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Merge jdlogicman/galaxy-central-startup-integration-apis

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This commit is contained in:
Nate Coraor
2012-01-24 12:18:21 -05:00
parent 997a00b766 1341cc9989
commit 0354480bd2
7 changed files with 92 additions and 19 deletions
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create_db.sh
Executable
+4
View File
@@ -0,0 +1,4 @@
#!/bin/sh
cd `dirname $0`
python ./scripts/create_db.py $@
lib/galaxy/web/api/histories.py
+1 -1
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@@ -88,8 +88,8 @@ class HistoriesController( BaseAPIController, UsesHistory ):
state = states.QUEUED
elif summary[states.OK] == num_sets:
state = states.OK
item['contents_url'] = url_for( 'history_contents', history_id=history_id )
item['state_details'] = summary
item['contents_url'] = url_for( 'history_contents', history_id=history_id )
item['state'] = state
except Exception, e:
item = "Error in history API at showing history detail"
lib/galaxy/web/api/users.py
+15 -9
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@@ -32,12 +32,11 @@ class UserAPIController( BaseAPIController ):
# special case: user can see only their own user
if not trans.user_is_admin():
item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
item['url'] = url_for( route, id=encoded_id )
item['url'] = url_for( route, id=item['id'] )
return item
for user in query:
item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } )
encoded_id = trans.security.encode_id( user.id )
item['url'] = url_for( route, id=encoded_id )
item['url'] = url_for( route, id=item['id'] )
rval.append( item )
return rval
@@ -63,18 +62,25 @@ class UserAPIController( BaseAPIController ):
'total_disk_usage': float } )
return item
@web.expose
def create( self, trans, **kwd ):
raise HTTPNotImplemented()
@web.expose_api
def create( self, trans, payload, **kwd ):
"""
/api/users
Creates a remote user
"""
user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email'])
item = user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id,
'total_disk_usage': float } )
return item
@web.expose
@web.expose_api
def update( self, trans, **kwd ):
raise HTTPNotImplemented()
@web.expose
@web.expose_api
def delete( self, trans, **kwd ):
raise HTTPNotImplemented()
@web.expose
@web.expose_api
def undelete( self, trans, **kwd ):
raise HTTPNotImplemented()
lib/galaxy/web/api/workflows.py
+16
View File
@@ -77,7 +77,23 @@ class WorkflowsAPIController(BaseAPIController):
"""
POST /api/workflows
We're not creating workflows from the api. Just execute for now.
However, we will import them if installed_repository_file is specified
"""
if 'workflow_id' not in payload:
# create new
if 'installed_repository_file' in payload:
workflow_controller = trans.webapp.controllers[ 'workflow' ]
result = workflow_controller.import_workflow( trans=trans,
cntrller='api',
**payload)
return result
trans.response.status = 403
return "Either workflow_id or installed_repository_file must be specified"
if 'installed_repository_file' in payload:
trans.response.status = 403
return "installed_repository_file may not be specified with workflow_id"
stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(
trans.security.decode_id(payload['workflow_id']))
if stored_workflow.user != trans.user and not trans.user_is_admin():
lib/galaxy/web/controllers/workflow.py
+12 -3
View File
@@ -1094,7 +1094,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
trans.response.set_content_type( 'application/galaxy-archive' )
return stored_dict
@web.expose
def import_workflow( self, trans, **kwd ):
def import_workflow( self, trans, cntrller='workflow', **kwd ):
"""
Import a workflow by reading an url, uploading a file, opening and reading the contents
of a local file, or receiving the textual representation of a workflow via http.
@@ -1115,7 +1115,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
if workflow_name:
workflow_name = tool_shed_decode( workflow_name )
# The following parameters will have a value only if the import originated
# from a tool shed repository installed locally.
# from a tool shed repository installed locally or from the API.
installed_repository_file = kwd.get( 'installed_repository_file', '' )
repository_id = kwd.get( 'repository_id', '' )
if installed_repository_file and not import_button:
@@ -1172,8 +1172,13 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
if data:
# Create workflow if possible. If a required tool is not available in the local
# Galaxy instance, the tool information will be available in the step_dict.
workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="uploaded file" )
src = None
if cntrller != 'api':
src="uploaded file"
workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src )
workflow = workflow.latest_workflow
if workflow_name:
workflow.name = workflow_name
# Provide user feedback and show workflow list.
if workflow.has_errors:
message += "Imported, but some steps in this workflow have validation errors. "
@@ -1230,12 +1235,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
elif installed_repository_file:
# The workflow was read from a file included with an installed tool shed repository.
message = "Workflow <b>%s</b> imported successfully." % workflow.name
if cntrller == 'api':
return status, message
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='browse_repository',
id=repository_id,
message=message,
status=status ) )
return self.list( trans )
if cntrller == 'api':
return status, message
return trans.fill_template( "workflow/import.mako",
url=url,
message=message,
lib/galaxy/web/framework/__init__.py
+8 -6
View File
@@ -359,17 +359,17 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ):
# An existing session, make sure correct association exists
if galaxy_session.user is None:
# No user, associate
galaxy_session.user = self.__get_or_create_remote_user( remote_user_email )
galaxy_session.user = self.get_or_create_remote_user( remote_user_email )
galaxy_session_requires_flush = True
elif galaxy_session.user.email != remote_user_email:
# Session exists but is not associated with the correct remote user
invalidate_existing_session = True
user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
user_for_new_session = self.get_or_create_remote_user( remote_user_email )
log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
remote_user_email, galaxy_session.user.email )
else:
# No session exists, get/create user for new session
user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
user_for_new_session = self.get_or_create_remote_user( remote_user_email )
else:
if galaxy_session is not None and galaxy_session.user and galaxy_session.user.external:
# Remote user support is not enabled, but there is an existing
@@ -461,11 +461,13 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ):
# The new session should be associated with the user
galaxy_session.user = user_for_new_session
return galaxy_session
def __get_or_create_remote_user( self, remote_user_email ):
def get_or_create_remote_user( self, remote_user_email ):
"""
Return the user in $HTTP_REMOTE_USER and create if necessary
Create a remote user with the email remote_user_email and return it
"""
# remote_user middleware ensures HTTP_REMOTE_USER exists
if not self.app.config.use_remote_user:
return None
user = self.sa_session.query( self.app.model.User ) \
.filter( self.app.model.User.table.c.email==remote_user_email ) \
.first()
scripts/create_db.py
Executable
+36
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@@ -0,0 +1,36 @@
import sys, os.path, logging
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
from galaxy.model.migrate.check import create_or_verify_database as create_db
import pkg_resources
from ConfigParser import SafeConfigParser
log = logging.getLogger( __name__ )
# Poor man's optparse
config_file = 'universe_wsgi.ini'
if '-c' in sys.argv:
pos = sys.argv.index( '-c' )
sys.argv.pop(pos)
config_file = sys.argv.pop( pos )
if not os.path.exists( config_file ):
print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
sys.exit( 1 )
cp = SafeConfigParser()
cp.read( config_file )
if cp.has_option( "app:main", "database_connection" ):
db_url = cp.get( "app:main", "database_connection" )
elif cp.has_option( "app:main", "database_file" ):
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" )
else:
db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
create_db(db_url, config_file)