def install_repository( self, repository_info_dict, install_tool_dependencies=True, install_repository_dependencies=True,
strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[],
post_submit_strings_displayed=[], new_tool_panel_section=None, **kwd ):
name = repository_info_dict[ 'name' ]
owner = repository_info_dict[ 'owner' ]
changeset_revision = repository_info_dict[ 'changeset_revision' ]
encoded_repository_id = repository_info_dict[ 'repository_id' ]
tool_shed_url = repository_info_dict[ 'tool_shed_url' ]
preview_params = urllib.urlencode( dict( repository_id=encoded_repository_id, changeset_revision=changeset_revision ) )
self.visit_url( '%s/repository/preview_tools_in_changeset?%s' % ( tool_shed_url, preview_params ) )
install_params = urllib.urlencode( dict( repository_ids=encoded_repository_id,
changeset_revisions=changeset_revision,
galaxy_url=self.url ) )
# If the tool shed does not have the same hostname as the Galaxy server being used for these tests,
# twill will not carry over previously set cookies for the Galaxy server when following the
# install_repositories_by_revision redirect, so we have to include 403 in the allowed HTTP
# status codes and log in again.
url = '%s/repository/install_repositories_by_revision?%s' % ( tool_shed_url, install_params )
self.visit_url( url, allowed_codes=[ 200, 403 ] )
self.logout()
self.login( email='*****@*****.**', username='******' )
install_params = urllib.urlencode( dict( repository_ids=encoded_repository_id,
changeset_revisions=changeset_revision,
tool_shed_url=tool_shed_url ) )
url = '/admin_toolshed/prepare_for_install?%s' % install_params
self.visit_url( url )
# This section is tricky, due to the way twill handles form submission. The tool dependency checkbox needs to
# be hacked in through tc.browser, putting the form field in kwd doesn't work.
if 'install_tool_dependencies' in self.last_page():
form = tc.browser.get_form( 'select_tool_panel_section' )
checkbox = form.find_control( id="install_tool_dependencies" )
checkbox.disabled = False
if install_tool_dependencies:
checkbox.selected = True
kwd[ 'install_tool_dependencies' ] = 'True'
else:
checkbox.selected = False
kwd[ 'install_tool_dependencies' ] = 'False'
if 'install_repository_dependencies' in self.last_page():
form = tc.browser.get_form( 'select_tool_panel_section' )
checkbox = form.find_control( id="install_repository_dependencies" )
checkbox.disabled = False
if install_repository_dependencies:
checkbox.selected = True
kwd[ 'install_repository_dependencies' ] = 'True'
else:
checkbox.selected = False
kwd[ 'install_repository_dependencies' ] = 'False'
if 'shed_tool_conf' not in kwd:
kwd[ 'shed_tool_conf' ] = self.shed_tool_conf
if new_tool_panel_section:
kwd[ 'new_tool_panel_section' ] = new_tool_panel_section
self.submit_form( 1, 'select_tool_panel_section_button', **kwd )
self.check_for_strings( post_submit_strings_displayed, strings_not_displayed )
repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section )
self.wait_for_repository_installation( repository_ids )
def install_repository( self, repository_info_dict, install_tool_dependencies=True, install_repository_dependencies=True,
strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[],
post_submit_strings_displayed=[], new_tool_panel_section_label=None, **kwd ):
name = repository_info_dict[ 'name' ]
owner = repository_info_dict[ 'owner' ]
changeset_revision = repository_info_dict[ 'changeset_revision' ]
encoded_repository_id = repository_info_dict[ 'repository_id' ]
tool_shed_url = repository_info_dict[ 'tool_shed_url' ]
# Pass galaxy_url to the tool shed in order to set cookies and redirects correctly.
install_params = urllib.urlencode( dict( repository_ids=encoded_repository_id,
changeset_revisions=changeset_revision,
galaxy_url=self.url ) )
# If the tool shed does not have the same hostname as the Galaxy server being used for these tests,
# twill will not carry over previously set cookies for the Galaxy server when following the
# install_repositories_by_revision redirect, so we have to include 403 in the allowed HTTP
# status codes and log in again.
url = '%s/repository/install_repositories_by_revision?%s' % ( tool_shed_url, install_params )
self.visit_url( url, allowed_codes=[ 200, 403 ] )
self.logout()
self.login( email='*****@*****.**', username='******' )
install_params = urllib.urlencode( dict( repository_ids=encoded_repository_id,
changeset_revisions=changeset_revision,
tool_shed_url=tool_shed_url ) )
url = '/admin_toolshed/prepare_for_install?%s' % install_params
self.visit_url( url )
# This section is tricky, due to the way twill handles form submission. The tool dependency checkbox needs to
# be hacked in through tc.browser, putting the form field in kwd doesn't work.
form = tc.browser.get_form( 'select_tool_panel_section' )
if form is None:
form = tc.browser.get_form( 'select_shed_tool_panel_config' )
assert form is not None, 'Could not find form select_shed_tool_panel_config or select_tool_panel_section.'
kwd = self.set_form_value( form, kwd, 'install_tool_dependencies', install_tool_dependencies )
kwd = self.set_form_value( form, kwd, 'install_repository_dependencies', install_repository_dependencies )
kwd = self.set_form_value( form, kwd, 'shed_tool_conf', self.shed_tool_conf )
if new_tool_panel_section_label is not None:
kwd = self.set_form_value( form, kwd, 'new_tool_panel_section_label', new_tool_panel_section_label )
submit_button_control = form.find_control( type='submit' )
assert submit_button_control is not None, 'No submit button found for form %s.' % form.attrs.get( 'id' )
self.submit_form( form.attrs.get( 'id' ), str( submit_button_control.name ), **kwd )
self.check_for_strings( post_submit_strings_displayed, strings_not_displayed )
repository_ids = self.initiate_installation_process( new_tool_panel_section_label=new_tool_panel_section_label )
log.debug( 'Waiting for the installation of repository IDs: %s' % str( repository_ids ) )
self.wait_for_repository_installation( repository_ids )
