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Update tool shed to use newer configuration schema.

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- Implement kwalify schema to validate/define the schema.
 - Replace ini configuration with YAML (completely backward compatible).
 - Rebuild a sample configuration from the schema (config/tool_shed.yml.sample).
This commit is contained in:
John Chilton
2017-08-10 13:15:29 -04:00
parent 7973a914e0
commit 90e899d68f
6 changed files with 602 additions and 181 deletions
Download Patch File Download Diff File Expand all files Collapse all files
config/tool_shed.ini.sample
-178
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@@ -1,178 +0,0 @@
# ---- HTTP Server ----------------------------------------------------------
[server:main]
use = egg:Paste#http
port = 9009
# The address on which to listen. By default, only listen to localhost
# (the Tool Shed will not be accessible over the network).
# Use '0.0.0.0' to listen on all available network interfaces.
#host = 0.0.0.0
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10
# Set the number of seconds a thread can work before you should kill it
# (assuming it will never finish) to 3 hours.
threadpool_kill_thread_limit = 10800
# ---- Galaxy Tool Shed -----------------------------------------------------
[app:main]
# Specifies the factory for the universe WSGI application
paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory
# Verbosity of console log messages. Acceptable values can be found here:
# https://docs.python.org/2/library/logging.html#logging-levels
#log_level = DEBUG
# By default, the Tool Shed uses a SQLite database at 'database/community.sqlite'. You
# may use a SQLAlchemy connection string to specify an external database
# instead. This string takes many options which are explained in detail in the
# config file documentation.
#database_connection = sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
# Where the hgweb.config file is stored.
# The default is the Galaxy installation directory.
#hgweb_config_dir = None
# Where tool shed repositories are stored.
#file_path = database/community_files
# Temporary storage for additional datasets,
# this should be shared through the cluster
#new_file_path = database/tmp
# File containing old-style genome builds
#builds_file_path = tool-data/shared/ucsc/builds.txt
# Format string used when showing date and time information.
# The string may contain:
# - the directives used by Python time.strftime() function (see
# https://docs.python.org/2/library/time.html#time.strftime ),
# - $locale (complete format string for the server locale),
# - $iso8601 (complete format string as specified by ISO 8601 international
# standard).
#pretty_datetime_format = $locale (UTC)
# -- Repository and Tool search
# Using the script located at scripts/build_ts_whoosh_index.py
# you can generate search index and allow full text API searching over
# the repositories and tools within the Tool Shed given that you specify
# the following two config options.
#toolshed_search_on = True
#whoosh_index_dir = database/toolshed_whoosh_indexes
# The following boosts are used to customize this instance's TS search.
# The higher the boost, the more importance the scoring algorithm gives to the
# given field.
# For searching repositories at /api/repositories:
#repo_name_boost = 0.9
#repo_description_boost = 0.6
#repo_long_description_boost = 0.5
#repo_homepage_url_boost = 0.3
#repo_remote_repository_url_boost = 0.2
#repo_owner_username_boost = 0.3
# For searching tools at /api/tools
#tool_name_boost = 1.2
#tool_description_boost = 0.6
#tool_help_boost = 0.4
#tool_repo_owner_username = 0.3
# -- Analytics
# You can enter tracking code here to track visitor's behavior
# through your Google Analytics account. Example: UA-XXXXXXXX-Y
#ga_code = None
# -- Users and Security
# The Tool Shed encodes various internal values when these values will be output in
# some format (for example, in a URL or cookie). You should set a key to be
# used by the algorithm that encodes and decodes these values. It can be any
# string. If left unchanged, anyone could construct a cookie that would grant
# them access to others' sessions.
# One simple way to generate a value for this is with the shell command:
# python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' '
#id_secret = changethisinproductiontoo
# User authentication can be delegated to an upstream proxy server (usually
# Apache). The upstream proxy should set a REMOTE_USER header in the request.
# Enabling remote user disables regular logins. For more information, see:
# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
#use_remote_user = False
# If use_remote_user is enabled, anyone who can log in to the Galaxy host may
# impersonate any other user by simply sending the appropriate header. Thus a
# secret shared between the upstream proxy server, and Galaxy is required.
# If anyone other than the Galaxy user is using the server, then apache/nginx
# should pass a value in the header 'GX_SECRET' that is identical the one below
#remote_user_secret = changethisinproductiontoo
# Configuration for debugging middleware
#debug = False
# Check for WSGI compliance.
#use_lint = False
# NEVER enable this on a public site (even test or QA)
#use_interactive = true
# Administrative users - set this to a comma-separated list of valid Tool Shed
# users (email addresses). These users will have access to the Admin section
# of the server, and will have access to create users, groups, roles,
# libraries, and more.
#admin_users = None
# Force everyone to log in (disable anonymous access)
#require_login = False
# For use by email messages sent from the tool shed
#smtp_server = smtp.your_tool_shed_server
#email_from = your_tool_shed_email@server
# If your SMTP server requires a username and password, you can provide them
# here (password in cleartext here, but if your server supports STARTTLS it
# will be sent over the network encrypted).
#smtp_username = None
#smtp_password = None
# If your SMTP server requires SSL from the beginning of the connection
#smtp_ssl = False
# The URL linked by the "Support" link in the "Help" menu.
#support_url = https://wiki.galaxyproject.org/Support
# Address to join mailing list
#mailing_join_addr = galaxy-announce-join@bx.psu.edu
# Write thread status periodically to 'heartbeat.log' (careful, uses disk
# space rapidly!)
#use_heartbeat = True
# Profiling middleware (cProfile based)
#use_profile = True
# Enable creation of Galaxy flavor Docker Image
#enable_galaxy_flavor_docker_image = False
# Show a message box under the masthead.
#message_box_visible = False
#message_box_content = None
#message_box_class = info
# Serving static files (needed if running standalone)
#static_enabled = True
#static_cache_time = 360
#static_dir = static/
#static_images_dir = static/images
#static_favicon_dir = static/favicon.ico
#static_scripts_dir = static/scripts/
#static_style_dir = static/style/blue
# Sentry (getsentry.com) DSN for catching bugs.
#sentry_dsn = None
config/tool_shed.yml.sample
+208
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@@ -0,0 +1,208 @@
uwsgi:
# The address and port on which to listen. By default, only listen to
# localhost (tool_shed will not be accessible over the network). Use
# '0.0.0.0' to listen on all available network interfaces.
http: 127.0.0.1:9009
threads: 8
http-raw-body: True
offload-threads: 8
module: galaxy.webapps.tool_shed.buildapp:uwsgi_app()
tool_shed:
# Verbosity of console log messages. Acceptable values can be found
# here: https://docs.python.org/2/library/logging.html#logging-levels
#log_level: DEBUG
# By default, the Tool Shed uses a SQLite database at
# 'database/community.sqlite'. You may use a SQLAlchemy connection
# string to specify an external database instead. This string takes
# many options which are explained in detail in the config file
# documentation.
#database_connection: sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
# Where the hgweb.config file is stored. The default is the Galaxy
# installation directory.
#hgweb_config_dir: None
# Where tool shed repositories are stored.
#file_path: database/community_files
# Temporary storage for additional datasets, this should be shared
# through the cluster
#new_file_path: database/tmp
# File containing old-style genome builds
#builds_file_path: tool-data/shared/ucsc/builds.txt
# Format string used when showing date and time information. The
# string may contain: - the directives used by Python time.strftime()
# function (see
# https://docs.python.org/2/library/time.html#time.strftime ), -
# $locale (complete format string for the server locale), - $iso8601
# (complete format string as specified by ISO 8601 international
# standard).
#pretty_datetime_format: $locale (UTC)
# -- Repository and Tool search Using the script located at
# scripts/build_ts_whoosh_index.py you can generate search index and
# allow full text API searching over the repositories and tools within
# the Tool Shed given that you specify the following two config
# options.
#toolshed_search_on: True
# -- Repository and Tool search Using the script located at
# scripts/build_ts_whoosh_index.py you can generate search index and
# allow full text API searching over the repositories and tools within
# the Tool Shed given that you specify the following two config
# options.
#whoosh_index_dir: database/toolshed_whoosh_indexes
# For searching repositories at /api/repositories:
#repo_name_boost: 0.9
# For searching repositories at /api/repositories:
#repo_description_boost: 0.6
# For searching repositories at /api/repositories:
#repo_long_description_boost: 0.5
# For searching repositories at /api/repositories:
#repo_homepage_url_boost: 0.3
# For searching repositories at /api/repositories:
#repo_remote_repository_url_boost: 0.2
# For searching repositories at /api/repositories:
#repo_owner_username_boost: 0.3
# For searching tools at /api/tools
#tool_name_boost: 1.2
# For searching tools at /api/tools
#tool_description_boost: 0.6
# For searching tools at /api/tools
#tool_help_boost: 0.4
# For searching tools at /api/tools
#tool_repo_owner_username: 0.3
# You can enter tracking code here to track visitor's behavior through
# your Google Analytics account. Example: UA-XXXXXXXX-Y
#ga_code: None
# The Tool Shed encodes various internal values when these values will
# be output in some format (for example, in a URL or cookie). You
# should set a key to be used by the algorithm that encodes and
# decodes these values. It can be any string. If left unchanged,
# anyone could construct a cookie that would grant them access to
# others' sessions. One simple way to generate a value for this is
# with the shell command: python -c 'import time; print time.time()'
# | md5sum | cut -f 1 -d ' '
#id_secret: changethisinproductiontoo
# User authentication can be delegated to an upstream proxy server
# (usually Apache). The upstream proxy should set a REMOTE_USER
# header in the request. Enabling remote user disables regular logins.
# For more information, see:
# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
#use_remote_user: False
# If use_remote_user is enabled, anyone who can log in to the Galaxy
# host may impersonate any other user by simply sending the
# appropriate header. Thus a secret shared between the upstream proxy
# server, and Galaxy is required. If anyone other than the Galaxy user
# is using the server, then apache/nginx should pass a value in the
# header 'GX_SECRET' that is identical the one below
#remote_user_secret: changethisinproductiontoo
# Configuration for debugging middleware
#debug: False
# Check for WSGI compliance.
#use_lint: False
# NEVER enable this on a public site (even test or QA)
#use_interactive: True
# Administrative users - set this to a comma-separated list of valid
# Tool Shed users (email addresses). These users will have access to
# the Admin section of the server, and will have access to create
# users, groups, roles, libraries, and more.
#admin_users: None
# Force everyone to log in (disable anonymous access)
#require_login: False
# 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
#email_from: your_tool_shed_email@server
# If your SMTP server requires a username and password, you can
# provide them here (password in cleartext here, but if your server
# supports STARTTLS it will be sent over the network encrypted).
#smtp_username: None
# If your SMTP server requires a username and password, you can
# provide them here (password in cleartext here, but if your server
# supports STARTTLS it will be sent over the network encrypted).
#smtp_password: None
# If your SMTP server requires SSL from the beginning of the
# connection
#smtp_ssl: False
# The URL linked by the "Support" link in the "Help" menu.
#support_url: https://wiki.galaxyproject.org/Support
# Address to join mailing list
#mailing_join_addr: galaxy-announce-join@bx.psu.edu
# Write thread status periodically to 'heartbeat.log' (careful, uses
# disk space rapidly!)
#use_heartbeat: True
# Profiling middleware (cProfile based)
#use_profile: True
# Enable creation of Galaxy flavor Docker Image
#enable_galaxy_flavor_docker_image: False
# Show a message box under the masthead.
#message_box_visible: False
# Show a message box under the masthead.
#message_box_content: None
# Show a message box under the masthead.
#message_box_class: info
# Serving static files (needed if running standalone)
#static_enabled: True
# Serving static files (needed if running standalone)
#static_cache_time: 360
# Serving static files (needed if running standalone)
#static_dir: static/
# Serving static files (needed if running standalone)
#static_images_dir: static/images
# Serving static files (needed if running standalone)
#static_favicon_dir: static/favicon.ico
# Serving static files (needed if running standalone)
#static_scripts_dir: static/scripts/
# Serving static files (needed if running standalone)
#static_style_dir: static/style/blue
lib/galaxy/webapps/tool_shed/buildapp.py
+3 -2
View File
@@ -53,12 +53,13 @@ def add_ui_controllers( webapp, app ):
webapp.add_ui_controller( name, T( app ) )
def app_factory( global_conf, **kwargs ):
def app_factory( global_conf, load_app_kwds={}, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
kwargs = load_app_properties(
kwds=kwargs,
config_prefix='TOOL_SHED_CONFIG_'
config_prefix='TOOL_SHED_CONFIG_',
**load_app_kwds
)
if 'app' in kwargs:
app = kwargs.pop( 'app' )
lib/galaxy/webapps/tool_shed/config_schema.yml
+387
View File
@@ -0,0 +1,387 @@
type: map
mapping:
uwsgi: !include uwsgi_schema.yml
tool_shed:
type: map
required: true
desc: |
Tool Shed configuration options.
mapping:
log_level:
type: str
default: DEBUG
required: false
desc: |
Verbosity of console log messages. Acceptable values can be found here:
https://docs.python.org/2/library/logging.html#logging-levels
database_connection:
type: str
default: sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
required: false
desc: |
By default, the Tool Shed uses a SQLite database at 'database/community.sqlite'. You
may use a SQLAlchemy connection string to specify an external database
instead. This string takes many options which are explained in detail in the
config file documentation.
hgweb_config_dir:
type: str
required: false
desc: |
Where the hgweb.config file is stored.
The default is the Galaxy installation directory.
file_path:
type: str
default: database/community_files
required: false
desc: |
Where tool shed repositories are stored.
new_file_path:
type: str
default: database/tmp
required: false
desc: |
Temporary storage for additional datasets,
this should be shared through the cluster
builds_file_path:
type: str
default: tool-data/shared/ucsc/builds.txt
required: false
desc: |
File containing old-style genome builds
pretty_datetime_format:
type: str
default: $locale (UTC)
required: false
desc: |
Format string used when showing date and time information.
The string may contain:
- the directives used by Python time.strftime() function (see
https://docs.python.org/2/library/time.html#time.strftime ),
- $locale (complete format string for the server locale),
- $iso8601 (complete format string as specified by ISO 8601 international
standard).
toolshed_search_on:
type: bool
default: true
required: false
desc: |
-- Repository and Tool search
Using the script located at scripts/build_ts_whoosh_index.py
you can generate search index and allow full text API searching over
the repositories and tools within the Tool Shed given that you specify
the following two config options.
whoosh_index_dir:
type: str
default: database/toolshed_whoosh_indexes
required: false
desc: |
-- Repository and Tool search
Using the script located at scripts/build_ts_whoosh_index.py
you can generate search index and allow full text API searching over
the repositories and tools within the Tool Shed given that you specify
the following two config options.
repo_name_boost:
type: float
default: 0.9
required: false
desc: |
For searching repositories at /api/repositories:
repo_description_boost:
type: float
default: 0.6
required: false
desc: |
For searching repositories at /api/repositories:
repo_long_description_boost:
type: float
default: 0.5
required: false
desc: |
For searching repositories at /api/repositories:
repo_homepage_url_boost:
type: float
default: 0.3
required: false
desc: |
For searching repositories at /api/repositories:
repo_remote_repository_url_boost:
type: float
default: 0.2
required: false
desc: |
For searching repositories at /api/repositories:
repo_owner_username_boost:
type: float
default: 0.3
required: false
desc: |
For searching repositories at /api/repositories:
tool_name_boost:
type: float
default: 1.2
required: false
desc: |
For searching tools at /api/tools
tool_description_boost:
type: float
default: 0.6
required: false
desc: |
For searching tools at /api/tools
tool_help_boost:
type: float
default: 0.4
required: false
desc: |
For searching tools at /api/tools
tool_repo_owner_username:
type: float
default: 0.3
required: false
desc: |
For searching tools at /api/tools
ga_code:
type: str
required: false
desc: |
You can enter tracking code here to track visitor's behavior
through your Google Analytics account. Example: UA-XXXXXXXX-Y
id_secret:
type: str
default: changethisinproductiontoo
required: false
desc: |
The Tool Shed encodes various internal values when these values will be output in
some format (for example, in a URL or cookie). You should set a key to be
used by the algorithm that encodes and decodes these values. It can be any
string. If left unchanged, anyone could construct a cookie that would grant
them access to others' sessions.
One simple way to generate a value for this is with the shell command:
python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' '
use_remote_user:
type: bool
default: false
required: false
desc: |
User authentication can be delegated to an upstream proxy server (usually
Apache). The upstream proxy should set a REMOTE_USER header in the request.
Enabling remote user disables regular logins. For more information, see:
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
remote_user_secret:
type: str
default: changethisinproductiontoo
required: false
desc: |
If use_remote_user is enabled, anyone who can log in to the Galaxy host may
impersonate any other user by simply sending the appropriate header. Thus a
secret shared between the upstream proxy server, and Galaxy is required.
If anyone other than the Galaxy user is using the server, then apache/nginx
should pass a value in the header 'GX_SECRET' that is identical the one below
debug:
type: bool
default: false
required: false
desc: |
Configuration for debugging middleware
use_lint:
type: bool
default: false
required: false
desc: |
Check for WSGI compliance.
use_printdebug:
type: bool
default: true
required: false
desc: |
Intercept print statements and show them on the returned page.
use_interactive:
type: bool
default: true
required: false
desc: |
NEVER enable this on a public site (even test or QA)
admin_users:
type: str
required: false
desc: |
Administrative users - set this to a comma-separated list of valid Tool Shed
users (email addresses). These users will have access to the Admin section
of the server, and will have access to create users, groups, roles,
libraries, and more.
require_login:
type: bool
default: false
required: false
desc: |
Force everyone to log in (disable anonymous access)
smtp_server:
type: str
default: smtp.your_tool_shed_server
required: false
desc: |
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
smtp_username:
type: str
required: false
desc: |
If your SMTP server requires a username and password, you can provide them
here (password in cleartext here, but if your server supports STARTTLS it
will be sent over the network encrypted).
smtp_password:
type: str
required: false
desc: |
If your SMTP server requires a username and password, you can provide them
here (password in cleartext here, but if your server supports STARTTLS it
will be sent over the network encrypted).
smtp_ssl:
type: bool
default: false
required: false
desc: |
If your SMTP server requires SSL from the beginning of the connection
support_url:
type: str
default: https://wiki.galaxyproject.org/Support
required: false
desc: |
The URL linked by the "Support" link in the "Help" menu.
mailing_join_addr:
type: str
default: galaxy-announce-join@bx.psu.edu
required: false
desc: |
Address to join mailing list
use_heartbeat:
type: bool
default: true
required: false
desc: |
Write thread status periodically to 'heartbeat.log' (careful, uses disk
space rapidly!)
use_profile:
type: bool
default: true
required: false
desc: |
Profiling middleware (cProfile based)
enable_galaxy_flavor_docker_image:
type: bool
default: false
required: false
desc: |
Enable creation of Galaxy flavor Docker Image
message_box_visible:
type: bool
default: false
required: false
desc: |
Show a message box under the masthead.
message_box_content:
type: str
required: false
desc: |
Show a message box under the masthead.
message_box_class:
type: str
default: info
required: false
desc: |
Show a message box under the masthead.
static_enabled:
type: bool
default: true
required: false
desc: |
Serving static files (needed if running standalone)
static_cache_time:
type: int
default: 360
required: false
desc: |
Serving static files (needed if running standalone)
static_dir:
type: str
default: static/
required: false
desc: |
Serving static files (needed if running standalone)
static_images_dir:
type: str
default: static/images
required: false
desc: |
Serving static files (needed if running standalone)
static_favicon_dir:
type: str
default: static/favicon.ico
required: false
desc: |
Serving static files (needed if running standalone)
static_scripts_dir:
type: str
default: static/scripts/
required: false
desc: |
Serving static files (needed if running standalone)
static_style_dir:
type: str
default: static/style/blue
required: false
desc: |
Serving static files (needed if running standalone)
lib/galaxy/webapps/tool_shed/uwsgi_schema.yml
Symlink
+1
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@@ -0,0 +1 @@
../uwsgi_schema.yml
run_tool_shed.sh
+3 -1
View File
@@ -30,8 +30,10 @@ if [ -z "$TOOL_SHED_CONFIG_FILE" ]; then
TOOL_SHED_CONFIG_FILE=tool_shed_wsgi.ini
elif [ -f config/tool_shed.ini ]; then
TOOL_SHED_CONFIG_FILE=config/tool_shed.ini
elif [ -f config/tool_shed.yml ]; then
TOOL_SHED_CONFIG_FILE=config/tool_shed.yml
else
TOOL_SHED_CONFIG_FILE=config/tool_shed.ini.sample
TOOL_SHED_CONFIG_FILE=config/tool_shed.yml.sample
fi
export TOOL_SHED_CONFIG_FILE
fi