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Merge pull request #1462 from jmchilton/release_16.01_merge_4

Browse Source 
[16.01] Full merge of 15.10 into 16.01.
This commit is contained in:
Martin Cech
2016-01-11 12:22:13 -05:00
parent cea1f9e617 3dda415fb9
commit 24cb97cdbf
34 changed files with 182 additions and 878 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/galaxy/scripts/mvc/collection/list-collection-creator.js
+1 -1
View File
@@ -1008,7 +1008,7 @@ var collectionCreatorModal = function _collectionCreatorModal( elements, options
title : options.title || _l( 'Create a collection' ),
body : creator.$el,
width : '80%',
height : 'min-content',
height : '100%',
closing_events: true
});
creator.render();
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+5 -1
View File
@@ -550,7 +550,11 @@ var FolderToolbarView = Backbone.View.extend({
},
error: function(model, response){
if (typeof response.responseJSON !== "undefined"){
mod_toastr.error(response.responseJSON.err_msg);
if (response.responseJSON.err_code === 404001){
mod_toastr.warning(response.responseJSON.err_msg);
} else{
mod_toastr.error(response.responseJSON.err_msg);
}
} else {
mod_toastr.error('An error ocurred.');
}
lib/galaxy/config.py
+4 -2
View File
@@ -258,7 +258,9 @@ class Configuration( object ):
self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
self.sanitize_whitelist_file = resolve_path( kwargs.get( 'sanitize_whitelist_file', "config/sanitize_whitelist.txt" ), self.root )
self.reload_sanitize_whitelist()
self.sanitize_whitelist = []
if kwargs.get('sanitize_whitelist_file', None) is not None:
self.reload_sanitize_whitelist()
self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
self.trust_ipython_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) )
self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
@@ -480,7 +482,7 @@ class Configuration( object ):
if not line.startswith("#"):
self.sanitize_whitelist.append(line.strip())
except IOError:
log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.")
log.warning("Sanitize log file %s does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
def __parse_config_file_options( self, kwargs ):
"""
lib/galaxy/tools/__init__.py
+4 -2
View File
@@ -1673,7 +1673,7 @@ class Tool( object, Dictifiable ):
if isinstance( input, Conditional ):
cond_messages = {}
if not input.is_job_resource_conditional:
cond_messages = { input.test_param.name: "No value found for '%s%s', using default" % ( prefix, input.label ) }
cond_messages = { input.test_param.name: "No value found for '%s%s', using default" % ( prefix, input.test_param.label ) }
messages[ input.name ] = cond_messages
test_value = input.test_param.get_initial_value( trans, context )
current_case = input.get_current_case( test_value, trans )
@@ -1687,6 +1687,7 @@ class Tool( object, Dictifiable ):
messages[ input.name ].append( rep_dict )
self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, allow_workflow_parameters=allow_workflow_parameters )
elif isinstance( input, Section ):
messages[ input.name ] = {}
self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix, allow_workflow_parameters=allow_workflow_parameters )
else:
messages[ input.name ] = "No value found for '%s%s', using default" % ( prefix, input.label )
@@ -1716,7 +1717,8 @@ class Tool( object, Dictifiable ):
current = group_values["__current_case__"]
self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, allow_workflow_parameters=allow_workflow_parameters )
elif isinstance( input, Section ):
self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages, context, prefix, allow_workflow_parameters=allow_workflow_parameters )
messages[ input.name ] = {}
self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix, allow_workflow_parameters=allow_workflow_parameters )
else:
# Regular tool parameter, no recursion needed
try:
lib/galaxy/tools/parameters/basic.py
+3 -2
View File
@@ -2212,14 +2212,15 @@ class DataToolParameter( BaseDataToolParameter ):
return d
# add datasets
visible_hda = other_values.get( self.name )
for hda in history.active_datasets_children_and_roles:
match = dataset_matcher.hda_match( hda )
match = dataset_matcher.hda_match( hda, ensure_visible=visible_hda != hda )
if match:
m = match.hda
d['options']['hda'].append({
'id' : trans.security.encode_id( m.id ),
'hid' : m.hid,
'name' : m.name,
'name' : m.name if m.visible else '(hidden) %s' % m.name,
'src' : 'hda'
})
lib/galaxy/tools/toolbox/base.py
+1
View File
@@ -17,6 +17,7 @@ from galaxy.util import string_as_bool
from galaxy.util.bunch import Bunch
from .parser import get_toolbox_parser, ensure_tool_conf_item
from .panel import ToolPanelElements
from .panel import ToolSectionLabel
from .panel import ToolSection
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+2 -2
View File
@@ -413,7 +413,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
:param encoded_folder_id: the encoded id of the folder to import dataset(s) to
:type encoded_folder_id: an encoded id string
:param source: source the datasets should be loaded form
:param source: source the datasets should be loaded from
:type source: str
:param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy
while linking is set to True all symlinks will be resolved _once_
@@ -434,7 +434,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
kwd[ 'to_posix_lines' ] = 'True'
kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' )
kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
kwd['link_data_only'] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
encoded_folder_id = kwd.get( 'encoded_folder_id', None )
if encoded_folder_id is not None:
folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id )
lib/galaxy/webapps/galaxy/api/remote_files.py
+4
View File
@@ -42,6 +42,8 @@ class RemoteFilesAPIController( BaseAPIController ):
if user_base_dir is None:
raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' )
full_import_dir = os.path.join( user_base_dir, user_login )
if not os.path.exists(full_import_dir):
raise exceptions.ObjectNotFound('You do not have any files in your user directory. Use FTP to upload there.')
if full_import_dir is not None:
if format == 'jstree':
disable = kwd.get( 'disable', 'folders')
@@ -51,6 +53,8 @@ class RemoteFilesAPIController( BaseAPIController ):
except Exception, exception:
log.debug( str( exception ) )
raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) )
if not response:
raise exceptions.ObjectNotFound('You do not have any files in your user directory. Use FTP to upload there.')
elif format == 'ajax':
raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' )
else:
lib/galaxy/workflow/extract.py
+14 -8
View File
@@ -14,7 +14,8 @@ from galaxy.tools.parameters.basic import (
from galaxy.tools.parser import ToolOutputCollectionPart
from galaxy.tools.parameters.grouping import (
Conditional,
Repeat
Repeat,
Section
)
from .steps import (
attach_ordered_steps,
@@ -341,10 +342,11 @@ def __cleanup_param_values( inputs, values ):
if k.startswith( key ):
del root_values[k]
elif isinstance( input, Repeat ):
group_values = values[key]
for i, rep_values in enumerate( group_values ):
rep_index = rep_values['__index__']
cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
if key in values:
group_values = values[key]
for i, rep_values in enumerate( group_values ):
rep_index = rep_values['__index__']
cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
elif isinstance( input, Conditional ):
# Scrub dynamic resource related parameters from workflows,
# they cause problems and the workflow probably should include
@@ -353,9 +355,13 @@ def __cleanup_param_values( inputs, values ):
if input.name in values:
del values[input.name]
return
group_values = values[input.name]
current_case = group_values['__current_case__']
cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
if input.name in values:
group_values = values[input.name]
current_case = group_values['__current_case__']
cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
elif isinstance( input, Section ):
if input.name in values:
cleanup( "%s%s|" % ( prefix, key ), input.inputs, values[input.name] )
cleanup( "", inputs, values )
return associations
static/maps/mvc/collection/list-collection-creator.js.map
+1 -1
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static/maps/mvc/library/library-foldertoolbar-view.js.map
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/bundled/analysis.bundled.js
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/bundled/analysis.bundled.js.map
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/bundled/libs.bundled.js
+17 -17
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File diff suppressed because one or more lines are too long
static/scripts/bundled/libs.bundled.js.map
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/mvc/collection/list-collection-creator.js
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/mvc/library/library-foldertoolbar-view.js
+2 -2
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File diff suppressed because one or more lines are too long
templates/webapps/reports/jobs_errors_per_tool.mako
+11 -77
View File
@@ -25,13 +25,7 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages( sort_id, order,
page_specs,
'jobs',
'errors_per_tool',
spark_time=time_period )
}
${get_pages(sort_id, order, page_specs, 'jobs', 'errors_per_tool', spark_time=time_period)}
</td>
<td>
<h4 align="center">Jobs In Error Per Tool</h4>
@@ -41,30 +35,12 @@ ${get_css()}
Click error number to view job details.
</p>
Graph goes from present to past for
${
make_spark_settings(
"jobs",
"errors_per_tool",
spark_limit,
sort_id,
order,
time_period,
page=page,
offset=offset,
entries=entries)
}
Graph goes from present to past for
${make_spark_settings("jobs", "errors_per_tool", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"errors_per_tool",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "errors_per_tool", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -78,59 +54,23 @@ ${get_css()}
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'tool_id',
'jobs',
'errors_per_tool',
'Tool ID',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow tool_id'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'errors_per_tool',
'User Jobs in Error',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'errors_per_tool',
'User and Monitor Jobs in Error',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -158,18 +98,12 @@ ${get_css()}
</a>
</td>
%try:
${
make_sparkline(
key,
trends[key],
"bar",
"/ " + time_period[:-1])
}
${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
%except KeyError:
%endtry
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
@@ -178,4 +112,4 @@ ${get_css()}
</table>
</div>
</div>
<!--End jobs_errors_per_tool.mako-->
<!--End jobs_errors_per_tool.mako-->
templates/webapps/reports/jobs_per_month_all.mako
+8 -61
View File
@@ -22,14 +22,7 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'jobs',
'per_month_all')
}
${get_pages(sort_id, order, page_specs, 'jobs', 'per_month_all')}
</td>
<td>
<h4 align="center">Jobs Per Month</h4>
@@ -39,68 +32,28 @@ ${get_css()}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"per_month_all",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "per_month_all", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
<table align="center" width="60%" class="colored">
%if len( jobs ) == 0:
<tr><td colspan="4">There are no jobs.</td></tr>
%else:
<tr class="header">
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'date',
'jobs',
'per_month_all',
'Month',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'date', 'jobs', 'per_month_all', 'Month', page=page, offset=offset, entries=entries)}
<span class='dir_arrow date'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_month_all',
'User Jobs',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_all', 'User Jobs', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_month_all',
'User and Monitor Jobs',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_all', 'User and Monitor Jobs', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
@@ -129,16 +82,10 @@ ${get_css()}
</a>
</td>
<td>${job[1]}</td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ day")
}
${make_sparkline(key, trends[key], "bar", "/ day")}
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/jobs_per_month_in_error.mako
+8 -61
View File
@@ -22,28 +22,14 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'jobs',
'per_month_in_error')
}
${get_pages(sort_id, order, page_specs, 'jobs', 'per_month_in_error')}
</td>
<td>
<h4 align="center">Jobs In Error Per Month</h4>
<h5 align="center">Click Month to view details.</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"per_month_in_error",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "per_month_in_error", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -57,56 +43,23 @@ ${get_css()}
%else:
<tr class="header">
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'date',
'jobs',
'per_month_in_error',
'Month',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'date', 'jobs', 'per_month_in_error', 'Month', page=page, offset=offset, entries=entries)}
<span class='dir_arrow date'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_month_in_error',
'User Jobs',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url( sort_id, order, 'total_jobs', 'jobs', 'per_month_in_error', 'User Jobs', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_month_in_error',
'User and Monitor Jobs',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_in_error', 'User and Monitor Jobs', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -125,16 +78,10 @@ ${get_css()}
<td><a href="${h.url_for( controller='jobs', action='specified_month_in_error', specified_date=job[0]+'-01', sort_id='default', order='default' )}">${job[2]}&nbsp;${job[3]}</a></td>
<td>${job[1]}</td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ day")
}
${make_sparkline(key, trends[key], "bar", "/ day")}
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/jobs_per_tool.mako
+11 -79
View File
@@ -25,44 +25,18 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'jobs',
'per_tool',
spark_time=time_period)
}
${get_pages(sort_id, order, page_specs, 'jobs', 'per_tool', spark_time=time_period)}
</td>
<td>
<h4 align="center">Jobs Per Tool</h4>
<h5 align="center">
Click Tool ID to view details.
Graph goes from present to past
${
make_spark_settings(
"jobs",
"per_tool",
spark_limit,
sort_id,
order,
time_period,
page=page,
offset=offset,
entries=entries)
}
Click Tool ID to view details.
Graph goes from present to past
${make_spark_settings("jobs", "per_tool", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"per_tool",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "per_tool", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -72,59 +46,23 @@ ${get_css()}
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'tool_id',
'jobs',
'per_tool',
'Tool ID',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow tool_id'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_tool',
'User Jobs',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_tool',
'User and Monitor Jobs',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -148,18 +86,12 @@ ${get_css()}
</td>
<td>${job[1]}</td>
%try:
${
make_sparkline(
key,
trends[key],
"bar",
"/ " + time_period[:-1])
}
${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
%except KeyError:
%endtry
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/jobs_per_user.mako
+8 -65
View File
@@ -26,44 +26,18 @@ ${q1time}, ${q2time}, ${ttime}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'jobs',
'per_user',
spark_time=time_period)
}
${get_pages(sort_id, order, page_specs, 'jobs', 'per_user', spark_time=time_period)}
</td>
<td>
<h4 align="center">Jobs Per User</h4>
<h5 align="center">
Click User to view details.
Graph goes from present to past
${
make_spark_settings(
"jobs",
"per_user",
spark_limit,
sort_id,
order,
time_period,
page=page,
offset=offset,
entries=entries)
}
${make_spark_settings("jobs", "per_user", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"per_user",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "per_user", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -73,40 +47,16 @@ ${q1time}, ${q2time}, ${ttime}
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'user_email',
'jobs',
'per_user',
'User',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow user_email'>${arrow}</span>
</td>
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'per_user',
'Total Jobs',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -130,18 +80,12 @@ ${q1time}, ${q2time}, ${ttime}
</td>
<td>${job[1]}</td>
%try:
${
make_sparkline(
key,
trends[key],
"bar",
"/ " + time_period[:-1])
}
${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
%except KeyError:
%endtry
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
@@ -151,4 +95,3 @@ ${q1time}, ${q2time}, ${ttime}
</div>
</div>
<!--End jobs_per_user.mako-->
templates/webapps/reports/jobs_specified_month_all.mako
+8 -61
View File
@@ -22,14 +22,7 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'jobs',
'specified_month_all')
}
${get_pages(sort_id, order, page_specs, 'jobs', 'specified_month_all')}
</td>
<td>
<h4 align="center">
@@ -43,14 +36,7 @@ ${get_css()}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"specified_month_all",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "specified_month_all", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -65,56 +51,23 @@ ${get_css()}
<tr class="header">
<td class="quarter_width">Day</td>
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'date',
'jobs',
'specified_month_all',
'Date',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'date', 'jobs', 'specified_month_all', 'Date', page=page, offset=offset, entries=entries)}
<span class='dir_arrow date'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'specified_month_all',
'User Jobs',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_all', 'User Jobs', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'specified_month_all',
'User and Monitor Jobs',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_all', 'User and Monitor Jobs', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -138,16 +91,10 @@ ${get_css()}
${job[2]}
</a>
</td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ hour")
}
${make_sparkline(key, trends[key], "bar", "/ hour")}
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/jobs_specified_month_in_error.mako
+8 -61
View File
@@ -21,14 +21,7 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'jobs',
'specified_month_in_error')
}
${get_pages(sort_id, order, page_specs, 'jobs', 'specified_month_in_error')}
</td>
<td>
<h4 align="center">
@@ -39,14 +32,7 @@ ${get_css()}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"jobs",
"specified_month_in_error",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("jobs", "specified_month_in_error", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -62,56 +48,23 @@ ${get_css()}
<tr class="header">
<td class="quarter_width">Day</td>
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'date',
'jobs',
'specified_month_in_error',
'Date',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'date', 'jobs', 'specified_month_in_error', 'Date', page=page, offset=offset, entries=entries)}
<span class='dir_arrow date'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'specified_month_in_error',
'User Jobs in Error',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_in_error', 'User Jobs in Error', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'specified_month_in_error',
'User and Monitor Jobs in Error',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_in_error', 'User and Monitor Jobs in Error', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -137,16 +90,10 @@ ${get_css()}
${job[2]}
</a>
</td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ hour")
}
${make_sparkline(key, trends[key], "bar", "/ hour")}
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/jobs_tool_per_month.mako
+5 -39
View File
@@ -7,7 +7,7 @@
${render_msg( message, 'done' )}
%endif
${get_css()}
${get_css()}
<!--jobs_tool_per_month.mako-->
@@ -28,44 +28,17 @@ ${get_css()}
%else:
<tr class="header">
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'date',
'jobs',
'tool_per_month',
'Month',
tool_id=tool_id)
}
${get_sort_url(sort_id, order, 'date', 'jobs', 'tool_per_month', 'Month', tool_id=tool_id)}
<span class='dir_arrow date'>${arrow}</span>
</td>
%if is_user_jobs_only:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'tool_per_month',
'User Jobs',
tool_id=tool_id)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'tool_per_month', 'User Jobs', tool_id=tool_id)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%else:
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'tool_per_month',
'User and Monitor Jobs',
tool_id=tool_id)
}
${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'tool_per_month', 'User and Monitor Jobs', tool_id=tool_id)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
%endif
@@ -81,13 +54,7 @@ ${get_css()}
%endif
<td>${job[2]}&nbsp;${job[3]}</td>
<td><a href="${h.url_for( controller='jobs', action='specified_date_handler', operation='tool_for_month', tool_id=tool_id, specified_date=job[0] )}">${job[1]}</a></td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ day")
}
${make_sparkline(key, trends[key], "bar", "/ day")}
<td id="${key}"></td>
</tr>
<% ctr += 1 %>
@@ -97,4 +64,3 @@ ${get_css()}
</div>
</div>
<!--End jobs_tool_per_month.mako-->
templates/webapps/reports/jobs_user_per_month.mako
+6 -30
View File
@@ -3,8 +3,8 @@
<%namespace file="/spark_base.mako" import="make_sparkline" />
<%namespace file="/sorting_base.mako" import="get_sort_url, get_css" />
<%
from galaxy import util
<%
from galaxy import util
%>
%if message:
@@ -16,7 +16,7 @@ ${get_css()}
<%
_email = util.restore_text( email )
%>
<!--jobs_user_per_month.mako-->
<div class="report">
<div class="reportBody">
@@ -35,29 +35,11 @@ ${get_css()}
%else:
<tr class="header">
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'date',
'jobs',
'user_per_month',
'Month',
email=email)
}
${get_sort_url(sort_id, order, 'date', 'jobs', 'user_per_month', 'Month', email=email)}
<span class='dir_arrow date'>${arrow}</span>
</td>
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_jobs',
'jobs',
'user_per_month',
'Total Jobs',
email=email)
}
${get_sort_url( sort_id, order, 'total_jobs', 'jobs', 'user_per_month', 'Total Jobs', email=email)}
<span class='dir_arrow total_jobs'>${arrow}</span>
</td>
<td></td>
@@ -76,13 +58,7 @@ ${get_css()}
${job[1]}
</a>
</td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ day")
}
${make_sparkline(key, trends[key], "bar", "/ day")}
<td id="${key}"></td>
</tr>
<% ctr += 1 %>
templates/webapps/reports/registered_users_per_month.mako
+2 -18
View File
@@ -21,27 +21,11 @@ ${get_css()}
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'date',
'users',
'registered_users_per_month',
'Month')
}
${get_sort_url(sort_id, order, 'date', 'users', 'registered_users_per_month', 'Month')}
<span class='dir_arrow date'>${arrow}</span>
</td>
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'num_users',
'users',
'registered_users_per_month',
'Number of Registrations')
}
${get_sort_url(sort_id, order, 'num_users', 'users', 'registered_users_per_month', 'Number of Registrations')}
<span class='dir_arrow num_users'>${arrow}</span>
</td>
</tr>
templates/webapps/reports/requests_user_per_month.mako
+3 -19
View File
@@ -9,7 +9,7 @@
%if message:
${render_msg( message, 'done' )}
%endif
${get_css()}
<div class="report">
@@ -29,27 +29,11 @@ ${get_css()}
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'date',
'users',
'requests_users_per_month',
'Month')
}
${get_sort_url(sort_id, order, 'date', 'users', 'requests_users_per_month', 'Month')}
<span class='dir_arrow date'>${arrow}</span>
</td>
<td class="half_width">Total
${
get_sort_url(
sort_id,
order,
'num_users',
'users',
'requests_users_per_month',
'Month')
}
${get_sort_url(sort_id, order, 'num_users', 'users', 'requests_users_per_month', 'Month')}
<span class='dir_arrow num_users'>${arrow}</span>
</td>
</tr>
templates/webapps/reports/users_last_access_date.mako
+5 -23
View File
@@ -24,9 +24,9 @@ ${get_css()}
${len( users ) }
%else:
0
%endif
&nbsp;users have not logged in to Galaxy for
<input type="textfield"
%endif
&nbsp;users have not logged in to Galaxy for
<input type="textfield"
value="${days_not_logged_in}"
size="3"
name="days_not_logged_in">
@@ -46,29 +46,11 @@ ${get_css()}
%if users:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'zero',
'users',
'last_access_date',
'Email',
days_not_logged_in=days_not_logged_in)
}
${get_sort_url(sort_id, order, 'zero', 'users', 'last_access_date', 'Email', days_not_logged_in=days_not_logged_in)}
<span class='dir_arrow zero'>${arrow}</span>
</td>
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'one',
'users',
'last_access_date',
'Date of last Login',
days_not_logged_in=days_not_logged_in)
}
${get_sort_url(sort_id, order, 'one', 'users', 'last_access_date', 'Date of last Login', days_not_logged_in=days_not_logged_in)}
<span class='dir_arrow one'>${arrow}</span>
</td>
</tr>
templates/webapps/reports/users_user_disk_usage.mako
+4 -20
View File
@@ -15,11 +15,11 @@ ${get_css()}
<table class="colored diskUsageForm">
<tr>
<td>
<form method="post"
<form method="post"
controller="users"
action="user_disk_usage">
<p>
Top <input type="textfield"
Top <input type="textfield"
value="${user_cutoff}"
size="3"
name="user_cutoff">
@@ -36,27 +36,11 @@ ${get_css()}
%if users:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'email',
'users',
'user_disk_usage',
'Email')
}
${get_sort_url(sort_id, order, 'email', 'users', 'user_disk_usage', 'Email')}
<span class='dir_arrow email'>${arrow}</span>
</td>
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'disk_usage',
'users',
'user_disk_usage',
'Disk Usage')
}
${get_sort_url(sort_id, order, 'disk_usage', 'users', 'user_disk_usage', 'Disk Usage')}
<span class='dir_arrow disk_usage'>${arrow}</span>
</td>
</tr>
templates/webapps/reports/workflows_per_month_all.mako
+7 -49
View File
@@ -21,27 +21,13 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'workflows',
'per_month_all')
}
${get_pages(sort_id, order, page_specs, 'workflows', 'per_month_all')}
</td>
<td>
<h3 align="center">Workflows Per Month</h3>
</td>
<td align="right">
${
get_entry_selector(
"workflows",
"per_month_all",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("workflows", "per_month_all", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
@@ -52,33 +38,11 @@ ${get_css()}
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'date',
'workflows',
'per_month_all',
'Month',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'date', 'workflows', 'per_month_all', 'Month', page=page, offset=offset, entries=entries)}
<span class='dir_arrow date'>${arrow}</span>
</td>
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'total_workflows',
'workflows',
'per_month_all',
'Total',
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_month_all', 'Total', page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_workflows'>${arrow}</span>
</td>
<td></td>
@@ -104,22 +68,16 @@ ${get_css()}
%else:
<tr class="tr">
%endif
<td>${month}</td>
<td>${total}</td>
%try:
${
make_sparkline(
key,
trends[key],
"bar",
"/ day")
}
${make_sparkline(key, trends[key], "bar", "/ day")}
%except KeyError:
%endtry
<td id=${key}></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/workflows_per_user.mako
+10 -65
View File
@@ -26,86 +26,37 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'workflows',
'per_user',
spark_time=time_period)
}
${get_pages(sort_id, order, page_specs, 'workflows', 'per_user', spark_time=time_period)}
</td>
<td>
<h3 align="center">Workflows Per User</h3>
<h5 align="center">
Graph goes from present to past
${
make_spark_settings(
"jobs",
"per_user",
spark_limit,
sort_id, order,
time_period,
page=page,
offset=offset,
entries=entries)
}
Graph goes from present to past
${make_spark_settings("jobs", "per_user", spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"workflows",
"per_user",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("workflows", "per_user", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
<table align="center" width="60%" class="colored">
%if len( workflows ) == 0:
<tr><td colspan="2">There are no workflows</td></tr>
%else:
<tr class="header">
<td class="half_width">
${
get_sort_url(
sort_id,
order,
'user_email',
'workflows',
'per_user',
'User',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'user_email', 'workflows', 'per_user', 'User', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow user_email'>${arrow}</span>
</td>
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_workflows',
'workflows',
'per_user',
'Total Workflows',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_user', 'Total Workflows', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_workflows'>${arrow}</span>
</td>
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -136,18 +87,12 @@ ${get_css()}
</td>
<td>${total}</td>
%try:
${
make_sparkline(
key,
trends[key],
"bar",
"/ " + time_period[:-1])
}
${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
%except KeyError:
%endtry
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/workflows_per_workflow.mako
+11 -79
View File
@@ -25,103 +25,41 @@ ${get_css()}
<table id="formHeader">
<tr>
<td>
${
get_pages(
sort_id,
order,
page_specs,
'workflows',
'per_workflow',
spark_time=time_period)
}
${get_pages(sort_id, order, page_specs, 'workflows', 'per_workflow', spark_time=time_period)}
</td>
<td>
<h4 align="center">Runs per Workflow</h4>
<h5 align="center">
Graph goes from present to past
${
make_spark_settings(
'workflows',
'per_workflow',
spark_limit,
sort_id,
order,
time_period,
page=page,
offset=offset,
entries=entries)
}
Graph goes from present to past
${make_spark_settings('workflows', 'per_workflow', spark_limit, sort_id, order, time_period, page=page, offset=offset, entries=entries)}
</h5>
</td>
<td align="right">
${
get_entry_selector(
"workflows",
"per_workflow",
page_specs.entries,
sort_id,
order)
}
${get_entry_selector("workflows", "per_workflow", page_specs.entries, sort_id, order)}
</td>
</tr>
</table>
<table align="center" width="60%" class="colored">
%if len( runs ) == 0:
<tr><td colspan="2">There are no runs.</td></tr>
%else:
<tr class="header">
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'workflow_id',
'workflows',
'per_workflow',
'Workflow ID',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'workflow_id', 'workflows', 'per_workflow', 'Workflow ID', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow workflow_id'>${arrow}</span>
</td>
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'workflow_name',
'workflows',
'per_workflow',
'Workflow Name',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'workflow_name', 'workflows', 'per_workflow', 'Workflow Name', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow workflow_name'>${arrow}</span>
</td>
<td class="quarter_width">
${
get_sort_url(
sort_id,
order,
'total_runs',
'workflows',
'per_workflow',
'Workflow Runs',
spark_time=time_period,
page=page,
offset=offset,
entries=entries)
}
${get_sort_url(sort_id, order, 'total_runs', 'workflows', 'per_workflow', 'Workflow Runs', spark_time=time_period, page=page, offset=offset, entries=entries)}
<span class='dir_arrow total_runs'>${arrow}</span>
</td>
<td></td>
</tr>
<%
<%
ctr = 0
entries = 1
%>
@@ -142,18 +80,12 @@ ${get_css()}
<td>${run[0]}</td>
<td>${run[1]}</td>
%try:
${
make_sparkline(
key,
trends[key],
"bar",
"/ " + time_period[:-1])
}
${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])}
%except KeyError:
%endtry
<td id="${key}"></td>
</tr>
<%
<%
ctr += 1
entries += 1
%>
templates/webapps/reports/workflows_user_per_month.mako
+4 -28
View File
@@ -12,7 +12,7 @@
%endif
${get_css()}
<%
_email = util.restore_text( email )
%>
@@ -33,29 +33,11 @@ ${get_css()}
%else:
<tr class="header">
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'date',
'workflows',
'user_per_month',
'Month',
email=util.sanitize_text( email ))
}
${get_sort_url(sort_id, order, 'date', 'workflows', 'user_per_month', 'Month', email=util.sanitize_text( email ))}
<span class='dir_arrow date'>${arrow}</span>
</td>
<td class="third_width">
${
get_sort_url(
sort_id,
order,
'total_workflows',
'workflows',
'user_per_month',
'Total',
email=util.sanitize_text( email ))
}
${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'user_per_month', 'Total', email=util.sanitize_text( email ))}
<span class='dir_arrow total_workflows'>${arrow}</span>
</td>
<td></td>
@@ -74,13 +56,7 @@ ${get_css()}
%endif
<td>${month}</td>
<td>${total}</td>
${
make_sparkline(
key,
trends[key],
"bar",
"/ day")
}
${make_sparkline(key, trends[key], "bar", "/ day")}
<td id="${key}"></td>
</tr>
<% ctr += 1 %>