def biostar_logout(self, trans):
"""
Log out of biostar
"""
try:
url = biostar.biostar_log_out(trans)
except Exception as e:
return error(str(e))
if url:
return trans.response.send_redirect(url)
return error("Could not determine Biostar logout URL.")
def biostar_logout(self, trans):
"""
Log out of biostar
"""
try:
url = biostar.biostar_log_out(trans)
except Exception as e:
return error(str(e))
if url:
return trans.response.send_redirect(url)
return error("Could not determine Biostar logout URL.")
def biostar_redirect( self, trans, payload=None, biostar_action=None ):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool.
"""
payload = payload or {}
# Ensure biostar integration is enabled
if not trans.app.config.biostar_url:
return error( "Biostar integration is not enabled" )
# Start building up the payload
payload = dict( DEFAULT_PAYLOAD, **payload )
# Do the best we can of providing user information for the payload
if trans.user:
payload['username'] = "******" + trans.security.encode_id( trans.user.id )
payload['email'] = trans.user.email
if trans.user.username:
payload['display_name'] = trans.user.username
else:
payload['display_name'] = trans.user.email.split( "@" )[0]
else:
encoded = trans.security.encode_id( trans.galaxy_session.id )
payload['username'] = "******" + encoded
payload['display_name'] = "Anonymous Galaxy User"
data, digest = encode_data( trans.app.config.biostar_key, payload )
return trans.response.send_redirect( url_for( trans.app.config.biostar_url, data=data, digest=digest, name=trans.app.config.biostar_key_name, action=biostar_action ) )
def biostar_redirect(self, trans, payload={}, biostar_action=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool.
"""
# Ensure biostar integration is enabled
if not trans.app.config.biostar_url:
return error("Biostar integration is not enabled")
# Start building up the payload
payload = dict(DEFAULT_PAYLOAD, **payload)
# Do the best we can of providing user information for the payload
if trans.user:
payload['username'] = "******" + trans.security.encode_id(
trans.user.id)
payload['email'] = trans.user.email
if trans.user.username:
payload['display_name'] = trans.user.username
else:
payload['display_name'] = trans.user.email.split("@")[0]
else:
encoded = trans.security.encode_id(trans.galaxy_session.id)
payload['username'] = "******" + encoded
payload['display_name'] = "Anonymous Galaxy User"
data, digest = encode_data(trans.app.config.biostar_key, payload)
return trans.response.send_redirect(
url_for(trans.app.config.biostar_url,
data=data,
digest=digest,
name=trans.app.config.biostar_key_name,
action=biostar_action))
def biostar_tool_tag_redirect(self, trans, tool_id=None):
"""
Generate a redirect to a Biostar site using tag for tool.
"""
# tool_id is required
if tool_id is None:
return error("No tool_id provided")
# Load the tool
tool_version_select_field, tools, tool = \
self.app.toolbox.get_tool_components(tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True)
# No matching tool, unlikely
if not tool:
return error("No tool found matching '%s'" % tool_id)
# Tool specific information for payload
payload = biostar.populate_tag_payload(tool=tool)
# Pass on to standard redirect method
return self.biostar_redirect(trans, payload=payload, biostar_action='show_tags')
def biostar_tool_tag_redirect( self, trans, tool_id=None ):
"""
Generate a redirect to a Biostar site using tag for tool.
"""
# tool_id is required
if tool_id is None:
return error( "No tool_id provided" )
# Load the tool
tool_version_select_field, tools, tool = \
self.app.toolbox.get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True )
# No matching tool, unlikely
if not tool:
return error( "No tool found matching '%s'" % tool_id )
# Tool specific information for payload
payload = biostar.populate_tag_payload( tool=tool )
# Pass on to standard redirect method
return self.biostar_redirect( trans, payload=payload, biostar_action='show_tags' )
def biostar_logout(self, trans):
"""
Log out of biostar
"""
try:
url = biostar.biostar_log_out(trans)
except Exception, e:
return error(str(e))
def biostar_logout(self, trans):
"""
Log out of biostar
"""
try:
url = biostar.biostar_log_out(trans)
except Exception, e:
return error(str(e))
def biostar_redirect( self, trans, payload=None, biostar_action=None ):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and optional information about a specific tool.
"""
try:
url, payload = biostar.get_biostar_url( trans.app, payload=payload, biostar_action=biostar_action )
except Exception, e:
return error( str( e ) )
def biostar_redirect(self, trans, payload=None, biostar_action=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and optional information about a specific tool.
"""
try:
url, payload = biostar.get_biostar_url(trans.app, payload=payload, biostar_action=biostar_action)
except Exception, e:
return error(str(e))
def biostar_tool_question_redirect(self, trans, tool_id=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool.
"""
# tool_id is required
if tool_id is None:
return error("No tool_id provided")
# Load the tool
tool_version_select_field, tools, tool = \
self.app.toolbox.get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True )
# No matching tool, unlikely
if not tool:
return error("No tool found matching '%s'" % tool_id)
# Tool specific information for payload
payload = biostar.populate_tool_payload(tool=tool)
# Pass on to regular question method
return self.biostar_question_redirect(trans, payload)
def biostar_tool_question_redirect(self, trans, tool_id=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool.
"""
# tool_id is required
if tool_id is None:
return error("No tool_id provided")
# Load the tool
tool_version_select_field, tools, tool = \
self.app.toolbox.get_tool_components(tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True)
# No matching tool, unlikely
if not tool:
return error("No tool found matching '%s'" % tool_id)
# Tool specific information for payload
payload = biostar.populate_tool_payload(tool=tool)
# Pass on to regular question method
return self.biostar_question_redirect(trans, payload)
def biostar_tool_bug_report( self, trans, hda=None, email=None, message=None ):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool error.
"""
try:
error_reporter = biostar.BiostarErrorReporter( hda, trans.app )
payload = error_reporter.send_report( trans.user, email=email, message=message )
except Exception, e:
return error( str( e ) )
def biostar_tool_bug_report(self, trans, hda=None, email=None, message=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool error.
"""
try:
error_reporter = biostar.BiostarErrorReporter(hda, trans.app)
payload = error_reporter.send_report(trans.user, email=email, message=message)
except Exception, e:
return error(str(e))
def biostar_redirect(self, trans, payload=None, biostar_action=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and optional information about a specific tool.
"""
try:
url, payload = biostar.get_biostar_url(trans.app, payload=payload, biostar_action=biostar_action)
except Exception as e:
return error(str(e))
# Only create/log in biostar user if is registered Galaxy user
if trans.user:
biostar.create_cookie(trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, trans.user.email)
if payload:
return trans.fill_template("biostar/post_redirect.mako", post_url=url, form_inputs=payload)
return trans.response.send_redirect(url)
def biostar_redirect(self, trans, payload=None, biostar_action=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and optional information about a specific tool.
"""
try:
url, payload = biostar.get_biostar_url(trans.app, payload=payload, biostar_action=biostar_action)
except Exception as e:
return error(str(e))
# Only create/log in biostar user if is registered Galaxy user
if trans.user:
biostar.create_cookie(trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, trans.user.email)
if payload:
return trans.fill_template("biostar/post_redirect.mako", post_url=url, form_inputs=payload)
return trans.response.send_redirect(url)
# Tool specific information for payload
payload = biostar.populate_tool_payload(tool=tool)
# Pass on to regular question method
return self.biostar_question_redirect(trans, payload)
@web.expose
def biostar_tool_bug_report(self, trans, hda=None, email=None, message=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool error.
"""
try:
error_reporter = biostar.BiostarErrorReporter(hda, trans.app)
payload = error_reporter.send_report(trans.user, email=email, message=message)
except Exception, e:
return error(str(e))
return self.biostar_redirect(trans, payload=payload, biostar_action="new_post")
@web.expose
def biostar_logout(self, trans):
"""
Log out of biostar
"""
try:
url = biostar.biostar_log_out(trans)
except Exception, e:
return error(str(e))
if url:
return trans.response.send_redirect(url)
return error("Could not determine Biostar logout URL.")
hda=None,
email=None,
message=None):
"""
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool error.
"""
try:
error_reporter = biostar.BiostarErrorReporter(hda, trans.app)
payload = error_reporter.send_report(trans.user,
email=email,
message=message)
except Exception, e:
return error(str(e))
return self.biostar_redirect(trans,
payload=payload,
biostar_action='new_post')
@web.expose
def biostar_logout(self, trans):
"""
Log out of biostar
"""
try:
url = biostar.biostar_log_out(trans)
except Exception, e:
return error(str(e))
if url:
return trans.response.send_redirect(url)
return error("Could not determine Biostar logout URL.")
