[hg] galaxy 3487: Make fastqAggregator a new style class.
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/b4dc8ea68ac7
changeset: 3487:b4dc8ea68ac7
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Fri Mar 05 10:13:36 2010 -0500
description:
Make fastqAggregator a new style class.
diffstat:
lib/galaxy_utils/sequence/fastq.py | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (12 lines):
diff -r 1cd52787c0bb -r b4dc8ea68ac7 lib/galaxy_utils/sequence/fastq.py
--- a/lib/galaxy_utils/sequence/fastq.py Fri Mar 05 09:09:26 2010 -0500
+++ b/lib/galaxy_utils/sequence/fastq.py Fri Mar 05 10:13:36 2010 -0500
@@ -264,7 +264,7 @@
FASTQ_FORMATS[ format.format ] = format
-class fastqAggregator():
+class fastqAggregator( object ):
VALID_FORMATS = FASTQ_FORMATS.keys()
def __init__( self, ):
self.ascii_values_used = [] #quick lookup of all ascii chars used
12 years, 5 months
[hg] galaxy 3486: Handle dialog box overflow gracefully by scrol...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/1cd52787c0bb
changeset: 3486:1cd52787c0bb
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Fri Mar 05 09:09:26 2010 -0500
description:
Handle dialog box overflow gracefully by scrolling body; this fix makes it possible to place item selection grids in dialog boxes without poor overflow. Also fixed msg when displaying an empty history.
diffstat:
static/june_2007_style/blue/panel_layout.css | 3 ++-
static/june_2007_style/panel_layout.css.tmpl | 8 +++++++-
templates/base_panels.mako | 2 +-
templates/history/display.mako | 2 +-
4 files changed, 11 insertions(+), 4 deletions(-)
diffs (56 lines):
diff -r ef90fbe0eda1 -r 1cd52787c0bb static/june_2007_style/blue/panel_layout.css
--- a/static/june_2007_style/blue/panel_layout.css Thu Mar 04 18:33:11 2010 -0500
+++ b/static/june_2007_style/blue/panel_layout.css Fri Mar 05 09:09:26 2010 -0500
@@ -27,7 +27,8 @@
.dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;}
.dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;}
.dialog-box{border:solid #999 1px;background:white;z-index:80000;}
-.dialog-box .body,.dialog-box .buttons{padding:5px;}
+.dialog-box .body{padding:5px;overflow:auto;max-height:500px;}
+.dialog-box .buttons{padding:5px;}
.panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;}
.panel-warning-message{background-image:url(warn_small.png);background-color:#FFFFCC;}
.panel-done-message{background-image:url(done_small.png);background-color:#CCFFCC;}
diff -r ef90fbe0eda1 -r 1cd52787c0bb static/june_2007_style/panel_layout.css.tmpl
--- a/static/june_2007_style/panel_layout.css.tmpl Thu Mar 04 18:33:11 2010 -0500
+++ b/static/june_2007_style/panel_layout.css.tmpl Fri Mar 05 09:09:26 2010 -0500
@@ -190,7 +190,13 @@
z-index: 80000;
}
-.dialog-box .body, .dialog-box .buttons {
+.dialog-box .body {
+ padding: 5px;
+ overflow: auto;
+ max-height: 500px;
+}
+
+.dialog-box .buttons {
padding: 5px;
}
diff -r ef90fbe0eda1 -r 1cd52787c0bb templates/base_panels.mako
--- a/templates/base_panels.mako Thu Mar 04 18:33:11 2010 -0500
+++ b/templates/base_panels.mako Fri Mar 05 09:09:26 2010 -0500
@@ -314,7 +314,7 @@
<div class="unified-panel-header">
<div class="unified-panel-header-inner"><span class='title'>${title}</span></div>
</div>
- <div class="body" style="max-height: 600px;">${content}</div>
+ <div class="body">${content}</div>
<div>
<div class="buttons" style="display: none; float: right;"></div>
<div class="extra_buttons" style="display: none; padding: 5px;"></div>
diff -r ef90fbe0eda1 -r 1cd52787c0bb templates/history/display.mako
--- a/templates/history/display.mako Thu Mar 04 18:33:11 2010 -0500
+++ b/templates/history/display.mako Fri Mar 05 09:09:26 2010 -0500
@@ -277,7 +277,7 @@
</table>
<div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;">
%endif
- ${_("Your history is empty. Click 'Get Data' on the left pane to start")}
+ ${_("This history is empty.")}
</div>
</%def>
\ No newline at end of file
12 years, 5 months
[hg] galaxy 3485: Add boxplot tool to tool_conf.xml.main
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/ef90fbe0eda1
changeset: 3485:ef90fbe0eda1
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Thu Mar 04 18:33:11 2010 -0500
description:
Add boxplot tool to tool_conf.xml.main
diffstat:
tool_conf.xml.main | 1 +
1 files changed, 1 insertions(+), 0 deletions(-)
diffs (11 lines):
diff -r d1900a25eb45 -r ef90fbe0eda1 tool_conf.xml.main
--- a/tool_conf.xml.main Thu Mar 04 16:16:42 2010 -0500
+++ b/tool_conf.xml.main Thu Mar 04 18:33:11 2010 -0500
@@ -119,6 +119,7 @@
<tool file="plotting/histogram2.xml" />
<tool file="plotting/scatterplot.xml" />
<tool file="plotting/xy_plot.xml" />
+ <tool file="plotting/boxplot.xml" />
<tool file="visualization/GMAJ.xml" />
<tool file="visualization/build_ucsc_custom_track.xml" />
</section>
12 years, 5 months
[hg] galaxy 3484: Better handling of workflow step annotations.
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/d1900a25eb45
changeset: 3484:d1900a25eb45
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Thu Mar 04 16:16:42 2010 -0500
description:
Better handling of workflow step annotations.
diffstat:
static/scripts/galaxy.workflow_editor.canvas.js | 8 +++++++-
templates/workflow/editor.mako | 7 +++----
2 files changed, 10 insertions(+), 5 deletions(-)
diffs (43 lines):
diff -r c349f517ffb8 -r d1900a25eb45 static/scripts/galaxy.workflow_editor.canvas.js
--- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Mar 04 13:55:21 2010 -0500
+++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Mar 04 16:16:42 2010 -0500
@@ -308,6 +308,7 @@
this.tool_state = data.tool_state;
this.form_html = data.form_html;
this.tool_errors = data.tool_errors;
+ this.annotation = data['annotation'];
if ( this.tool_errors ) {
el.addClass( "tool-node-error" );
} else {
@@ -447,7 +448,12 @@
// If active form has changed, save it
if (this.active_form_has_changes) {
this.has_changes = true;
- $("#right-content").find("form").submit();
+ // Get annotation and add to form.
+ var annotation = $("textarea[name=annotation]").val();
+ var tool_form = $("#right-content").find("form");
+ tool_form.append( "<input type='hidden' name='annotation' value='"+annotation+"' />" );
+ // Submit form.
+ tool_form.submit();
this.active_form_has_changes = false;
}
},
diff -r c349f517ffb8 -r d1900a25eb45 templates/workflow/editor.mako
--- a/templates/workflow/editor.mako Thu Mar 04 13:55:21 2010 -0500
+++ b/templates/workflow/editor.mako Thu Mar 04 16:16:42 2010 -0500
@@ -367,11 +367,10 @@
</div> \
</div> \
</div>");
- // When metadata is changed, update node and set workflow changes flag.
+ // See above comment: this is necessary to handle autosaving.
var textarea = $(metadata_div).find("textarea");
- textarea.change( function () {
- node.annotation = $(this).val();
- workflow.has_changes = true;
+ textarea.focus( function () {
+ workflow.active_form_has_changes = true;
});
$("#right-content").find(".toolForm").after( metadata_div );
}
12 years, 5 months
[hg] galaxy 3483: Fix for running workflows with steps that don'...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/c349f517ffb8
changeset: 3483:c349f517ffb8
user: James Taylor <james(a)jamestaylor.org>
date: Thu Mar 04 13:55:21 2010 -0500
description:
Fix for running workflows with steps that don't have jobs
diffstat:
lib/galaxy/model/mapping.py | 2 +-
lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py | 62 ++++++++++
2 files changed, 63 insertions(+), 1 deletions(-)
diffs (79 lines):
diff -r 66fda01625f3 -r c349f517ffb8 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Thu Mar 04 13:49:09 2010 -0500
+++ b/lib/galaxy/model/mapping.py Thu Mar 04 13:55:21 2010 -0500
@@ -571,7 +571,7 @@
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False )
+ Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True )
)
StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata,
diff -r 66fda01625f3 -r c349f517ffb8 lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py Thu Mar 04 13:55:21 2010 -0500
@@ -0,0 +1,62 @@
+"""
+Drop and readd workflow invocation tables, allowing null jobs
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import logging
+logging.basicConfig( level=logging.DEBUG )
+log = logging.getLogger( __name__ )
+
+import datetime
+now = datetime.datetime.utcnow
+
+def upgrade():
+ print __doc__
+
+ metadata = MetaData( migrate_engine )
+ db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+ metadata.reflect()
+
+ # 1) Drop
+
+ for table_name in [ "workflow_invocation_step", "workflow_invocation" ]:
+ try:
+ t = Table( table_name, metadata, autoload=True ).drop()
+ except:
+ log.exception( "Failed to drop table '%s', ignoring (might result in wrong schema)" % table_name )
+
+ # 2) Readd
+
+ metadata = MetaData( migrate_engine )
+ db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+ metadata.reflect()
+
+ WorkflowInvocation_table = Table( "workflow_invocation", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
+ )
+
+ WorkflowInvocationStep_table = Table( "workflow_invocation_step", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "create_time", DateTime, default=now ),
+ Column( "update_time", DateTime, default=now, onupdate=now ),
+ Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ),
+ Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
+ Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True ),
+ )
+
+ for table in [ WorkflowInvocation_table, WorkflowInvocationStep_table ]:
+ try:
+ table.create()
+ except:
+ log.exception( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
+
+def downgrade():
+ # No downgrade
+ pass
\ No newline at end of file
12 years, 5 months
[hg] galaxy 3482: Refactor page, history, workflow display code ...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/66fda01625f3
changeset: 3482:66fda01625f3
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Thu Mar 04 13:49:09 2010 -0500
description:
Refactor page, history, workflow display code to use same security code as get() methods.
diffstat:
lib/galaxy/web/base/controller.py | 3 +--
lib/galaxy/web/controllers/history.py | 10 +++-------
lib/galaxy/web/controllers/page.py | 10 +++-------
lib/galaxy/web/controllers/workflow.py | 12 +++---------
4 files changed, 10 insertions(+), 25 deletions(-)
diffs (79 lines):
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/base/controller.py Thu Mar 04 13:49:09 2010 -0500
@@ -110,8 +110,7 @@
if check_accessible:
# Verify accessible.
if ( item.user != user ) and ( not item.importable ) and ( user not in item.users_shared_with_dot_users ):
- raise "hi"
- error( "%s is not accessible by current user" % item.__class__.__name__ )
+ error( "%s is not accessible to current user" % item.__class__.__name__ )
return item
class UsesHistoryDatasetAssociation:
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/controllers/history.py Thu Mar 04 13:49:09 2010 -0500
@@ -589,15 +589,11 @@
# Get history.
session = trans.sa_session
user = session.query( model.User ).filter_by( username=username ).first()
- history_query_base = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False )
- if user is not None:
- # User can view history if it's importable or if it's shared with him/her.
- history = history_query_base.filter( or_( model.History.importable==True, model.History.users_shared_with.any( model.HistoryUserShareAssociation.user==trans.get_user() ) ) ).first()
- else:
- # User not logged in, so only way to view history is if it's importable.
- history = history_query_base.filter_by( importable=True ).first()
+ history = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False ).first()
if history is None:
raise web.httpexceptions.HTTPNotFound()
+ # Security check raises error if user cannot access history.
+ self.security_check( trans.get_user(), history, False, True)
# Get datasets.
datasets = self.get_history_datasets( trans, history )
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/controllers/page.py
--- a/lib/galaxy/web/controllers/page.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/controllers/page.py Thu Mar 04 13:49:09 2010 -0500
@@ -555,15 +555,11 @@
# Get page.
session = trans.sa_session
user = session.query( model.User ).filter_by( username=username ).first()
- page_query_base = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False )
- if user is not None:
- # User can view page if it's importable or if it's shared with him/her.
- page = page_query_base.filter( or_( model.Page.user==trans.get_user(), model.Page.importable==True, model.Page.users_shared_with.any( model.PageUserShareAssociation.user==trans.get_user() ) ) ).first()
- else:
- # User not logged in, so only way to view page is if it's importable.
- page = page_query_base.filter_by( importable=True ).first()
+ page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False ).first()
if page is None:
raise web.httpexceptions.HTTPNotFound()
+ # Security check raises error if user cannot access page.
+ self.security_check( trans.get_user(), page, False, True)
# Process page content.
processor = _PageContentProcessor( trans, 'utf-8', 'text/html', self._get_embed_html )
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:49:09 2010 -0500
@@ -169,15 +169,9 @@
# Get workflow.
session = trans.sa_session
user = session.query( model.User ).filter_by( username=username ).first()
- workflow_query_base = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False )
- if user is not None:
- # User can view workflow if it's importable or if it's shared with him/her.
- stored_workflow = workflow_query_base.filter( or_( model.StoredWorkflow.importable==True, model.StoredWorkflow.users_shared_with.any( model.StoredWorkflowUserShareAssociation.user==trans.get_user() ) ) ).first()
- else:
- # User not logged in, so only way to view workflow is if it's importable.
- stored_workflow = workflow_query_base.filter_by( importable=True ).first()
- if stored_workflow is None:
- raise web.httpexceptions.HTTPNotFound()
+ stored_workflow = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False ).first()
+ # Security check raises error if user cannot access workflow.
+ self.security_check( trans.get_user(), stored_workflow, False, True)
# Get data for workflow's steps.
self.get_stored_workflow_steps( trans, stored_workflow )
12 years, 5 months
[hg] galaxy 3481: Update default tool action execute() method to...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/2e025a8d71d0
changeset: 3481:2e025a8d71d0
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Thu Mar 04 13:19:14 2010 -0500
description:
Update default tool action execute() method to only wrap incoming values once per call. It was previously wrapping once per output data label generated and for each change_format tag.
diffstat:
lib/galaxy/tools/actions/__init__.py | 20 ++++++++++++--------
1 files changed, 12 insertions(+), 8 deletions(-)
diffs (44 lines):
diff -r 39aac31a841b -r 2e025a8d71d0 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py Thu Mar 04 13:10:09 2010 -0500
+++ b/lib/galaxy/tools/actions/__init__.py Thu Mar 04 13:19:14 2010 -0500
@@ -182,6 +182,7 @@
on_text = ""
# Add the dbkey to the incoming parameters
incoming[ "dbkey" ] = input_dbkey
+ params = None #wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed
# Keep track of parent / child relationships, we'll create all the
# datasets first, then create the associations
parent_to_child_pairs = []
@@ -213,8 +214,9 @@
ext = input_ext
#process change_format tags
if output.change_format:
- params = make_dict_copy( incoming ) #FIXME: The wrapping of inputs should only be done once per call to execute; currently happens here and possibly when generating output dataset name
- wrap_values( tool.inputs, params )
+ if params is None:
+ params = make_dict_copy( incoming )
+ wrap_values( tool.inputs, params )
for change_elem in output.change_format:
for when_elem in change_elem.findall( 'when' ):
check = when_elem.get( 'input', None )
@@ -258,12 +260,14 @@
data.blurb = "queued"
# Set output label
if output.label:
- params = make_dict_copy( incoming )
- # wrapping the params allows the tool config to contain things like
- # <outputs>
- # <data format="input" name="output" label="Blat on ${<input_param>.name}" />
- # </outputs>
- wrap_values( tool.inputs, params )
+ if params is None:
+ params = make_dict_copy( incoming )
+ # wrapping the params allows the tool config to contain things like
+ # <outputs>
+ # <data format="input" name="output" label="Blat on ${<input_param>.name}" />
+ # </outputs>
+ wrap_values( tool.inputs, params )
+ #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined
params['tool'] = tool
params['on_string'] = on_text
data.name = fill_template( output.label, context=params )
12 years, 5 months
[hg] galaxy 3479: Converted space to tab on mm5 declaration line...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/723de1e2dbe7
changeset: 3479:723de1e2dbe7
user: gua110
date: Thu Mar 04 13:02:56 2010 -0500
description:
Converted space to tab on mm5 declaration line in manual_builds.txt.
diffstat:
tool-data/shared/ucsc/manual_builds.txt | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (10 lines):
diff -r 11dcd9d18663 -r 723de1e2dbe7 tool-data/shared/ucsc/manual_builds.txt
--- a/tool-data/shared/ucsc/manual_builds.txt Thu Mar 04 11:48:10 2010 -0500
+++ b/tool-data/shared/ucsc/manual_builds.txt Thu Mar 04 13:02:56 2010 -0500
@@ -668,4 +668,4 @@
arabidopsis Arabidopsis thaliana TAIR9
arabidopsis_tair8 Arabidopsis thaliana TAIR8
araTha1 Arabidopsis thaliana TAIR7
-mm5 Mouse May 2004 (mm5)
\ No newline at end of file
+mm5 Mouse May 2004 (mm5)
12 years, 5 months
[hg] galaxy 3480: Provide workflow annotation field when creatin...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/39aac31a841b
changeset: 3480:39aac31a841b
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Thu Mar 04 13:10:09 2010 -0500
description:
Provide workflow annotation field when creating a workflow.
diffstat:
lib/galaxy/web/controllers/workflow.py | 10 +++++++---
1 files changed, 7 insertions(+), 3 deletions(-)
diffs (34 lines):
diff -r 723de1e2dbe7 -r 39aac31a841b lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:02:56 2010 -0500
+++ b/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:10:09 2010 -0500
@@ -441,7 +441,7 @@
@web.expose
@web.require_login( "create workflows" )
- def create( self, trans, workflow_name=None ):
+ def create( self, trans, workflow_name=None, workflow_annotation="" ):
"""
Create a new stored workflow with name `workflow_name`.
"""
@@ -456,6 +456,9 @@
workflow.name = workflow_name
workflow.stored_workflow = stored_workflow
stored_workflow.latest_workflow = workflow
+ # Add annotation.
+ workflow_annotation = sanitize_html( workflow_annotation, 'utf-8', 'text/html' )
+ self.add_item_annotation( trans, stored_workflow, workflow_annotation )
# Persist
session = trans.sa_session
session.add( stored_workflow )
@@ -464,8 +467,9 @@
trans.set_message( "Workflow '%s' created" % stored_workflow.name )
return self.list( trans )
else:
- return form( url_for(), "Create new workflow", submit_text="Create" ) \
- .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" )
+ return form( url_for(), "Create New Workflow", submit_text="Create" ) \
+ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \
+ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." )
@web.expose
def delete( self, trans, id=None ):
12 years, 5 months
[hg] galaxy 3477: Provide minimum width for columns in published...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/d9afcaa386f6
changeset: 3477:d9afcaa386f6
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Wed Mar 03 17:05:56 2010 -0500
description:
Provide minimum width for columns in published items grids so that tags/annotations do not squish other columns too much.
diffstat:
templates/history/list_published.mako | 9 +++++++++
templates/page/list_published.mako | 13 +++++++++++++
templates/workflow/list_published.mako | 9 +++++++++
3 files changed, 31 insertions(+), 0 deletions(-)
diffs (61 lines):
diff -r adda1b9e31fa -r d9afcaa386f6 templates/history/list_published.mako
--- a/templates/history/list_published.mako Wed Mar 03 17:00:50 2010 -0500
+++ b/templates/history/list_published.mako Wed Mar 03 17:05:56 2010 -0500
@@ -13,6 +13,15 @@
Galaxy :: Published Histories
</%def>
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .grid td {
+ min-width: 100px;
+ }
+ </style>
+</%def>
+
<%def name="center_panel()">
## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe>
diff -r adda1b9e31fa -r d9afcaa386f6 templates/page/list_published.mako
--- a/templates/page/list_published.mako Wed Mar 03 17:00:50 2010 -0500
+++ b/templates/page/list_published.mako Wed Mar 03 17:05:56 2010 -0500
@@ -9,6 +9,19 @@
%>
</%def>
+<%def name="title()">
+ Galaxy :: Published Pages
+</%def>
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .grid td {
+ min-width: 100px;
+ }
+ </style>
+</%def>
+
<%def name="center_panel()">
## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe>
diff -r adda1b9e31fa -r d9afcaa386f6 templates/workflow/list_published.mako
--- a/templates/workflow/list_published.mako Wed Mar 03 17:00:50 2010 -0500
+++ b/templates/workflow/list_published.mako Wed Mar 03 17:05:56 2010 -0500
@@ -13,6 +13,15 @@
Galaxy :: Published Workflows
</%def>
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .grid td {
+ min-width: 100px;
+ }
+ </style>
+</%def>
+
<%def name="center_panel()">
## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe>
12 years, 5 months