def set_peek(self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=True):
"""
Set the peek. This method is used by various subclasses of Text.
"""
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap)
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
dataset.blurb = "%s %s" % (util.commaify(str(dataset.metadata.data_lines)), inflector.cond_plural(dataset.metadata.data_lines, self.line_class))
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
# This can happen when the file is larger than max_optional_metadata_filesize.
if int(dataset.get_size()) <= 1048576:
# Small dataset, recount all lines and reset peek afterward.
lc = self.count_data_lines(dataset)
dataset.metadata.data_lines = lc
dataset.blurb = "%s %s" % (util.commaify(str(lc)), inflector.cond_plural(lc, self.line_class))
else:
est_lines = self.estimate_file_lines(dataset)
dataset.blurb = "~%s %s" % (util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class))
else:
dataset.blurb = "%s %s" % (util.commaify(str(line_count)), inflector.cond_plural(line_count, self.line_class))
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ):
"""
Set the peek. This method is used by various subclasses of Text.
"""
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars )
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, self.line_class) )
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
# This can happen when the file is larger than max_optional_metadata_filesize.
if int(dataset.get_size()) <= 1048576:
#Small dataset, recount all lines and reset peek afterward.
lc = self.count_data_lines(dataset)
dataset.metadata.data_lines = lc
dataset.blurb = "%s %s" % ( util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) )
else:
est_lines = self.estimate_file_lines(dataset)
dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) )
else:
dataset.blurb = "%s %s" % ( util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
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 delete_repository_metadata(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = get_repository_metadata_by_id(
trans, 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 delete_repository( self, trans, **kwd ):
message = 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, 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 )
repository.deleted = True
trans.sa_session.add( repository )
trans.sa_session.flush()
count += 1
deleted_repositories += " %s " % repository.name
if count:
message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), 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 undelete_repository(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.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 = get_repository(trans, repository_id)
if repository.deleted:
repository.deleted = False
trans.sa_session.add(repository)
trans.sa_session.flush()
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 undelete_repository( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.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 = get_repository( trans, repository_id )
if repository.deleted:
repository.deleted = False
trans.sa_session.add( repository )
trans.sa_session.flush()
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 reset_metadata_on_all_repositories( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
if 'reset_metadata_on_all_repositories_button' in kwd:
successful_count = 0
unsuccessful_count = 0
for repository in trans.sa_session.query( trans.model.Repository ) \
.filter( trans.model.Repository.table.c.deleted == False ):
try:
error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
if status not in [ 'ok' ] and error_message:
log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, error_message ) )
unsuccessful_count += 1
elif status in [ 'ok' ] and error_message:
log.debug( "Successfully reset metadata on repository %s, but encountered this problem: %s" % ( repository.name, error_message ) )
successful_count += 1
else:
log.debug( "Successfully reset metadata on repository %s" % repository.name )
successful_count += 1
except Exception, e:
log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) )
unsuccessful_count += 1
message = "Successfully reset metadata on %d %s. " % ( successful_count,
inflector.cond_plural( successful_count, "repository" ) )
if unsuccessful_count:
message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count,
inflector.cond_plural( unsuccessful_count,
"repository" ) )
trans.response.send_redirect( web.url_for( controller='admin',
action='browse_repository_metadata',
webapp='community',
message=util.sanitize_text( message ),
status=status ) )
def reset_metadata_on_selected_repositories(self, user, **kwd):
"""
Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
This method is called from both Galaxy and the Tool Shed.
"""
repository_ids = util.listify(kwd.get('repository_ids', None))
message = ''
status = 'done'
if repository_ids:
successful_count = 0
unsuccessful_count = 0
for repository_id in repository_ids:
try:
repository = get_installed_tool_shed_repository(
self.app, repository_id)
self.set_repository(repository)
self.reset_all_metadata_on_installed_repository()
if self.invalid_file_tups:
message = generate_message_for_invalid_tools(
self.app,
self.invalid_file_tups,
repository,
None,
as_html=False)
log.debug(message)
unsuccessful_count += 1
else:
log.debug(
"Successfully reset metadata on repository %s owned by %s"
% (str(repository.name), str(repository.owner)))
successful_count += 1
except Exception:
log.exception(
"Error attempting to reset metadata on repository %s",
str(repository.name))
unsuccessful_count += 1
message = "Successfully reset metadata on %d %s. " % \
(successful_count, inflector.cond_plural(successful_count, "repository"))
if unsuccessful_count:
message += "Error setting metadata on %d %s - see the paster log for details. " % \
(unsuccessful_count, inflector.cond_plural(unsuccessful_count, "repository"))
else:
message = 'Select at least one repository to on which to reset all metadata.'
status = 'error'
return message, status
def reset_metadata_on_selected_repositories( self, user, **kwd ):
"""
Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
This method is called from both Galaxy and the Tool Shed.
"""
repository_ids = util.listify( kwd.get( 'repository_ids', None ) )
message = ''
status = 'done'
if repository_ids:
successful_count = 0
unsuccessful_count = 0
for repository_id in repository_ids:
try:
repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id )
self.set_repository( repository )
self.reset_all_metadata_on_installed_repository()
if self.invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools( self.app,
self.invalid_file_tups,
repository,
None,
as_html=False )
log.debug( message )
unsuccessful_count += 1
else:
log.debug( "Successfully reset metadata on repository %s owned by %s" %
( str( repository.name ), str( repository.owner ) ) )
successful_count += 1
except:
log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) )
unsuccessful_count += 1
message = "Successfully reset metadata on %d %s. " % \
( successful_count, inflector.cond_plural( successful_count, "repository" ) )
if unsuccessful_count:
message += "Error setting metadata on %d %s - see the paster log for details. " % \
( unsuccessful_count, inflector.cond_plural( unsuccessful_count, "repository" ) )
else:
message = 'Select at least one repository to on which to reset all metadata.'
status = 'error'
return message, 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 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_user_password(self, trans, **kwd):
user_id = kwd.get('id', None)
if not user_id:
message = "No users received for resetting passwords."
trans.response.send_redirect(
web.url_for(controller='admin',
action='users',
message=message,
status='error'))
user_ids = util.listify(user_id)
if 'reset_user_password_button' in kwd:
message = ''
status = ''
for user_id in user_ids:
user = get_user(trans, user_id)
password = kwd.get('password', None)
confirm = kwd.get('confirm', None)
if len(password) < 6:
message = "Use a password of at least 6 characters."
status = 'error'
break
elif password != confirm:
message = "Passwords do not match."
status = 'error'
break
else:
user.set_password_cleartext(password)
trans.sa_session.add(user)
trans.sa_session.flush()
if not message and not status:
message = "Passwords reset for %d %s." % (len(
user_ids), inflector.cond_plural(len(user_ids), 'user'))
status = 'done'
trans.response.send_redirect(
web.url_for(controller='admin',
action='users',
message=util.sanitize_text(message),
status=status))
users = [get_user(trans, user_id) for user_id in user_ids]
if len(user_ids) > 1:
user_id = ','.join(user_ids)
return trans.fill_template(
'/webapps/tool_shed/admin/user/reset_password.mako',
id=user_id,
users=users,
password='',
confirm='')
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 reset_user_password(self, trans, **kwd):
user_id = kwd.get('id', None)
if not user_id:
message = "No users received for resetting passwords."
trans.response.send_redirect(web.url_for(controller='admin',
action='users',
message=message,
status='error'))
user_ids = util.listify(user_id)
if 'reset_user_password_button' in kwd:
message = ''
status = ''
for user_id in user_ids:
user = get_user(trans, user_id)
password = kwd.get('password', None)
confirm = kwd.get('confirm', None)
if len(password) < 6:
message = "Use a password of at least 6 characters."
status = 'error'
break
elif password != confirm:
message = "Passwords do not match."
status = 'error'
break
else:
user.set_password_cleartext(password)
trans.sa_session.add(user)
trans.sa_session.flush()
if not message and not status:
message = "Passwords reset for %d %s." % (len(user_ids), inflector.cond_plural(len(user_ids), 'user'))
status = 'done'
trans.response.send_redirect(web.url_for(controller='admin',
action='users',
message=util.sanitize_text(message),
status=status))
users = [get_user(trans, user_id) for user_id in user_ids]
if len(user_ids) > 1:
user_id = ','.join(user_ids)
return trans.fill_template('/webapps/tool_shed/admin/user/reset_password.mako',
id=user_id,
users=users,
password='',
confirm='')
def delete_repository_metadata( self, trans, **kwd ):
message = 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 undelete_repository( self, trans, **kwd ):
message = 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, 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 )
repository.deleted = False
trans.sa_session.add( repository )
trans.sa_session.flush()
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' ) )