1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ada35462ea04/
changeset: ada35462ea04
user: dannon
date: 2012-04-20 17:16:14
summary: Fix heavy handed removal of PJAs when not using outputs.
affected #: 1 file
diff -r 600fbbf082c1efcf6bacfabd685ccb0c60d2f5f4 -r ada35462ea041bb7fa6de53035eaf615eda068fd static/scripts/galaxy.workflow_editor.canvas.js
--- a/static/scripts/galaxy.workflow_editor.canvas.js
+++ b/static/scripts/galaxy.workflow_editor.canvas.js
@@ -492,8 +492,23 @@
// Using workflow outputs, or has existing pjas. Remove all PJAs and recreate based on outputs.
$.each(this.nodes, function (k, node ){
if (node.type === 'tool'){
- node.post_job_actions = {};
- node_changed = true;
+ var node_changed = false;
+ if (node.post_job_actions == null){
+ node.post_job_actions = {};
+ node_changed = true;
+ }
+ var pjas_to_rem = [];
+ $.each(node.post_job_actions, function(pja_id, pja){
+ if (pja.action_type == "HideDatasetAction"){
+ pjas_to_rem.push(pja_id);
+ }
+ });
+ if (pjas_to_rem.length > 0 && node == workflow.active_node) {
+ $.each(pjas_to_rem, function(i, pja_name){
+ node_changed = true;
+ delete node.post_job_actions[pja_name];
+ });
+ }
if (using_workflow_outputs){
$.each(node.output_terminals, function(ot_id, ot){
var create_pja = true;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8d94b528fb0f/
changeset: 8d94b528fb0f
user: jgoecks
date: 2012-04-19 18:46:31
summary: Trackster: do not subset data with no detail.
affected #: 1 file
diff -r c32b71dcfc84965dc6dacd80495b0b7bac3089cc -r 8d94b528fb0fca25d6f65eba6e507d094854ed57 static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4956,8 +4956,8 @@
* Returns true if data can be subsetted.
*/
can_subset: function(data) {
- // Do not subset summary tree data or entries with a message.
- if (data.dataset_type === "summary_tree" || data.message) {
+ // Do not subset summary tree data, entries with a message, or data with no detail.
+ if (data.dataset_type === "summary_tree" || data.message || data.extra_info === "no_detail") {
return false;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/c32b71dcfc84/
changeset: c32b71dcfc84
user: dan
date: 2012-04-19 18:07:31
summary: Fix for clearing implicitly converted dataset association when converted dataset is deleted.
affected #: 2 files
diff -r 0b52c4f1bf4673ebbd762fe84d09c2edd1d798df -r c32b71dcfc84965dc6dacd80495b0b7bac3089cc lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1125,7 +1125,7 @@
return ldda
def clear_associated_files( self, metadata_safe = False, purge = False ):
# metadata_safe = True means to only clear when assoc.metadata_safe == False
- for assoc in self.implicitly_converted_datasets:
+ for assoc in self.implicitly_converted_datasets + self.implicitly_converted_parent_datasets:
if not metadata_safe or not assoc.metadata_safe:
assoc.clear( purge = purge )
def get_display_name( self ):
diff -r 0b52c4f1bf4673ebbd762fe84d09c2edd1d798df -r c32b71dcfc84965dc6dacd80495b0b7bac3089cc lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -1204,6 +1204,9 @@
implicitly_converted_datasets=relation(
ImplicitlyConvertedDatasetAssociation,
primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ),
+ implicitly_converted_parent_datasets=relation(
+ ImplicitlyConvertedDatasetAssociation,
+ primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_id == HistoryDatasetAssociation.table.c.id ) ),
children=relation(
HistoryDatasetAssociation,
primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0b52c4f1bf46/
changeset: 0b52c4f1bf46
user: jgoecks
date: 2012-04-19 17:49:59
summary: Trackster: correctly handle navigation when only chrom name is used and name is the same as chrom currently being viewed.
affected #: 1 file
diff -r bdea1a9aa7fc594785f69dfae3c9a63dbe510d6c -r 0b52c4f1bf4673ebbd762fe84d09c2edd1d798df static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1669,6 +1669,11 @@
view.low = Math.max(low, 0);
view.high = Math.min(high, view.max_high);
}
+ else {
+ // Low and high undefined, so view is whole chome.
+ view.low = 0;
+ view.high = view.max_high;
+ }
view.reset_overview();
view.request_redraw();
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/bdea1a9aa7fc/
changeset: bdea1a9aa7fc
user: dan
date: 2012-04-19 17:05:10
summary: Tweak for 7079:7ca527380818.
affected #: 1 file
diff -r 7ca52738081826b32f57d43eff6510bd2cc1bdba -r bdea1a9aa7fc594785f69dfae3c9a63dbe510d6c lib/galaxy/security/validate_user_input.py
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -42,6 +42,7 @@
elif publicname not in [ 'None', None, '' ]:
publicname = publicname.lower()
publicname = re.sub( VALID_PUBLICNAME_SUB, FILL_CHAR, publicname )
+ publicname = publicname.ljust( 4, FILL_CHAR )[:255]
if not trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first():
return publicname
return ''
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7ca527380818/
changeset: 7ca527380818
user: dan
date: 2012-04-19 16:16:30
summary: Add a transform_publicname method that coerces a provided string into a valid username. This is now used during user creation.
affected #: 2 files
diff -r d346bd2efc9798547ba9a4ac80d305ee6d7aedcc -r 7ca52738081826b32f57d43eff6510bd2cc1bdba 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 +1,8 @@
import re
VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9\-]+$" )
+VALID_PUBLICNAME_SUB = re.compile( "[^a-z0-9\-]" )
+FILL_CHAR = '-'
def validate_email( trans, email, user=None, check_dup=True ):
message = ''
@@ -31,6 +33,19 @@
return "Public name is taken; please choose another"
return ''
+def transform_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.
+ #TODO: Enhance to allow generation of semi-random publicnnames e.g., when valid but taken
+ if user and user.username == publicname:
+ return publicname
+ elif publicname not in [ 'None', None, '' ]:
+ publicname = publicname.lower()
+ publicname = re.sub( VALID_PUBLICNAME_SUB, FILL_CHAR, publicname )
+ if not trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first():
+ return publicname
+ return ''
+
def validate_password( trans, password, confirm ):
if len( password ) < 6:
return "Use a password of at least 6 characters"
diff -r d346bd2efc9798547ba9a4ac80d305ee6d7aedcc -r 7ca52738081826b32f57d43eff6510bd2cc1bdba 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_publicname, validate_password
+from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password, transform_publicname
log = logging.getLogger( __name__ )
@@ -341,7 +341,7 @@
email=email,
password='',
confirm='',
- username=username,
+ username=transform_publicname( trans, username ),
header='',
use_panels=use_panels,
redirect=redirect,
@@ -581,7 +581,7 @@
email=email,
password=password,
confirm=confirm,
- username=username,
+ username=transform_publicname( trans, username ),
subscribe_checked=subscribe_checked,
user_type_fd_id_select_field=user_type_fd_id_select_field,
user_type_form_definition=user_type_form_definition,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d346bd2efc97/
changeset: d346bd2efc97
user: dan
date: 2012-04-19 01:38:34
summary: Slightly more unique automatically generated filename for GenomeSpace export.
affected #: 1 file
diff -r bb1d639c4db59c50f7384c8b2ef22a7b8da896ee -r d346bd2efc9798547ba9a4ac80d305ee6d7aedcc tools/genomespace/genomespace_exporter.xml
--- a/tools/genomespace/genomespace_exporter.xml
+++ b/tools/genomespace/genomespace_exporter.xml
@@ -27,7 +27,7 @@
#if $filename:
--filename "${filename}"
#else:
- --filename "Galaxy History Item ${__app__.security.encode_id( $input1.id )} - ${input1.hid}: ${input1.name}.${input1.ext}"
+ --filename "Galaxy History Item ${__app__.security.encode_id( $input1.id )} (${__app__.security.encode_id( $output_log.id )}) - ${input1.hid}: ${input1.name}.${input1.ext}"
#end if
--file_type "${input1.ext}"
--content_type "${input1.get_mime()}"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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