mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-13 00:44:55 +08:00
Apply the improvements for generation of tool shed URLs to the repository controller.
This commit is contained in:
Greg Von Kuster
@@ -392,8 +392,9 @@ class AdminToolshed( AdminGalaxy ):
|
||||
# Send a request to the relevant tool shed to see if there are any updates.
|
||||
repository = get_repository( trans, kwd[ 'id' ] )
|
||||
tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
|
||||
url = url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
|
||||
url = url_join( tool_shed_url,
|
||||
'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
|
||||
return trans.response.send_redirect( url )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
@@ -634,8 +635,9 @@ class AdminToolshed( AdminGalaxy ):
|
||||
tool_shed_repository,
|
||||
trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
|
||||
tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
|
||||
url = url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
|
||||
url = url_join( tool_shed_url,
|
||||
'/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
|
||||
response = urllib2.urlopen( url )
|
||||
text = response.read()
|
||||
response.close()
|
||||
@@ -954,7 +956,9 @@ class AdminToolshed( AdminGalaxy ):
|
||||
repository_ids = kwd.get( 'repository_ids', None )
|
||||
changeset_revisions = kwd.get( 'changeset_revisions', None )
|
||||
# Get the information necessary to install each repository.
|
||||
url = url_join( tool_shed_url, 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % ( repository_ids, changeset_revisions ) )
|
||||
url = url_join( tool_shed_url,
|
||||
'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % \
|
||||
( repository_ids, changeset_revisions ) )
|
||||
response = urllib2.urlopen( url )
|
||||
raw_text = response.read()
|
||||
response.close()
|
||||
@@ -1097,8 +1101,9 @@ class AdminToolshed( AdminGalaxy ):
|
||||
name = repo_info_dict.keys()[ 0 ]
|
||||
repo_info_tuple = repo_info_dict[ name ]
|
||||
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
|
||||
url = url_join( tool_shed_url, 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( name, repository_owner, changeset_revision ) )
|
||||
url = url_join( tool_shed_url,
|
||||
'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( name, repository_owner, changeset_revision ) )
|
||||
response = urllib2.urlopen( url )
|
||||
raw_text = response.read()
|
||||
response.close()
|
||||
@@ -1273,8 +1278,9 @@ class AdminToolshed( AdminGalaxy ):
|
||||
tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
|
||||
# Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset
|
||||
# revision to see if it was previously installed using one of them.
|
||||
url = url_join( tool_shed_url, 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) )
|
||||
url = url_join( tool_shed_url,
|
||||
'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) )
|
||||
response = urllib2.urlopen( url )
|
||||
text = response.read()
|
||||
response.close()
|
||||
@@ -1350,8 +1356,9 @@ class AdminToolshed( AdminGalaxy ):
|
||||
# Get the tool_versions from the tool shed for each tool in the installed change set.
|
||||
repository = get_repository( trans, kwd[ 'id' ] )
|
||||
tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
|
||||
url = url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( repository.name, repository.owner, repository.changeset_revision ) )
|
||||
url = url_join( tool_shed_url,
|
||||
'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
|
||||
( repository.name, repository.owner, repository.changeset_revision ) )
|
||||
response = urllib2.urlopen( url )
|
||||
text = response.read()
|
||||
response.close()
|
||||
|
||||
@@ -11,7 +11,7 @@ from galaxy.util.json import from_json_string, to_json_string
|
||||
from galaxy.model.orm import *
|
||||
from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, NOT_TOOL_CONFIGS
|
||||
from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path
|
||||
from galaxy.util.shed_util import to_html_escaped, update_repository
|
||||
from galaxy.util.shed_util import to_html_escaped, update_repository, url_join
|
||||
from galaxy.tool_shed.encoding_util import *
|
||||
from common import *
|
||||
|
||||
@@ -749,9 +749,10 @@ class RepositoryController( BaseUIController, ItemRatings ):
|
||||
update = 'true'
|
||||
no_update = 'false'
|
||||
else:
|
||||
# Start building up the url to redirect back to the calling Galaxy instance.
|
||||
url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) )
|
||||
url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision )
|
||||
# Start building up the url to redirect back to the calling Galaxy instance.
|
||||
url = url_join( galaxy_url,
|
||||
'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
|
||||
( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
|
||||
if changeset_revision == repository.tip:
|
||||
# If changeset_revision is the repository tip, there are no additional updates.
|
||||
if from_update_manager:
|
||||
@@ -1395,10 +1396,9 @@ class RepositoryController( BaseUIController, ItemRatings ):
|
||||
"""Send the list of repository_ids and changeset_revisions to Galaxy so it can begin the installation process."""
|
||||
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
|
||||
# Redirect back to local Galaxy to perform install.
|
||||
url = '%sadmin_toolshed/prepare_for_install' % galaxy_url
|
||||
url += '?tool_shed_url=%s' % url_for( '/', qualified=True )
|
||||
url += '&repository_ids=%s' % ','.join( util.listify( repository_ids ) )
|
||||
url += '&changeset_revisions=%s' % ','.join( util.listify( changeset_revisions ) )
|
||||
url = url_join( galaxy_url,
|
||||
'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \
|
||||
( url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) )
|
||||
return trans.response.send_redirect( url )
|
||||
@web.expose
|
||||
def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
|
||||
|
||||
Reference in New Issue
Block a user