[galaxy-dev] [hg] galaxy 3107: Fixed table migration bug encountered with Pos...

23 Nov 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/5fbda2fdb3ca
changeset: 3107:5fbda2fdb3ca
user:      Enis Afgan <afgane@gmail.com>
date:      Wed Nov 18 13:36:37 2009 -0500
description:
Fixed table migration bug encountered with PostgreSQL.

diffstat:

 lib/galaxy/cloud/__init__.py                           |  12 ++++++++++--
 lib/galaxy/cloud/providers/ec2.py                      |   8 ++++++--
 lib/galaxy/cloud/providers/eucalyptus.py               |  14 +++++++++-----
 lib/galaxy/model/__init__.py                           |   1 -
 lib/galaxy/model/mapping.py                            |   6 +++---
 lib/galaxy/model/migrate/versions/0026_cloud_tables.py |   4 ++--
 templates/cloud/view_instance.mako                     |   6 ++++--
 universe_wsgi.ini.sample                               |  12 ++++++------
 8 files changed, 40 insertions(+), 23 deletions(-)

diffs (258 lines):

diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/__init__.py

--- a/lib/galaxy/cloud/__init__.py	Wed Nov 18 10:57:24 2009 -0500
+++ b/lib/galaxy/cloud/__init__.py	Wed Nov 18 13:36:37 2009 -0500
@@ -45,6 +45,14 @@
     ERROR = "error"
 )
 
+store_status = Bunch(
+    WAITING = "waiting",
+    IN_USE = "in-use",
+    CREATING = "creating",
+    DELETED = 'deleted',
+    ERROR = "error"
+)
+
 snapshot_status = Bunch(
     SUBMITTED = 'submitted',
     PENDING = 'pending',
@@ -413,7 +421,7 @@
         be given in following format: 'vol-78943248'
         """
         vol = self.sa_session.query( model.CloudStore ).filter( model.CloudStore.table.c.volume_id == vol_id ).first()
-        vol.i_id = instance_id
+        vol.inst.instance_id = instance_id
         self.sa_session.add( vol )
         self.sa_session.flush()
                 
@@ -559,7 +567,7 @@
     def get_mi_id( self, instance_id=0 ):
         uci = self.sa_session.query( model.UCI ).get( self.uci_id )
         self.sa_session.refresh( uci )
-        return uci.instance[instance_id].mi_id
+        return uci.instance[instance_id].image.image_id
     
     def get_public_dns( self, instance_id=0 ):
         uci = self.sa_session.query( model.UCI ).get( self.uci_id )
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/providers/ec2.py
--- a/lib/galaxy/cloud/providers/ec2.py	Wed Nov 18 10:57:24 2009 -0500
+++ b/lib/galaxy/cloud/providers/ec2.py	Wed Nov 18 13:36:37 2009 -0500
@@ -49,6 +49,7 @@
 )
 
 store_status = Bunch(
+    WAITING = "waiting",
     IN_USE = "in-use",
     CREATING = "creating",
     DELETED = 'deleted',
@@ -441,6 +442,8 @@
                                     s = reservation.instances[0].state 
                                     uci_wrapper.change_state( s, i_id, s )
                                     uci_wrapper.set_security_group_name( self.security_group, i_id=i_id )
+                                    vol_id = uci_wrapper.get_store_volume_id( store_id=0 ) # TODO: Once more that one vol/UCI is allowed, update this!
+                                    uci_wrapper.set_store_status( vol_id, store_status.WAITING )
                                     log.debug( "Instance of UCI '%s' started, current state: '%s'" % ( uci_wrapper.get_name(), uci_wrapper.get_uci_state() ) )
                                 except boto.exception.EC2ResponseError, e:
                                     err = "EC2 response error when retrieving instance information for UCI '" + uci_wrapper.get_name() + "': " + str( e )
@@ -560,6 +563,7 @@
         stores = self.sa_session.query( model.CloudStore ) \
             .filter( or_( model.CloudStore.table.c.status==store_status.IN_USE, 
                           model.CloudStore.table.c.status==store_status.CREATING,
+                          model.CloudStore.table.c.status==store_status.WAITING,
                           model.CloudStore.table.c.status==None ) ) \
             .all()
         for store in stores:
@@ -717,8 +721,8 @@
                     store.status = vl[0].status
                     self.sa_session.add( store )
                     self.sa_session.flush()
-                if store.i_id != vl[0].instance_id:
-                    store.i_id = vl[0].instance_id
+                if store.inst.instance_id != vl[0].instance_id:
+                    store.inst.instance_id = vl[0].instance_id
                     self.sa_session.add( store )
                     self.sa_session.flush()
                 if store.attach_time != vl[0].attach_time:
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/providers/eucalyptus.py
--- a/lib/galaxy/cloud/providers/eucalyptus.py	Wed Nov 18 10:57:24 2009 -0500
+++ b/lib/galaxy/cloud/providers/eucalyptus.py	Wed Nov 18 13:36:37 2009 -0500
@@ -49,6 +49,7 @@
 )
 
 store_status = Bunch(
+    WAITING = "waiting",
     IN_USE = "in-use",
     CREATING = "creating",
     DELETED = 'deleted',
@@ -428,6 +429,8 @@
                                 uci_wrapper.set_instance_id( i_index, i_id )
                                 s = reservation.instances[0].state
                                 uci_wrapper.change_state( s, i_id, s )
+                                vol_id = uci_wrapper.get_store_volume_id( store_id=0 ) # TODO: Once more that one vol/UCI is allowed, update this!
+                                uci_wrapper.set_store_status( vol_id, store_status.WAITING )
                                 log.debug( "Instance of UCI '%s' started, current state: '%s'" % ( uci_wrapper.get_name(), uci_wrapper.get_uci_state() ) )
                             except boto.exception.EC2ResponseError, e:
                                 err = "EC2 response error when retrieving instance information for UCI '" + uci_wrapper.get_name() + "': " + str( e )
@@ -497,7 +500,7 @@
 ##                log.debug ( 'Error detaching volume; still going to try and stop instance %s.' % dbInstances.instance_id )
 #            store.attach_time = None
 #            store.device = None
-#            store.i_id = None
+#            store.inst.instance_id = None
 #            store.status = volStat
 #            log.debug ( '***** volume status: %s' % volStat )
 #        
@@ -549,6 +552,7 @@
         stores = self.sa_session.query( model.CloudStore ) \
             .filter( or_( model.CloudStore.table.c.status==store_status.IN_USE, 
                           model.CloudStore.table.c.status==store_status.CREATING,
+                          model.CloudStore.table.c.status==store_status.WAITING,
                           model.CloudStore.table.c.status==None ) ) \
             .all()
         for store in stores:
@@ -691,7 +695,7 @@
             # Update store status in local DB with info from cloud provider
             if len(vl) > 0:
                 try:
-                    if store.status != vl[0].status:
+                    if store.status != vl[0].status and store.availability_zone != 'epc':
                         # In case something failed during creation of UCI but actual storage volume was created and yet 
                         #  UCI state remained as 'new', try to remedy this by updating UCI state here 
                         if ( store.status == None ) and ( store.volume_id != None ):
@@ -714,8 +718,8 @@
                         store.status = vl[0].status
                         self.sa_session.add( store )
                         self.sa_session.flush()
-                    if store.i_id != vl[0].instance_id:
-                        store.i_id = vl[0].instance_id
+                    if store.inst.instance_id != vl[0].instance_id:
+                        store.inst.instance_id = vl[0].instance_id
                         self.sa_session.add( store )
                         self.sa_session.flush()
                     if store.attach_time != vl[0].attach_time:
@@ -981,7 +985,7 @@
 #        try:
 #            volumes = conn.get_all_volumes( vols )
 #            for i, v in enumerate( volumes ):
-#                uci.store[i].i_id = v.instance_id
+#                uci.store[i].inst.instance_id = v.instance_id
 #                uci.store[i].status = v.status
 #                uci.store[i].device = v.device
 #                uci.store[i].flush()
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py	Wed Nov 18 10:57:24 2009 -0500
+++ b/lib/galaxy/model/__init__.py	Wed Nov 18 13:36:37 2009 -0500
@@ -1077,7 +1077,6 @@
     def __init__( self ):
         self.id = None
         self.volume_id = None
-        self.i_id = None
         self.user = None
         self.size = None
         self.availability_zone = None
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py	Wed Nov 18 10:57:24 2009 -0500
+++ b/lib/galaxy/model/mapping.py	Wed Nov 18 13:36:37 2009 -0500
@@ -429,7 +429,7 @@
     Column( "type", TEXT ),
     Column( "reservation_id", TEXT ),
     Column( "instance_id", TEXT ),
-    Column( "mi_id", TEXT, ForeignKey( "cloud_image.image_id" ), index=True ),
+    Column( "mi_id", Integer, ForeignKey( "cloud_image.id" ), index=True ),
     Column( "state", TEXT ),
     Column( "error", TEXT ),
     Column( "public_dns", TEXT ),
@@ -447,7 +447,7 @@
     Column( "volume_id", TEXT ),
     Column( "size", Integer, nullable=False ),
     Column( "availability_zone", TEXT ),
-    Column( "i_id", TEXT, ForeignKey( "cloud_instance.instance_id" ) ),
+    Column( "inst_id", Integer, ForeignKey( "cloud_instance.id" ) ),
     Column( "status", TEXT ),
     Column( "device", TEXT ),
     Column( "space_consumed", Integer ),
@@ -1133,7 +1133,7 @@
 
 assign_mapper( context, CloudStore, CloudStore.table,
     properties=dict( user=relation( User ),
-                     i=relation( CloudInstance ),
+                     inst=relation( CloudInstance ),
                      snapshot=relation( CloudSnapshot, backref="store" )
                     ) )
 
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/migrate/versions/0026_cloud_tables.py
--- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py	Wed Nov 18 10:57:24 2009 -0500
+++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py	Wed Nov 18 13:36:37 2009 -0500
@@ -56,7 +56,7 @@
     Column( "type", TEXT ),
     Column( "reservation_id", TEXT ),
     Column( "instance_id", TEXT ),
-    Column( "mi_id", TEXT, ForeignKey( "cloud_image.id" ), index=True ),
+    Column( "mi_id", Integer, ForeignKey( "cloud_image.id" ), index=True ),
     Column( "state", TEXT ),
     Column( "error", TEXT ),
     Column( "public_dns", TEXT ),
@@ -74,7 +74,7 @@
     Column( "volume_id", TEXT ),
     Column( "size", Integer, nullable=False ),
     Column( "availability_zone", TEXT ),
-    Column( "i_id", TEXT, ForeignKey( "cloud_instance.id" ) ),
+    Column( "inst_id", Integer, ForeignKey( "cloud_instance.id" ) ),
     Column( "status", TEXT ),
     Column( "device", TEXT ),
     Column( "space_consumed", Integer ),
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca templates/cloud/view_instance.mako
--- a/templates/cloud/view_instance.mako	Wed Nov 18 10:57:24 2009 -0500
+++ b/templates/cloud/view_instance.mako	Wed Nov 18 13:36:37 2009 -0500
@@ -67,7 +67,7 @@
 	   %endif
 	   <tr>
 	   		<td> AMI: </td>
-	   		<td> ${liveInstance.mi_id} </td>
+	   		<td> ${liveInstance.image.image_id} </td>
 	   </tr>
 	   <tr>
 	   		<td> State:</td>
@@ -81,6 +81,7 @@
 	   		<td> Storage size:</td>
 			<td> ${liveInstance.uci.total_size} </td>
 	   </tr>
+	   %if liveInstance.public_dns != None and liveInstance.public_dns != '':
 	   <tr>
 	   		<td> Public DNS:</td>
 			<%
@@ -88,7 +89,8 @@
 			%>
 			<td> <a href="${lnk}" target="_blank">${liveInstance.public_dns}</a></td>
 	   </tr>
-	   %if liveInstance.private_dns != None:
+	   %endif
+	   %if liveInstance.private_dns != None and liveInstance.private_dns != '':
 	   <tr>
 	   		<td> Private DNS:</td>
 			<td> ${liveInstance.private_dns}</td>
diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample	Wed Nov 18 10:57:24 2009 -0500
+++ b/universe_wsgi.ini.sample	Wed Nov 18 13:36:37 2009 -0500
@@ -31,15 +31,15 @@
 paste.app_factory = galaxy.web.buildapp:app_factory
 
 # By default, Galaxy uses a SQLite database found here
-database_file = database/universe.sqlite
+#database_file = database/universe.sqlite
 
 # You may use a SQLAlchemy connection string to specify an external database
 # instead.  PostgreSQL and MySQL are supported.
-#database_connection = postgres:///galaxy
-#database_engine_option_echo = true
-#database_engine_option_echo_pool = true
-#database_engine_option_pool_size = 10
-#database_engine_option_max_overflow = 20
+database_connection = postgres:///galaxy
+database_engine_option_echo = true
+database_engine_option_echo_pool = true
+database_engine_option_pool_size = 10
+database_engine_option_max_overflow = 20
 
 # If using MySQL, see:
 # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-20...

    

[galaxy-dev] [hg] galaxy 3107: Fixed table migration bug encountered with Pos...

Greg Von Kuster