1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/6cbf38099b71/
changeset: 6cbf38099b71
user: natefoo
date: 2012-01-12 22:30:27
summary: Add missing distributed object store config file option to the sample universe_wsgi.ini.
affected #: 1 file
diff -r 0cc2440265bd85f95eab3f05b81dc60a5478543d -r 6cbf38099b7102b3547595d9949df24b4c699a3c universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -446,16 +446,21 @@
# -- Beta features
# Object store mode (valid options are: disk, s3, distributed, hierarchical)
-#object_store = s3
+#object_store = disk
#aws_access_key = <AWS access key>
#aws_secret_key = <AWS secret key>
#s3_bucket = <name of an existing S3 bucket>
#use_reduced_redundancy = True
+
# Size (in GB) that the cache used by object store should be limited to.
# If the value is not specified, the cache size will be limited only by the file
# system size.
#object_store_cache_size = 100
+# Configuration file for the distributed object store, if object_store =
+# distributed. See the sample at distributed_object_store_conf.xml.sample
+#distributed_object_store_config_file = None
+
# Enable Galaxy to communicate directly with a sequencer
#enable_sequencer_communication = False
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/831237b1a552/
changeset: 831237b1a552
user: jgoecks
date: 2012-01-11 20:19:27
summary: Trackster: bug fix when padding tiles for display.
affected #: 1 file
diff -r b716dc5d0e0eea1f8414cc75743852c02800b0d6 -r 831237b1a55211232eff0daf19501933748f0523 static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2511,11 +2511,13 @@
// Attribute init.
Tile.call(this, track, index, resolution, canvas, data);
this.mode = mode;
- this.message = message;
this.feature_mapper = feature_mapper;
+ this.has_icons = false;
// Add message + action icons to tile's html.
if (this.message || !all_slotted) {
+ this.has_icons = true;
+
var
tile = this;
canvas = this.html_elt.children()[0],
@@ -3145,21 +3147,20 @@
var track = this;
//
- // If some tiles have messages, set padding of tiles without messages
- // so features and rows align.
+ // If some tiles have icons, set padding of tiles without icons so features and rows align.
//
- var messages_to_show = false;
+ var icons_present = false;
for (var tile_index = 0; tile_index < tiles.length; tile_index++) {
- if (tiles[tile_index].message) {
- messages_to_show = true;
+ if (tiles[tile_index].has_icons) {
+ icons_present = true;
break;
}
}
- if (messages_to_show) {
+ if (icons_present) {
for (var tile_index = 0; tile_index < tiles.length; tile_index++) {
tile = tiles[tile_index];
- if (!tile.message) {
- // Need to align with other tile(s) that have message(s).
+ if (!tile.has_icons) {
+ // Need to align with other tile(s) that have icons.
tile.html_elt.css("padding-top", ERROR_PADDING);
}
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0d1d62b8be2e/
changeset: 0d1d62b8be2e
user: jgoecks
date: 2012-01-11 15:44:39
summary: Standardize code and error messages on 'public name' rather than 'username'
affected #: 3 files
diff -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 lib/galaxy/security/validate_user_input.py
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -1,6 +1,6 @@
import re
-VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" )
+VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9\-]+$" )
def validate_email( trans, email, user=None, check_dup=True ):
message = ''
@@ -14,21 +14,21 @@
message = "User with that email already exists"
return message
-def validate_username( trans, username, user=None ):
+def validate_publicname( trans, publicname, user=None ):
# User names must be at least four characters in length and contain only lower-case
# letters, numbers, and the '-' character.
- if username in [ 'None', None, '' ]:
+ if publicname in [ 'None', None, '' ]:
return ''
- if user and user.username == username:
+ if user and user.username == publicname:
return ''
- if len( username ) < 4:
- return "User name must be at least 4 characters in length"
- if len( username ) > 255:
- return "User name cannot be more than 255 characters in length"
- if not( VALID_USERNAME_RE.match( username ) ):
- return "User name must contain only lower-case letters, numbers and '-'"
- if trans.sa_session.query( trans.app.model.User ).filter_by( username=username ).first():
- return "This user name is not available"
+ if len( publicname ) < 4:
+ return "Public name must be at least 4 characters in length"
+ if len( publicname ) > 255:
+ return "Public name cannot be more than 255 characters in length"
+ if not( VALID_PUBLICNAME_RE.match( publicname ) ):
+ return "Public name must contain only lower-case letters, numbers and '-'"
+ if trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first():
+ return "Public name is taken; please choose another"
return ''
def validate_password( trans, password, confirm ):
diff -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -16,7 +16,7 @@
from galaxy.web.form_builder import WorkflowField, WorkflowMappingField, HistoryField, PasswordField, build_select_field
from galaxy.visualization.tracks.data_providers import get_data_provider
from galaxy.visualization.tracks.visual_analytics import get_tool_def
-from galaxy.security.validate_user_input import validate_username
+from galaxy.security.validate_user_input import validate_publicname
from paste.httpexceptions import *
from galaxy.exceptions import *
@@ -1222,7 +1222,7 @@
def set_public_username( self, trans, id, username, **kwargs ):
""" Set user's public username and delegate to sharing() """
user = trans.get_user()
- message = validate_username( trans, username, user )
+ message = validate_publicname( trans, username, user )
if message:
return trans.fill_template( '/sharing_base.mako', item=self.get_item( trans, id ), message=message, status='error' )
user.username = username
diff -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -10,7 +10,7 @@
from galaxy.web.form_builder import *
from galaxy.util.json import from_json_string, to_json_string
from galaxy.web.framework.helpers import iff
-from galaxy.security.validate_user_input import validate_email, validate_username, validate_password
+from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password
log = logging.getLogger( __name__ )
@@ -698,7 +698,7 @@
if user and params.get( 'change_username_button', False ):
username = kwd.get( 'username', '' )
if username:
- message = validate_username( trans, username, user )
+ message = validate_publicname( trans, username, user )
if message:
status = 'error'
else:
@@ -736,7 +736,7 @@
# Validate the new values for email and username
message = validate_email( trans, email, user )
if not message and username:
- message = validate_username( trans, username, user )
+ message = validate_publicname( trans, username, user )
if message:
status = 'error'
else:
@@ -878,7 +878,7 @@
if not message:
message = validate_password( trans, password, confirm )
if not message and username:
- message = validate_username( trans, username )
+ message = validate_publicname( trans, username )
if not message:
if webapp == 'galaxy':
if self.get_all_forms( trans,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/67a8349ff9b9/
changeset: 67a8349ff9b9
user: dannon
date: 2012-01-11 15:04:42
summary: Fix for Dan's issues with the GATK tools not behaving properly in 'set at runtime' mode in workflows.
affected #: 1 file
diff -r 4ce50b22cabaf7257c774eb5ae4bb171a731bb7f -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -757,7 +757,15 @@
# If we got this far, we can actually look at the dependencies
# to see if their values will not be available until runtime.
for dep_name in self.get_dependencies():
- dep_value = context[ dep_name ]
+ if dep_name in context:
+ dep_value = context[ dep_name ]
+ else:
+ # Quick hack to check deeper in the context.
+ # TODO: Context should really be scoped and the correct subset passed along.
+ # This happens specifically in all the GATK tools, the way the reference genome is handled.
+ for layer in context.itervalues():
+ if isinstance( layer, dict ) and self.name in layer and dep_name in layer:
+ dep_value = layer[dep_name]
# Dependency on a dataset that does not yet exist
if isinstance( dep_value, DummyDataset ):
return True
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/82115950072c/
changeset: 82115950072c
user: jgoecks
date: 2012-01-10 23:47:18
summary: Fix bug in saving visualizations.
affected #: 1 file
diff -r 2ef6a78863f1ab7e1364762eb114e5f8442f9687 -r 82115950072cf4114619fe1e9c693c83d8e4c9ed lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -692,7 +692,7 @@
session.add( vis_rev )
session.flush()
encoded_id = trans.security.encode_id(vis.id)
- return { "id": encoded_id, "url": url_for( action='browser', id=encoded_id ) }
+ return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) }
@web.expose
@web.require_login( "see all available libraries" )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.