b/lib/galaxy/webapps/config_manage.py index 3bd5dbc3dbe..be7f5e4a075 100644 --- a/lib/galaxy/webapps/config_manage.py +++ b/lib/galaxy/webapps/config_manage.py @@ -111,6 +111,16 @@ UWSGI_OPTIONS = OrderedDict([ 'default': '$uwsgi_module', 'type': 'str', }), + ('#mount', { + 'desc': """Mount the web application (e.g. Galaxy, Reports, etc.) at the given prefix. Cannot be used together with 'module:' above.""", + 'default': '/galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()', + 'type': 'str', + }), + ('manage-script-name', { + 'desc': """Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-points. Set this to true if a prefix is used.""", + 'default': False, + 'type': 'bool', + }), ('thunder-lock', { 'desc': """It is usually a good idea to set this to ``true`` if processes is greater than 1.""", 'default': False, diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index ad44ea8d7c5..873e00bd0cc 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -40,8 +40,8 @@ mapping: required: false desc: | If running behind a proxy server and Galaxy is served from a subdirectory, - enable the proxy-prefix filter and set the prefix in the - [filter:proxy-prefix] section above. + enable the proxy-prefix filter, uncomment the 'mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()' + line and enable `manage-script-name` in the uwsgi config section. cookie_path: type: str From d72f82de98f464ace59db312fe9db398793c3494 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 19 Feb 2019 10:37:34 -0500 Subject: [PATCH 2/6] remove Paste config option, reword URL prefix --- config/galaxy.yml.sample | 24 ++++++++++----------- config/reports.yml.sample | 4 ++-- config/tool_shed.yml.sample | 4 ++-- doc/source/admin/galaxy_options.rst | 20 ++++++++--------- lib/galaxy/webapps/config_manage.py | 4 ++-- lib/galaxy/webapps/galaxy/config_schema.yml | 11 +--------- 6 files changed, 29 insertions(+), 38 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index 593d6179faf..75bb1d10c4d 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -67,11 +67,11 @@ uwsgi: module: galaxy.webapps.galaxy.buildapp:uwsgi_app() # Mount the web application (e.g. Galaxy, Reports, etc.) at the given - # prefix. Cannot be used together with 'module:' above. + # URL prefix. Cannot be used together with 'module:' above. #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount- - # points. Set this to true if a prefix is used. + # points. Set this to true if a URL prefix is used. manage-script-name: false # It is usually a good idea to set this to ``true`` if processes is @@ -98,17 +98,17 @@ uwsgi: galaxy: - # If running behind a proxy server and Galaxy is served from a - # subdirectory, enable the proxy-prefix filter, uncomment the 'mount: - # /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()' line and enable - # `manage-script-name` in the uwsgi config section. - #filter-with: proxy-prefix + # If not running behind a proxy server, you may want to enable gzip + # compression to decrease the size of data transferred over the + # network. If using a proxy server, please enable gzip compression + # there instead. + #filter-with: gzip - # If proxy-prefix is enabled and you're running more than one Galaxy - # instance behind one hostname, you will want to set this to the same - # path as the prefix in the filter above. This value becomes the - # "path" attribute set in the cookie so the cookies from each instance - # will not clobber each other. + # If you serve Galaxy at a URL prefix and you're running more than one + # Galaxy instance behind one hostname, you will want to set this to + # the same path as the prefix in the filter above. This value becomes + # the "path" attribute set in the cookie so the cookies from each + # instance will not clobber each other. #cookie_path: '' # By default, Galaxy uses a SQLite database at diff --git a/config/reports.yml.sample b/config/reports.yml.sample index 3f426e10135..b4288fa4ca6 100644 --- a/config/reports.yml.sample +++ b/config/reports.yml.sample @@ -49,11 +49,11 @@ uwsgi: module: galaxy.webapps.reports.buildapp:uwsgi_app() # Mount the web application (e.g. Galaxy, Reports, etc.) at the given - # prefix. Cannot be used together with 'module:' above. + # URL prefix. Cannot be used together with 'module:' above. #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount- - # points. Set this to true if a prefix is used. + # points. Set this to true if a URL prefix is used. manage-script-name: false # It is usually a good idea to set this to ``true`` if processes is diff --git a/config/tool_shed.yml.sample b/config/tool_shed.yml.sample index 619729600f8..857869709a8 100644 --- a/config/tool_shed.yml.sample +++ b/config/tool_shed.yml.sample @@ -49,11 +49,11 @@ uwsgi: module: galaxy.webapps.tool_shed.buildapp:uwsgi_app() # Mount the web application (e.g. Galaxy, Reports, etc.) at the given - # prefix. Cannot be used together with 'module:' above. + # URL prefix. Cannot be used together with 'module:' above. #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount- - # points. Set this to true if a prefix is used. + # points. Set this to true if a URL prefix is used. manage-script-name: false # It is usually a good idea to set this to ``true`` if processes is diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 45230831bbc..b89b455f6b8 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -3,11 +3,11 @@ ~~~~~~~~~~~~~~~ :Description: - If running behind a proxy server and Galaxy is served from a - subdirectory, enable the proxy-prefix filter, uncomment the - 'mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()' line - and enable `manage-script-name` in the uwsgi config section. -:Default: ``proxy-prefix`` + If not running behind a proxy server, you may want to enable gzip + compression to decrease the size of data transferred over the + network. If using a proxy server, please enable gzip compression + there instead. +:Default: ``gzip`` :Type: str @@ -16,11 +16,11 @@ ~~~~~~~~~~~~~~~ :Description: - If proxy-prefix is enabled and you're running more than one Galaxy - instance behind one hostname, you will want to set this to the - same path as the prefix in the filter above. This value becomes - the "path" attribute set in the cookie so the cookies from each - instance will not clobber each other. + If you serve Galaxy at a URL prefix and you're running more than + one Galaxy instance behind one hostname, you will want to set this + to the same path as the prefix in the filter above. This value + becomes the "path" attribute set in the cookie so the cookies from + each instance will not clobber each other. :Default: ```` :Type: str diff --git a/lib/galaxy/webapps/config_manage.py b/lib/galaxy/webapps/config_manage.py index be7f5e4a075..fc0beae88a1 100644 --- a/lib/galaxy/webapps/config_manage.py +++ b/lib/galaxy/webapps/config_manage.py @@ -112,12 +112,12 @@ UWSGI_OPTIONS = OrderedDict([ 'type': 'str', }), ('#mount', { - 'desc': """Mount the web application (e.g. Galaxy, Reports, etc.) at the given prefix. Cannot be used together with 'module:' above.""", + 'desc': """Mount the web application (e.g. Galaxy, Reports, etc.) at the given URL prefix. Cannot be used together with 'module:' above.""", 'default': '/galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()', 'type': 'str', }), ('manage-script-name', { - 'desc': """Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-points. Set this to true if a prefix is used.""", + 'desc': """Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-points. Set this to true if a URL prefix is used.""", 'default': False, 'type': 'bool', }), diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 873e00bd0cc..664402636cd 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -34,21 +34,12 @@ mapping: to decrease the size of data transferred over the network. If using a proxy server, please enable gzip compression there instead. - filter-with: - type: str - default: proxy-prefix - required: false - desc: | - If running behind a proxy server and Galaxy is served from a subdirectory, - enable the proxy-prefix filter, uncomment the 'mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()' - line and enable `manage-script-name` in the uwsgi config section. - cookie_path: type: str default: '' required: false desc: | - If proxy-prefix is enabled and you're running more than one Galaxy instance + If you serve Galaxy at a URL prefix and you're running more than one Galaxy instance behind one hostname, you will want to set this to the same path as the prefix in the filter above. This value becomes the "path" attribute set in the cookie so the cookies from each instance will not clobber each other. From 8c9c27b7f6bd14581af870b0d38339d90501e464 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 21 Feb 2019 17:45:56 +0100 Subject: [PATCH 3/6] Drop filter-with from docs / .sample --- config/galaxy.yml.sample | 6 ------ doc/source/admin/galaxy_options.rst | 13 ------------- 2 files changed, 19 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index 75bb1d10c4d..c6c7eb107c0 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -98,12 +98,6 @@ uwsgi: galaxy: - # If not running behind a proxy server, you may want to enable gzip - # compression to decrease the size of data transferred over the - # network. If using a proxy server, please enable gzip compression - # there instead. - #filter-with: gzip - # If you serve Galaxy at a URL prefix and you're running more than one # Galaxy instance behind one hostname, you will want to set this to # the same path as the prefix in the filter above. This value becomes diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index b89b455f6b8..726d63ca89d 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -1,16 +1,3 @@ -~~~~~~~~~~~~~~~ -``filter-with`` -~~~~~~~~~~~~~~~ - -:Description: - If not running behind a proxy server, you may want to enable gzip - compression to decrease the size of data transferred over the - network. If using a proxy server, please enable gzip compression - there instead. -:Default: ``gzip`` -:Type: str - - ~~~~~~~~~~~~~~~ ``cookie_path`` ~~~~~~~~~~~~~~~ From 1a0f067590d8dcd88857e38d58f62b95a467c641 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 21 Feb 2019 12:26:31 -0500 Subject: [PATCH 4/6] change config schema to reflect removing paste options --- config/galaxy.yml.sample | 6 +++--- doc/source/admin/galaxy_options.rst | 6 +++--- lib/galaxy/webapps/galaxy/config_schema.yml | 11 +---------- 3 files changed, 7 insertions(+), 16 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index c6c7eb107c0..cfed6347d90 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -100,9 +100,9 @@ galaxy: # If you serve Galaxy at a URL prefix and you're running more than one # Galaxy instance behind one hostname, you will want to set this to - # the same path as the prefix in the filter above. This value becomes - # the "path" attribute set in the cookie so the cookies from each - # instance will not clobber each other. + # the same path as the prefix in the mount uWSGI configuration above. + # This value becomes the "path" attribute set in the cookie so the + # cookies from each instance will not clobber each other. #cookie_path: '' # By default, Galaxy uses a SQLite database at diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 726d63ca89d..3383515e1f6 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -5,9 +5,9 @@ :Description: If you serve Galaxy at a URL prefix and you're running more than one Galaxy instance behind one hostname, you will want to set this - to the same path as the prefix in the filter above. This value - becomes the "path" attribute set in the cookie so the cookies from - each instance will not clobber each other. + to the same path as the prefix in the mount uWSGI configuration + above. This value becomes the "path" attribute set in the cookie + so the cookies from each instance will not clobber each other. :Default: ```` :Type: str diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 664402636cd..58380cca392 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -25,15 +25,6 @@ mapping: required: true mapping: - filter-with: - type: str - default: gzip - required: false - desc: | - If not running behind a proxy server, you may want to enable gzip compression - to decrease the size of data transferred over the network. If using a proxy - server, please enable gzip compression there instead. - cookie_path: type: str default: '' @@ -41,7 +32,7 @@ mapping: desc: | If you serve Galaxy at a URL prefix and you're running more than one Galaxy instance behind one hostname, you will want to set this to the same path as the prefix - in the filter above. This value becomes the "path" attribute set in the + in the mount uWSGI configuration above. This value becomes the "path" attribute set in the cookie so the cookies from each instance will not clobber each other. database_connection: From 351c188830793946ce6fa71dfaab95fe3af7cf7a Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 22 Feb 2019 12:07:16 +0000 Subject: [PATCH 5/6] Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports --- config/galaxy.yml.sample | 10 +++--- config/reports.yml.sample | 26 +++++++-------- config/tool_shed.yml.sample | 17 +++++----- doc/source/admin/galaxy_options.rst | 2 +- doc/source/admin/reports_options.rst | 33 +++++++------------ lib/galaxy/webapps/galaxy/config_schema.yml | 2 +- lib/galaxy/webapps/reports/config_schema.yml | 24 +++++--------- .../webapps/tool_shed/config_schema.yml | 10 +++--- 8 files changed, 51 insertions(+), 73 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index cfed6347d90..bc73ee43045 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -98,11 +98,11 @@ uwsgi: galaxy: - # If you serve Galaxy at a URL prefix and you're running more than one - # Galaxy instance behind one hostname, you will want to set this to - # the same path as the prefix in the mount uWSGI configuration above. - # This value becomes the "path" attribute set in the cookie so the - # cookies from each instance will not clobber each other. + # If Galaxy is served at a URL prefix and you are running more than + # one Galaxy instance behind one hostname, you will want to set this + # to the same path as the prefix in the mount uWSGI configuration + # above. This value becomes the "path" attribute set in the cookie so + # the cookies from each instance will not clobber each other. #cookie_path: '' # By default, Galaxy uses a SQLite database at diff --git a/config/reports.yml.sample b/config/reports.yml.sample index b4288fa4ca6..06b315cf134 100644 --- a/config/reports.yml.sample +++ b/config/reports.yml.sample @@ -80,34 +80,30 @@ uwsgi: reports: - # If running behind a proxy server and Galaxy is served from a - # subdirectory, enable the proxy-prefix filter and set the prefix in - # the [filter:proxy-prefix] section above. - #filter-with: proxy-prefix - - # If proxy-prefix is enabled and you're running more than one Galaxy - # instance behind one hostname, you will want to set this to the same - # path as the prefix in the filter above. This value becomes the - # "path" attribute set in the cookie so the cookies from each instance - # will not clobber each other. + # If Galaxy Reports is served at a URL prefix and you are running more + # than one Galaxy Reports instance behind one hostname, you will want + # to set this to the same path as the prefix in the mount uWSGI + # configuration above. This value becomes the "path" attribute set in + # the cookie so the cookies from each instance will not clobber each + # other. #cookie_path: null # Verbosity of console log messages. Acceptable values can be found # here: https://docs.python.org/2/library/logging.html#logging-levels #log_level: DEBUG - # Database connection Galaxy reports are intended for production + # Database connection. Galaxy Reports are intended for production # Galaxy instances, so sqlite (and the default value below) is not # supported. An SQLAlchemy connection string should be used specify an # external database. #database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE' - # Where dataset files are saved Temporary storage for additional - # datasets, this should be shared through the cluster + # Where dataset files are saved. Temporary storage for additional + # datasets, this should be shared through the cluster. #file_path: database/files - # Where dataset files are saved Temporary storage for additional - # datasets, this should be shared through the cluster + # Where dataset files are saved. Temporary storage for additional + # datasets, this should be shared through the cluster. #new_file_path: database/tmp # Mako templates are compiled as needed and cached for reuse, this diff --git a/config/tool_shed.yml.sample b/config/tool_shed.yml.sample index 857869709a8..90dbb628abd 100644 --- a/config/tool_shed.yml.sample +++ b/config/tool_shed.yml.sample @@ -95,7 +95,7 @@ tool_shed: # installation directory. #hgweb_config_dir: null - # Where tool shed repositories are stored. + # Where Tool Shed repositories are stored. #file_path: database/community_files # Temporary storage for additional datasets, this should be shared @@ -233,10 +233,10 @@ tool_shed: # Allow administrators to delete accounts. #allow_user_deletion: false - # For use by email messages sent from the tool shed + # For use by email messages sent from the Tool Shed. #smtp_server: smtp.your_tool_shed_server - # For use by email messages sent from the tool shed + # For use by email messages sent from the Tool Shed. #email_from: your_tool_shed_email@server # If your SMTP server requires a username and password, you can @@ -351,11 +351,12 @@ tool_shed: # store this information. #citation_cache_lock_dir: database/citations/lock - # If proxy-prefix is enabled and you're running more than one Galaxy - # instance behind one hostname, you will want to set this to the same - # path as the prefix in the filter above. This value becomes the - # "path" attribute set in the cookie so the cookies from each instance - # will not clobber each other. + # If the Tool Shed is served at a URL prefix and you are running more + # than one Tool Shed instance behind one hostname, you will want to + # set this to the same path as the prefix in the mount uWSGI + # configuration above. This value becomes the "path" attribute set in + # the cookie so the cookies from each instance will not clobber each + # other. #cookie_path: null # Enable authentication via OpenID. Allows users to log in to their diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 3383515e1f6..f3e49bab46c 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -3,7 +3,7 @@ ~~~~~~~~~~~~~~~ :Description: - If you serve Galaxy at a URL prefix and you're running more than + If Galaxy is served at a URL prefix and you are running more than one Galaxy instance behind one hostname, you will want to set this to the same path as the prefix in the mount uWSGI configuration above. This value becomes the "path" attribute set in the cookie diff --git a/doc/source/admin/reports_options.rst b/doc/source/admin/reports_options.rst index d3cc03e683e..d3512952d51 100644 --- a/doc/source/admin/reports_options.rst +++ b/doc/source/admin/reports_options.rst @@ -1,25 +1,14 @@ -~~~~~~~~~~~~~~~ -``filter-with`` -~~~~~~~~~~~~~~~ - -:Description: - If running behind a proxy server and Galaxy is served from a - subdirectory, enable the proxy-prefix filter and set the prefix in - the [filter:proxy-prefix] section above. -:Default: ``proxy-prefix`` -:Type: str - - ~~~~~~~~~~~~~~~ ``cookie_path`` ~~~~~~~~~~~~~~~ :Description: - If proxy-prefix is enabled and you're running more than one Galaxy - instance behind one hostname, you will want to set this to the - same path as the prefix in the filter above. This value becomes - the "path" attribute set in the cookie so the cookies from each - instance will not clobber each other. + If Galaxy Reports is served at a URL prefix and you are running + more than one Galaxy Reports instance behind one hostname, you + will want to set this to the same path as the prefix in the mount + uWSGI configuration above. This value becomes the "path" attribute + set in the cookie so the cookies from each instance will not + clobber each other. :Default: ``None`` :Type: str @@ -41,7 +30,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Database connection Galaxy reports are intended for production + Database connection. Galaxy Reports are intended for production Galaxy instances, so sqlite (and the default value below) is not supported. An SQLAlchemy connection string should be used specify an external database. @@ -54,8 +43,8 @@ ~~~~~~~~~~~~~ :Description: - Where dataset files are saved Temporary storage for additional - datasets, this should be shared through the cluster + Where dataset files are saved. Temporary storage for additional + datasets, this should be shared through the cluster. :Default: ``database/files`` :Type: str @@ -65,8 +54,8 @@ ~~~~~~~~~~~~~~~~~ :Description: - Where dataset files are saved Temporary storage for additional - datasets, this should be shared through the cluster + Where dataset files are saved. Temporary storage for additional + datasets, this should be shared through the cluster. :Default: ``database/tmp`` :Type: str diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 58380cca392..761a8fc5973 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -30,7 +30,7 @@ mapping: default: '' required: false desc: | - If you serve Galaxy at a URL prefix and you're running more than one Galaxy instance + If Galaxy is served at a URL prefix and you are running more than one Galaxy instance behind one hostname, you will want to set this to the same path as the prefix in the mount uWSGI configuration above. This value becomes the "path" attribute set in the cookie so the cookies from each instance will not clobber each other. diff --git a/lib/galaxy/webapps/reports/config_schema.yml b/lib/galaxy/webapps/reports/config_schema.yml index c02b31d9e06..62003f5aebb 100644 --- a/lib/galaxy/webapps/reports/config_schema.yml +++ b/lib/galaxy/webapps/reports/config_schema.yml @@ -7,20 +7,12 @@ mapping: desc: | Galaxy Reports configuration options. mapping: - filter-with: - type: str - default: proxy-prefix - desc: | - If running behind a proxy server and Galaxy is served from a subdirectory, - enable the proxy-prefix filter and set the prefix in the - [filter:proxy-prefix] section above. - cookie_path: type: str desc: | - If proxy-prefix is enabled and you're running more than one Galaxy instance + If Galaxy Reports is served at a URL prefix and you are running more than one Galaxy Reports instance behind one hostname, you will want to set this to the same path as the prefix - in the filter above. This value becomes the "path" attribute set in the + in the mount uWSGI configuration above. This value becomes the "path" attribute set in the cookie so the cookies from each instance will not clobber each other. log_level: @@ -34,8 +26,8 @@ mapping: type: str default: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE desc: | - Database connection - Galaxy reports are intended for production Galaxy instances, so sqlite (and the default value + Database connection. + Galaxy Reports are intended for production Galaxy instances, so sqlite (and the default value below) is not supported. An SQLAlchemy connection string should be used specify an external database. @@ -43,15 +35,15 @@ mapping: type: str default: database/files desc: | - Where dataset files are saved - Temporary storage for additional datasets, this should be shared through the cluster + Where dataset files are saved. + Temporary storage for additional datasets, this should be shared through the cluster. new_file_path: type: str default: database/tmp desc: | - Where dataset files are saved - Temporary storage for additional datasets, this should be shared through the cluster + Where dataset files are saved. + Temporary storage for additional datasets, this should be shared through the cluster. template_cache_path: type: str diff --git a/lib/galaxy/webapps/tool_shed/config_schema.yml b/lib/galaxy/webapps/tool_shed/config_schema.yml index 03f6eb74666..86e6212a105 100644 --- a/lib/galaxy/webapps/tool_shed/config_schema.yml +++ b/lib/galaxy/webapps/tool_shed/config_schema.yml @@ -37,7 +37,7 @@ mapping: default: database/community_files required: false desc: | - Where tool shed repositories are stored. + Where Tool Shed repositories are stored. new_file_path: type: str @@ -293,14 +293,14 @@ mapping: default: smtp.your_tool_shed_server required: false desc: | - For use by email messages sent from the tool shed + For use by email messages sent from the Tool Shed. email_from: type: str default: your_tool_shed_email@server required: false desc: | - For use by email messages sent from the tool shed + For use by email messages sent from the Tool Shed. smtp_username: type: str @@ -521,9 +521,9 @@ mapping: default: null required: false desc: | - If proxy-prefix is enabled and you're running more than one Galaxy instance + If the Tool Shed is served at a URL prefix and you are running more than one Tool Shed instance behind one hostname, you will want to set this to the same path as the prefix - in the filter above. This value becomes the "path" attribute set in the + in the mount uWSGI configuration above. This value becomes the "path" attribute set in the cookie so the cookies from each instance will not clobber each other. enable_openid: From a83eb67775442f37b22ff20203b88a234ab11bec Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Fri, 22 Feb 2019 11:31:44 -0500 Subject: [PATCH 6/6] Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions. --- config/galaxy.yml.sample | 17 ++++++++++------- config/reports.yml.sample | 17 +++++++---------- config/tool_shed.yml.sample | 14 ++++++-------- doc/source/admin/galaxy_options.rst | 18 +++++++++++------- doc/source/admin/reports_options.rst | 18 ++++++++---------- lib/galaxy/webapps/galaxy/config_schema.yml | 15 +++++++++------ lib/galaxy/webapps/reports/config_schema.yml | 15 +++++++-------- lib/galaxy/webapps/tool_shed/config_schema.yml | 12 ++++++------ 8 files changed, 64 insertions(+), 62 deletions(-) diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample index bc73ee43045..6de3271e013 100644 --- a/config/galaxy.yml.sample +++ b/config/galaxy.yml.sample @@ -98,11 +98,11 @@ uwsgi: galaxy: - # If Galaxy is served at a URL prefix and you are running more than - # one Galaxy instance behind one hostname, you will want to set this - # to the same path as the prefix in the mount uWSGI configuration - # above. This value becomes the "path" attribute set in the cookie so - # the cookies from each instance will not clobber each other. + # When running multiple Galaxy instances under separate URL prefixes + # on a single hostname, you will want to set this to the same path as + # the prefix set in the uWSGI "mount" configuration option above. This + # value becomes the "path" attribute set in the cookie so the cookies + # from one instance will not clobber those from another. #cookie_path: '' # By default, Galaxy uses a SQLite database at @@ -170,10 +170,13 @@ galaxy: # not recommended for production use. #database_auto_migrate: false - # Dataset files are stored in this directory. + # Where dataset files are stored. It must accessible at the same path + # on any cluster nodes that will run Galaxy jobs, unless using Pulsar. #file_path: database/files - # Temporary files are stored in this directory. + # Where temporary files are stored. It must accessible at the same + # path on any cluster nodes that will run Galaxy jobs, unless using + # Pulsar. #new_file_path: database/tmp # Tool config files, defines what tools are available in Galaxy. Tools diff --git a/config/reports.yml.sample b/config/reports.yml.sample index 06b315cf134..fa9e533bcfd 100644 --- a/config/reports.yml.sample +++ b/config/reports.yml.sample @@ -80,12 +80,11 @@ uwsgi: reports: - # If Galaxy Reports is served at a URL prefix and you are running more - # than one Galaxy Reports instance behind one hostname, you will want - # to set this to the same path as the prefix in the mount uWSGI - # configuration above. This value becomes the "path" attribute set in - # the cookie so the cookies from each instance will not clobber each - # other. + # When running multiple Galaxy Reports instances under separate URL + # prefixes on a single hostname, you will want to set this to the same + # path as the prefix set in the uWSGI "mount" configuration option + # above. This value becomes the "path" attribute set in the cookie so + # the cookies from one instance will not clobber those from another. #cookie_path: null # Verbosity of console log messages. Acceptable values can be found @@ -98,12 +97,10 @@ reports: # external database. #database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE' - # Where dataset files are saved. Temporary storage for additional - # datasets, this should be shared through the cluster. + # Where dataset files are stored. #file_path: database/files - # Where dataset files are saved. Temporary storage for additional - # datasets, this should be shared through the cluster. + # Where temporary files are stored. #new_file_path: database/tmp # Mako templates are compiled as needed and cached for reuse, this diff --git a/config/tool_shed.yml.sample b/config/tool_shed.yml.sample index 90dbb628abd..fc709bc0c01 100644 --- a/config/tool_shed.yml.sample +++ b/config/tool_shed.yml.sample @@ -98,8 +98,7 @@ tool_shed: # Where Tool Shed repositories are stored. #file_path: database/community_files - # Temporary storage for additional datasets, this should be shared - # through the cluster + # Where temporary files are stored. #new_file_path: database/tmp # File containing old-style genome builds @@ -351,12 +350,11 @@ tool_shed: # store this information. #citation_cache_lock_dir: database/citations/lock - # If the Tool Shed is served at a URL prefix and you are running more - # than one Tool Shed instance behind one hostname, you will want to - # set this to the same path as the prefix in the mount uWSGI - # configuration above. This value becomes the "path" attribute set in - # the cookie so the cookies from each instance will not clobber each - # other. + # When running multiple Tool Shed instances under separate URL + # prefixes on a single hostname, you will want to set this to the same + # path as the prefix set in the uWSGI "mount" configuration option + # above. This value becomes the "path" attribute set in the cookie so + # the cookies from one instance will not clobber those from another. #cookie_path: null # Enable authentication via OpenID. Allows users to log in to their diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index f3e49bab46c..d95bcd682a1 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -3,11 +3,11 @@ ~~~~~~~~~~~~~~~ :Description: - If Galaxy is served at a URL prefix and you are running more than - one Galaxy instance behind one hostname, you will want to set this - to the same path as the prefix in the mount uWSGI configuration - above. This value becomes the "path" attribute set in the cookie - so the cookies from each instance will not clobber each other. + When running multiple Galaxy instances under separate URL prefixes + on a single hostname, you will want to set this to the same path + as the prefix set in the uWSGI "mount" configuration option above. + This value becomes the "path" attribute set in the cookie so the + cookies from one instance will not clobber those from another. :Default: ```` :Type: str @@ -161,7 +161,9 @@ ~~~~~~~~~~~~~ :Description: - Dataset files are stored in this directory. + Where dataset files are stored. It must accessible at the same + path on any cluster nodes that will run Galaxy jobs, unless using + Pulsar. :Default: ``database/files`` :Type: str @@ -171,7 +173,9 @@ ~~~~~~~~~~~~~~~~~ :Description: - Temporary files are stored in this directory. + Where temporary files are stored. It must accessible at the same + path on any cluster nodes that will run Galaxy jobs, unless using + Pulsar. :Default: ``database/tmp`` :Type: str diff --git a/doc/source/admin/reports_options.rst b/doc/source/admin/reports_options.rst index d3512952d51..1a0a7b83032 100644 --- a/doc/source/admin/reports_options.rst +++ b/doc/source/admin/reports_options.rst @@ -3,12 +3,12 @@ ~~~~~~~~~~~~~~~ :Description: - If Galaxy Reports is served at a URL prefix and you are running - more than one Galaxy Reports instance behind one hostname, you - will want to set this to the same path as the prefix in the mount - uWSGI configuration above. This value becomes the "path" attribute - set in the cookie so the cookies from each instance will not - clobber each other. + When running multiple Galaxy Reports instances under separate URL + prefixes on a single hostname, you will want to set this to the + same path as the prefix set in the uWSGI "mount" configuration + option above. This value becomes the "path" attribute set in the + cookie so the cookies from one instance will not clobber those + from another. :Default: ``None`` :Type: str @@ -43,8 +43,7 @@ ~~~~~~~~~~~~~ :Description: - Where dataset files are saved. Temporary storage for additional - datasets, this should be shared through the cluster. + Where dataset files are stored. :Default: ``database/files`` :Type: str @@ -54,8 +53,7 @@ ~~~~~~~~~~~~~~~~~ :Description: - Where dataset files are saved. Temporary storage for additional - datasets, this should be shared through the cluster. + Where temporary files are stored. :Default: ``database/tmp`` :Type: str diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 761a8fc5973..ace6732a500 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -30,10 +30,11 @@ mapping: default: '' required: false desc: | - If Galaxy is served at a URL prefix and you are running more than one Galaxy instance - behind one hostname, you will want to set this to the same path as the prefix - in the mount uWSGI configuration above. This value becomes the "path" attribute set in the - cookie so the cookies from each instance will not clobber each other. + When running multiple Galaxy instances under separate URL prefixes on a + single hostname, you will want to set this to the same path as the prefix set + in the uWSGI "mount" configuration option above. This value becomes the "path" + attribute set in the cookie so the cookies from one instance will not clobber + those from another. database_connection: type: str @@ -143,14 +144,16 @@ mapping: default: database/files required: false desc: | - Dataset files are stored in this directory. + Where dataset files are stored. It must accessible at the same path on any cluster + nodes that will run Galaxy jobs, unless using Pulsar. new_file_path: type: str default: database/tmp required: false desc: | - Temporary files are stored in this directory. + Where temporary files are stored. It must accessible at the same path on any cluster + nodes that will run Galaxy jobs, unless using Pulsar. tool_config_file: type: str diff --git a/lib/galaxy/webapps/reports/config_schema.yml b/lib/galaxy/webapps/reports/config_schema.yml index 62003f5aebb..91be030da36 100644 --- a/lib/galaxy/webapps/reports/config_schema.yml +++ b/lib/galaxy/webapps/reports/config_schema.yml @@ -10,10 +10,11 @@ mapping: cookie_path: type: str desc: | - If Galaxy Reports is served at a URL prefix and you are running more than one Galaxy Reports instance - behind one hostname, you will want to set this to the same path as the prefix - in the mount uWSGI configuration above. This value becomes the "path" attribute set in the - cookie so the cookies from each instance will not clobber each other. + When running multiple Galaxy Reports instances under separate URL prefixes on a + single hostname, you will want to set this to the same path as the prefix set + in the uWSGI "mount" configuration option above. This value becomes the "path" + attribute set in the cookie so the cookies from one instance will not clobber + those from another. log_level: type: str @@ -35,15 +36,13 @@ mapping: type: str default: database/files desc: | - Where dataset files are saved. - Temporary storage for additional datasets, this should be shared through the cluster. + Where dataset files are stored. new_file_path: type: str default: database/tmp desc: | - Where dataset files are saved. - Temporary storage for additional datasets, this should be shared through the cluster. + Where temporary files are stored. template_cache_path: type: str diff --git a/lib/galaxy/webapps/tool_shed/config_schema.yml b/lib/galaxy/webapps/tool_shed/config_schema.yml index 86e6212a105..71309d85c89 100644 --- a/lib/galaxy/webapps/tool_shed/config_schema.yml +++ b/lib/galaxy/webapps/tool_shed/config_schema.yml @@ -44,8 +44,7 @@ mapping: default: database/tmp required: false desc: | - Temporary storage for additional datasets, - this should be shared through the cluster + Where temporary files are stored. builds_file_path: type: str @@ -521,10 +520,11 @@ mapping: default: null required: false desc: | - If the Tool Shed is served at a URL prefix and you are running more than one Tool Shed instance - behind one hostname, you will want to set this to the same path as the prefix - in the mount uWSGI configuration above. This value becomes the "path" attribute set in the - cookie so the cookies from each instance will not clobber each other. + When running multiple Tool Shed instances under separate URL prefixes on a + single hostname, you will want to set this to the same path as the prefix set + in the uWSGI "mount" configuration option above. This value becomes the "path" + attribute set in the cookie so the cookies from one instance will not clobber + those from another. enable_openid: type: bool