commit/galaxy-central: guerler: scratchbook: hide on disable
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9ddb3130b98d/
Changeset: 9ddb3130b98d
User: guerler
Date: 2013-07-01 01:29:04
Summary: scratchbook: hide on disable
Affected #: 2 files
diff -r 27a8341736452288e7324559ff74df38abaa3931 -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 static/scripts/galaxy.frame.js
--- a/static/scripts/galaxy.frame.js
+++ b/static/scripts/galaxy.frame.js
@@ -123,8 +123,8 @@
this.event_initialize();
// add
- $(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"});
- $(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"});
+ //$(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"});
+ //$(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"});
// catch window resize event
var self = this;
@@ -218,7 +218,7 @@
if (this.event.type === null)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// identify frame
@@ -340,6 +340,9 @@
if (this.event.type !== null)
return;
+ // prevent
+ e.preventDefault();
+
// get frame
var frame = this.event_get_frame(e.target);
var self = this;
@@ -375,7 +378,7 @@
if (this.event.type !== null)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// get frame
@@ -413,7 +416,7 @@
if (this.event.type !== null)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// load panel
@@ -427,7 +430,7 @@
if (this.event.type !== null)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// load panel
@@ -441,7 +444,7 @@
if (this.event.type !== null || !this.visible)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// get wheel delta
@@ -458,7 +461,7 @@
if (this.event.type !== null)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// scroll up
@@ -472,7 +475,7 @@
if (this.event.type !== null)
return;
- // prevent text selection
+ // prevent
e.preventDefault();
// scroll down
@@ -774,6 +777,10 @@
// untoggle
$(".galaxy-frame-active .icon").removeClass("f-toggle");
+
+ // hide panel
+ if (this.visible)
+ this.panel_show_hide();
} else {
// activate
this.active = true;
@@ -789,9 +796,6 @@
// adds and displays a new frame/window
frame_new: function(options)
{
- // trigger mouse leave
- $(document).trigger('mouseleave');
-
// validate
if (!this.active)
{
diff -r 27a8341736452288e7324559ff74df38abaa3931 -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 static/style/blue/galaxy.frame.css
--- a/static/style/blue/galaxy.frame.css
+++ b/static/style/blue/galaxy.frame.css
@@ -95,7 +95,7 @@
z-index : 34010;
position : absolute;
top : 6px;
- right : 165px;
+ right : 170px;
cursor : pointer;
color : #BCC800;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/27a834173645/
Changeset: 27a834173645
User: natefoo
Date: 2013-06-30 16:04:58
Summary: GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."
Use tool_conf.xml for running functional tests, rather than tool_conf.xml.sample.
Affected #: 3 files
diff -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb -r 27a8341736452288e7324559ff74df38abaa3931 buildbot_setup.sh
--- a/buildbot_setup.sh
+++ b/buildbot_setup.sh
@@ -65,6 +65,7 @@
"
SAMPLES="
+tool_conf.xml.sample
datatypes_conf.xml.sample
universe_wsgi.ini.sample
tool_data_table_conf.xml.sample
diff -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb -r 27a8341736452288e7324559ff74df38abaa3931 run_functional_tests.sh
--- a/run_functional_tests.sh
+++ b/run_functional_tests.sh
@@ -51,4 +51,3 @@
fi
echo "'run_functional_tests.sh help' for help"
-echo "Note: galaxy test framework uses tool_conf.xml.sample, not tool_conf.xml"
diff -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb -r 27a8341736452288e7324559ff74df38abaa3931 scripts/functional_tests.py
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -129,7 +129,7 @@
# Exclude all files except test_toolbox.py.
ignore_files = ( re.compile( r'^test_[adghlmsu]*' ), re.compile( r'^test_ta*' ) )
else:
- tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
+ tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml' )
galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir )
if not os.path.isabs( galaxy_test_file_dir ):
galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 10 months
commit/galaxy-central: guerler: Scratchbook: Improve event handling
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9c4b7f8d2f98/
Changeset: 9c4b7f8d2f98
User: guerler
Date: 2013-06-30 09:27:29
Summary: Scratchbook: Improve event handling
Affected #: 1 file
diff -r d748871f160f9bf1b13df57d34a9f3cf13a9f947 -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb static/scripts/galaxy.frame.js
--- a/static/scripts/galaxy.frame.js
+++ b/static/scripts/galaxy.frame.js
@@ -375,6 +375,9 @@
if (this.event.type !== null)
return;
+ // prevent text selection
+ e.preventDefault();
+
// get frame
var frame = this.event_get_frame(e.target);
@@ -404,23 +407,29 @@
},
// show/hide panel
- event_panel_load: function ()
+ event_panel_load: function (e)
{
// check
if (this.event.type !== null)
return;
+ // prevent text selection
+ e.preventDefault();
+
// load panel
this.panel_show_hide();
},
// activate/disable panel
- event_panel_active: function ()
+ event_panel_active: function (e)
{
// check
if (this.event.type !== null)
return;
+ // prevent text selection
+ e.preventDefault();
+
// load panel
this.panel_active_disable();
},
@@ -432,6 +441,9 @@
if (this.event.type !== null || !this.visible)
return;
+ // prevent text selection
+ e.preventDefault();
+
// get wheel delta
var delta = e.originalEvent.detail ? e.originalEvent.detail : e.originalEvent.wheelDelta / -3;
@@ -440,23 +452,29 @@
},
// scroll up
- event_panel_scroll_up: function()
+ event_panel_scroll_up: function(e)
{
// check
if (this.event.type !== null)
return;
+ // prevent text selection
+ e.preventDefault();
+
// scroll up
this.panel_scroll(-this.options.scroll);
},
// scroll down
- event_panel_scroll_down: function()
+ event_panel_scroll_down: function(e)
{
// check
if (this.event.type !== null)
return;
+ // prevent text selection
+ e.preventDefault();
+
// scroll down
this.panel_scroll(this.options.scroll);
},
@@ -771,6 +789,9 @@
// adds and displays a new frame/window
frame_new: function(options)
{
+ // trigger mouse leave
+ $(document).trigger('mouseleave');
+
// validate
if (!this.active)
{
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 10 months
commit/galaxy-central: guerler: Fix event handling, tooltip
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d748871f160f/
Changeset: d748871f160f
User: guerler
Date: 2013-06-30 08:34:19
Summary: Fix event handling, tooltip
Affected #: 1 file
diff -r 019ad31c3c2502005846dadc5c0457bbb6f80712 -r d748871f160f9bf1b13df57d34a9f3cf13a9f947 static/scripts/galaxy.frame.js
--- a/static/scripts/galaxy.frame.js
+++ b/static/scripts/galaxy.frame.js
@@ -91,8 +91,8 @@
$(this.el).append(this.frame_template_menu());
// load load button
- $(this.el_header).append(this.frame_template_load());
-
+ $(this.el_header).append(this.frame_template_header());
+
//
// define shadow frame
//
@@ -121,7 +121,11 @@
// link events
this.event_initialize();
-
+
+ // add
+ $(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"});
+ $(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"});
+
// catch window resize event
var self = this;
$(window).resize(function ()
@@ -162,7 +166,6 @@
{*/
this.events = {
// global page events
- 'mousedown' : 'event_frame_mouse_down',
'mousemove' : 'event_frame_mouse_move',
'mouseup' : 'event_frame_mouse_up',
'mouseleave' : 'event_frame_mouse_up',
@@ -170,13 +173,14 @@
'DOMMouseScroll' : 'event_panel_scroll',
// events fixed to elements
- 'mousedown .f-close' : 'event_frame_close',
- 'mousedown .f-pin' : 'event_frame_lock',
+ 'mousedown .galaxy-frame' : 'event_frame_mouse_down',
'mousedown .galaxy-frame-active' : 'event_panel_active',
'mousedown .galaxy-frame-load' : 'event_panel_load',
'mousedown .galaxy-frame-background' : 'event_panel_load',
'mousedown .galaxy-frame-scroll-up' : 'event_panel_scroll_up',
- 'mousedown .galaxy-frame-scroll-down' : 'event_panel_scroll_down'
+ 'mousedown .galaxy-frame-scroll-down' : 'event_panel_scroll_down',
+ 'mousedown .f-close' : 'event_frame_close',
+ 'mousedown .f-pin' : 'event_frame_lock'
};
/*} else {
this.events = {
@@ -197,9 +201,6 @@
// drag start
event_frame_mouse_down: function (e)
{
- // prevent text selection
- e.preventDefault();
-
// skip if event is already active
if (this.event.type !== null)
return;
@@ -212,11 +213,14 @@
// check for resize event
if ($(e.target).hasClass('f-resize'))
this.event.type = 'resize';
-
+
// skip if no event has to be handled
if (this.event.type === null)
return;
-
+
+ // prevent text selection
+ e.preventDefault();
+
// identify frame
this.event.target = this.event_get_frame(e.target);
@@ -1044,13 +1048,13 @@
},
// fill load button template
- frame_template_load: function()
+ frame_template_header: function()
{
return '<div class="galaxy-frame-load f-corner">' +
'<div class="number f-corner">0</div>' +
'<div class="icon fa-icon-2x"></div>' +
- '</div>'+
- '<div class="galaxy-frame-active f-corner">' +
+ '</div>' +
+ '<div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;">' +
'<div class="icon fa-icon-2x fa-icon-th"></div>' +
'</div>';
},
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/bf69f8db6dbb/
Changeset: bf69f8db6dbb
Branch: stable
User: dannon
Date: 2013-05-30 17:23:29
Summary: Add specific ami functionality (via GET param) to cloudlaunch. Prevent existing instance selection when using a share string.
Affected #: 2 files
diff -r be47a7f089f91c4b72c0c5f89182a62589389e1f -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -35,8 +35,8 @@
BaseUIController.__init__(self, app)
@web.expose
- def index(self, trans, share_string=None):
- return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string)
+ def index(self, trans, share_string=None, ami=None):
+ return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string, ami=ami)
@web.expose
def get_account_info(self, trans, key_id, secret, **kwargs):
@@ -92,7 +92,7 @@
return to_json_string(account_info)
@web.expose
- def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, zone=None, **kwargs):
+ def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, **kwargs):
ec2_error = None
try:
# Create security group & key pair used when starting an instance
@@ -113,11 +113,14 @@
user_provided_data['password'] = password
if share_string:
user_provided_data['share_string'] = share_string
+
rs = run_instance(ec2_conn=ec2_conn,
+ image_id = ami,
user_provided_data=user_provided_data,
key_name=kp_name,
security_groups=[sg_name],
- placement=zone)
+ placement=zone
+ )
if rs:
instance = rs.instances[0]
ct = 0
@@ -266,7 +269,7 @@
return None, None
return kp.name, kp.material
-def run_instance(ec2_conn, user_provided_data, image_id=DEFAULT_AMI,
+def run_instance(ec2_conn, user_provided_data, image_id=None,
kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR,
placement=None, security_groups=['CloudMan']):
""" Start an instance. If instance start was OK, return the ResultSet object
diff -r be47a7f089f91c4b72c0c5f89182a62589389e1f -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 templates/webapps/galaxy/cloud/index.mako
--- a/templates/webapps/galaxy/cloud/index.mako
+++ b/templates/webapps/galaxy/cloud/index.mako
@@ -202,12 +202,14 @@
</div><div id="hidden_options">
+ %if not share_string:
<div id='existing_instance_wrapper' style="display:none;" class="form-row"><label for="id_existing_instance">Instances in your account</label><select name="existing_instance" id="id_existing_instance"></select><input id='id_zone' type='hidden' name='zone' value=''/></div>
+ %endif
<div id='cluster_name_wrapper' class="form-row"><label for="id_cluster_name">Cluster Name</label><input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/>
@@ -244,6 +246,10 @@
</div>
%endif
+ %if ami:
+ <input type='hidden' name='ami' value='${ami}'/>
+ %endif
+
<div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type">
https://bitbucket.org/galaxy/galaxy-central/commits/51c57629182d/
Changeset: 51c57629182d
Branch: stable
User: dannon
Date: 2013-05-31 17:55:46
Summary: Add bucket_default userData (param-based only) to cloudlaunch.
Affected #: 2 files
diff -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 -r 51c57629182d2a77e5ddfe2742919a2412d42898 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -35,8 +35,12 @@
BaseUIController.__init__(self, app)
@web.expose
- def index(self, trans, share_string=None, ami=None):
- return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string, ami=ami)
+ def index(self, trans, share_string=None, ami=None, bucket_default = None):
+ return trans.fill_template("cloud/index.mako",
+ default_keypair = DEFAULT_KEYPAIR,
+ share_string=share_string,
+ ami=ami,
+ bucket_default=bucket_default)
@web.expose
def get_account_info(self, trans, key_id, secret, **kwargs):
@@ -92,7 +96,7 @@
return to_json_string(account_info)
@web.expose
- def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, **kwargs):
+ def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, bucket_default=None, **kwargs):
ec2_error = None
try:
# Create security group & key pair used when starting an instance
@@ -113,6 +117,8 @@
user_provided_data['password'] = password
if share_string:
user_provided_data['share_string'] = share_string
+ if bucket_default:
+ user_provided_data['bucket_default'] = bucket_default
rs = run_instance(ec2_conn=ec2_conn,
image_id = ami,
diff -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 -r 51c57629182d2a77e5ddfe2742919a2412d42898 templates/webapps/galaxy/cloud/index.mako
--- a/templates/webapps/galaxy/cloud/index.mako
+++ b/templates/webapps/galaxy/cloud/index.mako
@@ -250,6 +250,10 @@
<input type='hidden' name='ami' value='${ami}'/>
%endif
+ %if bucket_default:
+ <input type='hidden' name='bucket_default' value='${bucket_default}'/>
+ %endif
+
<div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type">
https://bitbucket.org/galaxy/galaxy-central/commits/64bc5a64b19e/
Changeset: 64bc5a64b19e
Branch: stable
User: dannon
Date: 2013-06-30 07:26:31
Summary: Make default ami configurable via universe
Affected #: 3 files
diff -r 51c57629182d2a77e5ddfe2742919a2412d42898 -r 64bc5a64b19ea3161f95e74702cc1d44fb50e4e3 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -251,6 +251,7 @@
self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
# Cloud configuration options
self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) )
+ self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-118bfc78' )
# Galaxy messaging (AMQP) configuration options
self.amqp = {}
try:
diff -r 51c57629182d2a77e5ddfe2742919a2412d42898 -r 64bc5a64b19ea3161f95e74702cc1d44fb50e4e3 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -26,7 +26,6 @@
PKEY_PREFIX = 'gxy_pkey'
DEFAULT_KEYPAIR = 'cloudman_keypair'
-DEFAULT_AMI = 'ami-da58aab3'
class CloudController(BaseUIController):
@@ -96,7 +95,7 @@
return to_json_string(account_info)
@web.expose
- def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, bucket_default=None, **kwargs):
+ def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=None, zone=None, bucket_default=None, **kwargs):
ec2_error = None
try:
# Create security group & key pair used when starting an instance
@@ -120,6 +119,9 @@
if bucket_default:
user_provided_data['bucket_default'] = bucket_default
+ if not ami:
+ ami = trans.app.config.cloudlaunch_default_ami
+
rs = run_instance(ec2_conn=ec2_conn,
image_id = ami,
user_provided_data=user_provided_data,
diff -r 51c57629182d2a77e5ddfe2742919a2412d42898 -r 64bc5a64b19ea3161f95e74702cc1d44fb50e4e3 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -316,9 +316,10 @@
# Note that this requires java > 1.4 for executing yuicompressor.jar
#pack_scripts = False
-# Enable Cloud Launch
+# Cloud Launch
#enable_cloud_launch = False
+#cloudlaunch_default_ami = ami-118bfc78
# -- Advanced proxy features
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 10 months
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/be47a7f089f9/
Changeset: be47a7f089f9
Branch: stable
User: jgoecks
Date: 2013-06-28 21:26:27
Summary: Enhance multi-value select parsing to split on all whitespace; this fixes a bug that prevents multi-value selects from being used in workflows due to web browsers using \r\n for newline designation.
Affected #: 1 file
diff -r 8c663e656f64a60dac55979841947e78ce23a473 -r be47a7f089f91c4b72c0c5f89182a62589389e1f lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -703,7 +703,10 @@
value = None
else:
if not isinstance( value, list ):
- value = value.split( "\n" )
+ # Split on all whitespace. This not only provides flexibility
+ # in interpreting values but also is needed because many browsers
+ # use \r\n to separate lines.
+ value = value.split()
return UnvalidatedValue( value )
legal_values = self.get_legal_values( trans, context )
if isinstance( value, list ):
https://bitbucket.org/galaxy/galaxy-central/commits/019ad31c3c25/
Changeset: 019ad31c3c25
User: jgoecks
Date: 2013-06-28 21:28:01
Summary: Automated merge of stable branch.
Affected #: 1 file
diff -r b89b721a0b3db47cdeddef35f03ce4c2ffcb47b5 -r 019ad31c3c2502005846dadc5c0457bbb6f80712 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -703,7 +703,10 @@
value = None
else:
if not isinstance( value, list ):
- value = value.split( "\n" )
+ # Split on all whitespace. This not only provides flexibility
+ # in interpreting values but also is needed because many browsers
+ # use \r\n to separate lines.
+ value = value.split()
return UnvalidatedValue( value )
legal_values = self.get_legal_values( trans, context )
if isinstance( value, list ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: When repairing a repository via the browser, display the ordered list of repositories that will be inspected and repaired.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4227472b7640/
Changeset: 4227472b7640
User: greg
Date: 2013-06-27 21:52:45
Summary: When repairing a repository via the browser, display the ordered list of repositories that will be inspected and repaired.
Affected #: 2 files
diff -r 43e609a791a13c37612e5e440d5890acc070a351 -r 4227472b7640e6689d13d428949be363b4bbc637 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1147,8 +1147,6 @@
Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as
each repository's tool dependencies.
"""
- # TODO: figure out how to handle installing repositories and tool dependencies consecutively since each redirects to an ajaxian grid. This
- # is not a problem in that Galaxy API.
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
@@ -1160,15 +1158,27 @@
message=message,
status=status ) )
tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id )
+ if kwd.get( 'repair_repository_button', False ):
+ repair_dict = kwd.get( 'repair_dict', None )
+ if not repair_dict:
+ repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository )
+ ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] )
+ ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] )
+ if ordered_tsr_ids and ordered_repo_info_dicts:
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='manage_repositories',
+ operation='repair',
+ ordered_tsr_ids=ordered_tsr_ids,
+ ordered_repo_info_dicts=ordered_repo_info_dicts ) )
+ tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id )
repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository )
ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] )
ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] )
- if ordered_tsr_ids and ordered_repo_info_dicts:
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='manage_repositories',
- operation='repair',
- ordered_tsr_ids=ordered_tsr_ids,
- ordered_repo_info_dicts=ordered_repo_info_dicts ) )
+ return trans.fill_template( 'admin/tool_shed_repository/repair_repository.mako',
+ repository=tool_shed_repository,
+ repair_dict=repair_dict,
+ message=message,
+ status=status )
@web.json
def repository_installation_status_updates( self, trans, ids=None, status_list=None ):
diff -r 43e609a791a13c37612e5e440d5890acc070a351 -r 4227472b7640e6689d13d428949be363b4bbc637 templates/admin/tool_shed_repository/repair_repository.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/repair_repository.mako
@@ -0,0 +1,51 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ ${h.css( "library" )}
+</%def>
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+</%def>
+
+${render_galaxy_repository_actions( repository )}
+
+%if message:
+ ${render_msg( message, status )}
+%endif
+
+<div class="warningmessage">
+ The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are correctly
+ installed. Click <b>Repair</b> to inspect and repair these repositories.
+</div>
+
+<div class="toolForm">
+ <div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div>
+ <br/><br/>
+ <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=repair_dict )}" method="post" >
+ <% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %>
+ <table class="grid">
+ <tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr>
+ %for repo_info_dict in ordered_repo_info_dicts:
+ <%
+ for name, repo_info_tuple in repo_info_dict.items():
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
+ break
+ %>
+ <tr>
+ <td>${name | h}</td>
+ <td>${repository_owner | h}</td>
+ <td>${changeset_revision | h}</td>
+ </tr>
+ %endfor
+ </table>
+ <div style="clear: both"></div>
+ <div class="form-row">
+ <input type="submit" name="repair_repository_button" value="Repair"/>
+ </div>
+ </form>
+ </div>
+</div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Add VCF visualization support for dataset viewer
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/43e609a791a1/
Changeset: 43e609a791a1
User: guerler
Date: 2013-06-27 20:35:37
Summary: Add VCF visualization support for dataset viewer
Affected #: 1 file
diff -r 507ac09f587d2e0c40c1d8f06ed385817a209626 -r 43e609a791a13c37612e5e440d5890acc070a351 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -120,7 +120,7 @@
initialize: function(options)
{
// load trackster button
- (new TabularButtonTracksterView(options)).render();
+ new TabularButtonTracksterView(options);
},
render: function()
@@ -252,23 +252,63 @@
// database key
genome_build: null,
+ // data type
+ data_type: null,
+
// backbone initialize
initialize: function (options)
{
- // verify that metadata exists
- var metadata = options.model.attributes.metadata.attributes;
- if (typeof metadata.chromCol === "undefined" || typeof metadata.startCol === "undefined" || typeof metadata.endCol === "undefined")
- console.log("TabularButtonTrackster : Metadata for column identification is missing.");
- else {
- // read in columns
- this.col.chrom = metadata.chromCol - 1;
- this.col.start = metadata.startCol - 1;
- this.col.end = metadata.endCol - 1;
+ // get options
+ var attributes = options.model.attributes;
+ var metadata = options.model.attributes.metadata.attributes;
+
+ // check for datatype
+ if (typeof attributes.data_type !== "undefined")
+ this.data_type = attributes.data_type;
+ else
+ console.log("TabularButtonTrackster : Data type missing.");
+
+ // check for bed-file format
+ if (this.data_type == "bed")
+ {
+ // verify that metadata exists
+ if (typeof metadata.chromCol !== "undefined" || typeof metadata.startCol !== "undefined" || typeof metadata.endCol !== "undefined")
+ {
+ // read in columns
+ this.col.chrom = metadata.chromCol - 1;
+ this.col.start = metadata.startCol - 1;
+ this.col.end = metadata.endCol - 1;
+ } else
+ console.log("TabularButtonTrackster : Bed-file metadata incomplete.");
+ }
+
+ // check for vcf-file format
+ if (this.data_type == "vcf")
+ {
+ // search array
+ function search (str, array)
+ {
+ for (var j = 0; j < array.length; j++)
+ if (array[j].match(str)) return j;
+ return -1;
+ };
+
+ // load
+ this.col.chrom = search("Chrom", metadata.column_names);
+ this.col.start = search("Pos", metadata.column_names);
+ this.col.end = null;
+
+ // verify that metadata exists
+ if (this.col.chrom == -1 || this.col.start == -1)
+ console.log("TabularButtonTrackster : VCF-file metadata incomplete.");
}
// check
if(this.col.chrom === null)
+ {
+ console.log("TabularButtonTrackster : Chromosome column undefined.");
return;
+ }
// get dataset id
if (typeof options.model.attributes.id === "undefined")
@@ -285,6 +325,19 @@
// get genome_build / database key
if (typeof options.model.attributes.genome_build !== "undefined")
this.genome_build = options.model.attributes.genome_build;
+
+ // render the icon from template
+ var btn_viz = new IconButtonView({ model : new IconButton({
+ title : 'Visualize',
+ icon_class : 'chart_curve',
+ id : 'btn_viz'
+ })});
+
+ // add it to the screen
+ this.$el.append(btn_viz.render().$el);
+
+ // hide the button
+ $('#btn_viz').hide();
},
// backbone events
@@ -297,29 +350,39 @@
// show button
btn_viz_show: function (e)
{
+ // is numeric
+ function is_numeric(n)
+ {
+ return !isNaN(parseFloat(n)) && isFinite(n);
+ };
+
// check
if(this.col.chrom === null)
return;
-
+
// get selected data line
var row = $(e.target).parent();
-
+
// verify that location has been found
var chrom = row.children().eq(this.col.chrom).html();
var start = row.children().eq(this.col.start).html();
- var end = row.children().eq(this.col.end).html();
- if (chrom !== "" && start !== "" && end !== "")
+
+ // end is optional
+ var end = this.col.end ? row.children().eq(this.col.end).html() : start;
+
+ // double check location
+ if (!chrom.match("^#") && chrom !== "" && is_numeric(start))
{
// get target gene region
var btn_viz_pars = {
dataset_id : this.dataset_id,
gene_region : chrom + ":" + start + "-" + end
};
-
+
// get button position
var offset = row.offset();
var left = offset.left - 10;
- var top = offset.top;
+ var top = offset.top - $(window).scrollTop();
// update css
$('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'});
@@ -328,6 +391,9 @@
// show the button
$('#btn_viz').show();
+ } else {
+ // hide the button
+ $('#btn_viz').hide();
}
},
@@ -401,24 +467,7 @@
});
return false;
};
- },
-
- // render frame
- render: function()
- {
- // render the icon from template
- var btn_viz = new IconButtonView({ model : new IconButton({
- title : 'Visualize',
- icon_class : 'chart_curve',
- id : 'btn_viz'
- })});
-
- // add it to the screen
- this.$el.append(btn_viz.render().$el);
-
- // hide the button
- $('#btn_viz').hide();
- }
+ }
});
// -- Utility functions. --
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8c663e656f64/
Changeset: 8c663e656f64
Branch: stable
User: jgoecks
Date: 2013-06-27 18:11:21
Summary: Fix unicode issues in page editor.
Affected #: 1 file
diff -r 53f9bc7009f4c7c93177eb1f71d014e822b43640 -r 8c663e656f64a60dac55979841947e78ce23a473 templates/webapps/galaxy/page/editor.mako
--- a/templates/webapps/galaxy/page/editor.mako
+++ b/templates/webapps/galaxy/page/editor.mako
@@ -782,7 +782,7 @@
</div><div class="unified-panel-body">
- <textarea name="page_content">${page.latest_revision.content.decode('utf-8')}</textarea>
+ <textarea name="page_content">${util.unicodify( page.latest_revision.content) }</textarea></div></%def>
https://bitbucket.org/galaxy/galaxy-central/commits/507ac09f587d/
Changeset: 507ac09f587d
User: jgoecks
Date: 2013-06-27 18:12:07
Summary: Automated merge of stable branch.
Affected #: 3 files
diff -r e1955f57e73a8ce096bf77fd6c9d0e0ad8c5f086 -r 507ac09f587d2e0c40c1d8f06ed385817a209626 templates/webapps/galaxy/page/editor.mako
--- a/templates/webapps/galaxy/page/editor.mako
+++ b/templates/webapps/galaxy/page/editor.mako
@@ -782,7 +782,7 @@
</div><div class="unified-panel-body">
- <textarea name="page_content">${page.latest_revision.content.decode('utf-8')}</textarea>
+ <textarea name="page_content">${util.unicodify( page.latest_revision.content) }</textarea></div></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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