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Merge pull request #9306 from dannon/blue-elimination

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Clean up old 'blue' style path, update documentation and samples
This commit is contained in:
Nate Coraor
2020-02-05 09:31:34 -05:00
committed by GitHub
parent 568b159524 d410d9e045
commit acb9bc1ea1
15 changed files with 53 additions and 76 deletions
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doc/source/admin/apache.md
-2
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@@ -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]
doc/source/admin/galaxy_options.rst
+7 -4
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@@ -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
doc/source/admin/nginx.md
+31 -35
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@@ -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 $galaxy_root/static/favicon.ico;
expires 24h;
}
# serve visualization and interactive environment plugin static content
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
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 {
doc/source/admin/scaling.md
-2
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@@ -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
```
lib/galaxy/config/config_manage.py
+2 -8
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@@ -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',
lib/galaxy/config/sample/galaxy.yml.sample
+7 -8
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@@ -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
lib/galaxy/config/sample/reports.yml.sample
+1 -4
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@@ -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.
lib/galaxy/config/sample/tool_shed.yml.sample
+2 -5
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@@ -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
lib/galaxy/config/script.py
-1
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@@ -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',
lib/galaxy/web/framework/webapp.py
-1
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@@ -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)
lib/galaxy_test/driver/driver_util.py
+1 -1
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@@ -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'),
)
lib/tool_shed/webapp/config_schema.yml
+1 -1
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@@ -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)
scripts/get_uwsgi_args.py
+1 -2
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@@ -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,
test/unit/config/config_manage/embedded/config/galaxy.yml
-1
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@@ -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
test/unit/config/config_manage/simple/config/galaxy.yml
-1
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@@ -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