def purge_category(self, trans, **kwd):
# This method should only be called for a Category that has previously been deleted.
# Purging a deleted Category deletes all of the following from the database:
# - RepoitoryCategoryAssociations where category_id == Category.id
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
purged_categories = ""
message = "Purged %d categories: " % len(ids)
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
# Delete RepositoryCategoryAssociations
for rca in category.repositories:
trans.sa_session.delete(rca)
trans.sa_session.flush()
purged_categories += " %s " % category.name
message = "Purged %d categories: %s" % (count, escape(purged_categories))
else:
message = "No category ids received for purging."
trans.response.send_redirect(web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
def undelete_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
undeleted_categories = ""
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
category.deleted = False
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
count += 1
undeleted_categories += " %s" % category.name
message = "Undeleted %d categories: %s" % (
count, escape(undeleted_categories))
else:
message = "No category ids received for undeleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
def undelete_category( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
ids = util.listify( id )
count = 0
undeleted_categories = ""
for category_id in ids:
category = suc.get_category( trans.app, category_id )
if category.deleted:
category.deleted = False
trans.sa_session.add( category )
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry( category )
count += 1
undeleted_categories += " %s" % category.name
message = "Undeleted %d categories: %s" % ( count, escape( undeleted_categories ) )
else:
message = "No category ids received for undeleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=util.sanitize_text( message ),
status='done' ) )
def create_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
name = kwd.get('name', '').strip()
description = kwd.get('description', '').strip()
if kwd.get('create_category_button', False):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_category_by_name(trans.app, name):
message = 'A category with that name already exists'
status = 'error'
else:
# Create the category
category = trans.app.model.Category(name=name, description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
message = "Category '%s' has been created" % escape(category.name)
status = 'done'
trans.response.send_redirect(web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template('/webapps/tool_shed/category/create_category.mako',
name=name,
description=description,
message=message,
status=status)
def create_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
name = kwd.get('name', '').strip()
description = kwd.get('description', '').strip()
if kwd.get('create_category_button', False):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_category_by_name(trans.app, name):
message = 'A category with that name already exists'
status = 'error'
else:
# Create the category
category = trans.app.model.Category(name=name,
description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
message = "Category '%s' has been created" % escape(
category.name)
status = 'done'
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/tool_shed/category/create_category.mako',
name=name,
description=description,
message=message,
status=status)
def mark_category_deleted( self, trans, **kwd ):
# TODO: We should probably eliminate the Category.deleted column since it really makes no
# sense to mark a category as deleted (category names and descriptions can be changed instead).
# If we do this, and the following 2 methods can be eliminated.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
ids = util.listify( id )
message = "Deleted %d categories: " % len( ids )
for category_id in ids:
category = suc.get_category( trans.app, category_id )
category.deleted = True
trans.sa_session.add( category )
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.remove_category_entry( category )
message += " %s " % escape( category.name )
else:
message = "No category ids received for deleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=util.sanitize_text( message ),
status='done' ) )
def create_component( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
name = kwd.get( 'name', '' )
description = kwd.get( 'description', '' )
if kwd.get( 'create_component_button', False ):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif review_util.get_component_by_name( trans.app, name ):
message = 'A component with that name already exists'
status = 'error'
else:
component = trans.app.model.Component( name=name, description=description )
trans.sa_session.add( component )
trans.sa_session.flush()
message = "Component '%s' has been created" % escape( component.name )
status = 'done'
trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_components',
message=message,
status=status ) )
return trans.fill_template( '/webapps/tool_shed/repository_review/create_component.mako',
name=name,
description=description,
message=message,
status=status )
def purge_category(self, trans, **kwd):
# This method should only be called for a Category that has previously been deleted.
# Purging a deleted Category deletes all of the following from the database:
# - RepoitoryCategoryAssociations where category_id == Category.id
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
purged_categories = ""
message = "Purged %d categories: " % len(ids)
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
# Delete RepositoryCategoryAssociations
for rca in category.repositories:
trans.sa_session.delete(rca)
trans.sa_session.flush()
purged_categories += " %s " % category.name
message = "Purged %d categories: %s" % (count,
escape(purged_categories))
else:
message = "No category ids received for purging."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
def create_category(self, trans, **kwd):
message = escape(kwd.get("message", ""))
status = kwd.get("status", "done")
name = kwd.get("name", "").strip()
description = kwd.get("description", "").strip()
if kwd.get("create_category_button", False):
if not name or not description:
message = "Enter a valid name and a description"
status = "error"
elif suc.get_category_by_name(trans.app, name):
message = "A category with that name already exists"
status = "error"
else:
# Create the category
category = trans.app.model.Category(name=name, description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
message = "Category '%s' has been created" % escape(category.name)
status = "done"
trans.response.send_redirect(
web.url_for(controller="admin", action="manage_categories", message=message, status=status)
)
return trans.fill_template(
"/webapps/tool_shed/category/create_category.mako",
name=name,
description=description,
message=message,
status=status,
)
def upload( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = escape( kwd.get( 'commit_message', 'Uploaded' ) )
category_ids = util.listify( kwd.get( 'category_id', '' ) )
categories = suc.get_categories( trans.app )
repository_id = kwd.get( 'repository_id', '' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) )
uploaded_file = None
upload_point = commit_util.get_upload_point( repository, **kwd )
tip = repository.tip( trans.app )
file_data = kwd.get( 'file_data', '' )
url = kwd.get( 'url', '' )
# Part of the upload process is sending email notification to those that have registered to
# receive them. One scenario occurs when the first change set is produced for the repository.
# See the suc.handle_email_alerts() method for the definition of the scenarios.
new_repo_alert = repository.is_new( trans.app )
uploaded_directory = None
if kwd.get( 'upload_button', False ):
if file_data == '' and url == '':
message = 'No files were entered on the upload form.'
status = 'error'
uploaded_file = None
elif url and url.startswith( 'hg' ):
# Use mercurial clone to fetch repository, contents will then be copied over.
uploaded_directory = tempfile.mkdtemp()
repo_url = 'http%s' % url[ len( 'hg' ): ]
repo_url = repo_url.encode( 'ascii', 'replace' )
try:
commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory )
except Exception, e:
message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string( str( e ) )
status = 'error'
basic_util.remove_dir( uploaded_directory )
uploaded_directory = None
elif url:
valid_url = True
try:
stream = urllib.urlopen( url )
except Exception, e:
valid_url = False
message = 'Error uploading file via http: %s' % str( e )
status = 'error'
uploaded_file = None
if valid_url:
fd, uploaded_file_name = tempfile.mkstemp()
uploaded_file = open( uploaded_file_name, 'wb' )
while 1:
chunk = stream.read( util.CHUNK_SIZE )
if not chunk:
break
uploaded_file.write( chunk )
uploaded_file.flush()
uploaded_file_filename = url.split( '/' )[ -1 ]
isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
def handle_role_associations(app, role, repository, **kwd):
sa_session = app.model.context.current
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository_owner = repository.user
if kwd.get('manage_role_associations_button', False):
in_users_list = util.listify(kwd.get('in_users', []))
in_users = [
sa_session.query(app.model.User).get(x) for x in in_users_list
]
# Make sure the repository owner is always associated with the repostory's admin role.
owner_associated = False
for user in in_users:
if user.id == repository_owner.id:
owner_associated = True
break
if not owner_associated:
in_users.append(repository_owner)
message += "The repository owner must always be associated with the repository's administrator role. "
status = 'error'
in_groups_list = util.listify(kwd.get('in_groups', []))
in_groups = [
sa_session.query(app.model.Group).get(x) for x in in_groups_list
]
in_repositories = [repository]
app.security_agent.set_entity_role_associations(
roles=[role],
users=in_users,
groups=in_groups,
repositories=in_repositories)
sa_session.refresh(role)
message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \
( escape( str( role.name ) ), len( in_users ), len( in_groups ), len( in_repositories ) )
in_users = []
out_users = []
in_groups = []
out_groups = []
for user in sa_session.query( app.model.User ) \
.filter( app.model.User.table.c.deleted == false() ) \
.order_by( app.model.User.table.c.email ):
if user in [x.user for x in role.users]:
in_users.append((user.id, user.email))
else:
out_users.append((user.id, user.email))
for group in sa_session.query( app.model.Group ) \
.filter( app.model.Group.table.c.deleted == false() ) \
.order_by( app.model.Group.table.c.name ):
if group in [x.group for x in role.groups]:
in_groups.append((group.id, group.name))
else:
out_groups.append((group.id, group.name))
associations_dict = dict(in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
message=message,
status=status)
return associations_dict
def upload( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = escape( kwd.get( 'commit_message', 'Uploaded' ) )
repository_id = kwd.get( 'repository_id', '' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) )
uploaded_file = None
upload_point = commit_util.get_upload_point( repository, **kwd )
tip = repository.tip( trans.app )
file_data = kwd.get( 'file_data', '' )
url = kwd.get( 'url', '' )
# Part of the upload process is sending email notification to those that have registered to
# receive them. One scenario occurs when the first change set is produced for the repository.
# See the suc.handle_email_alerts() method for the definition of the scenarios.
new_repo_alert = repository.is_new( trans.app )
uploaded_directory = None
if kwd.get( 'upload_button', False ):
if file_data == '' and url == '':
message = 'No files were entered on the upload form.'
status = 'error'
uploaded_file = None
elif url and url.startswith( 'hg' ):
# Use mercurial clone to fetch repository, contents will then be copied over.
uploaded_directory = tempfile.mkdtemp()
repo_url = 'http%s' % url[ len( 'hg' ): ]
repo_url = repo_url.encode( 'ascii', 'replace' )
try:
commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory )
except Exception, e:
message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string( str( e ) )
status = 'error'
basic_util.remove_dir( uploaded_directory )
uploaded_directory = None
elif url:
valid_url = True
try:
stream = urllib.urlopen( url )
except Exception, e:
valid_url = False
message = 'Error uploading file via http: %s' % str( e )
status = 'error'
uploaded_file = None
if valid_url:
fd, uploaded_file_name = tempfile.mkstemp()
uploaded_file = open( uploaded_file_name, 'wb' )
while 1:
chunk = stream.read( util.CHUNK_SIZE )
if not chunk:
break
uploaded_file.write( chunk )
uploaded_file.flush()
uploaded_file_filename = url.split( '/' )[ -1 ]
isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
def edit_category(self, trans, **kwd):
'''Handle requests to edit TS category name or description'''
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if not id:
message = "No category ids received for editing"
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status='error'))
category = suc.get_category(trans.app, id)
original_category_name = str(category.name)
original_category_description = str(category.description)
if kwd.get('edit_category_button', False):
flush_needed = False
new_name = kwd.get('name', '').strip()
new_description = kwd.get('description', '').strip()
if original_category_name != new_name:
if not new_name:
message = 'Enter a valid name'
status = 'error'
elif original_category_name != new_name and suc.get_category_by_name(
trans.app, new_name):
message = 'A category with that name already exists'
status = 'error'
else:
category.name = new_name
flush_needed = True
if original_category_description != new_description:
category.description = new_description
if not flush_needed:
flush_needed = True
if flush_needed:
trans.sa_session.add(category)
trans.sa_session.flush()
if original_category_name != new_name:
# Update the Tool Shed's repository registry.
trans.app.repository_registry.edit_category_entry(
original_category_name, new_name)
message = "The information has been saved for category '%s'" % escape(
category.name)
status = 'done'
return trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/tool_shed/category/edit_category.mako',
category=category,
message=message,
status=status)
def handle_role_associations( app, role, repository, **kwd ):
sa_session = app.model.context.current
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_owner = repository.user
if kwd.get( 'manage_role_associations_button', False ):
in_users_list = util.listify( kwd.get( 'in_users', [] ) )
in_users = [ sa_session.query( app.model.User ).get( x ) for x in in_users_list ]
# Make sure the repository owner is always associated with the repostory's admin role.
owner_associated = False
for user in in_users:
if user.id == repository_owner.id:
owner_associated = True
break
if not owner_associated:
in_users.append( repository_owner )
message += "The repository owner must always be associated with the repository's administrator role. "
status = 'error'
in_groups_list = util.listify( kwd.get( 'in_groups', [] ) )
in_groups = [ sa_session.query( app.model.Group ).get( x ) for x in in_groups_list ]
in_repositories = [ repository ]
app.security_agent.set_entity_role_associations( roles=[ role ],
users=in_users,
groups=in_groups,
repositories=in_repositories )
sa_session.refresh( role )
message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \
( escape( str( role.name ) ), len( in_users ), len( in_groups ), len( in_repositories ) )
in_users = []
out_users = []
in_groups = []
out_groups = []
for user in sa_session.query( app.model.User ) \
.filter( app.model.User.table.c.deleted==False ) \
.order_by( app.model.User.table.c.email ):
if user in [ x.user for x in role.users ]:
in_users.append( ( user.id, user.email ) )
else:
out_users.append( ( user.id, user.email ) )
for group in sa_session.query( app.model.Group ) \
.filter( app.model.Group.table.c.deleted==False ) \
.order_by( app.model.Group.table.c.name ):
if group in [ x.group for x in role.groups ]:
in_groups.append( ( group.id, group.name ) )
else:
out_groups.append( ( group.id, group.name ) )
associations_dict = dict( in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
message=message,
status=status )
return associations_dict
def edit_category(self, trans, **kwd):
'''Handle requests to edit TS category name or description'''
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if not id:
message = "No category ids received for editing"
trans.response.send_redirect(web.url_for(controller='admin',
action='manage_categories',
message=message,
status='error'))
category = suc.get_category(trans.app, id)
original_category_name = str(category.name)
original_category_description = str(category.description)
if kwd.get('edit_category_button', False):
flush_needed = False
new_name = kwd.get('name', '').strip()
new_description = kwd.get('description', '').strip()
if original_category_name != new_name:
if not new_name:
message = 'Enter a valid name'
status = 'error'
elif original_category_name != new_name and suc.get_category_by_name(trans.app, new_name):
message = 'A category with that name already exists'
status = 'error'
else:
category.name = new_name
flush_needed = True
if original_category_description != new_description:
category.description = new_description
if not flush_needed:
flush_needed = True
if flush_needed:
trans.sa_session.add(category)
trans.sa_session.flush()
if original_category_name != new_name:
# Update the Tool Shed's repository registry.
trans.app.repository_registry.edit_category_entry(original_category_name, new_name)
message = "The information has been saved for category '%s'" % escape(category.name)
status = 'done'
return trans.response.send_redirect(web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template('/webapps/tool_shed/category/edit_category.mako',
category=category,
message=message,
status=status)
def check_for_updates( app, model, repository_id=None ):
message = ''
status = 'ok'
if repository_id is None:
success_count = 0
repository_names_not_updated = []
updated_count = 0
for repository in model.context.query( model.ToolShedRepository ) \
.filter( model.ToolShedRepository.table.c.deleted == false() ):
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
success_count += 1
else:
repository_names_not_updated.append( '<b>%s</b>' % escape( str( repository.name ) ) )
if updated:
updated_count += 1
message = "Checked the status in the tool shed for %d repositories. " % success_count
message += "Updated the tool shed status for %d repositories. " % updated_count
if repository_names_not_updated:
message += "Unable to retrieve status from the tool shed for the following repositories:\n"
message += ", ".join( repository_names_not_updated )
else:
repository = suc.get_tool_shed_repository_by_id( app, repository_id )
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
if updated:
message = "The tool shed status for repository <b>%s</b> has been updated." % escape( str( repository.name ) )
else:
message = "The status has not changed in the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
else:
message = "Unable to retrieve status from the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
status = 'error'
return message, status
def regenerate_statistics(self, trans, **kwd):
message = escape(kwd.get("message", ""))
status = kwd.get("status", "done")
if "regenerate_statistics_button" in kwd:
trans.app.shed_counter.generate_statistics()
message = "Successfully regenerated statistics"
return trans.fill_template("/webapps/tool_shed/admin/statistics.mako", message=message, status=status)
def delete_repository_metadata(self, trans, **kwd):
message = escape(kwd.get("message", ""))
status = kwd.get("status", "done")
id = kwd.get("id", None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
trans.sa_session.delete(repository_metadata)
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record"))
else:
message = "No repository metadata ids received for deleting."
status = "error"
trans.response.send_redirect(
web.url_for(
controller="admin",
action="browse_repository_metadata",
message=util.sanitize_text(message),
status=status,
)
)
def edit_component( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if not id:
message = "No component ids received for editing"
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=message,
status='error' ) )
component = review_util.get_component( trans.app, id )
if kwd.get( 'edit_component_button', False ):
new_description = kwd.get( 'description', '' ).strip()
if component.description != new_description:
component.description = new_description
trans.sa_session.add( component )
trans.sa_session.flush()
message = "The information has been saved for the component named <b>%s</b>" % escape( component.name )
status = 'done'
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_components',
message=message,
status=status ) )
return trans.fill_template( '/webapps/tool_shed/repository_review/edit_component.mako',
component=component,
message=message,
status=status )
def repository_reviews_by_user(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'operation' in kwd:
operation = kwd['operation'].lower()
# The value of the received id is the encoded review id.
review = review_util.get_review(trans.app, kwd['id'])
repository = review.repository
kwd['id'] = trans.security.encode_id(repository.id)
if operation == "inspect repository revisions":
return trans.response.send_redirect(
web.url_for(controller='repository_review',
action='manage_repository_reviews',
**kwd))
if operation == "view_or_manage_repository":
kwd['changeset_revision'] = review.changeset_revision
return trans.response.send_redirect(
web.url_for(controller='repository_review',
action='view_or_manage_repository',
**kwd))
# The user may not be the current user. The value of the received id is the encoded user id.
user = suc.get_user(trans.app, kwd['id'])
self.repository_reviews_by_user_grid.title = "All repository revision reviews for user '%s'" % user.username
return self.repository_reviews_by_user_grid(trans, **kwd)
def review_tool_migration_stages( self, trans, **kwd ):
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
migration_stages_dict = odict()
migration_modules = []
migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions' ) )
migration_scripts_dir_contents = os.listdir( migration_scripts_dir )
for item in migration_scripts_dir_contents:
if os.path.isfile( os.path.join( migration_scripts_dir, item ) ) and item.endswith( '.py' ):
module = item.replace( '.py', '' )
migration_modules.append( module )
if migration_modules:
migration_modules.sort()
# Remove the 0001_tools.py script since it is the seed.
migration_modules = migration_modules[ 1: ]
# Reverse the list so viewing will be newest to oldest.
migration_modules.reverse()
for migration_module in migration_modules:
migration_stage = int( migration_module.replace( '_tools', '' ) )
repo_name_dependency_tups = self.check_for_tool_dependencies( trans, migration_stage )
open_file_obj, file_name, description = imp.find_module( migration_module, [ migration_scripts_dir ] )
imported_module = imp.load_module( 'upgrade', open_file_obj, file_name, description )
migration_info = imported_module.__doc__
open_file_obj.close()
migration_stages_dict[ migration_stage ] = ( migration_info, repo_name_dependency_tups )
return trans.fill_template( 'admin/review_tool_migration_stages.mako',
migration_stages_dict=migration_stages_dict,
message=message,
status=status )
def manage_repository_reviews(self, trans, mine=False, **kwd):
# The value of the received id is the encoded repository id.
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository_id = kwd.get('id', None)
if repository_id:
repository = suc.get_repository_in_tool_shed(
trans.app, repository_id)
repo = hg_util.get_repo_for_repository(trans.app,
repository=repository)
metadata_revision_hashes = [
metadata_revision.changeset_revision
for metadata_revision in repository.metadata_revisions
]
reviewed_revision_hashes = [
review.changeset_revision for review in repository.reviews
]
reviews_dict = OrderedDict()
for changeset in hg_util.get_reversed_changelog_changesets(repo):
changeset_revision = str(repo[changeset])
if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes:
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(
repo, changeset_revision)
if changeset_revision in reviewed_revision_hashes:
# Find the review for this changeset_revision
repository_reviews = \
review_util.get_reviews_by_repository_id_changeset_revision(trans.app,
repository_id,
changeset_revision)
# Determine if the current user can add a review to this revision.
can_add_review = trans.user not in [
repository_review.user
for repository_review in repository_reviews
]
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
trans.app, repository_id, changeset_revision)
if repository_metadata:
repository_metadata_reviews = util.listify(
repository_metadata.reviews)
else:
repository_metadata_reviews = []
else:
repository_reviews = []
repository_metadata_reviews = []
can_add_review = True
installable = changeset_revision in metadata_revision_hashes
revision_dict = dict(
changeset_revision_label=changeset_revision_label,
repository_reviews=repository_reviews,
repository_metadata_reviews=repository_metadata_reviews,
installable=installable,
can_add_review=can_add_review)
reviews_dict[changeset_revision] = revision_dict
return trans.fill_template(
'/webapps/tool_shed/repository_review/reviews_of_repository.mako',
repository=repository,
reviews_dict=reviews_dict,
mine=mine,
message=message,
status=status)
def manage_repository_reviews_of_revision(self, trans, **kwd):
# The value of the received id is the encoded repository id.
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
repository_id = kwd.get('id', None)
changeset_revision = kwd.get('changeset_revision', None)
repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
repo = hg_util.get_repo_for_repository(trans.app,
repository=repository,
repo_path=None,
create=False)
installable = changeset_revision in [
metadata_revision.changeset_revision
for metadata_revision in repository.metadata_revisions
]
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision(
repo, changeset_revision)
reviews = review_util.get_reviews_by_repository_id_changeset_revision(
trans.app, repository_id, changeset_revision)
return trans.fill_template(
'/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako',
repository=repository,
changeset_revision=changeset_revision,
changeset_revision_label=changeset_revision_label,
reviews=reviews,
installable=installable,
message=message,
status=status)
def create_repository(
app,
name,
type,
description,
long_description,
user_id,
category_ids=[],
remote_repository_url=None,
homepage_url=None,
):
"""Create a new ToolShed repository"""
sa_session = app.model.context.current
# Add the repository record to the database.
repository = app.model.Repository(
name=name,
type=type,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url,
description=description,
long_description=long_description,
user_id=user_id,
)
# Flush to get the id.
sa_session.add(repository)
sa_session.flush()
# Create an admin role for the repository.
repository_admin_role = create_repository_admin_role(app, repository)
# Determine the repository's repo_path on disk.
dir = os.path.join(app.config.file_path, *directory_hash_id(repository.id))
# Create directory if it does not exist.
if not os.path.exists(dir):
os.makedirs(dir)
# Define repo name inside hashed directory.
repository_path = os.path.join(dir, "repo_%d" % repository.id)
# Create local repository directory.
if not os.path.exists(repository_path):
os.makedirs(repository_path)
# Create the local repository.
repo = hg_util.get_repo_for_repository(app, repository=None, repo_path=repository_path, create=True)
# Add an entry in the hgweb.config file for the local repository.
lhs = "repos/%s/%s" % (repository.user.username, repository.name)
app.hgweb_config_manager.add_entry(lhs, repository_path)
# Create a .hg/hgrc file for the local repository.
hg_util.create_hgrc_file(app, repository)
flush_needed = False
if category_ids:
# Create category associations
for category_id in category_ids:
category = sa_session.query(app.model.Category).get(app.security.decode_id(category_id))
rca = app.model.RepositoryCategoryAssociation(repository, category)
sa_session.add(rca)
flush_needed = True
if flush_needed:
sa_session.flush()
# Update the repository registry.
app.repository_registry.add_entry(repository)
message = "Repository <b>%s</b> has been created." % escape(str(repository.name))
return repository, message
def delete_repository(self, trans, **kwd):
message = escape(kwd.get("message", ""))
status = kwd.get("status", "done")
id = kwd.get("id", None)
if id:
# Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
deleted_repositories = ""
for repository_id in ids:
repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
if repository:
if not repository.deleted:
# Mark all installable repository_metadata records as not installable.
for repository_metadata in repository.downloadable_revisions:
repository_metadata.downloadable = False
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = True
trans.sa_session.add(repository_admin_role)
repository.deleted = True
trans.sa_session.add(repository)
trans.sa_session.flush()
# Update the repository registry.
trans.app.repository_registry.remove_entry(repository)
count += 1
deleted_repositories += " %s " % repository.name
if count:
message = "Deleted %d %s: %s" % (
count,
inflector.cond_plural(len(ids), "repository"),
escape(deleted_repositories),
)
else:
message = "All selected repositories were already marked deleted."
else:
message = "No repository ids received for deleting."
status = "error"
trans.response.send_redirect(
web.url_for(
controller="admin", action="browse_repositories", message=util.sanitize_text(message), status=status
)
)
def regenerate_statistics(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'regenerate_statistics_button' in kwd:
trans.app.shed_counter.generate_statistics()
message = "Successfully regenerated statistics"
return trans.fill_template('/webapps/tool_shed/admin/statistics.mako',
message=message,
status=status)
def regenerate_statistics(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'regenerate_statistics_button' in kwd:
trans.app.shed_counter.generate_statistics()
message = "Successfully regenerated statistics"
return trans.fill_template('/webapps/tool_shed/admin/statistics.mako',
message=message,
status=status)
def edit_category(self, trans, **kwd):
message = escape(kwd.get("message", ""))
status = kwd.get("status", "done")
id = kwd.get("id", None)
if not id:
message = "No category ids received for editing"
trans.response.send_redirect(
web.url_for(controller="admin", action="manage_categories", message=message, status="error")
)
category = suc.get_category(trans.app, id)
original_category_name = str(category.name)
original_category_description = str(category.description)
if kwd.get("edit_category_button", False):
flush_needed = False
new_name = kwd.get("name", "").strip()
new_description = kwd.get("description", "").strip()
if original_category_name != new_name:
if not new_name:
message = "Enter a valid name"
status = "error"
elif original_category_name != new_name and suc.get_category_by_name(trans.app, new_name):
message = "A category with that name already exists"
status = "error"
else:
category.name = new_name
flush_needed = True
if original_category_description != new_description:
category.description = new_description
if not flush_needed:
flush_needed = True
if flush_needed:
trans.sa_session.add(category)
trans.sa_session.flush()
if original_category_name != new_name:
# Update the Tool Shed's repository registry.
trans.app.repository_registry.edit_category_entry(original_category_name, new_name)
message = "The information has been saved for category '%s'" % escape(category.name)
status = "done"
return trans.response.send_redirect(
web.url_for(controller="admin", action="manage_categories", message=message, status=status)
)
return trans.fill_template(
"/webapps/tool_shed/category/edit_category.mako", category=category, message=message, status=status
)
def delete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
# Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
deleted_repositories = ""
for repository_id in ids:
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository:
if not repository.deleted:
# Mark all installable repository_metadata records as not installable.
for repository_metadata in repository.downloadable_revisions:
repository_metadata.downloadable = False
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = True
trans.sa_session.add(repository_admin_role)
repository.deleted = True
trans.sa_session.add(repository)
trans.sa_session.flush()
# Update the repository registry.
trans.app.repository_registry.remove_entry(repository)
count += 1
deleted_repositories += " %s " % repository.name
if count:
message = "Deleted %d %s: %s" % (
count, inflector.cond_plural(
len(ids), "repository"), escape(deleted_repositories))
else:
message = "All selected repositories were already marked deleted."
else:
message = "No repository ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status=status))
def create_repository(app,
name,
type,
description,
long_description,
user_id,
category_ids=[]):
sa_session = app.model.context.current
# Add the repository record to the database.
repository = app.model.Repository(name=name,
type=type,
description=description,
long_description=long_description,
user_id=user_id)
# Flush to get the id.
sa_session.add(repository)
sa_session.flush()
# Create an admin role for the repository.
repository_admin_role = create_repository_admin_role(app, repository)
# Determine the repository's repo_path on disk.
dir = os.path.join(app.config.file_path, *directory_hash_id(repository.id))
# Create directory if it does not exist.
if not os.path.exists(dir):
os.makedirs(dir)
# Define repo name inside hashed directory.
repository_path = os.path.join(dir, "repo_%d" % repository.id)
# Create local repository directory.
if not os.path.exists(repository_path):
os.makedirs(repository_path)
# Create the local repository.
repo = hg_util.get_repo_for_repository(app,
repository=None,
repo_path=repository_path,
create=True)
# Add an entry in the hgweb.config file for the local repository.
lhs = "repos/%s/%s" % (repository.user.username, repository.name)
app.hgweb_config_manager.add_entry(lhs, repository_path)
# Create a .hg/hgrc file for the local repository.
hg_util.create_hgrc_file(app, repository)
flush_needed = False
if category_ids:
# Create category associations
for category_id in category_ids:
category = sa_session.query( app.model.Category ) \
.get( app.security.decode_id( category_id ) )
rca = app.model.RepositoryCategoryAssociation(repository, category)
sa_session.add(rca)
flush_needed = True
if flush_needed:
sa_session.flush()
# Update the repository registry.
app.repository_registry.add_entry(repository)
message = "Repository <b>%s</b> has been created." % escape(
str(repository.name))
return repository, message
def manage_repositories_reviewed_by_me( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if 'operation' in kwd:
kwd[ 'mine' ] = True
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_repositories_with_reviews',
**kwd ) )
self.repositories_reviewed_by_me_grid.title = 'Repositories reviewed by me'
return self.repositories_reviewed_by_me_grid( trans, **kwd )
def approve_repository_review( self, trans, **kwd ):
# The value of the received id is the encoded review id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
encoded_review_id = kwd[ 'id' ]
review = review_util.get_review( trans.app, encoded_review_id )
if kwd.get( 'approve_repository_review_button', False ):
approved_select_field_name = '%s%sapproved' % ( encoded_review_id, STRSEP )
approved_select_field_value = str( kwd[ approved_select_field_name ] )
review.approved = approved_select_field_value
trans.sa_session.add( review )
trans.sa_session.flush()
message = 'Approved value <b>%s</b> saved for this revision.' % escape( approved_select_field_value )
repository_id = trans.security.encode_id( review.repository_id )
changeset_revision = review.changeset_revision
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_repository_reviews_of_revision',
id=repository_id,
changeset_revision=changeset_revision,
message=message,
status=status ) )
def manage_repositories_reviewed_by_me(self, trans, **kwd):
# The value of the received id is the encoded repository id.
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'operation' in kwd:
kwd['mine'] = True
return trans.response.send_redirect(
web.url_for(controller='repository_review',
action='manage_repositories_with_reviews',
**kwd))
self.repositories_reviewed_by_me_grid.title = 'Repositories reviewed by me'
return self.repositories_reviewed_by_me_grid(trans, **kwd)
def browse_review( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
review = review_util.get_review( trans.app, kwd[ 'id' ] )
repository = review.repository
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako',
repository=repository,
changeset_revision_label=changeset_revision_label,
review=review,
message=message,
status=status )
def undelete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
# Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
undeleted_repositories = ""
for repository_id in ids:
repository = suc.get_repository_in_tool_shed(
trans.app, repository_id)
if repository:
if repository.deleted:
# Inspect all repository_metadata records to determine those that are installable, and mark
# them accordingly.
for repository_metadata in repository.metadata_revisions:
metadata = repository_metadata.metadata
if metadata:
if metadata_util.is_downloadable(metadata):
repository_metadata.downloadable = True
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as not deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = False
trans.sa_session.add(repository_admin_role)
repository.deleted = False
trans.sa_session.add(repository)
trans.sa_session.flush()
if not repository.deprecated:
# Update the repository registry.
trans.app.repository_registry.add_entry(repository)
count += 1
undeleted_repositories += " %s" % repository.name
if count:
message = "Undeleted %d %s: %s" % (
count, inflector.cond_plural(
count, "repository"), undeleted_repositories)
else:
message = "No selected repositories were marked deleted, so they could not be undeleted."
else:
message = "No repository ids received for undeleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status='done'))
def reviewed_repositories_i_own( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
# The value of the received id is the encoded repository id.
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "inspect repository revisions":
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_repository_reviews',
**kwd ) )
if operation == "view_or_manage_repository":
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='view_or_manage_repository',
**kwd ) )
return self.reviewed_repositories_i_own_grid( trans, **kwd )
def reset_metadata_on_selected_repositories_in_tool_shed(self, trans, **kwd):
rmm = repository_metadata_manager.RepositoryMetadataManager(trans.app, trans.user)
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = rmm.reset_metadata_on_selected_repositories(**kwd)
else:
message = escape(util.restore_text(kwd.get('message', '')))
status = kwd.get('status', 'done')
repositories_select_field = rmm.build_repository_ids_select_field(name='repository_ids',
multiple=True,
display='checkboxes',
my_writable=False)
return trans.fill_template('/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
status=status)
def reset_metadata_on_selected_repositories_in_tool_shed(self, trans, **kwd):
rmm = repository_metadata_manager.RepositoryMetadataManager(trans.app, trans.user)
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = rmm.reset_metadata_on_selected_repositories(**kwd)
else:
message = escape(util.restore_text(kwd.get('message', '')))
status = kwd.get('status', 'done')
repositories_select_field = rmm.build_repository_ids_select_field(name='repository_ids',
multiple=True,
display='checkboxes',
my_writable=False)
return trans.fill_template('/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
status=status)
def undelete_repository(self, trans, **kwd):
message = escape(kwd.get("message", ""))
id = kwd.get("id", None)
if id:
# Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
undeleted_repositories = ""
for repository_id in ids:
repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
if repository:
if repository.deleted:
# Inspect all repository_metadata records to determine those that are installable, and mark
# them accordingly.
for repository_metadata in repository.metadata_revisions:
metadata = repository_metadata.metadata
if metadata:
if metadata_util.is_downloadable(metadata):
repository_metadata.downloadable = True
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as not deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = False
trans.sa_session.add(repository_admin_role)
repository.deleted = False
trans.sa_session.add(repository)
trans.sa_session.flush()
if not repository.deprecated:
# Update the repository registry.
trans.app.repository_registry.add_entry(repository)
count += 1
undeleted_repositories += " %s" % repository.name
if count:
message = "Undeleted %d %s: %s" % (
count,
inflector.cond_plural(count, "repository"),
undeleted_repositories,
)
else:
message = "No selected repositories were marked deleted, so they could not be undeleted."
else:
message = "No repository ids received for undeleting."
trans.response.send_redirect(
web.url_for(
controller="admin", action="browse_repositories", message=util.sanitize_text(message), status="done"
)
)
def reset_metadata_on_selected_repositories_in_tool_shed(self, trans, **kwd):
rmm = repository_metadata_manager.RepositoryMetadataManager(trans.app, trans.user)
if "reset_metadata_on_selected_repositories_button" in kwd:
message, status = rmm.reset_metadata_on_selected_repositories(**kwd)
else:
message = escape(util.restore_text(kwd.get("message", "")))
status = kwd.get("status", "done")
repositories_select_field = rmm.build_repository_ids_select_field(
name="repository_ids", multiple=True, display="checkboxes", my_writable=False
)
return trans.fill_template(
"/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako",
repositories_select_field=repositories_select_field,
message=message,
status=status,
)
def reviewed_repositories_i_own(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
# The value of the received id is the encoded repository id.
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "inspect repository revisions":
return trans.response.send_redirect(
web.url_for(controller='repository_review',
action='manage_repository_reviews',
**kwd))
if operation == "view_or_manage_repository":
return trans.response.send_redirect(
web.url_for(controller='repository_review',
action='view_or_manage_repository',
**kwd))
return self.reviewed_repositories_i_own_grid(trans, **kwd)
def manage_repository_reviews( self, trans, mine=False, **kwd ):
# The value of the received id is the encoded repository id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
if repository_id:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
reviews_dict = odict()
for changeset in hg_util.get_reversed_changelog_changesets( repo ):
ctx = repo.changectx( changeset )
changeset_revision = str( ctx )
if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes:
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
if changeset_revision in reviewed_revision_hashes:
# Find the review for this changeset_revision
repository_reviews = \
review_util.get_reviews_by_repository_id_changeset_revision( trans.app,
repository_id,
changeset_revision )
# Determine if the current user can add a review to this revision.
can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ]
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if repository_metadata:
repository_metadata_reviews = util.listify( repository_metadata.reviews )
else:
repository_metadata_reviews = []
else:
repository_reviews = []
repository_metadata_reviews = []
can_add_review = True
installable = changeset_revision in metadata_revision_hashes
revision_dict = dict( changeset_revision_label=changeset_revision_label,
repository_reviews=repository_reviews,
repository_metadata_reviews=repository_metadata_reviews,
installable=installable,
can_add_review=can_add_review )
reviews_dict[ changeset_revision ] = revision_dict
return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_repository.mako',
repository=repository,
reviews_dict=reviews_dict,
mine=mine,
message=message,
status=status )
def select_previous_review( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
changeset_revision = kwd.get( 'changeset_revision', None )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
previous_reviews_dict = review_util.get_previous_repository_reviews( trans.app,
repository,
changeset_revision )
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako',
repository=repository,
changeset_revision=changeset_revision,
changeset_revision_label=changeset_revision_label,
previous_reviews_dict=previous_reviews_dict,
message=message,
status=status )
def manage_repository_reviews_of_revision( self, trans, **kwd ):
# The value of the received id is the encoded repository id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans.app,
repository_id,
changeset_revision )
return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako',
repository=repository,
changeset_revision=changeset_revision,
changeset_revision_label=changeset_revision_label,
reviews=reviews,
installable=installable,
message=message,
status=status )
def delete_repository_metadata(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
trans.sa_session.delete(repository_metadata)
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record"))
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect(web.url_for(controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text(message),
status=status))
def check_for_updates(app, model, repository_id=None):
message = ''
status = 'ok'
if repository_id is None:
success_count = 0
repository_names_not_updated = []
updated_count = 0
for repository in model.context.query( model.ToolShedRepository ) \
.filter( model.ToolShedRepository.table.c.deleted == false() ):
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
success_count += 1
else:
repository_names_not_updated.append(
'<b>%s</b>' % escape(str(repository.name)))
if updated:
updated_count += 1
message = "Checked the status in the tool shed for %d repositories. " % success_count
message += "Updated the tool shed status for %d repositories. " % updated_count
if repository_names_not_updated:
message += "Unable to retrieve status from the tool shed for the following repositories:\n"
message += ", ".join(repository_names_not_updated)
else:
repository = suc.get_tool_shed_repository_by_id(app, repository_id)
ok, updated = \
check_or_update_tool_shed_status_for_installed_repository( app, repository )
if ok:
if updated:
message = "The tool shed status for repository <b>%s</b> has been updated." % escape(
str(repository.name))
else:
message = "The status has not changed in the tool shed for repository <b>%s</b>." % escape(
str(repository.name))
else:
message = "Unable to retrieve status from the tool shed for repository <b>%s</b>." % escape(
str(repository.name))
status = 'error'
return message, status
def repository_reviews_by_user( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
if 'operation' in kwd:
operation = kwd['operation'].lower()
# The value of the received id is the encoded review id.
review = review_util.get_review( trans.app, kwd[ 'id' ] )
repository = review.repository
kwd[ 'id' ] = trans.security.encode_id( repository.id )
if operation == "inspect repository revisions":
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_repository_reviews',
**kwd ) )
if operation == "view_or_manage_repository":
kwd[ 'changeset_revision' ] = review.changeset_revision
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='view_or_manage_repository',
**kwd ) )
# The user may not be the current user. The value of the received id is the encoded user id.
user = suc.get_user( trans.app, kwd[ 'id' ] )
self.repository_reviews_by_user_grid.title = "All repository revision reviews for user '%s'" % user.username
return self.repository_reviews_by_user_grid( trans, **kwd )
def get_value( self, trans, grid, quota ):
if quota.description:
return escape(quota.description)
return ''
def get_value( self, trans, grid, user ):
return escape(user.email)
def get_value( self, trans, grid, quota ):
return escape(quota.name)
def get_value( self, trans, grid, user ):
if user.username:
return escape(user.username)
return 'not set'
def view_tool_data_tables( self, trans, **kwd ):
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status )