def create_category( self, trans, **kwd ):
message = 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" % 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 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_repository_and_import_archive( trans, repository_archive_dict, import_results_tups ):
"""
Create a new repository in the tool shed and populate it with the contents of a gzip compressed tar archive that was exported
as part or all of the contents of a capsule.
"""
results_message = ''
name = repository_archive_dict.get( 'name', None )
username = repository_archive_dict.get( 'owner', None )
if name is None or username is None:
results_message += 'Import failed: required repository name <b>%s</b> or owner <b>%s</b> is missing.' % ( str( name ), str( username ))
import_results_tups.append( ( ( str( name ), str( username ) ), results_message ) )
else:
if repository_archive_dict[ 'status' ] is None:
# The repository does not yet exist in this Tool Shed and the current user is authorized to import
# the current archive file.
type = repository_archive_dict.get( 'type', 'unrestricted' )
description = repository_archive_dict.get( 'description', '' )
long_description = repository_archive_dict.get( 'long_description', '' )
# The owner entry in the repository_archive_dict is the public username of the user associated with
# the exported repository archive.
user = suc.get_user_by_username( trans.app, username )
if user is None:
results_message += 'Import failed: repository owner <b>%s</b> does not have an account in this Tool Shed.' % str( username )
import_results_tups.append( ( ( str( name ), str( username ) ), results_message ) )
else:
user_id = user.id
# The categories entry in the repository_archive_dict is a list of category names. If a name does not
# exist in the current Tool Shed, the category will not be created, so it will not be associated with
# the repository.
category_ids = []
category_names = repository_archive_dict[ 'category_names' ]
for category_name in category_names:
category = suc.get_category_by_name( trans, category_name )
if category is None:
results_message += 'This Tool Shed does not have the category <b>%s</b> so it will not be associated with this repository.' % \
str( category_name )
else:
category_ids.append( trans.security.encode_id( category.id ) )
# Create the repository record in the database.
repository, create_message = create_repository( trans,
name,
type,
description,
long_description,
user_id=user_id,
category_ids=category_ids )
if create_message:
results_message += create_message
# Populate the new repository with the contents of exported repository archive.
results_dict = import_util.import_repository_archive( trans, repository, repository_archive_dict )
import_results_tups.append( ( ( str( name ), str( username ) ), results_message ) )
else:
# The repository either already exists in this Tool Shed or the current user is not authorized to create it.
results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % str( repository_archive_dict[ 'status' ] )
import_results_tups.append( ( ( str( name ), str( username ) ), results_message ) )
return import_results_tups
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 create(self, trans, payload, **kwd):
"""
POST /api/categories
Returns a dictionary of information about the created category.
: param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param name (required): the name of the category
:param description (optional): the description of the category (if not provided, the name will be used)
"""
category_dict = dict(message='', status='ok')
# Make sure the current user's API key proves he is an admin user in this Tool Shed.
if trans.user_is_admin():
# Get the information about the category to be created from the payload.
name = payload.get('name', '')
if name:
description = payload.get('description', '')
if not description:
# Default the description to the name.
description = name
if suc.get_category_by_name(trans.app, name):
category_dict[
'message'] = 'A category with that name already exists'
category_dict['status'] = 'error'
else:
# Create the category
category = trans.app.model.Category(
name=name, description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
category_dict = category.to_dict(
view='element',
value_mapper=self.__get_value_mapper(trans))
category_dict[
'message'] = "Category '%s' has been created" % str(
category.name)
category_dict['url'] = web.url_for(
controller='categories',
action='show',
id=trans.security.encode_id(category.id))
else:
category_dict['message'] = "Missing required parameter 'name'."
category_dict['status'] = 'error'
else:
category_dict[
'message'] = 'You are not authorized to create a category in this Tool Shed.'
category_dict['status'] = 'error'
return category_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 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 create(self, trans, payload, **kwd):
"""
POST /api/categories
Return a dictionary of information about the created category.
The following parameters are included in the payload:
:param name (required): the name of the category
:param description (optional): the description of the category (if not provided, the name will be used)
Example: POST /api/categories/?key=XXXYYYXXXYYY
Content-Disposition: form-data; name="name" Category_Name
Content-Disposition: form-data; name="description" Category_Description
"""
category_dict = dict(message='', status='ok')
name = payload.get('name', '')
if name:
description = payload.get('description', '')
if not description:
# Default the description to the name.
description = name
if suc.get_category_by_name(self.app, name):
raise exceptions.Conflict(
'A category with that name already exists.')
else:
# Create the category
category = self.app.model.Category(name=name,
description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
category_dict = category.to_dict(
view='element',
value_mapper=self.__get_value_mapper(trans))
category_dict[
'message'] = "Category '%s' has been created" % str(
category.name)
category_dict['url'] = web.url_for(controller='categories',
action='show',
id=trans.security.encode_id(
category.id))
else:
raise exceptions.RequestParameterMissingException(
'Missing required parameter "name".')
return category_dict
def create( self, trans, payload, **kwd ):
"""
POST /api/categories
Returns a dictionary of information about the created category.
: param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param name (required): the name of the category
:param description (optional): the description of the category (if not provided, the name will be used)
"""
category_dict = dict( message = '',
status = 'ok' )
# Make sure the current user's API key proves he is an admin user in this Tool Shed.
if trans.user_is_admin():
# Get the information about the category to be created from the payload.
name = payload.get( 'name', '' )
if name:
description = payload.get( 'description', '' )
if not description:
# Default the description to the name.
description = name
if suc.get_category_by_name( trans.app, name ):
category_dict[ 'message' ] = 'A category with that name already exists'
category_dict[ 'status' ] = 'error'
else:
# Create the category
category = trans.app.model.Category( name=name, description=description )
trans.sa_session.add( category )
trans.sa_session.flush()
category_dict = category.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
category_dict[ 'message' ] = "Category '%s' has been created" % str( category.name )
category_dict[ 'url' ] = web.url_for( controller='categories',
action='show',
id=trans.security.encode_id( category.id ) )
else:
category_dict[ 'message' ] = "Missing required parameter 'name'."
category_dict[ 'status' ] = 'error'
else:
category_dict[ 'message' ] = 'You are not authorized to create a category in this Tool Shed.'
category_dict[ 'status' ] = 'error'
return category_dict
def create( self, trans, payload, **kwd ):
"""
POST /api/categories
Return a dictionary of information about the created category.
The following parameters are included in the payload:
:param name (required): the name of the category
:param description (optional): the description of the category (if not provided, the name will be used)
Example: POST /api/categories/?key=XXXYYYXXXYYY
Content-Disposition: form-data; name="name" Category_Name
Content-Disposition: form-data; name="description" Category_Description
"""
category_dict = dict( message='', status='ok' )
name = payload.get( 'name', '' )
if name:
description = payload.get( 'description', '' )
if not description:
# Default the description to the name.
description = name
if suc.get_category_by_name( self.app, name ):
raise exceptions.Conflict( 'A category with that name already exists.' )
else:
# Create the category
category = self.app.model.Category( name=name, description=description )
trans.sa_session.add( category )
trans.sa_session.flush()
category_dict = category.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
category_dict[ 'message' ] = "Category '%s' has been created" % str( category.name )
category_dict[ 'url' ] = web.url_for( controller='categories',
action='show',
id=trans.security.encode_id( category.id ) )
else:
raise exceptions.RequestParameterMissingException( 'Missing required parameter "name".' )
return category_dict
def edit_category( self, trans, **kwd ):
message = 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, id )
if kwd.get( 'edit_category_button', False ):
new_name = kwd.get( 'name', '' ).strip()
new_description = kwd.get( 'description', '' ).strip()
if category.name != new_name or category.description != new_description:
if not new_name:
message = 'Enter a valid name'
status = 'error'
elif category.name != new_name and suc.get_category_by_name( trans, new_name ):
message = 'A category with that name already exists'
status = 'error'
else:
category.name = new_name
category.description = new_description
trans.sa_session.add( category )
trans.sa_session.flush()
message = "The information has been saved for category '%s'" % ( 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 )
