diff --git a/doc/source/admin/apache.md b/doc/source/admin/apache.md index 6494473a8e5..40370e9ceec 100644 --- a/doc/source/admin/apache.md +++ b/doc/source/admin/apache.md @@ -150,7 +150,6 @@ SSLStaplingCache shmcb:/var/run/ocsp(128000) # serve framework static content RewriteEngine On - RewriteRule ^/static/style/(.*) ${galaxy_root}/static/style/blue/$1 [L] RewriteRule ^/static/(.*) ${galaxy_root}/static/$1 [L] RewriteRule ^/favicon.ico ${galaxy_root}/static/favicon.ico [L] RewriteRule ^/robots.txt ${galaxy_root}/static/robots.txt [L] @@ -216,7 +215,6 @@ previous section: # serve framework static content RewriteEngine On RewriteRule ^/galaxy/$ /galaxy [R,L] - RewriteRule ^/galaxy/static/style/(.*) ${galaxy_root}/static/style/blue/$1 [L] RewriteRule ^/galaxy/static/(.*) ${galaxy_root}/static/$1 [L] RewriteRule ^/galaxy/favicon.ico ${galaxy_root}/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt ${galaxy_root}/static/robots.txt [L] diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index c36c95d5cac..7d2c1bc7763 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -226,7 +226,7 @@ Where dataset files are stored. It must be accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar. -:Default: ``files`` +:Default: ``objects`` :Type: str @@ -1078,9 +1078,12 @@ :Description: What Dataset attribute is used to reference files in an - ObjectStore implementation, default is 'id' but can also be set to - 'uuid' for more de-centralized usage. -:Default: ``id`` + ObjectStore implementation, this can be 'uuid' or 'id'. The + default will depend on how the object store is configured, + starting with 20.05 Galaxy will try to default to 'uuid' if it can + be sure this is a new Galaxy instance - but the default will be + 'id' in many cases. +:Default: ``None`` :Type: str diff --git a/doc/source/admin/nginx.md b/doc/source/admin/nginx.md index 33763b63095..ff204970d5e 100644 --- a/doc/source/admin/nginx.md +++ b/doc/source/admin/nginx.md @@ -117,7 +117,7 @@ http { server_name _; # use a variable for convenience - set $galaxy_root /srv/galaxy/server; + set $galaxy_root /srv/galaxy/server; # Enable HSTS add_header Strict-Transport-Security "max-age=15552000; includeSubdomains"; @@ -129,28 +129,24 @@ http { include uwsgi_params; } - # serve framework static content - location /static/style { - alias $galaxy_root/static/style/blue; - expires 24h; - } - location /static { - alias $galaxy_root/static; - expires 24h; - } - location /robots.txt { - alias $galaxy_root/static/robots.txt; - expires 24h; - } - location /favicon.ico { - alias $galaxy_root/static/favicon.ico; - expires 24h; - } + # serve framework static content + location /static { + alias $galaxy_root/static; + expires 24h; + } + location /robots.txt { + alias $galaxy_root/static/robots.txt; + expires 24h; + } + location /favicon.ico { + alias $galaxy_root/static/favicon.ico; + expires 24h; + } # serve visualization and interactive environment plugin static content - location ~ ^/plugins/(?.+?)/(?.+?)/static/(?.*?)$ { + location ~ ^/plugins/(?.+?)/(?.+?)/static/(?.*?)$ { alias $galaxy_root/config/plugins/$plug_type/$vis_name/static/$static_file; - expires 24; + expires 24; } } } @@ -203,8 +199,8 @@ previous section: } # serve framework static content - location /galaxy/static/style { - alias $galaxy_root/static/style/blue; + location /galaxy/static { + alias $galaxy_root/static; expires 24h; } @@ -307,24 +303,24 @@ user galaxy; http { - #... + #... server { - #... + #... # handle file uploads via the upload module - location /_upload { - upload_store /srv/galaxy/upload_store; - upload_store_access user:rw group:rw; - upload_pass_form_field ""; - upload_set_form_field "__${upload_field_name}__is_composite" "true"; - upload_set_form_field "__${upload_field_name}__keys" "name path"; - upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; - upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; - upload_pass_args on; - upload_pass /_upload_done; - } + location /_upload { + upload_store /srv/galaxy/upload_store; + upload_store_access user:rw group:rw; + upload_pass_form_field ""; + upload_set_form_field "__${upload_field_name}__is_composite" "true"; + upload_set_form_field "__${upload_field_name}__keys" "name path"; + upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; + upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; + upload_pass_args on; + upload_pass /_upload_done; + } # once upload is complete, redirect to the proper galaxy path location /_upload_done { diff --git a/doc/source/admin/scaling.md b/doc/source/admin/scaling.md index aa2c5c1a8b7..e50aa6963ec 100644 --- a/doc/source/admin/scaling.md +++ b/doc/source/admin/scaling.md @@ -355,7 +355,6 @@ uWSGI can be configured to serve HTTP and/or HTTPS directly: # listening options http: :8080 https: :8443,server.crt,server.key - static-map: /static/style=static/style/blue static-map: /static=static ``` @@ -370,7 +369,6 @@ user and drop privileges to the Galaxy user with a configuration such as: https: =1 uid: galaxy gid: galaxy - static-map: /static/style=static/style/blue static-map: /static=static ``` diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py index c3adebbcf59..8ae4035bc63 100644 --- a/lib/galaxy/config/config_manage.py +++ b/lib/galaxy/config/config_manage.py @@ -88,17 +88,11 @@ UWSGI_OPTIONS = OrderedDict([ }), ('static-map.1', { 'key': 'static-map', - 'desc': """Mapping to serve style content.""", - 'default': '/static/style=static/style/blue', - 'type': 'str', - }), - ('static-map.2', { - 'key': 'static-map', - 'desc': """Mapping to serve the remainder of the static content.""", + 'desc': """Mapping to serve static content.""", 'default': '/static=static', 'type': 'str', }), - ('static-map.3', { + ('static-map.2', { 'key': 'static-map', 'desc': """Mapping to serve the favicon.""", 'default': '/favicon.ico=static/favicon.ico', diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index d52bf131207..dfbac923fad 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -41,10 +41,7 @@ uwsgi: # routing requests. offload-threads: 2 - # Mapping to serve style content. - static-map: /static/style=static/style/blue - - # Mapping to serve the remainder of the static content. + # Mapping to serve static content. static-map: /static=static # Mapping to serve the favicon. @@ -211,7 +208,7 @@ galaxy: # Where dataset files are stored. It must be accessible at the same # path on any cluster nodes that will run Galaxy jobs, unless using # Pulsar. - #file_path: files + #file_path: objects # Where temporary files are stored. It must be accessible at the same # path on any cluster nodes that will run Galaxy jobs, unless using @@ -620,9 +617,11 @@ galaxy: #object_store_config_file: object_store_conf.xml # What Dataset attribute is used to reference files in an ObjectStore - # implementation, default is 'id' but can also be set to 'uuid' for - # more de-centralized usage. - #object_store_store_by: id + # implementation, this can be 'uuid' or 'id'. The default will depend + # on how the object store is configured, starting with 20.05 Galaxy + # will try to default to 'uuid' if it can be sure this is a new Galaxy + # instance - but the default will be 'id' in many cases. + #object_store_store_by: null # Galaxy sends mail for various things: subscribing users to the # mailing list if they request it, password resets, reporting dataset diff --git a/lib/galaxy/config/sample/reports.yml.sample b/lib/galaxy/config/sample/reports.yml.sample index b207fd53bd7..b1e950bee6a 100644 --- a/lib/galaxy/config/sample/reports.yml.sample +++ b/lib/galaxy/config/sample/reports.yml.sample @@ -23,10 +23,7 @@ uwsgi: # routing requests. offload-threads: 2 - # Mapping to serve style content. - static-map: /static/style=static/style/blue - - # Mapping to serve the remainder of the static content. + # Mapping to serve static content. static-map: /static=static # Mapping to serve the favicon. diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample index 236e4b7430c..2e1934d55fa 100644 --- a/lib/galaxy/config/sample/tool_shed.yml.sample +++ b/lib/galaxy/config/sample/tool_shed.yml.sample @@ -23,10 +23,7 @@ uwsgi: # routing requests. offload-threads: 2 - # Mapping to serve style content. - static-map: /static/style=static/style/blue - - # Mapping to serve the remainder of the static content. + # Mapping to serve static content. static-map: /static=static # Mapping to serve the favicon. @@ -313,7 +310,7 @@ tool_shed: #static_scripts_dir: static/scripts/ # Serving static files (needed if running standalone) - #static_style_dir: static/style/blue + #static_style_dir: static/style # Enables GDPR Compliance mode. This makes several changes to the way # Galaxy logs and exposes data externally such as removing diff --git a/lib/galaxy/config/script.py b/lib/galaxy/config/script.py index 03cfc0cd22f..5a90a36a862 100644 --- a/lib/galaxy/config/script.py +++ b/lib/galaxy/config/script.py @@ -53,7 +53,6 @@ Start Galaxy by running the command from directory [{}]: # configs differently. GALAXY_CONFIG_SUBSTITUTIONS = { ' http: 127.0.0.1:8080': ' ${uwsgi_transport}: ${host}:${port}', - ' static-map: /static/style=static/style/blue': ' static-map: /static=${static_path}/style/blue', ' static-map: /static=static': ' static-map: /static=${static_path}', ' static-map: /favicon.ico=static/favicon.ico': ' static-map: /static=${static_path}/favicon.ico', ' static-safe: client/galaxy/images': ' ${client_path}/galaxy/images', diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py index 273eb40cc69..cf9b52e7e0e 100644 --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -1013,7 +1013,6 @@ def build_url_map(app, global_conf, local_conf): urlmap["/static"] = Static(conf.get("static_dir", default_url_path("static/")), cache_time) urlmap["/images"] = Static(conf.get("static_images_dir", default_url_path("static/images")), cache_time) urlmap["/static/scripts"] = Static(conf.get("static_scripts_dir", default_url_path("static/scripts/")), cache_time) - urlmap["/static/style"] = Static(conf.get("static_style_dir", default_url_path("static/style/blue")), cache_time) urlmap["/static/welcome.html"] = Static(conf.get("static_welcome_html", default_url_path("static/welcome.html")), cache_time) urlmap["/favicon.ico"] = Static(conf.get("static_favicon_dir", default_url_path("static/favicon.ico")), cache_time) urlmap["/robots.txt"] = Static(conf.get("static_robots_txt", default_url_path("static/robots.txt")), cache_time) diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py index ed06f13cdb2..cdd9b3d1f0f 100644 --- a/lib/galaxy_test/driver/driver_util.py +++ b/lib/galaxy_test/driver/driver_util.py @@ -459,7 +459,7 @@ def _get_static_settings(): static_images_dir=os.path.join(static_dir, 'images', ''), static_favicon_dir=os.path.join(static_dir, 'favicon.ico'), static_scripts_dir=os.path.join(static_dir, 'scripts', ''), - static_style_dir=os.path.join(static_dir, 'style', 'blue'), + static_style_dir=os.path.join(static_dir, 'style'), static_robots_txt=os.path.join(static_dir, 'robots.txt'), ) diff --git a/lib/tool_shed/webapp/config_schema.yml b/lib/tool_shed/webapp/config_schema.yml index c0ea126a737..cc014e2c630 100644 --- a/lib/tool_shed/webapp/config_schema.yml +++ b/lib/tool_shed/webapp/config_schema.yml @@ -425,7 +425,7 @@ mapping: static_style_dir: type: str - default: static/style/blue + default: static/style required: false desc: | Serving static files (needed if running standalone) diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py index ec2c4f6953c..3206711ee66 100644 --- a/scripts/get_uwsgi_args.py +++ b/scripts/get_uwsgi_args.py @@ -91,8 +91,7 @@ def _get_uwsgi_args(cliargs, kwargs): 'threads': '4', 'buffer-size': '16384', # https://github.com/galaxyproject/galaxy/issues/1530 'http': 'localhost:{port}'.format(port=DEFAULT_PORTS[cliargs.app]), - 'static-map': ('/static/style={here}/static/style/blue'.format(here=os.getcwd()), - '/static={here}/static'.format(here=os.getcwd()), + 'static-map': ('/static={here}/static'.format(here=os.getcwd()), '/favicon.ico={here}/static/favicon.ico'.format(here=os.getcwd())), 'static-safe': ('{here}/client/galaxy/images'.format(here=os.getcwd())), 'die-on-term': True, diff --git a/test/unit/config/config_manage/embedded/config/galaxy.yml b/test/unit/config/config_manage/embedded/config/galaxy.yml index 97896d126d3..b8b5cf225b5 100644 --- a/test/unit/config/config_manage/embedded/config/galaxy.yml +++ b/test/unit/config/config_manage/embedded/config/galaxy.yml @@ -4,7 +4,6 @@ uwsgi: processes: 1 threads: 4 offload-threads: 2 - static-map: /static/style=static/style/blue static-map: /static=static static-map: /favicon.ico=static/favicon.ico master: false diff --git a/test/unit/config/config_manage/simple/config/galaxy.yml b/test/unit/config/config_manage/simple/config/galaxy.yml index cbb51747c6d..1fb983b57dc 100644 --- a/test/unit/config/config_manage/simple/config/galaxy.yml +++ b/test/unit/config/config_manage/simple/config/galaxy.yml @@ -4,7 +4,6 @@ uwsgi: processes: 1 threads: 4 offload-threads: 2 - static-map: /static/style=static/style/blue static-map: /static=static static-map: /favicon.ico=static/favicon.ico master: false