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Merge remote-tracking branch 'upstream/release_18.05' into release_18.09

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This commit is contained in:
Dannon Baker
2018-09-26 09:25:54 -04:00
parent eb1980ec08 cf62a1dafd
commit c3d4be2e2c
3 changed files with 63 additions and 47 deletions
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lib/galaxy/security/__init__.py
+2 -1
View File
@@ -799,7 +799,8 @@ class GalaxyRBACAgent(RBACAgent):
def get_private_user_role(self, user, auto_create=False):
role = self.sa_session.query(self.model.Role) \
.filter(and_(self.model.Role.table.c.name == user.email,
.filter(and_(self.model.UserRoleAssociation.table.c.user_id == user.id,
self.model.Role.table.c.id == self.model.UserRoleAssociation.table.c.role_id,
self.model.Role.table.c.type == self.model.Role.types.PRIVATE)) \
.first()
if not role:
lib/galaxy/webapps/galaxy/api/workflows.py
+9 -3
View File
@@ -777,7 +777,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
decoded_workflow_invocation_id = self.decode_id(invocation_id)
workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
if workflow_invocation:
return self.__encode_invocation(workflow_invocation, **kwd)
step_details = util.string_as_bool(kwd.get('step_details', 'False'))
legacy_job_state = util.string_as_bool(kwd.get('legacy_job_state', 'False'))
return self.__encode_invocation(trans, workflow_invocation, step_details=step_details, legacy_job_state=legacy_job_state)
return None
@expose_api
@@ -867,5 +869,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
def __get_stored_workflow(self, trans, workflow_id):
return self.workflow_manager.get_stored_workflow(trans, workflow_id)
def __encode_invocation(self, invocation, **kwd):
return self.workflow_manager.serialize_workflow_invocation(invocation, **kwd)
def __encode_invocation(self, trans, invocation, view="element", step_details=False, legacy_job_state=False):
return self.encode_all_ids(
trans,
invocation.to_dict(view, step_details=step_details, legacy_job_state=legacy_job_state),
True
)
lib/galaxy/webapps/galaxy/config_schema.yml
+52 -43
View File
@@ -45,7 +45,7 @@ mapping:
cookie_path:
type: str
default: null
default: ''
required: false
desc: |
If proxy-prefix is enabled and you're running more than one Galaxy instance
@@ -109,7 +109,7 @@ mapping:
database_template:
type: str
default: null
default: ''
required: false
desc: |
If auto-creating a postgres database on startup - it can be based on an existing
@@ -343,7 +343,7 @@ mapping:
watch_tools:
type: str
default: false
default: 'false'
required: false
desc: |
Set to True to enable monitoring of tools and tool directories
@@ -394,7 +394,7 @@ mapping:
containers_resolvers_config_file:
type: str
default: null
default: ''
required: false
desc: |
Container resolvers configuration (beta). Setup a file describing container
@@ -490,7 +490,7 @@ mapping:
watch_tool_data_dir:
type: str
default: false
default: 'false'
required: false
desc: |
Set to True to enable monitoring of the tool_data and shed_tool_data_path
@@ -653,7 +653,7 @@ mapping:
Number of checks to execute if check_job_script_integrity is enabled.
check_job_script_integrity_sleep:
type: str
type: float
default: .25
required: false
desc: |
@@ -720,7 +720,7 @@ mapping:
smtp_server:
type: str
default: null
default: ''
required: false
desc: |
Galaxy sends mail for various things: subscribing users to the mailing list
@@ -731,7 +731,7 @@ mapping:
smtp_username:
type: str
default: null
default: ''
required: false
desc: |
If your SMTP server requires a username and password, you can provide them
@@ -740,7 +740,7 @@ mapping:
smtp_password:
type: str
default: null
default: ''
required: false
desc: |
If your SMTP server requires a username and password, you can provide them
@@ -765,7 +765,7 @@ mapping:
error_email_to:
type: str
default: null
default: ''
required: false
desc: |
Datasets in an error state include a link to report the error. Those reports
@@ -775,7 +775,7 @@ mapping:
email_from:
type: str
default: null
default: ''
required: false
desc: |
Email address to use in the 'From' field when sending emails for
@@ -859,7 +859,7 @@ mapping:
ga_code:
type: str
default: null
default: ''
required: false
desc: |
You can enter tracking code here to track visitor's behavior
@@ -911,7 +911,7 @@ mapping:
message_box_content:
type: str
default: null
default: ''
required: false
desc: |
Show a message box under the masthead.
@@ -925,7 +925,7 @@ mapping:
brand:
type: str
default: null
default: ''
required: false
desc: |
Append "/{brand}" to the "Galaxy" text in the masthead.
@@ -1013,21 +1013,21 @@ mapping:
biostar_url:
type: str
default: null
default: ''
required: false
desc: |
Enable integration with a custom Biostar instance.
biostar_key_name:
type: str
default: null
default: ''
required: false
desc: |
Enable integration with a custom Biostar instance.
biostar_key:
type: str
default: null
default: ''
required: false
desc: |
Enable integration with a custom Biostar instance.
@@ -1084,7 +1084,7 @@ mapping:
terms_url:
type: str
default: null
default: ''
required: false
desc: |
The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
@@ -1198,7 +1198,7 @@ mapping:
nginx_x_accel_redirect_base:
type: str
default: null
default: ''
required: false
desc: |
The same download handling can be done by nginx using X-Accel-Redirect. This
@@ -1230,7 +1230,7 @@ mapping:
nginx_upload_store:
type: str
default: null
default: ''
required: false
desc: |
nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
@@ -1240,7 +1240,7 @@ mapping:
nginx_upload_path:
type: str
default: null
default: ''
required: false
desc: |
This value overrides the action set on the file upload form, e.g. the web
@@ -1249,7 +1249,7 @@ mapping:
nginx_upload_job_files_store:
type: str
default: null
default: ''
required: false
desc: |
Galaxy can also use nginx_upload_module to receive files staged out upon job
@@ -1259,7 +1259,7 @@ mapping:
nginx_upload_job_files_path:
type: str
default: null
default: ''
required: false
desc: |
Galaxy can also use nginx_upload_module to receive files staged out upon job
@@ -1374,7 +1374,7 @@ mapping:
dynamic_proxy_golang_api_key:
type: str
default: null
default: ''
required: false
desc: |
The golang proxy uses a RESTful HTTP API for communication with Galaxy
@@ -1401,7 +1401,7 @@ mapping:
logging:
type: map
default: galaxy.config.LOGGING_CONFIG_DEFAULT
allowempty: True
desc: |
Controls where and how the server logs messages. If unset, the default is to log all messages to standard
output at the level defined by the `log_level` configuration option. Configuration is described in the
@@ -1494,7 +1494,7 @@ mapping:
allowed_origin_hostnames:
type: str
default: null
default: ''
required: false
desc: |
Return a Access-Control-Allow-Origin response header that matches the Origin
@@ -1591,7 +1591,7 @@ mapping:
sentry_dsn:
type: str
default: null
default: ''
required: false
desc: |
Log to Sentry
@@ -1658,7 +1658,7 @@ mapping:
library_import_dir:
type: str
default: null
default: ''
required: false
desc: |
Add an option to the library upload form which allows administrators to
@@ -1666,7 +1666,7 @@ mapping:
user_library_import_dir:
type: str
default: null
default: ''
required: false
desc: |
Add an option to the library upload form which allows authorized
@@ -1685,7 +1685,7 @@ mapping:
user_library_import_symlink_whitelist:
type: str
default: null
default: ''
required: false
desc: |
For security reasons, users may not import any files that actually lie
@@ -1739,7 +1739,7 @@ mapping:
tool_name_boost:
type: float
default: 9
default: 9.0
required: false
desc: |
Boosts are used to customize this instance's toolbox search.
@@ -1749,7 +1749,7 @@ mapping:
tool_section_boost:
type: float
default: 3
default: 3.0
required: false
desc: |
Boosts are used to customize this instance's toolbox search.
@@ -1759,7 +1759,7 @@ mapping:
tool_description_boost:
type: float
default: 2
default: 2.0
required: false
desc: |
Boosts are used to customize this instance's toolbox search.
@@ -1769,7 +1769,7 @@ mapping:
tool_label_boost:
type: float
default: 1
default: 1.0
required: false
desc: |
Boosts are used to customize this instance's toolbox search.
@@ -1779,7 +1779,7 @@ mapping:
tool_stub_boost:
type: float
default: 5
default: 5.0
required: false
desc: |
Boosts are used to customize this instance's toolbox search.
@@ -1865,7 +1865,7 @@ mapping:
remote_user_maildomain:
type: str
default: null
default: ''
required: false
desc: |
If use_remote_user is enabled and your external authentication
@@ -1897,7 +1897,7 @@ mapping:
remote_user_logout_href:
type: str
default: null
default: ''
required: false
desc: |
If use_remote_user is enabled, you can set this to a URL that will log your
@@ -1924,7 +1924,7 @@ mapping:
admin_users:
type: str
default: null
default: ''
required: false
desc: |
Administrative users - set this to a comma-separated list of valid Galaxy
@@ -2155,7 +2155,7 @@ mapping:
invocation to schedule indefinitely. The default corresponds to 1 month.
maximum_workflow_jobs_per_scheduling_iteration:
type: str
type: int
default: -1
required: false
desc: |
@@ -2228,7 +2228,7 @@ mapping:
api_allow_run_as:
type: str
default: null
default: ''
required: false
desc: |
Optional list of email addresses of API users who can make calls on behalf of
@@ -2274,7 +2274,7 @@ mapping:
ftp_upload_dir:
type: str
default: null
default: ''
required: false
desc: |
Enable Galaxy's "Upload via FTP" interface. You'll need to install and
@@ -2285,7 +2285,7 @@ mapping:
ftp_upload_site:
type: str
default: null
default: ''
required: false
desc: |
This should be the hostname of your FTP server, which will be provided to
@@ -2565,7 +2565,7 @@ mapping:
environment_setup_file:
type: str
default: null
default: ''
required: false
desc: |
File to source to set up the environment when running jobs. By default, the
@@ -2720,3 +2720,12 @@ mapping:
required: false
desc: |
persistent_communication_rooms is a comma-separated list of rooms that should be always available.
use_pbkdf2:
type: bool
default: true
required: false
desc: |
Allow disabling pbkdf2 hashing of passwords for legacy situations.
This should normally be left enabled unless there is a specific
reason to disable it.