1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/538745257362/ Changeset: 538745257362 User: dan Date: 2014-03-03 15:11:38 Summary: Update Biostar interaction to use new cookie-based method. Affected #: 1 file
diff -r eafb4208db665dfeed7d8f3e6f0d2b61ce2f4fc8 -r 538745257362eebda5caf25c8c16793caa90fec7 lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -7,6 +7,7 @@ import base64 from galaxy.util import json import hmac +import urlparse
# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/)
@@ -15,6 +16,11 @@
_punct_re = re.compile(r'[\t !"#$%&'()*-/<=>?@[\]^_`{|},.]+')
+BIOSTAR_ACTIONS = { + 'new': 'p/new/post/', + None: '' +} +
def slugify(text, delim=u'-'): """Generates an slightly worse ASCII-only slug.""" @@ -28,12 +34,9 @@
# Biostar requires all keys to be present, so we start with a template DEFAULT_PAYLOAD = { - 'email': "", - 'title': "", - 'tags': 'galaxy', - 'tool_name': '', - 'tool_version': '', - 'tool_id': '' + 'title': '', + 'tag_val': 'galaxy', + 'content': '', }
@@ -49,10 +52,32 @@
def tag_for_tool( tool ): """ - Generate a reasonavle biostar tag for a tool. + Generate a reasonable biostar tag for a tool. """ return slugify( unicode( tool.name ) )
+def determine_cookie_domain( galaxy_hostname, biostar_hostname ): + if galaxy_hostname == biostar_hostname: + return galaxy_hostname + + sub_biostar_hostname = biostar_hostname.split( '.', 1 )[-1] + if sub_biostar_hostname == galaxy_hostname: + return galaxy_hostname + + sub_galaxy_hostname = galaxy_hostname.split( '.', 1 )[-1] + if sub_biostar_hostname == sub_galaxy_hostname: + return sub_galaxy_hostname + + return galaxy_hostname + +def create_cookie( trans, key_name, key, email ): + digest = hmac.new( key, email ).hexdigest() + value = "%s:%s" % (email, digest) + trans.set_cookie( value, name=key_name, path='/', age=90, version='1' ) + #We need to explicitly set the domain here, in order to allow for biostar in a subdomain to work + galaxy_hostname = urlparse.urlsplit( url_for( '/', qualified=True ) ).hostname + biostar_hostname = urlparse.urlsplit( trans.app.config.biostar_url ).hostname + trans.response.cookies[ key_name ][ 'domain' ] = determine_cookie_domain( galaxy_hostname, biostar_hostname )
class BiostarController( BaseUIController ): """ @@ -65,26 +90,22 @@ 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" ) + if biostar_action not in BIOSTAR_ACTIONS: + return error( "Invalid action specified (%s)." % ( biostar_action ) ) + # Start building up the payload + payload = payload or {} payload = dict( DEFAULT_PAYLOAD, **payload ) # Do the best we can of providing user information for the payload if trans.user: - payload['username'] = "user-" + 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] + email = trans.user.email else: - encoded = trans.security.encode_id( trans.galaxy_session.id ) - payload['username'] = "anon-" + 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 ) ) + email = "anon-%s" % ( trans.security.encode_id( trans.galaxy_session.id ) ) + create_cookie( trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, email ) + return trans.response.send_redirect( url_for( urlparse.urljoin( trans.app.config.biostar_url, BIOSTAR_ACTIONS[ biostar_action ] ), **payload ) )
@web.expose def biostar_question_redirect( self, trans, payload=None ): @@ -111,9 +132,8 @@ if not tool: return error( "No tool found matching '%s'" % tool_id ) # Tool specific information for payload - payload = { 'tool_name': tool.name, - 'tool_version': tool.version, - 'tool_id': tool.id, - 'tags': 'galaxy ' + tag_for_tool( tool ) } + payload = { 'title':'Need help with "%s" tool' % ( tool.name ), + 'content': '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ), + 'tag_val': 'galaxy ' + tag_for_tool( tool ) } # Pass on to regular question method return self.biostar_question_redirect( trans, payload )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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