SMTP Authentication support for all places where Galaxy sends mail. Use STARTTLS where available, too.

lib/galaxy/config.py

@@ -76,6 +76,8 @@ class Configuration( object ):
         self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu")
         self.error_email_to = kwargs.get( 'error_email_to', None )
         self.smtp_server = kwargs.get( 'smtp_server', None )
+        self.smtp_username = kwargs.get( 'smtp_username', None )
+        self.smtp_password = kwargs.get( 'smtp_password', None )
         self.start_job_runners = kwargs.get( 'start_job_runners', None )
         # External Service types used in sample tracking
         self.external_service_type_config_file = resolve_path( kwargs.get( 'external_service_type_config_file', 'external_service_types_conf.xml' ), self.root )

lib/galaxy/jobs/actions/post.py

@@ -1,5 +1,5 @@
-import logging, datetime, smtplib
-from email.MIMEText import MIMEText
+import logging, datetime
+from galaxy.util import send_mail
 from galaxy.util.json import to_json_string
 
 log = logging.getLogger( __name__ )
@@ -58,35 +58,17 @@ class EmailAction(DefaultJobAction):
     
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict):
-        smtp_server = app.config.smtp_server
         if action.action_arguments and action.action_arguments.has_key('host'):
             host = action.action_arguments['host']
         else:
             host = 'usegalaxy.org'
-        if smtp_server is None:
-            log.error("Mail is not configured for this galaxy instance.  Workflow action aborting after logging mail to info.")
-            frm = 'galaxy-noreply@%s' % host
-            to  = job.user.email
-            outdata = ', '.join(ds.dataset.display_name() for ds in job.output_datasets)
-            msg = MIMEText( "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime( "%I:%M" )))
-            msg[ 'To' ] = to
-            msg[ 'From' ] = frm
-            msg[ 'Subject' ] = "Galaxy notification regarding history '%s'" % (job.history.name)
-            log.info(msg)
-            return
-        # Build the email message
         frm = 'galaxy-noreply@%s' % host
         to  = job.user.email
+        subject = "Galaxy workflow step notification '%s'" % (job.history.name)
         outdata = ', '.join(ds.dataset.display_name() for ds in job.output_datasets)
-        msg = MIMEText( "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime( "%I:%M" )))
-        msg[ 'To' ] = to
-        msg[ 'From' ] = frm
-        msg[ 'Subject' ] = "Galaxy workflow step notification '%s'" % (job.history.name)
+        body = "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime( "%I:%M" ))
         try:
-            s = smtplib.SMTP()
-            s.connect( smtp_server )
-            s.sendmail( frm, [ to ], msg.as_string() )
-            s.close()
+            send_mail( frm, to, subject, body, app.config )
         except Exception, e:
             log.error("EmailAction PJA Failed, exception: %s" % e)
             

lib/galaxy/model/__init__.py

@@ -15,7 +15,7 @@ from galaxy.util.hash_util import *
 from galaxy.web.form_builder import *
 from galaxy.model.item_attrs import UsesAnnotations, APIItem
 from sqlalchemy.orm import object_session
-import os.path, os, errno, codecs, operator, smtplib, socket, pexpect, logging, time
+import os.path, os, errno, codecs, operator, socket, pexpect, logging, time
 
 log = logging.getLogger( __name__ )
 
@@ -1803,12 +1803,8 @@ All samples in state:     %(sample_state)s
             to = self.notification['email']
             frm = 'galaxy-no-reply@' + host
             subject = "Galaxy Sample Tracking notification: '%s' sequencing request" % self.name
-            message = "From: %s\r\nTo: %s\r\nSubject: %s\r\n\r\n%s" % ( frm, ", ".join( to ), subject, body )
             try:
-                s = smtplib.SMTP()
-                s.connect( trans.app.config.smtp_server )
-                s.sendmail( frm, to, message )
-                s.quit()
+                util.send_mail( frm, to, subject, body, trans.app.config )
                 comments = "Email notification sent to %s." % ", ".join( to ).strip().strip( ',' )
             except Exception,e:
                 comments = "Email notification failed. (%s)" % str(e)

lib/galaxy/util/__init__.py

@@ -2,7 +2,8 @@
 Utility functions used systemwide.
 
 """
-import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp
+import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib
+from email.MIMEText import MIMEText
 
 # Older py compatibility
 try:
@@ -540,6 +541,51 @@ def nice_size(size):
             return "%.1f %s" % (size, word)
     return '??? bytes'
 
+def send_mail( frm, to, subject, body, config ):
+    """
+    Sends an email.
+    """
+    msg = MIMEText( body )
+    msg[ 'To' ] = to
+    msg[ 'From' ] = frm
+    msg[ 'Subject' ] = subject
+    if config.smtp_server is None:
+        log.error( "Mail is not configured for this Galaxy instance." )
+        log.info( msg )
+        return
+    s = smtplib.SMTP()
+    s.connect( config.smtp_server )
+    try:
+        s.starttls()
+        log.debug( 'Initiated SSL/TLS connection to SMTP server: %s' % config.smtp_server )
+    except RuntimeError, e:
+        log.warning( 'SSL/TLS support is not available to your Python interpreter: %s' % e )
+    except smtplib.SMTPHeloError, e:
+        log.error( "The server didn't reply properly to the HELO greeting: %s" % e )
+        s.close()
+        raise
+    except smtplib.SMTPException, e:
+        log.warning( 'The server does not support the STARTTLS extension: %s' % e )
+    if config.smtp_username and config.smtp_password:
+        try:
+            s.login( config.smtp_username, config.smtp_password )
+        except smtplib.SMTPHeloError, e:
+            log.error( "The server didn't reply properly to the HELO greeting: %s" % e )
+            s.close()
+            raise
+        except smtplib.SMTPAuthenticationError, e:
+            log.error( "The server didn't accept the username/password combination: %s" % e )
+            s.close()
+            raise
+        except smtplib.SMTPError, e:
+            log.error( "No suitable authentication method was found: %s" % e )
+            s.close()
+            raise
+    if isinstance( to, basestring ):
+        to = [ to ]
+    s.sendmail( frm, to, msg.as_string() )
+    s.quit()
+
 galaxy_root_path = os.path.join(__path__[0], "..","..","..")
 # The dbnames list is used in edit attributes and the upload tool
 dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) )

lib/galaxy/web/controllers/dataset.py

@@ -1,4 +1,4 @@
-import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob, sys
+import logging, os, string, shutil, re, socket, mimetypes, urllib, tempfile, zipfile, glob, sys
 
 from galaxy.web.base.controller import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
@@ -10,7 +10,6 @@ from galaxy.util import inflector
 from galaxy.model.item_attrs import *
 from galaxy.model import LibraryDatasetDatasetAssociation, HistoryDatasetAssociation
 
-from email.MIMEText import MIMEText
 import pkg_resources; 
 pkg_resources.require( "Paste" )
 import paste.httpexceptions
@@ -174,7 +173,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
         host = trans.request.host
         history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) )
         # Build the email message
-        msg = MIMEText( string.Template( error_report_template )
+        body = string.Template( error_report_template ) \
             .safe_substitute( host=host,
                               dataset_id=hda.dataset_id,
                               history_id=hda.history_id,
@@ -189,7 +188,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
                               job_info=job.info,
                               job_traceback=job.traceback,
                               email=email, 
-                              message=message ) )
+                              message=message )
         frm = to_address
         # Check email a bit
         email = email.strip()
@@ -198,15 +197,10 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistory, UsesHistor
             to = to_address + ", " + email
         else:
             to = to_address
-        msg[ 'To' ] = to
-        msg[ 'From' ] = frm
-        msg[ 'Subject' ] = "Galaxy tool error report from " + email
+        subject = "Galaxy tool error report from " + email
         # Send it
         try:
-            s = smtplib.SMTP()
-            s.connect( smtp_server )
-            s.sendmail( frm, [ to ], msg.as_string() )
-            s.close()
+            util.send_mail( frm, to, subject, body, trans.app.config )
             return trans.show_ok_message( "Your error report has been sent" )
         except Exception, e:
             return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) )

lib/galaxy/web/controllers/user.py

@@ -5,9 +5,8 @@ from galaxy.web.framework.helpers import time_ago, grids
 from galaxy.web.base.controller import *
 from galaxy.model.orm import *
 from galaxy import util, model
-import logging, os, string, re, smtplib, socket, glob
+import logging, os, string, re, socket, glob
 from random import choice
-from email.MIMEText import MIMEText
 from galaxy.web.form_builder import * 
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.web.framework.helpers import iff
@@ -560,15 +559,12 @@ class User( BaseController, UsesFormDefinitions ):
                 if trans.app.config.smtp_server is None:
                     error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance."
                 else:
-                    msg = MIMEText( 'Join Mailing list.\n' )
-                    to = msg[ 'To' ] = trans.app.config.mailing_join_addr
-                    frm = msg[ 'From' ] = email
-                    msg[ 'Subject' ] = 'Join Mailing List'
+                    body = 'Join Mailing list.\n'
+                    to = trans.app.config.mailing_join_addr
+                    frm = email
+                    subject = 'Join Mailing List'
                     try:
-                        s = smtplib.SMTP()
-                        s.connect( trans.app.config.smtp_server )
-                        s.sendmail( frm, [ to ], msg.as_string() )
-                        s.close()
+                        util.send_mail( frm, to, subject, body, trans.app.config )
                     except:
                         error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed."
             if not error and not is_admin:
@@ -888,15 +884,12 @@ class User( BaseController, UsesFormDefinitions ):
                     host = trans.request.host.split(':')[0]
                     if host == 'localhost':
                         host = socket.getfqdn()
-                    msg = MIMEText( 'Your password on %s has been reset to:\n\n  %s\n' % ( host, new_pass ) )
-                    to = msg[ 'To' ] = email
-                    frm = msg[ 'From' ] = 'galaxy-no-reply@' + host
-                    msg[ 'Subject' ] = 'Galaxy Password Reset'
+                    body = 'Your password on %s has been reset to:\n\n  %s\n' % ( host, new_pass )
+                    to = email
+                    frm = 'galaxy-no-reply@' + host
+                    subject = 'Galaxy Password Reset'
                     try:
-                        s = smtplib.SMTP()
-                        s.connect( trans.app.config.smtp_server )
-                        s.sendmail( frm, [ to ], msg.as_string() )
-                        s.close()
+                        util.send_mail( frm, to, subject, body, trans.app.config )
                         reset_user.set_password_cleartext( new_pass )
                         trans.sa_session.add( reset_user )
                         trans.sa_session.flush()

universe_wsgi.ini.sample

@@ -161,9 +161,16 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Galaxy sends mail for various things: Subscribing users to the mailing list
 # if they request it, emailing password resets, notification from the Galaxy
 # Sample Tracking system, and reporting dataset errors.  To do this, it needs
-# to send mail through an SMTP server, which you may define here.
+# to send mail through an SMTP server, which you may define here (host:port).
+# Galaxy will automatically try STARTTLS but will continue upon failure.
 #smtp_server = None
 
+# If your SMTP server requires a username and password, you can provide them
+# here (password in cleartext here, but if your server supports STARTTLS it
+# will be sent over the network encrypted).
+#smtp_username = None
+#smtp_password = None
+
 # On the user registration form, users may choose to join the mailing list.
 # This is the address of the list they'll be subscribed to.
 #mailing_join_addr = galaxy-user-join@bx.psu.edu