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January 2014
- 1 participants
- 280 discussions
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f2ee4ba93917/
Changeset: f2ee4ba93917
User: dannon
Date: 2014-01-31 15:36:37
Summary: Require pytz in web framework where Babel depends on it.
Affected #: 1 file
diff -r b3e8c0ab30c94906be2bb5d76776b22f120c9c8e -r f2ee4ba93917f89e95971f198f96117ed67fda55 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -37,6 +37,7 @@
import mako.lookup
import mako.runtime
+pkg_resources.require( "pytz" ) # Used by Babel.
pkg_resources.require( "Babel" )
from babel.support import Translations
from babel import Locale, UnknownLocaleError
https://bitbucket.org/galaxy/galaxy-central/commits/00810d29c09d/
Changeset: 00810d29c09d
User: dannon
Date: 2014-01-31 15:42:24
Summary: Slight import cleanup in galaxy.web.framework, remove unsafe relative imports.
Affected #: 1 file
diff -r f2ee4ba93917f89e95971f198f96117ed67fda55 -r 00810d29c09d351e6e582d4868907b989e686059 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -5,7 +5,6 @@
import hashlib
import inspect
import os
-import pkg_resources
import random
import socket
import string
@@ -14,40 +13,39 @@
from Cookie import CookieError
from functools import wraps
-pkg_resources.require( "Cheetah" )
+from galaxy import eggs
+
+eggs.require( "Cheetah" )
from Cheetah.Template import Template
-#TODO: Relative imports to be removed
-import base
-import helpers
-
from galaxy import util
+from galaxy.exceptions import error_codes
from galaxy.exceptions import MessageException
-from galaxy.exceptions import error_codes
from galaxy.util import asbool
from galaxy.util import safe_str_cmp
from galaxy.util.backports.importlib import import_module
from galaxy.util.json import from_json_string, to_json_string
from galaxy.util.sanitize_html import sanitize_html
+from galaxy.web.framework import base, helpers
import paste.httpexceptions
-pkg_resources.require( "Mako" )
+eggs.require( "Mako" )
import mako.template
import mako.lookup
import mako.runtime
-pkg_resources.require( "pytz" ) # Used by Babel.
-pkg_resources.require( "Babel" )
+eggs.require( "pytz" ) # Used by Babel.
+eggs.require( "Babel" )
from babel.support import Translations
from babel import Locale, UnknownLocaleError
-pkg_resources.require( "SQLAlchemy >= 0.4" )
+eggs.require( "SQLAlchemy >= 0.4" )
from sqlalchemy import and_
from sqlalchemy.orm.exc import NoResultFound
-pkg_resources.require( "pexpect" )
-pkg_resources.require( "amqplib" )
+eggs.require( "pexpect" )
+eggs.require( "amqplib" )
import logging
log = logging.getLogger( __name__ )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Update guppy egg to 0.1.10. This resolves issues encountered on particular platforms (http://sourceforge.net/p/guppy-pe/bugs/10/)
by commits-noreply＠bitbucket.org 31 Jan '14
by commits-noreply＠bitbucket.org 31 Jan '14
31 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b3e8c0ab30c9/
Changeset: b3e8c0ab30c9
User: dannon
Date: 2014-01-31 15:29:24
Summary: Update guppy egg to 0.1.10. This resolves issues encountered on particular platforms (http://sourceforge.net/p/guppy-pe/bugs/10/)
Affected #: 1 file
diff -r b99981d64dc4d214032a059f7d0302b96bf9e2ad -r b3e8c0ab30c94906be2bb5d76776b22f120c9c8e eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -27,7 +27,7 @@
pysqlite = 2.5.6
python_lzo = 1.08_2.03_static
threadframe = 0.2
-guppy = 0.1.8
+guppy = 0.1.10
SQLAlchemy = 0.7.9
; msgpack_python = 0.2.4
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/324474c3c17f/
Changeset: 324474c3c17f
User: dannon
Date: 2014-01-31 15:26:07
Summary: Add pytz egg.
Affected #: 1 file
diff -r 4368f2b00150fd01840773711600c73abb8590ca -r 324474c3c17f3569bc7d9a715b8195727fb3f3b7 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -53,6 +53,7 @@
pexpect = 2.4
python_openid = 2.2.5
python_daemon = 1.5.5
+pytz = 2013.9
Routes = 1.12.3
sqlalchemy_migrate = 0.7.2
ssh = 1.7.14
https://bitbucket.org/galaxy/galaxy-central/commits/b99981d64dc4/
Changeset: b99981d64dc4
User: dannon
Date: 2014-01-31 15:26:21
Summary: Merge
Affected #: 2 files
diff -r 324474c3c17f3569bc7d9a715b8195727fb3f3b7 -r b99981d64dc4d214032a059f7d0302b96bf9e2ad static/scripts/mvc/grid/grid-template.js
--- a/static/scripts/mvc/grid/grid-template.js
+++ b/static/scripts/mvc/grid/grid-template.js
@@ -548,16 +548,16 @@
if (size < 20) {
size = 20;
}
- // +4 to account for search icon/button.
+ // +4 to account for space after placeholder
size = size + 4;
}
// print input field for column
tmpl += '<span class="search-box">' +
'<input class="search-box-input" id="input-' + column_key + '-filter" name="f-' + column_key + '" type="text" placeholder="' + value + '" size="' + size + '"/>' +
- //'<button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;">' +
- // '<i class="fa fa-plus-circle" style="font-size: 1.2em;"></i>' +
- //'</button>' +
+ '<button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;">' +
+ '<i class="fa fa-plus-circle"></i>' +
+ '</button>' +
'</span>' +
'</form>';
} else {
diff -r 324474c3c17f3569bc7d9a715b8195727fb3f3b7 -r b99981d64dc4d214032a059f7d0302b96bf9e2ad static/scripts/packed/mvc/grid/grid-template.js
--- a/static/scripts/packed/mvc/grid/grid-template.js
+++ b/static/scripts/packed/mvc/grid/grid-template.js
@@ -1,1 +1,1 @@
-define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
+define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-plus-circle"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Grids: Add search button
by commits-noreply＠bitbucket.org 31 Jan '14
by commits-noreply＠bitbucket.org 31 Jan '14
31 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4b6a0e598c54/
Changeset: 4b6a0e598c54
User: guerler
Date: 2014-01-31 15:02:33
Summary: Grids: Add search button
Affected #: 2 files
diff -r 4368f2b00150fd01840773711600c73abb8590ca -r 4b6a0e598c5400e5bc4f731f153e32c46da5d98e static/scripts/mvc/grid/grid-template.js
--- a/static/scripts/mvc/grid/grid-template.js
+++ b/static/scripts/mvc/grid/grid-template.js
@@ -548,16 +548,16 @@
if (size < 20) {
size = 20;
}
- // +4 to account for search icon/button.
+ // +4 to account for space after placeholder
size = size + 4;
}
// print input field for column
tmpl += '<span class="search-box">' +
'<input class="search-box-input" id="input-' + column_key + '-filter" name="f-' + column_key + '" type="text" placeholder="' + value + '" size="' + size + '"/>' +
- //'<button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;">' +
- // '<i class="fa fa-plus-circle" style="font-size: 1.2em;"></i>' +
- //'</button>' +
+ '<button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;">' +
+ '<i class="fa fa-plus-circle"></i>' +
+ '</button>' +
'</span>' +
'</form>';
} else {
diff -r 4368f2b00150fd01840773711600c73abb8590ca -r 4b6a0e598c5400e5bc4f731f153e32c46da5d98e static/scripts/packed/mvc/grid/grid-template.js
--- a/static/scripts/packed/mvc/grid/grid-template.js
+++ b/static/scripts/packed/mvc/grid/grid-template.js
@@ -1,1 +1,1 @@
-define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
+define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-plus-circle"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Grids: Remove url generation from js template
by commits-noreply＠bitbucket.org 31 Jan '14
by commits-noreply＠bitbucket.org 31 Jan '14
31 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4368f2b00150/
Changeset: 4368f2b00150
User: guerler
Date: 2014-01-31 14:24:39
Summary: Grids: Remove url generation from js template
Affected #: 4 files
diff -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 -r 4368f2b00150fd01840773711600c73abb8590ca static/scripts/mvc/grid/grid-template.js
--- a/static/scripts/mvc/grid/grid-template.js
+++ b/static/scripts/mvc/grid/grid-template.js
@@ -230,7 +230,7 @@
},
// template
- footer: function(grid_model, options) {
+ footer: function(options) {
// create template string
var tmpl = '';
@@ -284,7 +284,7 @@
'Page:';
if (min_page > 1) {
- tmpl += '<span class="page-link" id="page-link-1"><a href="' + grid_model.get_url({page : page_index}) + '" page_num="1" onclick="return false;">1</a></span> ...';
+ tmpl += '<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...';
}
// create page urls
@@ -293,19 +293,19 @@
if (page_index == options.cur_page_num) {
tmpl += '<span class="page-link inactive-link" id="page-link-' + page_index + '">' + page_index + '</span>';
} else {
- tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="' + grid_model.get_url({page : page_index}) + '" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>';
+ tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="javascript:void(0);" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>';
}
}
// show last page
if (max_page < num_pages) {
tmpl += '...' +
- '<span class="page-link" id="page-link-' + num_pages + '"><a href="' + grid_model.get_url({page : num_pages}) + '" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>';
+ '<span class="page-link" id="page-link-' + num_pages + '"><a href="javascript:void(0);" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>';
}
tmpl += '</span>';
// Show all link
- tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="' + grid_model.get_url({page : 'all'}) + '" onclick="return false;" page_num="all">Show All</a></span>' +
+ tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span>' +
'</td>' +
'</tr>';
}
diff -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 -r 4368f2b00150fd01840773711600c73abb8590ca static/scripts/mvc/grid/grid-view.js
--- a/static/scripts/mvc/grid/grid-view.js
+++ b/static/scripts/mvc/grid/grid-view.js
@@ -63,7 +63,7 @@
// update div contents
this.$el.find('#grid-table-header').html(Templates.header(options));
this.$el.find('#grid-table-body').html(Templates.body(options));
- this.$el.find('#grid-table-footer').html(Templates.footer(this.grid, options));
+ this.$el.find('#grid-table-footer').html(Templates.footer(options));
// update message
if (options.message) {
diff -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 -r 4368f2b00150fd01840773711600c73abb8590ca static/scripts/packed/mvc/grid/grid-template.js
--- a/static/scripts/packed/mvc/grid/grid-template.js
+++ b/static/scripts/packed/mvc/grid/grid-template.js
@@ -1,1 +1,1 @@
-define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(h,p){var l="";if(p.use_paging&&p.num_pages>1){var n=p.num_page_links;var a=p.cur_page_num;var o=p.num_pages;var k=n/2;var g=a-k;var e=0;if(g==0){g=1;e=k-(a-g)}var d=k+e;var c=a+d;if(c<=o){max_offset=0}else{c=o;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}l+='<tr id="page-links-row">';if(p.show_item_checkboxes){l+="<td></td>"}l+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){l+='<span class="page-link" id="page-link-1"><a href="'+h.get_url({page:m})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var m=g;m<c+1;m++){if(m==p.cur_page_num){l+='<span class="page-link inactive-link" id="page-link-'+m+'">'+m+"</span>"}else{l+='<span class="page-link" id="page-link-'+m+'"><a href="'+h.get_url({page:m})+'" onclick="return false;" page_num="'+m+'">'+m+"</a></span>"}}if(c<o){l+='...<span class="page-link" id="page-link-'+o+'"><a href="'+h.get_url({page:o})+'" onclick="return false;" page_num="'+o+'">'+o+"</a></span>"}l+="</span>";l+='<span class="page-link" id="show-all-link-span"> | <a href="'+h.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(p.show_item_checkboxes){l+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+p.get_class_plural+": ";for(i in p.operations){var b=p.operations[i];if(b.allow_multiple){l+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}l+="</td></tr>"}var f=false;for(i in p.operations){if(p.operations[i].global_operation){f=true;break}}if(f){l+='<tr><td colspan="100">';for(i in p.operations){var b=p.operations[i];if(b.global_operation){l+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}l+="</td></tr>"}if(p.legend){l+='<tr><td colspan="100">'+p.legend+"</td></tr>"}return l},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
+define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
diff -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 -r 4368f2b00150fd01840773711600c73abb8590ca static/scripts/packed/mvc/grid/grid-view.js
--- a/static/scripts/packed/mvc/grid/grid-view.js
+++ b/static/scripts/packed/mvc/grid/grid-view.js
@@ -1,1 +1,1 @@
-jQuery.ajaxSettings.traditional=true;define(["mvc/grid/grid-model","mvc/grid/grid-template","mvc/ui"],function(b,a){return Backbone.View.extend({grid:null,initialize:function(c){this.setElement("#grid-container");if(c.use_panels){$("#center").css({padding:"10px",overflow:"auto"})}this.init_grid(c)},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(f){this.grid=new b(f);var e=this.grid.attributes;this.handle_refresh(e.refresh_frames);var d=this.grid.get("url_base");d=d.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",d);this.$el.html(a.grid(e));this.$el.find("#grid-table-header").html(a.header(e));this.$el.find("#grid-table-body").html(a.body(e));this.$el.find("#grid-table-footer").html(a.footer(this.grid,e));if(e.message){this.$el.find("#grid-message").html(a.message(e));var c=this;if(e.use_hide_message){setTimeout(function(){c.$el.find("#grid-message").html("")},5000)}}this.init_grid_elements();this.init_grid_controls();init_refresh_on_change()},init_grid_controls:function(){var c=this;this.$el.find(".operation-button").each(function(){$(this).off();$(this).click(function(){c.submit_operation(this,operation.confirm);return false})});this.$el.find("input[type=text]").each(function(){$(this).off();$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})});this.$el.find(".sort-link").each(function(){$(this).off();$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});this.$el.find(".text-filter-form").each(function(){$(this).off();$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});this.$el.find(".text-filter-val > a").each(function(){$(this).off();$(this).click(function(){$(this).parent().remove();c.remove_filter_condition($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});this.$el.find(".categorical-filter > a").each(function(){$(this).off();$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});var e=this.$el.find("#input-tags-filter");if(e.length){e.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var d=this.$el.find("#input-name-filter");if(d.length){d.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}this.$el.find(".advanced-search-toggle").each(function(){$(this).off();$(this).click(function(){c.$el.find("#standard-search").slideToggle("fast");c.$el.find("#advanced-search").slideToggle("fast");return false})});this.$el.find("#check_all").off();this.$el.find("#check_all").on("click",function(){c.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var j=$(this).find("input.grid-row-select-checkbox");var i=$(this).find("span.grid-selected-count");var r=function(){i.text($(j).filter(":checked").length)};$(j).each(function(){$(this).change(r)});r()});if(this.$el.find(".community_rating_star").length!==0){this.$el.find(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;this.$el.find(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});this.$el.find(".use-inbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href"),inbound:true});return false})});this.$el.find(".use-outbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=this.$el.find("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(r){r.preventDefault();var j=$(r.target).html();var i=this.findItemByHtml(j);p.execute(i)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$(a.filter_element(e,g));var d=this;f.click(function(){$(this).remove();d.remove_filter_condition(e,g)});var c=this.$el.find("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},remove_filter_condition:function(c,d){this.grid.remove_filter(c,d);this.go_page_one();this.execute()},set_sort_condition:function(g){var f=this.grid.get("sort_key");var e=g;if(f.indexOf(g)!==-1){if(f.substring(0,1)!=="-"){e="-"+g}}this.$el.find(".sort-arrow").remove();var d=(e.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+d+"</span>").addClass("sort-arrow");this.$el.find("#"+g+"-header").append(c);this.grid.set("sort_key",e);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;this.$el.find("."+e+"-filter").each(function(){var k=$.trim($(this).text());var i=d[k];var j=i[e];if(j==g){$(this).empty();$(this).addClass("current-filter");$(this).append(k)}else{if(j==f){$(this).empty();var h=$('<a href="#">'+k+"</a>");h.click(function(){c.set_categorical_filter(e,j)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;this.$el.find(".page-link").each(function(){var i=$(this).attr("id"),g=parseInt(i.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$('<a href="#">'+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(d,g){var e=$(d).val();var f=this.$el.find('input[name="id"]:checked').length;if(!f>0){return false}var c=[];this.$el.find("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:e,id:c,confirmation_text:g});return true},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},execute:function(l){var f=null;var e=null;var g=null;var c=null;var k=null;if(l){e=l.href;g=l.operation;f=l.id;c=l.confirmation_text;k=l.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var j=e.split("?");if(j.length>1){var i=j[1];var d=i.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(k,"")}return false}if(e){this.go_to(k,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(k,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=this.$el.find("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");this.$el.find(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){var g=c.grid.get("embedded");var h=c.grid.get("insert");var f=$.parseJSON(e);f.embedded=g;f.insert=h;c.init_grid(f);c.$el.find(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})}})});
\ No newline at end of file
+jQuery.ajaxSettings.traditional=true;define(["mvc/grid/grid-model","mvc/grid/grid-template","mvc/ui"],function(b,a){return Backbone.View.extend({grid:null,initialize:function(c){this.setElement("#grid-container");if(c.use_panels){$("#center").css({padding:"10px",overflow:"auto"})}this.init_grid(c)},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(f){this.grid=new b(f);var e=this.grid.attributes;this.handle_refresh(e.refresh_frames);var d=this.grid.get("url_base");d=d.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",d);this.$el.html(a.grid(e));this.$el.find("#grid-table-header").html(a.header(e));this.$el.find("#grid-table-body").html(a.body(e));this.$el.find("#grid-table-footer").html(a.footer(e));if(e.message){this.$el.find("#grid-message").html(a.message(e));var c=this;if(e.use_hide_message){setTimeout(function(){c.$el.find("#grid-message").html("")},5000)}}this.init_grid_elements();this.init_grid_controls();init_refresh_on_change()},init_grid_controls:function(){var c=this;this.$el.find(".operation-button").each(function(){$(this).off();$(this).click(function(){c.submit_operation(this,operation.confirm);return false})});this.$el.find("input[type=text]").each(function(){$(this).off();$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})});this.$el.find(".sort-link").each(function(){$(this).off();$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});this.$el.find(".text-filter-form").each(function(){$(this).off();$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});this.$el.find(".text-filter-val > a").each(function(){$(this).off();$(this).click(function(){$(this).parent().remove();c.remove_filter_condition($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});this.$el.find(".categorical-filter > a").each(function(){$(this).off();$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});var e=this.$el.find("#input-tags-filter");if(e.length){e.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var d=this.$el.find("#input-name-filter");if(d.length){d.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}this.$el.find(".advanced-search-toggle").each(function(){$(this).off();$(this).click(function(){c.$el.find("#standard-search").slideToggle("fast");c.$el.find("#advanced-search").slideToggle("fast");return false})});this.$el.find("#check_all").off();this.$el.find("#check_all").on("click",function(){c.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var j=$(this).find("input.grid-row-select-checkbox");var i=$(this).find("span.grid-selected-count");var r=function(){i.text($(j).filter(":checked").length)};$(j).each(function(){$(this).change(r)});r()});if(this.$el.find(".community_rating_star").length!==0){this.$el.find(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;this.$el.find(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});this.$el.find(".use-inbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href"),inbound:true});return false})});this.$el.find(".use-outbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=this.$el.find("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(r){r.preventDefault();var j=$(r.target).html();var i=this.findItemByHtml(j);p.execute(i)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$(a.filter_element(e,g));var d=this;f.click(function(){$(this).remove();d.remove_filter_condition(e,g)});var c=this.$el.find("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},remove_filter_condition:function(c,d){this.grid.remove_filter(c,d);this.go_page_one();this.execute()},set_sort_condition:function(g){var f=this.grid.get("sort_key");var e=g;if(f.indexOf(g)!==-1){if(f.substring(0,1)!=="-"){e="-"+g}}this.$el.find(".sort-arrow").remove();var d=(e.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+d+"</span>").addClass("sort-arrow");this.$el.find("#"+g+"-header").append(c);this.grid.set("sort_key",e);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;this.$el.find("."+e+"-filter").each(function(){var k=$.trim($(this).text());var i=d[k];var j=i[e];if(j==g){$(this).empty();$(this).addClass("current-filter");$(this).append(k)}else{if(j==f){$(this).empty();var h=$('<a href="#">'+k+"</a>");h.click(function(){c.set_categorical_filter(e,j)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;this.$el.find(".page-link").each(function(){var i=$(this).attr("id"),g=parseInt(i.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$('<a href="#">'+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(d,g){var e=$(d).val();var f=this.$el.find('input[name="id"]:checked').length;if(!f>0){return false}var c=[];this.$el.find("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:e,id:c,confirmation_text:g});return true},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},execute:function(l){var f=null;var e=null;var g=null;var c=null;var k=null;if(l){e=l.href;g=l.operation;f=l.id;c=l.confirmation_text;k=l.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var j=e.split("?");if(j.length>1){var i=j[1];var d=i.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(k,"")}return false}if(e){this.go_to(k,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(k,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=this.$el.find("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");this.$el.find(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){var g=c.grid.get("embedded");var h=c.grid.get("insert");var f=$.parseJSON(e);f.embedded=g;f.insert=h;c.init_grid(f);c.$el.find(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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31 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2abb0622cf6a/
Changeset: 2abb0622cf6a
User: guerler
Date: 2014-01-31 13:52:49
Summary: Grids: Fix pages
Affected #: 5 files
diff -r 50012b1e7bbc5c181d6678f56cd2899d6a6b4511 -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 static/scripts/mvc/grid/grid-template.js
--- a/static/scripts/mvc/grid/grid-template.js
+++ b/static/scripts/mvc/grid/grid-template.js
@@ -230,7 +230,7 @@
},
// template
- footer: function(options) {
+ footer: function(grid_model, options) {
// create template string
var tmpl = '';
@@ -284,7 +284,7 @@
'Page:';
if (min_page > 1) {
- tmpl += '<span class="page-link" id="page-link-1"><a href="' + this.grid.get_url({page : page_index}) + '" page_num="1" onclick="return false;">1</a></span> ...';
+ tmpl += '<span class="page-link" id="page-link-1"><a href="' + grid_model.get_url({page : page_index}) + '" page_num="1" onclick="return false;">1</a></span> ...';
}
// create page urls
@@ -293,19 +293,19 @@
if (page_index == options.cur_page_num) {
tmpl += '<span class="page-link inactive-link" id="page-link-' + page_index + '">' + page_index + '</span>';
} else {
- tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="' + this.grid.get_url({page : page_index}) + '" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>';
+ tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="' + grid_model.get_url({page : page_index}) + '" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>';
}
}
// show last page
if (max_page < num_pages) {
tmpl += '...' +
- '<span class="page-link" id="page-link-' + num_pages + '"><a href="' + this.grid.get_url({page : num_pages}) + '" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>';
+ '<span class="page-link" id="page-link-' + num_pages + '"><a href="' + grid_model.get_url({page : num_pages}) + '" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>';
}
tmpl += '</span>';
// Show all link
- tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="' + this.grid.get_url({page : 'all'}) + '" onclick="return false;" page_num="all">Show All</a></span>' +
+ tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="' + grid_model.get_url({page : 'all'}) + '" onclick="return false;" page_num="all">Show All</a></span>' +
'</td>' +
'</tr>';
}
diff -r 50012b1e7bbc5c181d6678f56cd2899d6a6b4511 -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 static/scripts/mvc/grid/grid-view.js
--- a/static/scripts/mvc/grid/grid-view.js
+++ b/static/scripts/mvc/grid/grid-view.js
@@ -63,7 +63,7 @@
// update div contents
this.$el.find('#grid-table-header').html(Templates.header(options));
this.$el.find('#grid-table-body').html(Templates.body(options));
- this.$el.find('#grid-table-footer').html(Templates.footer(options));
+ this.$el.find('#grid-table-footer').html(Templates.footer(this.grid, options));
// update message
if (options.message) {
diff -r 50012b1e7bbc5c181d6678f56cd2899d6a6b4511 -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 static/scripts/packed/mvc/grid/grid-template.js
--- a/static/scripts/packed/mvc/grid/grid-template.js
+++ b/static/scripts/packed/mvc/grid/grid-template.js
@@ -1,1 +1,1 @@
-define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:l})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="'+this.grid.get_url({page:l})+'" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
+define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(h,p){var l="";if(p.use_paging&&p.num_pages>1){var n=p.num_page_links;var a=p.cur_page_num;var o=p.num_pages;var k=n/2;var g=a-k;var e=0;if(g==0){g=1;e=k-(a-g)}var d=k+e;var c=a+d;if(c<=o){max_offset=0}else{c=o;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}l+='<tr id="page-links-row">';if(p.show_item_checkboxes){l+="<td></td>"}l+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){l+='<span class="page-link" id="page-link-1"><a href="'+h.get_url({page:m})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var m=g;m<c+1;m++){if(m==p.cur_page_num){l+='<span class="page-link inactive-link" id="page-link-'+m+'">'+m+"</span>"}else{l+='<span class="page-link" id="page-link-'+m+'"><a href="'+h.get_url({page:m})+'" onclick="return false;" page_num="'+m+'">'+m+"</a></span>"}}if(c<o){l+='...<span class="page-link" id="page-link-'+o+'"><a href="'+h.get_url({page:o})+'" onclick="return false;" page_num="'+o+'">'+o+"</a></span>"}l+="</span>";l+='<span class="page-link" id="show-all-link-span"> | <a href="'+h.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(p.show_item_checkboxes){l+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+p.get_class_plural+": ";for(i in p.operations){var b=p.operations[i];if(b.allow_multiple){l+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}l+="</td></tr>"}var f=false;for(i in p.operations){if(p.operations[i].global_operation){f=true;break}}if(f){l+='<tr><td colspan="100">';for(i in p.operations){var b=p.operations[i];if(b.global_operation){l+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}l+="</td></tr>"}if(p.legend){l+='<tr><td colspan="100">'+p.legend+"</td></tr>"}return l},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
diff -r 50012b1e7bbc5c181d6678f56cd2899d6a6b4511 -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 static/scripts/packed/mvc/grid/grid-view.js
--- a/static/scripts/packed/mvc/grid/grid-view.js
+++ b/static/scripts/packed/mvc/grid/grid-view.js
@@ -1,1 +1,1 @@
-jQuery.ajaxSettings.traditional=true;define(["mvc/grid/grid-model","mvc/grid/grid-template","mvc/ui"],function(b,a){return Backbone.View.extend({grid:null,initialize:function(c){this.setElement("#grid-container");if(c.use_panels){$("#center").css({padding:"10px",overflow:"auto"})}this.init_grid(c)},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(f){this.grid=new b(f);var e=this.grid.attributes;this.handle_refresh(e.refresh_frames);var d=this.grid.get("url_base");d=d.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",d);this.$el.html(a.grid(e));this.$el.find("#grid-table-header").html(a.header(e));this.$el.find("#grid-table-body").html(a.body(e));this.$el.find("#grid-table-footer").html(a.footer(e));if(e.message){this.$el.find("#grid-message").html(a.message(e));var c=this;if(e.use_hide_message){setTimeout(function(){c.$el.find("#grid-message").html("")},5000)}}this.init_grid_elements();this.init_grid_controls();init_refresh_on_change()},init_grid_controls:function(){var c=this;this.$el.find(".operation-button").each(function(){$(this).off();$(this).click(function(){c.submit_operation(this,operation.confirm);return false})});this.$el.find("input[type=text]").each(function(){$(this).off();$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})});this.$el.find(".sort-link").each(function(){$(this).off();$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});this.$el.find(".text-filter-form").each(function(){$(this).off();$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});this.$el.find(".text-filter-val > a").each(function(){$(this).off();$(this).click(function(){$(this).parent().remove();c.remove_filter_condition($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});this.$el.find(".categorical-filter > a").each(function(){$(this).off();$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});var e=this.$el.find("#input-tags-filter");if(e.length){e.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var d=this.$el.find("#input-name-filter");if(d.length){d.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}this.$el.find(".advanced-search-toggle").each(function(){$(this).off();$(this).click(function(){c.$el.find("#standard-search").slideToggle("fast");c.$el.find("#advanced-search").slideToggle("fast");return false})});this.$el.find("#check_all").off();this.$el.find("#check_all").on("click",function(){c.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var j=$(this).find("input.grid-row-select-checkbox");var i=$(this).find("span.grid-selected-count");var r=function(){i.text($(j).filter(":checked").length)};$(j).each(function(){$(this).change(r)});r()});if(this.$el.find(".community_rating_star").length!==0){this.$el.find(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;this.$el.find(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});this.$el.find(".use-inbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href"),inbound:true});return false})});this.$el.find(".use-outbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=this.$el.find("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(r){r.preventDefault();var j=$(r.target).html();var i=this.findItemByHtml(j);p.execute(i)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$(a.filter_element(e,g));var d=this;f.click(function(){$(this).remove();d.remove_filter_condition(e,g)});var c=this.$el.find("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},remove_filter_condition:function(c,d){this.grid.remove_filter(c,d);this.go_page_one();this.execute()},set_sort_condition:function(g){var f=this.grid.get("sort_key");var e=g;if(f.indexOf(g)!==-1){if(f.substring(0,1)!=="-"){e="-"+g}}this.$el.find(".sort-arrow").remove();var d=(e.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+d+"</span>").addClass("sort-arrow");this.$el.find("#"+g+"-header").append(c);this.grid.set("sort_key",e);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;this.$el.find("."+e+"-filter").each(function(){var k=$.trim($(this).text());var i=d[k];var j=i[e];if(j==g){$(this).empty();$(this).addClass("current-filter");$(this).append(k)}else{if(j==f){$(this).empty();var h=$('<a href="#">'+k+"</a>");h.click(function(){c.set_categorical_filter(e,j)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;this.$el.find(".page-link").each(function(){var i=$(this).attr("id"),g=parseInt(i.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$('<a href="#">'+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(d,g){var e=$(d).val();var f=this.$el.find('input[name="id"]:checked').length;if(!f>0){return false}var c=[];this.$el.find("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:e,id:c,confirmation_text:g});return true},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},execute:function(l){var f=null;var e=null;var g=null;var c=null;var k=null;if(l){e=l.href;g=l.operation;f=l.id;c=l.confirmation_text;k=l.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var j=e.split("?");if(j.length>1){var i=j[1];var d=i.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(k,"")}return false}if(e){this.go_to(k,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(k,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=this.$el.find("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");this.$el.find(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){var g=c.grid.get("embedded");var h=c.grid.get("insert");var f=$.parseJSON(e);f.embedded=g;f.insert=h;c.init_grid(f);c.$el.find(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})}})});
\ No newline at end of file
+jQuery.ajaxSettings.traditional=true;define(["mvc/grid/grid-model","mvc/grid/grid-template","mvc/ui"],function(b,a){return Backbone.View.extend({grid:null,initialize:function(c){this.setElement("#grid-container");if(c.use_panels){$("#center").css({padding:"10px",overflow:"auto"})}this.init_grid(c)},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(f){this.grid=new b(f);var e=this.grid.attributes;this.handle_refresh(e.refresh_frames);var d=this.grid.get("url_base");d=d.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",d);this.$el.html(a.grid(e));this.$el.find("#grid-table-header").html(a.header(e));this.$el.find("#grid-table-body").html(a.body(e));this.$el.find("#grid-table-footer").html(a.footer(this.grid,e));if(e.message){this.$el.find("#grid-message").html(a.message(e));var c=this;if(e.use_hide_message){setTimeout(function(){c.$el.find("#grid-message").html("")},5000)}}this.init_grid_elements();this.init_grid_controls();init_refresh_on_change()},init_grid_controls:function(){var c=this;this.$el.find(".operation-button").each(function(){$(this).off();$(this).click(function(){c.submit_operation(this,operation.confirm);return false})});this.$el.find("input[type=text]").each(function(){$(this).off();$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})});this.$el.find(".sort-link").each(function(){$(this).off();$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});this.$el.find(".text-filter-form").each(function(){$(this).off();$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});this.$el.find(".text-filter-val > a").each(function(){$(this).off();$(this).click(function(){$(this).parent().remove();c.remove_filter_condition($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});this.$el.find(".categorical-filter > a").each(function(){$(this).off();$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});var e=this.$el.find("#input-tags-filter");if(e.length){e.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var d=this.$el.find("#input-name-filter");if(d.length){d.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}this.$el.find(".advanced-search-toggle").each(function(){$(this).off();$(this).click(function(){c.$el.find("#standard-search").slideToggle("fast");c.$el.find("#advanced-search").slideToggle("fast");return false})});this.$el.find("#check_all").off();this.$el.find("#check_all").on("click",function(){c.check_all_items()})},init_grid_elements:function(){this.$el.find(".grid").each(function(){var j=$(this).find("input.grid-row-select-checkbox");var i=$(this).find("span.grid-selected-count");var r=function(){i.text($(j).filter(":checked").length)};$(j).each(function(){$(this).change(r)});r()});if(this.$el.find(".community_rating_star").length!==0){this.$el.find(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;this.$el.find(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});this.$el.find(".use-inbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href"),inbound:true});return false})});this.$el.find(".use-outbound").each(function(){$(this).click(function(i){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=this.$el.find("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(r){r.preventDefault();var j=$(r.target).html();var i=this.findItemByHtml(j);p.execute(i)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$(a.filter_element(e,g));var d=this;f.click(function(){$(this).remove();d.remove_filter_condition(e,g)});var c=this.$el.find("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},remove_filter_condition:function(c,d){this.grid.remove_filter(c,d);this.go_page_one();this.execute()},set_sort_condition:function(g){var f=this.grid.get("sort_key");var e=g;if(f.indexOf(g)!==-1){if(f.substring(0,1)!=="-"){e="-"+g}}this.$el.find(".sort-arrow").remove();var d=(e.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+d+"</span>").addClass("sort-arrow");this.$el.find("#"+g+"-header").append(c);this.grid.set("sort_key",e);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;this.$el.find("."+e+"-filter").each(function(){var k=$.trim($(this).text());var i=d[k];var j=i[e];if(j==g){$(this).empty();$(this).addClass("current-filter");$(this).append(k)}else{if(j==f){$(this).empty();var h=$('<a href="#">'+k+"</a>");h.click(function(){c.set_categorical_filter(e,j)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;this.$el.find(".page-link").each(function(){var i=$(this).attr("id"),g=parseInt(i.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$('<a href="#">'+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(d,g){var e=$(d).val();var f=this.$el.find('input[name="id"]:checked').length;if(!f>0){return false}var c=[];this.$el.find("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:e,id:c,confirmation_text:g});return true},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},execute:function(l){var f=null;var e=null;var g=null;var c=null;var k=null;if(l){e=l.href;g=l.operation;f=l.id;c=l.confirmation_text;k=l.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var j=e.split("?");if(j.length>1){var i=j[1];var d=i.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(k,"")}return false}if(e){this.go_to(k,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(k,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=this.$el.find("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");this.$el.find(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){var g=c.grid.get("embedded");var h=c.grid.get("insert");var f=$.parseJSON(e);f.embedded=g;f.insert=h;c.init_grid(f);c.$el.find(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})}})});
\ No newline at end of file
diff -r 50012b1e7bbc5c181d6678f56cd2899d6a6b4511 -r 2abb0622cf6ad5172a14a85c450230b8f5df2070 templates/grid_base.mako
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -97,7 +97,7 @@
'url' : url(dict())
}
- # add refresh frames
+ ## add refresh frames
if refresh_frames:
self.grid_config['refresh_frames'] = refresh_frames
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Upgrade Babel egg from 0.9.4 to 1.3. This resolves several known issues with utf-8 for particular distributions.
by commits-noreply＠bitbucket.org 31 Jan '14
by commits-noreply＠bitbucket.org 31 Jan '14
31 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/50012b1e7bbc/
Changeset: 50012b1e7bbc
User: dannon
Date: 2014-01-31 13:43:28
Summary: Upgrade Babel egg from 0.9.4 to 1.3. This resolves several known issues with utf-8 for particular distributions.
Affected #: 1 file
diff -r b20d93e643068f3154752582db3d17e16c499633 -r 50012b1e7bbc5c181d6678f56cd2899d6a6b4511 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -63,7 +63,7 @@
WebHelpers = 1.3
WebOb = 0.8.5
wsgiref = 0.1.2
-Babel = 0.9.4
+Babel = 1.3
wchartype = 0.1
Whoosh = 0.3.18
; fluent_logger = 0.3.3
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Grids: Finalize code separation, refactor filters and apply coding conventions
by commits-noreply＠bitbucket.org 31 Jan '14
by commits-noreply＠bitbucket.org 31 Jan '14
31 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b20d93e64306/
Changeset: b20d93e64306
User: guerler
Date: 2014-01-31 11:20:23
Summary: Grids: Finalize code separation, refactor filters and apply coding conventions
iG: removed static/scripts/packed/galaxy.grids.js
Affected #: 12 files
diff -r be7ece9454471d655668f3997c29b90c2f6c312d -r b20d93e643068f3154752582db3d17e16c499633 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -41,6 +41,7 @@
cur_sort_key_pref_name = ".sort_key"
pass_through_operations = {}
legend = None
+ info_text = None
def __init__( self ):
# Determine if any multiple row operations are defined
self.has_multiple_item_operations = False
@@ -286,6 +287,7 @@
url = url,
status = status,
message = message,
+ info_text=self.info_text,
use_panels=self.use_panels,
use_hide_message=self.use_hide_message,
advanced_search=self.advanced_search,
diff -r be7ece9454471d655668f3997c29b90c2f6c312d -r b20d93e643068f3154752582db3d17e16c499633 lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -104,6 +104,7 @@
preserve_state = False
use_async = True
use_paging = True
+ info_text = "Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted."
def get_current_item( self, trans, **kwargs ):
return trans.get_history()
diff -r be7ece9454471d655668f3997c29b90c2f6c312d -r b20d93e643068f3154752582db3d17e16c499633 static/scripts/galaxy.grids.js
--- a/static/scripts/galaxy.grids.js
+++ /dev/null
@@ -1,984 +0,0 @@
-// External dependencies (for module management eventually): jQuery, Backbone, underscore
-
-// This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are
-// not appended to the identifier of a nested array.
-jQuery.ajaxSettings.traditional = true;
-
-// dependencies
-define(['mvc/ui'], function() {
-
-/**
- * A Galaxy grid.
- */
-var Grid = Backbone.Model.extend({
- defaults: {
- url_base: '',
- async: false,
- async_ops: [],
- categorical_filters: [],
- filters: {},
- sort_key: null,
- show_item_checkboxes: false,
- advanced_search: false,
- cur_page: 1,
- num_pages: 1,
- operation: undefined,
- item_ids: undefined
- },
-
- /**
- * Return true if operation can be done asynchronously.
- */
- can_async_op: function(op) {
- return _.indexOf(this.attributes.async_ops, op) !== -1;
- },
-
- /**
- * Add filtering criterion.
- */
- add_filter: function(key, value, append) {
- // Update URL arg with new condition.
- if (append) {
- // Update or append value.
- var cur_val = this.attributes.filters[key],
- new_val;
- if (cur_val === null || cur_val === undefined) {
- new_val = value;
- }
- else if (typeof(cur_val) == "string") {
- if (cur_val == "All") {
- new_val = value;
- } else {
- // Replace string with array.
- var values = [];
- values[0] = cur_val;
- values[1] = value;
- new_val = values;
- }
- }
- else {
- // Current value is an array.
- new_val = cur_val;
- new_val.push(value);
- }
- this.attributes.filters[key] = new_val;
- }
- else {
- // Replace value.
- this.attributes.filters[key] = value;
- }
- },
-
- /**
- * Remove filtering criterion.
- */
- remove_filter: function(key, condition) {
- var cur_val = this.attributes.filters[key];
- if (cur_val === null || cur_val === undefined) {
- return false;
- }
-
- var removed = true;
- if (typeof(cur_val) === "string") {
- if (cur_val == "All") {
- // Unexpected. Throw error?
- removed = false;
- }
- else {
- // Remove condition.
- delete this.attributes.filters[key];
- }
- }
- else {
- // Filter contains an array of conditions.
- var condition_index = _.indexOf(cur_val, condition);
- if (condition_index !== -1) {
- cur_val.splice(condition_index, 1);
- }
- else {
- removed = false;
- }
- }
-
- return removed;
- },
-
- /**
- * Returns URL data for obtaining a new grid.
- */
- get_url_data: function() {
- var url_data = {
- async: this.attributes.async,
- sort: this.attributes.sort_key,
- page: this.attributes.cur_page,
- show_item_checkboxes: this.attributes.show_item_checkboxes,
- advanced_search: this.attributes.advanced_search
- };
-
- // Add operation, item_ids only if they have values.
- if (this.attributes.operation) {
- url_data.operation = this.attributes.operation;
- }
- if (this.attributes.item_ids) {
- url_data.id = this.attributes.item_ids;
- }
-
- // Add filter arguments to data, placing "f-" in front of all arguments.
- var self = this;
- _.each(_.pairs(self.attributes.filters), function(k) {
- url_data['f-' + k[0]] = k[1];
- });
-
- return url_data;
- },
-
- // Return URL for obtaining a new grid
- get_url: function (args) {
- return this.get('url_base') + "?" + $.param(this.get_url_data()) + '&' + $.param(args);
- }
-
-});
-
-// grid view
-var GridView = Backbone.View.extend({
-
- // model
- grid: null,
-
- // Initialize
- initialize: function(grid_config)
- {
- // initialize controls
- this.init_grid(grid_config);
- this.init_grid_controls();
-
- // Initialize text filters to select text on click and use normal font when user is typing.
- $('input[type=text]').each(function() {
- $(this).click(function() { $(this).select(); } )
- .keyup(function () { $(this).css("font-style", "normal"); });
- });
- },
-
- // refresh frames
- handle_refresh: function (refresh_frames) {
- if (refresh_frames) {
- if ($.inArray('history', refresh_frames) > -1) {
- if( top.Galaxy && top.Galaxy.currHistoryPanel ){
- top.Galaxy.currHistoryPanel.loadCurrentHistory();
- }
- }
- }
- },
-
- // Initialize
- init_grid: function(grid_config)
- {
- // link grid model
- this.grid = new Grid(grid_config);
-
- // get options
- var options = this.grid.attributes;
-
- // handle refresh requests
- this.handle_refresh(options.refresh_frames);
-
- // strip protocol and domain
- var url = this.grid.get('url_base');
- url = url.replace(/^.*\/\/[^\/]+/, '');
- this.grid.set('url_base', url);
-
- // update div contents
- $('#grid-table-body').html(this.template_body(options));
- $('#grid-table-footer').html(this.template_footer(options));
-
- // update message
- if (options.message) {
- $('#grid-message').html(this.template_message(options));
- if (options.use_hide_message) {
- setTimeout( function() { $('#grid-message').html(''); }, 5000);
- }
- }
-
- // configure elements
- this.init_grid_elements();
-
- // attach global event handler
- init_refresh_on_change();
- },
-
- // Initialize grid controls
- init_grid_controls: function() {
- // Initialize submit image elements.
- $('.submit-image').each( function() {
- // On mousedown, add class to simulate click.
- $(this).mousedown( function() {
- $(this).addClass('gray-background');
- });
-
- // On mouseup, add class to simulate click.
- $(this).mouseup( function() {
- $(this).removeClass('gray-background');
- });
- });
-
- // link
- var self = this;
-
- // Initialize sort links.
- $('.sort-link').each( function() {
- $(this).click( function() {
- self.set_sort_condition( $(this).attr('sort_key') );
- return false;
- });
- });
-
- // Initialize categorical filters.
- $('.categorical-filter > a').each( function() {
- $(this).click( function() {
- self.set_categorical_filter( $(this).attr('filter_key'), $(this).attr('filter_val') );
- return false;
- });
- });
-
- // Initialize text filters.
- $('.text-filter-form').each( function() {
- $(this).submit( function() {
- var column_key = $(this).attr('column_key');
- var text_input_obj = $('#input-' + column_key + '-filter');
- var text_input = text_input_obj.val();
- text_input_obj.val('');
- self.add_filter_condition(column_key, text_input);
- return false;
- });
- });
-
- // Initialize autocomplete for text inputs in search UI.
- var t = $("#input-tags-filter");
- if (t.length) {
- t.autocomplete(this.grid.history_tag_autocomplete_url,
- { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
- }
-
- var t2 = $("#input-name-filter");
- if (t2.length) {
- t2.autocomplete(this.grid.history_name_autocomplete_url,
- { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
- }
-
- // Initialize standard, advanced search toggles.
- $('.advanced-search-toggle').each( function() {
- $(this).click( function() {
- $('#standard-search').slideToggle('fast');
- $('#advanced-search').slideToggle('fast');
- return false;
- });
- });
- },
-
- // Initialize grid elements.
- init_grid_elements : function() {
- // Initialize grid selection checkboxes.
- $(".grid").each( function() {
- var checkboxes = $(this).find("input.grid-row-select-checkbox");
- var check_count = $(this).find("span.grid-selected-count");
- var update_checked = function() {
- check_count.text( $(checkboxes).filter(":checked").length );
- };
-
- $(checkboxes).each( function() {
- $(this).change(update_checked);
- });
- update_checked();
- });
-
- // Initialize ratings.
- if ($('.community_rating_star').length !== 0)
- $('.community_rating_star').rating({});
-
- // get options
- var options = this.grid.attributes;
- var self = this;
-
- //
- // add page click events
- //
- $('.page-link > a').each( function() {
- $(this).click( function() {
- self.set_page( $(this).attr('page_num') );
- return false;
- });
- });
-
- //
- // add inbound/outbound events
- //
- $(".use-inbound").each( function() {
- $(this).click( function(e) {
- self.execute({
- href : $(this).attr('href'),
- inbound : true
- });
- return false;
-
- });
- });
-
- $(".use-outbound").each( function() {
- $(this).click( function(e) {
- self.execute({
- href : $(this).attr('href')
- });
- return false;
- });
- });
-
- // empty grid?
- var items_length = options.items.length;
- if (items_length == 0) {
- return;
- }
-
- //
- // add operation popup menus
- //
- for (var i in options.items)
- {
- // get items
- var item = options.items[i];
-
- // get identifiers
- var button = $('#grid-' + i + '-popup');
- button.off();
- var popup = new PopupMenu(button);
-
- // load details
- for (var j in options['operations'])
- {
- // get operation details
- var operation = options['operations'][j];
- var operation_id = operation['label'];
- var operation_settings = item['operation_config'][operation_id];
- var encode_id = item['encode_id'];
-
- // check
- if (operation_settings['allowed'] && operation['allow_popup'])
- {
- // popup configuration
- var popupConfig =
- {
- html : operation['label'],
- href : operation_settings['url_args'],
- target : operation_settings['target'],
- confirmation_text : operation['confirm'],
- inbound : operation['inbound']
- };
-
- // add popup function
- popupConfig.func = function(e)
- {
- e.preventDefault();
- var label = $(e.target).html();
- var options = this.findItemByHtml(label);
- self.execute(options);
- };
-
- // add item
- popup.addItem(popupConfig);
- }
- }
- }
- },
-
- // Add a condition to the grid filter; this adds the condition and refreshes the grid.
- add_filter_condition: function (name, value) {
- // Do nothing is value is empty.
- if (value === "") {
- return false;
- }
-
- // Add condition to grid.
- this.grid.add_filter(name, value, true);
-
- // Add button that displays filter and provides a button to delete it.
- var t = $("<span>" + value + "<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");
- t.addClass('text-filter-val');
- var self = this;
- t.click(function() {
- // Remove filter condition.
- self.grid.remove_filter(name, value);
-
- // Remove visible element.
- $(this).remove();
-
- self.go_page_one();
- self.execute();
- });
-
- var container = $('#' + name + "-filtering-criteria");
- container.append(t);
-
- this.go_page_one();
- this.execute();
- },
-
- // Set sort condition for grid.
- set_sort_condition: function (col_key) {
- // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on
- // currently sorted column, sort is reversed.
- var cur_sort = this.grid.get('sort_key');
- var new_sort = col_key;
- if (cur_sort.indexOf(col_key) !== -1) {
- // Reverse sort.
- if (cur_sort.substring(0,1) !== '-') {
- new_sort = '-' + col_key;
- } else {
- // Sort reversed by using just col_key.
- }
- }
-
- // Remove sort arrows elements.
- $('.sort-arrow').remove();
-
- // Add sort arrow element to new sort column.
- var sort_arrow = (new_sort.substring(0,1) == '-') ? "↑" : "↓";
- var t = $("<span>" + sort_arrow + "</span>").addClass('sort-arrow');
- var th = $("#" + col_key + '-header');
- th.append(t);
-
- // Update grid.
- this.grid.set('sort_key', new_sort);
- this.go_page_one();
- this.execute();
- },
-
- // Set new value for categorical filter.
- set_categorical_filter: function (name, new_value) {
- // Update filter hyperlinks to reflect new filter value.
- var category_filter = this.grid.get('categorical_filters')[name],
- cur_value = this.grid.get('filters')[name];
- var self = this;
- $("." + name + "-filter").each( function() {
- var text = $.trim( $(this).text() );
- var filter = category_filter[text];
- var filter_value = filter[name];
- if (filter_value == new_value) {
- // Remove filter link since grid will be using this filter. It is assumed that
- // this element has a single child, a hyperlink/anchor with text.
- $(this).empty();
- $(this).addClass("current-filter");
- $(this).append(text);
- } else if (filter_value == cur_value) {
- // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that
- // this element has a single child, a hyperlink/anchor.
- $(this).empty();
- var t = $("<a href='#'>" + text + "</a>");
- t.click(function() {
- self.set_categorical_filter( name, filter_value );
- });
- $(this).removeClass("current-filter");
- $(this).append(t);
- }
- });
-
- // Update grid.
- this.grid.add_filter(name, new_value);
- this.go_page_one();
- this.execute();
- },
-
- // Set page to view.
- set_page: function (new_page) {
- // Update page hyperlink to reflect new page.
- var self = this;
- $(".page-link").each( function() {
- var id = $(this).attr('id'),
- page_num = parseInt( id.split("-")[2], 10 ), // Id has form 'page-link-<page_num>
- cur_page = self.grid.get('cur_page'),
- text;
- if (page_num === new_page) {
- // Remove link to page since grid will be on this page. It is assumed that
- // this element has a single child, a hyperlink/anchor with text.
- text = $(this).children().text();
- $(this).empty();
- $(this).addClass("inactive-link");
- $(this).text(text);
- }
- else if (page_num === cur_page) {
- // Add hyperlink to this page since grid will no longer be on this page. It is assumed that
- // this element has a single child, a hyperlink/anchor.
- text = $(this).text();
- $(this).empty();
- $(this).removeClass("inactive-link");
- var t = $("<a href='#'>" + text + "</a>");
- t.click(function() {
- self.set_page(page_num);
- });
- $(this).append(t);
- }
- });
-
- if (new_page === "all") {
- this.grid.set('cur_page', new_page);
- } else {
- this.grid.set('cur_page', parseInt(new_page, 10));
- }
- this.execute();
- },
-
- // confirmation/submission of operation request
- submit_operation: function (selected_button, confirmation_text)
- {
- // verify in any item is selected
- var number_of_checked_ids = $('input[name="id"]:checked').length;
- if (!number_of_checked_ids > 0)
- return false;
-
- // collect ids
- var operation_name = $(selected_button).val();
- var item_ids = [];
- $('input[name=id]:checked').each(function() {
- item_ids.push( $(this).val() );
- });
- this.execute({
- operation: operation_name,
- id: item_ids,
- confirmation_text: confirmation_text
- });
-
- // return
- return true;
- },
-
- // execute operations and hyperlink requests
- execute: function (options) {
- // get url
- var id = null;
- var href = null;
- var operation = null;
- var confirmation_text = null;
- var inbound = null;
-
- // check for options
- if (options)
- {
- // get options
- href = options.href;
- operation = options.operation;
- id = options.id;
- confirmation_text = options.confirmation_text;
- inbound = options.inbound;
-
- // check if input contains the operation tag
- if (href !== undefined && href.indexOf('operation=') != -1) {
- // Get operation, id in hyperlink's href.
- var href_parts = href.split("?");
- if (href_parts.length > 1) {
- var href_parms_str = href_parts[1];
- var href_parms = href_parms_str.split("&");
- for (var index = 0; index < href_parms.length; index++) {
- if (href_parms[index].indexOf('operation') != -1) {
- // Found operation parm; get operation value.
- operation = href_parms[index].split('=')[1];
- operation = operation.replace (/\+/g, ' ');
- } else if (href_parms[index].indexOf('id') != -1) {
- // Found id parm; get id value.
- id = href_parms[index].split('=')[1];
- }
- }
- }
- }
- }
-
- // check for operation details
- if (operation && id) {
- // show confirmation box
- if (confirmation_text && confirmation_text != '' && confirmation_text != 'None' && confirmation_text != 'null')
- if(!confirm(confirmation_text))
- return false;
-
- // use small characters for operation?!
- operation = operation.toLowerCase();
-
- // Update grid.
- this.grid.set({
- operation: operation,
- item_ids: id
- });
-
- // Do operation. If operation cannot be performed asynchronously, redirect to location.
- if (this.grid.can_async_op(operation)) {
- this.update_grid();
- } else {
- this.go_to(inbound, '');
- }
-
- // done
- return false;
- }
-
- // check for href details
- if (href)
- {
- this.go_to(inbound, href);
- return false;
- }
-
- // refresh grid
- if (this.grid.get('async')) {
- this.update_grid();
- } else {
- this.go_to(inbound, '');
- }
-
- // done
- return false;
- },
-
- // go to url
- go_to: function (inbound, href) {
- // get aysnc status
- var async = this.grid.get('async');
- this.grid.set('async', false);
-
- // get slide status
- advanced_search = $('#advanced-search').is(":visible");
- this.grid.set('advanced_search', advanced_search);
-
- // get default url
- if(!href)
- href = this.grid.get('url_base') + "?" + $.param(this.grid.get_url_data());
-
- // clear grid of transient request attributes.
- this.grid.set({
- operation: undefined,
- item_ids: undefined,
- async: async
- });
-
- if (inbound) {
- // this currently assumes that there is only a single grid shown at a time
- var $div = $('.grid-header').closest('.inbound');
- if ($div.length !== 0) {
- $div.load(href);
- return;
- }
- }
-
- window.location = href;
- },
-
- // Update grid.
- update_grid: function () {
- // If there's an operation, do POST; otherwise, do GET.
- var method = (this.grid.get('operation') ? "POST" : "GET" );
- $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions.
- var self = this;
- $.ajax({
- type: method,
- url: self.grid.get('url_base'),
- data: self.grid.get_url_data(),
- error: function(response) { alert( 'Grid refresh failed' );},
- success: function(response_text) {
- // Initialize new grid config
- self.init_grid($.parseJSON(response_text));
-
- // Hide loading overlay.
- $('.loading-elt-overlay').hide();
- },
- complete: function() {
- // Clear grid of transient request attributes.
- self.grid.set({
- operation: undefined,
- item_ids: undefined
- });
- }
- });
- },
-
- check_all_items: function () {
- var chk_all = document.getElementById('check_all'),
- checks = document.getElementsByTagName('input'),
- total = 0,
- i;
- if ( chk_all.checked === true ) {
- for ( i=0; i < checks.length; i++ ) {
- if ( checks[i].name.indexOf( 'id' ) !== -1) {
- checks[i].checked = true;
- total++;
- }
- }
- }
- else {
- for ( i=0; i < checks.length; i++ ) {
- if ( checks[i].name.indexOf( 'id' ) !== -1) {
- checks[i].checked = false;
- }
-
- }
- }
- this.init_grid_elements();
- },
-
- // Go back to page one; this is useful when a filter is applied.
- go_page_one: function () {
- // Need to go back to page 1 if not showing all.
- var cur_page = this.grid.get('cur_page');
- if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') {
- this.grid.set('cur_page', 1);
- }
- },
-
- // template
- template_body: function(options) {
- // initialize
- var tmpl = '';
- var num_rows_rendered = 0;
- var items_length = options.items.length;
-
- // empty grid?
- if (items_length == 0) {
- // No results.
- tmpl += '<tr><td colspan="100"><em>No Items</em></td></tr>';
- num_rows_rendered = 1;
- }
-
- // create rows
- for (var i in options.items) {
-
- // encode ids
- var item = options.items[i];
- var encoded_id = item.encode_id;
- var popupmenu_id = 'grid-' + i + '-popup';
-
- // Tag current
- tmpl += '<tr ';
- if (options.current_item_id == item.id) {
- tmpl += 'class="current"';
- }
- tmpl += '>';
-
- // Item selection column
- if (options.show_item_checkboxes) {
- tmpl += '<td style="width: 1.5em;">' +
- '<input type="checkbox" name="id" value="' + encoded_id + '" id="' + encoded_id + '" class="grid-row-select-checkbox" />' +
- '</td>';
- }
-
- // Data columns
- for (j in options.columns) {
- var column = options.columns[j];
- if (column.visible) {
- // Nowrap
- var nowrap = '';
- if (column.nowrap) {
- nowrap = 'style="white-space:nowrap;"';
- }
-
- // get column settings
- var column_settings = item.column_config[column.label];
-
- // load attributes
- var link = column_settings.link;
- var value = column_settings.value;
- var inbound = column_settings.inbound;
-
- // unescape value
- if (jQuery.type( value ) === 'string') {
- value = value.replace(/\/\//g, '/');
- }
-
- // Attach popup menu?
- var id = "";
- var cls = "";
- if (column.attach_popup) {
- id = 'grid-' + i + '-popup';
- cls = "menubutton"
- if (link != '') {
- cls += " split";
- }
- cls += " popup";
- }
-
- // Check for row wrapping
- tmpl += '<td ' + nowrap + '>';
-
- // Link
- if (link) {
- if (options.operations.length != 0) {
- tmpl += '<div id="' + id + '" class="' + cls + '" style="float: left;">';
- }
-
- var label_class = "";
- if (inbound) {
- label_class = "use-inbound"
- } else {
- label_class = "use-outbound"
- }
- tmpl += '<a class="label ' + label_class + '" href="' + link + '" onclick="return false;">' + value + '</a>';
- if (options.operations.length != 0) {
- tmpl += '</div>';
- }
- } else {
- tmpl += '<div id="' + id + '" class="' + cls + '"><label id="' + column.label_id_prefix + encoded_id + '" for="' + encoded_id + '">' + value + '</label></div>';
- }
- tmpl += '</td>';
- }
- }
- tmpl += '</tr>';
- num_rows_rendered++;
- }
- return tmpl;
- },
-
- // template
- template_footer: function(options) {
-
- // create template string
- var tmpl = '';
-
- // paging
- if (options.use_paging && options.num_pages > 1) {
- // get configuration
- var num_page_links = options.num_page_links;
- var cur_page_num = options.cur_page_num;
- var num_pages = options.num_pages;
-
- // First pass on min page.
- var page_link_range = num_page_links / 2;
- var min_page = cur_page_num - page_link_range
- var min_offset = 0;
- if (min_page == 0) {
- // Min page is too low.
- min_page = 1;
- min_offset = page_link_range - ( cur_page_num - min_page );
- }
-
- // Set max page.
- var max_range = page_link_range + min_offset;
- var max_page = cur_page_num + max_range;
- if (max_page <= num_pages) {
- // Max page is fine.
- max_offset = 0;
- } else {
- // Max page is too high.
- max_page = num_pages;
- // +1 to account for the +1 in the loop below.
- max_offset = max_range - ( max_page + 1 - cur_page_num );
- }
-
- // Second and final pass on min page to add any unused
- // offset from max to min.
- if (max_offset != 0) {
- min_page -= max_offset
- if (min_page < 1) {
- min_page = 1
- }
- }
-
- // template header
- tmpl += '<tr id="page-links-row">';
- if (options.show_item_checkboxes) {
- tmpl += '<td></td>';
- }
- tmpl += '<td colspan="100">' +
- '<span id="page-link-container">' +
- 'Page:';
-
- if (min_page > 1) {
- tmpl += '<span class="page-link" id="page-link-1"><a href="' + this.grid.get_url({page : page_index}) + '" page_num="1" onclick="return false;">1</a></span> ...';
- }
-
- // create page urls
- for (var page_index = min_page; page_index < max_page + 1; page_index++) {
-
- if (page_index == options.cur_page_num) {
- tmpl += '<span class="page-link inactive-link" id="page-link-' + page_index + '">' + page_index + '</span>';
- } else {
- tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="' + this.grid.get_url({page : page_index}) + '" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>';
- }
- }
-
- // show last page
- if (max_page < num_pages) {
- tmpl += '...' +
- '<span class="page-link" id="page-link-' + num_pages + '"><a href="' + this.grid.get_url({page : num_pages}) + '" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>';
- }
- tmpl += '</span>';
-
- // Show all link
- tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="' + this.grid.get_url({page : 'all'}) + '" onclick="return false;" page_num="all">Show All</a></span>' +
- '</td>' +
- '</tr>';
- }
-
- // Grid operations for multiple items.
- if (options.show_item_checkboxes) {
- // start template
- tmpl += '<tr>' +
- '<input type="hidden" id="operation" name="operation" value="">' +
- '<td></td>' +
- '<td colspan="100">' +
- 'For <span class="grid-selected-count"></span> selected ' + options.get_class_plural + ': ';
-
- // configure buttons for operations
- for (i in options.operations) {
- var operation = options.operations[i];
- if (operation.allow_multiple) {
- tmpl += '<input type="button" value="' + operation.label + '" class="action-button" onclick="gridView.submit_operation(this, \'' + operation.confirm + '\')"> ';
- }
- }
-
- // finalize template
- tmpl += '</td>' +
- '</tr>';
- }
-
- // count global operations
- var found_global = false;
- for (i in options.operations) {
- if (options.operations[i].global_operation) {
- found_global = true;
- break;
- }
- }
-
- // add global operations
- if (found_global) {
- tmpl += '<tr>' +
- '<td colspan="100">';
- for (i in options.operations) {
- var operation = options.operations[i];
- if (operation.global_operation) {
- tmpl += '<a class="action-button" href="' + operation.global_operation + '">' + operation.label + '</a>';
- }
- }
- tmpl += '</td>' +
- '</tr>';
- }
-
- // add legend
- if (options.legend) {
- tmpl += '<tr>' +
- '<td colspan="100">' + options.legend + '</td>' +
- '</tr>';
- }
-
- // return
- return tmpl;
- },
-
- // template
- template_message: function(options) {
- return '<p>' +
- '<div class="' + options.status + 'message transient-message">' + options.message + '</div>' +
- '<div style="clear: both"></div>' +
- '</p>';
- }
-});
-
-return {
- Grid : Grid,
- GridView : GridView
-};
-
-});
\ No newline at end of file
diff -r be7ece9454471d655668f3997c29b90c2f6c312d -r b20d93e643068f3154752582db3d17e16c499633 static/scripts/mvc/grid/grid-model.js
--- /dev/null
+++ b/static/scripts/mvc/grid/grid-model.js
@@ -0,0 +1,134 @@
+// dependencies
+define([], function() {
+
+// grid model
+return Backbone.Model.extend({
+ defaults: {
+ url_base: '',
+ async: false,
+ async_ops: [],
+ categorical_filters: [],
+ filters: {},
+ sort_key: null,
+ show_item_checkboxes: false,
+ advanced_search: false,
+ cur_page: 1,
+ num_pages: 1,
+ operation: undefined,
+ item_ids: undefined
+ },
+
+ /**
+ * Return true if operation can be done asynchronously.
+ */
+ can_async_op: function(op) {
+ return _.indexOf(this.attributes.async_ops, op) !== -1;
+ },
+
+ /**
+ * Add filtering criterion.
+ */
+ add_filter: function(key, value, append) {
+ // Update URL arg with new condition.
+ if (append) {
+ // Update or append value.
+ var cur_val = this.attributes.filters[key],
+ new_val;
+ if (cur_val === null || cur_val === undefined) {
+ new_val = value;
+ }
+ else if (typeof(cur_val) == "string") {
+ if (cur_val == "All") {
+ new_val = value;
+ } else {
+ // Replace string with array.
+ var values = [];
+ values[0] = cur_val;
+ values[1] = value;
+ new_val = values;
+ }
+ }
+ else {
+ // Current value is an array.
+ new_val = cur_val;
+ new_val.push(value);
+ }
+ this.attributes.filters[key] = new_val;
+ }
+ else {
+ // Replace value.
+ this.attributes.filters[key] = value;
+ }
+ },
+
+ /**
+ * Remove filtering criterion.
+ */
+ remove_filter: function(key, condition) {
+ var cur_val = this.attributes.filters[key];
+ if (cur_val === null || cur_val === undefined) {
+ return false;
+ }
+
+ var removed = true;
+ if (typeof(cur_val) === "string") {
+ if (cur_val == "All") {
+ // Unexpected. Throw error?
+ removed = false;
+ }
+ else {
+ // Remove condition.
+ delete this.attributes.filters[key];
+ }
+ }
+ else {
+ // Filter contains an array of conditions.
+ var condition_index = _.indexOf(cur_val, condition);
+ if (condition_index !== -1) {
+ cur_val.splice(condition_index, 1);
+ }
+ else {
+ removed = false;
+ }
+ }
+
+ return removed;
+ },
+
+ /**
+ * Returns URL data for obtaining a new grid.
+ */
+ get_url_data: function() {
+ var url_data = {
+ async: this.attributes.async,
+ sort: this.attributes.sort_key,
+ page: this.attributes.cur_page,
+ show_item_checkboxes: this.attributes.show_item_checkboxes,
+ advanced_search: this.attributes.advanced_search
+ };
+
+ // Add operation, item_ids only if they have values.
+ if (this.attributes.operation) {
+ url_data.operation = this.attributes.operation;
+ }
+ if (this.attributes.item_ids) {
+ url_data.id = this.attributes.item_ids;
+ }
+
+ // Add filter arguments to data, placing "f-" in front of all arguments.
+ var self = this;
+ _.each(_.pairs(self.attributes.filters), function(k) {
+ url_data['f-' + k[0]] = k[1];
+ });
+
+ return url_data;
+ },
+
+ // Return URL for obtaining a new grid
+ get_url: function (args) {
+ return this.get('url_base') + "?" + $.param(this.get_url_data()) + '&' + $.param(args);
+ }
+
+});
+
+});
\ No newline at end of file
diff -r be7ece9454471d655668f3997c29b90c2f6c312d -r b20d93e643068f3154752582db3d17e16c499633 static/scripts/mvc/grid/grid-template.js
--- /dev/null
+++ b/static/scripts/mvc/grid/grid-template.js
@@ -0,0 +1,617 @@
+// dependencies
+define([], function() {
+
+// grid view templates
+return {
+ // template
+ grid: function(options) {
+ var tmpl = '';
+ if (options.embedded) {
+ tmpl = this.grid_header(options) + this.grid_table(options);
+ } else {
+ tmpl = '<div class="loading-elt-overlay"></div>' +
+ '<table>' +
+ '<tr>' +
+ '<td width="75%">' +
+ this.grid_header(options) +
+ '</td>' +
+ '<td></td>' +
+ '<td></td>' +
+ '</tr>' +
+ '<tr>' +
+ '<td width="100%" id="grid-message" valign="top"></td>' +
+ '<td></td>' +
+ '<td></td>' +
+ '</tr>' +
+ '</table>' +
+ this.grid_table(options);
+ }
+
+ // add info text
+ if (options.info_text) {
+ tmpl += '<br><div class="toolParamHelp" style="clear: both;">' + options.info_text + '</div>';
+ }
+
+ // return
+ return tmpl;
+ },
+
+ // template
+ grid_table: function(options) {
+ return '<form method="post" onsubmit="return false;">' +
+ '<table id="grid-table" class="grid">' +
+ '<thead id="grid-table-header"></thead>' +
+ '<tbody id="grid-table-body"></tbody>' +
+ '<tfoot id="grid-table-footer"></tfoot>' +
+ '</table>' +
+ '</form>';
+ },
+
+ // template
+ grid_header: function(options) {
+ var tmpl = '<div class="grid-header">';
+ if (!options.embedded) {
+ tmpl += '<h2>' + options.title + '</h2>';
+ }
+ if (options.global_actions) {
+ tmpl += '<ul class="manage-table-actions">';
+ var show_popup = (options.global_actions.length >= 3);
+ if (show_popup) {
+ tmpl += '<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li>' +
+ '<div popupmenu="popup-global-actions">';
+ }
+ for (i in options.global_actions) {
+ var action = options.global_actions[i];
+ var label_cls = '';
+ if (action.inbound) {
+ label_cls = 'use-inbound'
+ } else {
+ label_cls = 'use-outbound'
+ }
+ tmpl += '<li>' +
+ '<a class="action-button ' + label_cls + '" href="' + action.url_args + '" onclick="return false;">' + action.label + '</a>' +
+ '</li>';
+ }
+ if (show_popup) {
+ tmpl += '</div>';
+ }
+ tmpl += '</ul>';
+ }
+ if (options.insert) {
+ tmpl += options.insert;
+ }
+
+ // add grid filters
+ tmpl += this.grid_filters(options);
+ tmpl += '</div>'
+
+ // return template
+ return tmpl;
+ },
+
+ // template
+ header: function(options) {
+
+ // start
+ var tmpl = '<tr>';
+
+ // add checkbox
+ if (options.show_item_checkboxes) {
+ tmpl += '<th>';
+ if (options.items.length > 0) {
+ tmpl += '<input type="checkbox" id="check_all" name=select_all_checkbox value="true">' +
+ '<input type="hidden" name=select_all_checkbox value="true">';
+ }
+ tmpl += '</th>';
+ }
+
+ // create header elements
+ for (var i in options.columns) {
+ var column = options.columns[i];
+ if (column.visible) {
+ tmpl += '<th id="' + column.key + '-header">';
+ if (column.href) {
+ tmpl += '<a href="' + column.href + '" class="sort-link" sort_key="' + column.key + '">' + column.label + '</a>';
+ } else {
+ tmpl += column.label;
+ }
+ tmpl += '<span class="sort-arrow">' + column.extra + '</span>' +
+ '</th>';
+ }
+ }
+
+ // finalize
+ tmpl += '</tr>';
+
+ // return template
+ return tmpl;
+ },
+
+ // template
+ body: function(options) {
+ // initialize
+ var tmpl = '';
+ var num_rows_rendered = 0;
+ var items_length = options.items.length;
+
+ // empty grid?
+ if (items_length == 0) {
+ // No results.
+ tmpl += '<tr><td colspan="100"><em>No Items</em></td></tr>';
+ num_rows_rendered = 1;
+ }
+
+ // create rows
+ for (var i in options.items) {
+
+ // encode ids
+ var item = options.items[i];
+ var encoded_id = item.encode_id;
+ var popupmenu_id = 'grid-' + i + '-popup';
+
+ // Tag current
+ tmpl += '<tr ';
+ if (options.current_item_id == item.id) {
+ tmpl += 'class="current"';
+ }
+ tmpl += '>';
+
+ // Item selection column
+ if (options.show_item_checkboxes) {
+ tmpl += '<td style="width: 1.5em;">' +
+ '<input type="checkbox" name="id" value="' + encoded_id + '" id="' + encoded_id + '" class="grid-row-select-checkbox" />' +
+ '</td>';
+ }
+
+ // Data columns
+ for (j in options.columns) {
+ var column = options.columns[j];
+ if (column.visible) {
+ // Nowrap
+ var nowrap = '';
+ if (column.nowrap) {
+ nowrap = 'style="white-space:nowrap;"';
+ }
+
+ // get column settings
+ var column_settings = item.column_config[column.label];
+
+ // load attributes
+ var link = column_settings.link;
+ var value = column_settings.value;
+ var inbound = column_settings.inbound;
+
+ // unescape value
+ if (jQuery.type( value ) === 'string') {
+ value = value.replace(/\/\//g, '/');
+ }
+
+ // Attach popup menu?
+ var id = '';
+ var cls = '';
+ if (column.attach_popup) {
+ id = 'grid-' + i + '-popup';
+ cls = 'menubutton';
+ if (link != '') {
+ cls += ' split';
+ }
+ cls += ' popup';
+ }
+
+ // Check for row wrapping
+ tmpl += '<td ' + nowrap + '>';
+
+ // Link
+ if (link) {
+ if (options.operations.length != 0) {
+ tmpl += '<div id="' + id + '" class="' + cls + '" style="float: left;">';
+ }
+
+ var label_class = '';
+ if (inbound) {
+ label_class = 'use-inbound';
+ } else {
+ label_class = 'use-outbound';
+ }
+ tmpl += '<a class="label ' + label_class + '" href="' + link + '" onclick="return false;">' + value + '</a>';
+ if (options.operations.length != 0) {
+ tmpl += '</div>';
+ }
+ } else {
+ tmpl += '<div id="' + id + '" class="' + cls + '"><label id="' + column.label_id_prefix + encoded_id + '" for="' + encoded_id + '">' + value + '</label></div>';
+ }
+ tmpl += '</td>';
+ }
+ }
+ tmpl += '</tr>';
+ num_rows_rendered++;
+ }
+ return tmpl;
+ },
+
+ // template
+ footer: function(options) {
+
+ // create template string
+ var tmpl = '';
+
+ // paging
+ if (options.use_paging && options.num_pages > 1) {
+ // get configuration
+ var num_page_links = options.num_page_links;
+ var cur_page_num = options.cur_page_num;
+ var num_pages = options.num_pages;
+
+ // First pass on min page.
+ var page_link_range = num_page_links / 2;
+ var min_page = cur_page_num - page_link_range
+ var min_offset = 0;
+ if (min_page == 0) {
+ // Min page is too low.
+ min_page = 1;
+ min_offset = page_link_range - ( cur_page_num - min_page );
+ }
+
+ // Set max page.
+ var max_range = page_link_range + min_offset;
+ var max_page = cur_page_num + max_range;
+ if (max_page <= num_pages) {
+ // Max page is fine.
+ max_offset = 0;
+ } else {
+ // Max page is too high.
+ max_page = num_pages;
+ // +1 to account for the +1 in the loop below.
+ max_offset = max_range - ( max_page + 1 - cur_page_num );
+ }
+
+ // Second and final pass on min page to add any unused
+ // offset from max to min.
+ if (max_offset != 0) {
+ min_page -= max_offset
+ if (min_page < 1) {
+ min_page = 1
+ }
+ }
+
+ // template header
+ tmpl += '<tr id="page-links-row">';
+ if (options.show_item_checkboxes) {
+ tmpl += '<td></td>';
+ }
+ tmpl += '<td colspan="100">' +
+ '<span id="page-link-container">' +
+ 'Page:';
+
+ if (min_page > 1) {
+ tmpl += '<span class="page-link" id="page-link-1"><a href="' + this.grid.get_url({page : page_index}) + '" page_num="1" onclick="return false;">1</a></span> ...';
+ }
+
+ // create page urls
+ for (var page_index = min_page; page_index < max_page + 1; page_index++) {
+
+ if (page_index == options.cur_page_num) {
+ tmpl += '<span class="page-link inactive-link" id="page-link-' + page_index + '">' + page_index + '</span>';
+ } else {
+ tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="' + this.grid.get_url({page : page_index}) + '" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>';
+ }
+ }
+
+ // show last page
+ if (max_page < num_pages) {
+ tmpl += '...' +
+ '<span class="page-link" id="page-link-' + num_pages + '"><a href="' + this.grid.get_url({page : num_pages}) + '" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>';
+ }
+ tmpl += '</span>';
+
+ // Show all link
+ tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="' + this.grid.get_url({page : 'all'}) + '" onclick="return false;" page_num="all">Show All</a></span>' +
+ '</td>' +
+ '</tr>';
+ }
+
+ // Grid operations for multiple items.
+ if (options.show_item_checkboxes) {
+ // start template
+ tmpl += '<tr>' +
+ '<input type="hidden" id="operation" name="operation" value="">' +
+ '<td></td>' +
+ '<td colspan="100">' +
+ 'For <span class="grid-selected-count"></span> selected ' + options.get_class_plural + ': ';
+
+ // configure buttons for operations
+ for (i in options.operations) {
+ var operation = options.operations[i];
+ if (operation.allow_multiple) {
+ tmpl += '<input type="button" value="' + operation.label + '" class="operation-button action-button"> ';
+ }
+ }
+
+ // finalize template
+ tmpl += '</td>' +
+ '</tr>';
+ }
+
+ // count global operations
+ var found_global = false;
+ for (i in options.operations) {
+ if (options.operations[i].global_operation) {
+ found_global = true;
+ break;
+ }
+ }
+
+ // add global operations
+ if (found_global) {
+ tmpl += '<tr>' +
+ '<td colspan="100">';
+ for (i in options.operations) {
+ var operation = options.operations[i];
+ if (operation.global_operation) {
+ tmpl += '<a class="action-button" href="' + operation.global_operation + '">' + operation.label + '</a>';
+ }
+ }
+ tmpl += '</td>' +
+ '</tr>';
+ }
+
+ // add legend
+ if (options.legend) {
+ tmpl += '<tr>' +
+ '<td colspan="100">' + options.legend + '</td>' +
+ '</tr>';
+ }
+
+ // return
+ return tmpl;
+ },
+
+ // template
+ message: function(options) {
+ return '<p>' +
+ '<div class="' + options.status + 'message transient-message">' + options.message + '</div>' +
+ '<div style="clear: both"></div>' +
+ '</p>';
+ },
+
+ // template
+ grid_filters: function (options) {
+
+ // get filters
+ var default_filter_dict = options.default_filter_dict;
+ var filters = options.filters;
+
+ // show advanced search if flag set or if there are filters for advanced search fields
+ var advanced_search_display = 'none';
+ if (options.advanced_search) {
+ advanced_search_display = 'block';
+ }
+
+ // identify columns with advanced filtering
+ var show_advanced_search_link = false;
+ for (var i in options.columns) {
+ var column = options.columns[i];
+ if (column.filterable == 'advanced') {
+ var column_key = column.key;
+ var f_key = filters[column_key];
+ var d_key = default_filter_dict[column_key];
+ if (f_key && d_key && f_key != d_key) {
+ advanced_search_display = 'block';
+ }
+ show_advanced_search_link = true;
+ }
+ }
+
+ // hide standard search if advanced is shown
+ var standard_search_display = 'block';
+ if (advanced_search_display == 'block') {
+ standard_search_display = 'none';
+ }
+
+ //
+ // standard search
+ //
+ var tmpl = '<div id="standard-search" style="display: ' + standard_search_display + ';">' +
+ '<table>' +
+ '<tr>' +
+ '<td style="padding: 0;">' +
+ '<table>';
+
+ // add standard filters
+ for (var i in options.columns) {
+ var column = options.columns[i];
+ if (column.filterable == 'standard') {
+ tmpl += this.grid_column_filter(options, column);
+ }
+ }
+
+ // finalize standard search
+ tmpl += '</table>' +
+ '</td>' +
+ '</tr>' +
+ '<tr>' +
+ '<td>';
+
+ // show advanced search link in standard display
+ if (show_advanced_search_link) {
+ tmpl += '<a href="" class="advanced-search-toggle">Advanced Search</a>';
+ }
+
+ // finalize standard search display
+ tmpl += '</td>' +
+ '</tr>' +
+ '</table>' +
+ '</div>';
+
+ //
+ // advanced search
+ //
+ tmpl += '<div id="advanced-search" style="display: ' + advanced_search_display + '; margin-top: 5px; border: 1px solid #ccc;">' +
+ '<table>' +
+ '<tr>' +
+ '<td style="text-align: left" colspan="100">' +
+ '<a href="" class="advanced-search-toggle">Close Advanced Search</a>' +
+ '</td>' +
+ '</tr>';
+
+ // add advanced filters
+ for (var i in options.columns) {
+ var column = options.columns[i];
+ if (column.filterable == 'advanced') {
+ tmpl += this.grid_column_filter(options, column);
+ }
+ }
+
+ // finalize advanced search template
+ tmpl += '</table>' +
+ '</div>';
+
+ // return template
+ return tmpl;
+ },
+
+ // template
+ grid_column_filter: function(options, column) {
+
+ // collect parameters
+ var default_filter_dict = options.default_filter_dict;
+ var filters = options.filters;
+ var column_label = column.label;
+ var column_key = column.key;
+ if (column.filterable == 'advanced') {
+ column_label = column_label.toLowerCase();
+ }
+
+ // start
+ var tmpl = '<tr>';
+
+ if (column.filterable == 'advanced') {
+ tmpl += '<td align="left" style="padding-left: 10px">' + column_label + ':</td>';
+ }
+ tmpl += '<td style="padding-bottom: 1px;">';
+ if (column.is_text) {
+ tmpl += '<form class="text-filter-form" column_key="' + column_key + '" action="' + options.url + '" method="get" >';
+ // Carry forward filtering criteria with hidden inputs.
+ for (i in options.columns) {
+ var temp_column = options.columns[i];
+ var filter_value = filters[temp_column.key];
+ if (filter_value) {
+ if (filter_value != 'All') {
+ if (temp_column.is_text) {
+ filter_value = JSON.stringify( filter_value )
+ }
+ tmpl += '<input type="hidden" id="' + temp_column.key + '" name="f-' + temp_column.key + '" value="' + filter_value + '"/>';
+ }
+ }
+ }
+ // Print current filtering criteria and links to delete.
+ tmpl += '<span id="' + column_key + '-filtering-criteria">';
+
+ // add filters
+ var column_filter = filters[column_key];
+ if (column_filter) {
+ // identify type
+ var type = jQuery.type(column_filter);
+
+ // single filter value
+ if (type == 'string') {
+ if (column_filter != 'All') {
+ // append template
+ tmpl += this.filter_element(column_key, column_filter);
+ }
+ }
+
+ // multiple filter values
+ if (type == 'array') {
+ for (var i in column_filter ) {
+ // get filter
+ var filter = column_filter[i];
+
+ // copy filters and remove entry
+ var params = column_filter;
+ params = params.slice(i);
+
+ // append template
+ tmpl += this.filter_element(column_key, filter);
+ }
+ }
+ }
+
+ // close span
+ tmpl += '</span>';
+
+ // Set value, size of search input field. Minimum size is 20 characters.
+ var value = '';
+ if (column.filterable == 'standard') {
+ value = column.label.toLowerCase();
+ var size = value.length;
+ if (size < 20) {
+ size = 20;
+ }
+ // +4 to account for search icon/button.
+ size = size + 4;
+ }
+
+ // print input field for column
+ tmpl += '<span class="search-box">' +
+ '<input class="search-box-input" id="input-' + column_key + '-filter" name="f-' + column_key + '" type="text" placeholder="' + value + '" size="' + size + '"/>' +
+ //'<button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;">' +
+ // '<i class="fa fa-plus-circle" style="font-size: 1.2em;"></i>' +
+ //'</button>' +
+ '</span>' +
+ '</form>';
+ } else {
+ // filter criteria
+ tmpl += '<span id="' + column_key + '-filtering-criteria">';
+
+ // add category filters
+ var seperator = false;
+ for (cf_label in options.categorical_filters[column_key]) {
+ // get category filter
+ var cf = options.categorical_filters[column_key][cf_label];
+
+ // each filter will have only a single argument, so get that single argument
+ var cf_key = '';
+ var cf_arg = '';
+ for (key in cf) {
+ cf_key = key;
+ cf_arg = cf[key];
+ }
+
+ // add seperator
+ if (seperator) {
+ tmpl += ' | ';
+ }
+ seperator = true;
+
+ // add category
+ var filter = filters[column_key];
+ if (filter && cf[column_key] && filter == cf_arg) {
+ tmpl += '<span class="categorical-filter ' + column_key + '-filter current-filter">' + cf_label + '</span>';
+ } else {
+ tmpl += '<span class="categorical-filter ' + column_key + '-filter">' +
+ '<a href="javascript:void(0);" filter_key="' + cf_key + '" filter_val="' + cf_arg + '">' + cf_label + '</a>' +
+ '</span>';
+ }
+ }
+ tmpl += '</span>';
+ }
+ tmpl += '</td>' +
+ '</tr>';
+
+ // return template
+ return tmpl;
+ },
+
+ // template for filter items
+ filter_element: function(filter_key, filter_value) {
+ return '<span class="text-filter-val">' + filter_value +
+ '<a href="javascript:void(0);" filter_key="' + filter_key + '" filter_val="' + filter_value + '">' +
+ '<i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/>' +
+ '</a>' +
+ '</span>';
+
+ }
+};
+
+});
\ No newline at end of file
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7637cfbea32e/
Changeset: 7637cfbea32e
Branch: job-search
User: Kyle Ellrott
Date: 2014-01-29 21:51:37
Summary: Default Merge
Affected #: 429 files
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 buildbot_setup.sh
--- a/buildbot_setup.sh
+++ b/buildbot_setup.sh
@@ -4,28 +4,6 @@
: ${HOSTTYPE:=`uname -m`}
-# link to HYPHY is arch-dependent
-case "$OSTYPE" in
- linux-gnu)
- kernel=`uname -r | cut -f1,2 -d.`
- HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy"
- ;;
- darwin*)
- this_minor=`uname -r | awk -F. '{print ($1-4)}'`
- machine=`machine`
- for minor in `jot - 3 $this_minor 1`; do
- HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy"
- [ -d "$HYPHY" ] && break
- done
- [ ! -d "$HYPHY" ] && unset HYPHY
- ;;
- solaris2.10)
- # For the psu-production builder which is Solaris, but jobs run on a
- # Linux cluster
- HYPHY="/galaxy/software/linux2.6-x86_64/hyphy"
- ;;
-esac
-
LINKS="
/galaxy/data/location/add_scores.loc
/galaxy/data/location/all_fasta.loc
@@ -121,12 +99,6 @@
ln -sf $link tool-data
done
- if [ -d "$HYPHY" ]; then
- echo "Linking $HYPHY"
- rm -f tool-data/HYPHY
- ln -sf $HYPHY tool-data/HYPHY
- fi
-
if [ -d "$JARS" ]; then
echo "Linking $JARS"
rm -f tool-data/shared/jars
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -37,17 +37,27 @@
this.chart_view = new ChartView(this);
this.viewport_view = new ViewportView(this);
- // portlet
- this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'});
+ // append view port to charts viewer
+ this.charts_view.append(this.viewport_view.$el);
+
+ // create portlet
+ if (!this.options.config.widget) {
+ this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'});
+ } else {
+ this.portlet = $('<div></div>');
+ }
+
+ // append views
this.portlet.append(this.charts_view.$el);
this.portlet.append(this.group_view.$el);
this.portlet.append(this.chart_view.$el);
- // append main
- this.charts_view.append(this.viewport_view.$el);
-
- // set elements
- this.setElement(this.portlet.$el);
+ // set element
+ if (!this.options.config.widget) {
+ this.setElement(this.portlet.$el);
+ } else {
+ this.setElement(this.portlet);
+ }
// hide views
this.group_view.$el.hide();
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 config/plugins/visualizations/charts/static/library/portlet.js
--- a/config/plugins/visualizations/charts/static/library/portlet.js
+++ b/config/plugins/visualizations/charts/static/library/portlet.js
@@ -116,21 +116,38 @@
showOperation: function(id) {
this.$operations.find('#' + id).show();
},
-
+
+ // set operation
+ setOperation: function(id, callback) {
+ var $el = this.$operations.find('#' + id);
+ $el.off('click');
+ $el.on('click', callback);
+ },
+
+ // label
+ label: function(new_label) {
+ var $el = this.$el.find('#label');
+ if (new_label) {
+ $el.html(new_label);
+ }
+ return $el.html();
+ },
+
// fill regular modal template
template: function(options) {
var tmpl = '<div class="toolForm">';
- if (options.label) {
- tmpl += '<div id="title" class="toolFormTitle" style="padding-bottom: 7px;">' +
+ if (options.label || options.icon) {
+ tmpl += '<div id="title" class="toolFormTitle" style="overflow:hidden;">' +
'<div id="operations" style="float: right;"></div>' +
- '<div>';
+ '<div style="overflow: hidden">';
if (options.icon)
- tmpl += '<i style="font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>';
+ tmpl += '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>';
- tmpl += options.label +
- '</div>' +
+ tmpl += '<div id="label" style="padding-top: 2px; float: left;">' + options.label + '</div>';
+
+ tmpl += '</div>' +
'</div>';
}
tmpl += '<div id="body" class="toolFormBody">';
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 config/plugins/visualizations/charts/static/models/datasets.js
--- a/config/plugins/visualizations/charts/static/models/datasets.js
+++ b/config/plugins/visualizations/charts/static/models/datasets.js
@@ -6,9 +6,9 @@
{
// options
optionsDefault : {
- limit : 20,
+ limit : 500,
pace : 1000,
- max : 5
+ max : 2
},
// list
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 config/plugins/visualizations/charts/static/views/charts.js
--- a/config/plugins/visualizations/charts/static/views/charts.js
+++ b/config/plugins/visualizations/charts/static/views/charts.js
@@ -45,25 +45,6 @@
self.app.chart_view.$el.show();
}
}),
- 'edit' : new Ui.ButtonIcon({
- icon : 'fa-pencil',
- tooltip: 'Edit',
- onclick: function() {
- // check if element has been selected
- var chart_id = self.table.value();
- if (!chart_id) {
- return;
- }
-
- // get chart
- var chart = self.app.charts.get(chart_id);
- self.app.chart.copy(chart);
-
- // show edit
- self.$el.hide();
- self.app.chart_view.$el.show();
- }
- }),
'delete' : new Ui.ButtonIcon({
icon : 'fa-minus',
tooltip: 'Delete',
@@ -100,7 +81,9 @@
this.portlet.append(this.table.$el);
// append to main
- this.$el.append(this.portlet.$el);
+ if (!this.app.options.config.widget) {
+ this.$el.append(this.portlet.$el);
+ }
// events
var self = this;
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -25,8 +25,16 @@
// add table to portlet
this.portlet = new Portlet({
+ label : '',
+ icon : 'fa-signal',
height : this.options.height,
- overflow : 'hidden'
+ overflow : 'hidden',
+ operations : {
+ 'edit' : new Ui.ButtonIcon({
+ icon : 'fa-gear',
+ tooltip : 'Configure'
+ })
+ }
});
// set this element
@@ -53,15 +61,30 @@
},
// show
- show: function(id) {
+ show: function(chart_id) {
// hide all
this.$el.find('svg').hide();
- var item = this.list[id];
+ // identify selected item from list
+ var item = this.list[chart_id];
if (item) {
// show selected chart
this.$el.find(item.svg_id).show();
+ // get chart
+ var chart = self.app.charts.get(chart_id);
+
+ // update portlet
+ this.portlet.label(chart.get('title'));
+ this.portlet.setOperation('edit', function() {
+ // get chart
+ self.app.chart.copy(chart);
+
+ // show edit
+ self.app.charts_view.$el.hide();
+ self.app.chart_view.$el.show();
+ });
+
// this trigger d3 update events
$(window).trigger('resize');
}
@@ -69,11 +92,17 @@
// add
_addChart: function(chart) {
+ // link this
+ var self = this;
+
+ // backup chart details
+ var chart_id = chart.id;
+
// make sure that svg does not exist already
- this._removeChart(chart.id);
+ this._removeChart(chart_id);
// create id
- var svg_id = '#svg_' + chart.id;
+ var svg_id = '#svg_' + chart_id;
// create element
var chart_el = $(this._template({id: svg_id, height : this.options.height}));
@@ -82,7 +111,7 @@
this.portlet.append(chart_el);
// backup id
- this.list[chart.id] = {
+ this.list[chart_id] = {
svg_id : svg_id
}
@@ -129,8 +158,8 @@
chart_index++;
});
- // add view
- self.list[chart.id].view = view;
+ // show
+ self.show(chart_id);
});
},
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 doc/source/lib/galaxy.tools.util.rst
--- a/doc/source/lib/galaxy.tools.util.rst
+++ b/doc/source/lib/galaxy.tools.util.rst
@@ -9,14 +9,6 @@
:undoc-members:
:show-inheritance:
-:mod:`hyphy_util` Module
-------------------------
-
-.. automodule:: galaxy.tools.util.hyphy_util
- :members:
- :undoc-members:
- :show-inheritance:
-
:mod:`maf_utilities` Module
---------------------------
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 install_and_test_tool_shed_repositories.sh
--- a/install_and_test_tool_shed_repositories.sh
+++ b/install_and_test_tool_shed_repositories.sh
@@ -48,6 +48,14 @@
fi
fi
+if [ -z $GALAXY_INSTALL_TEST_SHED_TOOL_PATH ] ; then
+ export GALAXY_INSTALL_TEST_SHED_TOOL_PATH='/tmp/shed_tools'
+fi
+
+if [ ! -d $GALAXY_INSTALL_TEST_SHED_TOOL_PATH ] ; then
+ mkdir -p $GALAXY_INSTALL_TEST_SHED_TOOL_PATH
+fi
+
test_tool_dependency_definitions () {
# Test installation of repositories of type tool_dependency_definition.
if [ -f $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete ] ; then
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -58,7 +58,7 @@
self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root )
self.cookie_path = kwargs.get( "cookie_path", "/" )
self.genome_data_path = kwargs.get( "genome_data_path", "tool-data/genome" )
- self.rsync_url = kwargs.get( "rsync_url", "rsync://scofield.bx.psu.edu/indexes" )
+ self.rsync_url = kwargs.get( "rsync_url", "rsync://datacache.galaxyproject.org/indexes" )
# Galaxy OpenID settings
self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' )
@@ -122,6 +122,7 @@
self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) )
self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
+ self.normalize_remote_user_email = string_as_bool( kwargs.get( "normalize_remote_user_email", "False" ) )
self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
self.remote_user_header = kwargs.get( "remote_user_header", 'HTTP_REMOTE_USER' )
self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
@@ -151,6 +152,7 @@
h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ]
self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h )
self.admin_users = kwargs.get( "admin_users", "" )
+ self.reset_password_length = int( kwargs.get('reset_password_length', '15') )
self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu")
self.error_email_to = kwargs.get( 'error_email_to', None )
self.activation_email = kwargs.get( 'activation_email', None )
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/datatypes/converters/bam_to_bai.xml
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,4 +1,7 @@
<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" hidden="true">
+ <requirements>
+ <requirement type="package">samtools</requirement>
+ </requirements><command>samtools index $input1 $output1</command><inputs><page>
@@ -10,4 +13,4 @@
</outputs><help></help>
-</tool>
\ No newline at end of file
+</tool>
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/datatypes/converters/sam_to_bam.xml
--- a/lib/galaxy/datatypes/converters/sam_to_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bam.xml
@@ -5,6 +5,9 @@
To fix this: (a) merge sam_to_bam tool in tools with this conversion (like fasta_to_len
conversion); and (b) define a datatype-specific way to set converter parameters.
-->
+ <requirements>
+ <requirement type="package">samtools</requirement>
+ </requirements><command interpreter="python">sam_to_bam.py $input1 $output</command><inputs><param name="input1" type="data" format="sam" label="SAM file"/>
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -275,7 +275,7 @@
cursor = f.read(1)
return to_json_string( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } )
- def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None):
+ def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd):
preview = util.string_as_bool( preview )
if chunk:
return self.get_chunk(trans, dataset, chunk)
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -789,8 +789,8 @@
# If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
if self.tool:
self.tool.job_failed( self, message, exception )
- if self.app.config.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED):
- self.cleanup()
+ delete_files = self.app.config.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED)
+ self.cleanup( delete_files=delete_files )
def pause( self, job=None, message=None ):
if job is None:
@@ -883,11 +883,10 @@
# We set final_job_state to use for dataset management, but *don't* set
# job.state until after dataset collection to prevent history issues
- if job.states.ERROR != job.state:
- if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )):
- final_job_state = job.states.OK
- else:
- final_job_state = job.states.ERROR
+ if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ):
+ final_job_state = job.states.OK
+ else:
+ final_job_state = job.states.ERROR
if self.version_string_cmd:
version_filename = self.get_version_string_path()
@@ -1067,22 +1066,26 @@
self.sa_session.flush()
log.debug( 'job %d ended' % self.job_id )
- if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ):
- self.cleanup()
+ delete_files = self.app.config.cleanup_job == 'always' or ( job.state == job.states.OK and self.app.config.cleanup_job == 'onsuccess' )
+ self.cleanup( delete_files=delete_files )
def check_tool_output( self, stdout, stderr, tool_exit_code, job ):
return check_output( self.tool, stdout, stderr, tool_exit_code, job )
- def cleanup( self ):
- # remove temporary files
+ def cleanup( self, delete_files=True ):
+ # At least one of these tool cleanup actions (job import), is needed
+ # for thetool to work properly, that is why one might want to run
+ # cleanup but not delete files.
try:
- for fname in self.extra_filenames:
- os.remove( fname )
- self.external_output_metadata.cleanup_external_metadata( self.sa_session )
+ if delete_files:
+ for fname in self.extra_filenames:
+ os.remove( fname )
+ self.external_output_metadata.cleanup_external_metadata( self.sa_session )
galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session )
galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.app, self.job_id ).cleanup_after_job()
galaxy.tools.genome_index.GenomeIndexToolWrapper( self.job_id ).postprocessing( self.sa_session, self.app )
- self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id))
+ if delete_files:
+ self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id))
except:
log.exception( "Unable to cleanup job %d" % self.job_id )
@@ -1520,8 +1523,8 @@
# if the job was deleted, don't finish it
if task.state == task.states.DELETED:
# Job was deleted by an administrator
- if self.app.config.cleanup_job in ( 'always', 'onsuccess' ):
- self.cleanup()
+ delete_files = self.app.config.cleanup_job in ( 'always', 'onsuccess' )
+ self.cleanup( delete_files=delete_files )
return
elif task.state == task.states.ERROR:
self.fail( task.info )
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -35,7 +35,9 @@
PasswordField, SelectField, TextArea, TextField, WorkflowField,
WorkflowMappingField)
from sqlalchemy.orm import object_session
+from sqlalchemy.orm import joinedload
from sqlalchemy.sql.expression import func
+from sqlalchemy import not_
log = logging.getLogger( __name__ )
@@ -898,6 +900,22 @@
rval = galaxy.datatypes.data.nice_size( rval )
return rval
+ @property
+ def active_datasets_children_and_roles( self ):
+ if not hasattr(self, '_active_datasets_children_and_roles'):
+ db_session = object_session( self )
+ query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ). \
+ filter( not_( HistoryDatasetAssociation.deleted ) ). \
+ order_by( HistoryDatasetAssociation.table.c.hid.asc() ). \
+ options(
+ joinedload("children"),
+ joinedload("dataset"),
+ joinedload("dataset.actions"),
+ joinedload("dataset.actions.role"),
+ )
+ self._active_datasets_children_and_roles = query.all()
+ return self._active_datasets_children_and_roles
+
def contents_iter( self, **kwds ):
"""
Fetch filtered list of contents of history.
@@ -909,10 +927,10 @@
query = query.order_by( HistoryDatasetAssociation.table.c.hid.asc() )
deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) )
if deleted is not None:
- query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) )
+ query = query.filter( HistoryDatasetAssociation.deleted == deleted )
visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) )
if visible is not None:
- query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) )
+ query = query.filter( HistoryDatasetAssociation.visible == visible )
if 'ids' in kwds:
ids = kwds['ids']
max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH)
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -213,7 +213,7 @@
db_datasets[ "chromInfo" ] = db_dataset
incoming[ "chromInfo" ] = db_dataset.file_name
else:
- # -- Get chrom_info from either a custom or built-in build. --
+ # -- Get chrom_info (len file) from either a custom or built-in build. --
chrom_info = None
if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ):
@@ -226,9 +226,13 @@
# condition below to avoid getting chrom_info when running the
# fasta-to-len converter.
if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len':
+ # Build is defined by fasta; get len file, which is obtained from converting fasta.
build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
-
+ elif 'len' in custom_build_dict:
+ # Build is defined by len file, so use it.
+ chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
+
if not chrom_info:
# Default to built-in build.
chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey )
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -332,7 +332,7 @@
is_binary=is_binary,
link_data_only=link_data_only,
uuid=uuid_str,
- to_posix_lines=uploaded_dataset.to_posix_lines,
+ to_posix_lines=getattr(uploaded_dataset, "to_posix_lines", True),
space_to_tab=uploaded_dataset.space_to_tab,
in_place=trans.app.config.external_chown_script is None,
path=uploaded_dataset.path )
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/imp_exp/__init__.py
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -1,4 +1,8 @@
-import os, shutil, logging, tempfile, json
+import os
+import shutil
+import logging
+import tempfile
+import json
from galaxy import model
from galaxy.tools.parameters.basic import UnvalidatedValue
from galaxy.web.framework.helpers import to_unicode
@@ -8,6 +12,7 @@
log = logging.getLogger(__name__)
+
def load_history_imp_exp_tools( toolbox ):
""" Adds tools for importing/exporting histories to archives. """
# Use same process as that used in load_external_metadata_tool; see that
@@ -42,6 +47,7 @@
toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool
log.debug( "Loaded history import tool: %s", history_imp_tool.id )
+
class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ):
"""
Class provides support for performing jobs that import a history from
@@ -144,23 +150,23 @@
metadata = dataset_attrs['metadata']
# Create dataset and HDA.
- hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ),
- extension = dataset_attrs['extension'],
- info = dataset_attrs['info'].encode( 'utf-8' ),
- blurb = dataset_attrs['blurb'],
- peek = dataset_attrs['peek'],
- designation = dataset_attrs['designation'],
- visible = dataset_attrs['visible'],
- dbkey = metadata['dbkey'],
- metadata = metadata,
- history = new_history,
- create_dataset = True,
- sa_session = self.sa_session )
+ hda = model.HistoryDatasetAssociation( name=dataset_attrs['name'].encode( 'utf-8' ),
+ extension=dataset_attrs['extension'],
+ info=dataset_attrs['info'].encode( 'utf-8' ),
+ blurb=dataset_attrs['blurb'],
+ peek=dataset_attrs['peek'],
+ designation=dataset_attrs['designation'],
+ visible=dataset_attrs['visible'],
+ dbkey=metadata['dbkey'],
+ metadata=metadata,
+ history=new_history,
+ create_dataset=True,
+ sa_session=self.sa_session )
hda.state = hda.states.OK
self.sa_session.add( hda )
self.sa_session.flush()
- new_history.add_dataset( hda, genome_build = None )
- hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history.
+ new_history.add_dataset( hda, genome_build=None )
+ hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history.
# TODO: Is there a way to recover permissions? Is this needed?
#permissions = trans.app.security_agent.history_get_default_permissions( new_history )
#trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions )
@@ -273,6 +279,7 @@
jiha.job.stderr += "Error cleaning up history import job: %s" % e
self.sa_session.flush()
+
class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ):
"""
Class provides support for performing jobs that export a history to an
@@ -317,23 +324,23 @@
""" Encode an HDA, default encoding for everything else. """
if isinstance( obj, trans.app.model.HistoryDatasetAssociation ):
return {
- "__HistoryDatasetAssociation__" : True,
- "create_time" : obj.create_time.__str__(),
- "update_time" : obj.update_time.__str__(),
- "hid" : obj.hid,
- "name" : to_unicode( obj.name ),
- "info" : to_unicode( obj.info ),
- "blurb" : obj.blurb,
- "peek" : obj.peek,
- "extension" : obj.extension,
- "metadata" : prepare_metadata( dict( obj.metadata.items() ) ),
- "parent_id" : obj.parent_id,
- "designation" : obj.designation,
- "deleted" : obj.deleted,
- "visible" : obj.visible,
- "file_name" : obj.file_name,
- "annotation" : to_unicode( getattr( obj, 'annotation', '' ) ),
- "tags" : get_item_tag_dict( obj ),
+ "__HistoryDatasetAssociation__": True,
+ "create_time": obj.create_time.__str__(),
+ "update_time": obj.update_time.__str__(),
+ "hid": obj.hid,
+ "name": to_unicode( obj.name ),
+ "info": to_unicode( obj.info ),
+ "blurb": obj.blurb,
+ "peek": obj.peek,
+ "extension": obj.extension,
+ "metadata": prepare_metadata( dict( obj.metadata.items() ) ),
+ "parent_id": obj.parent_id,
+ "designation": obj.designation,
+ "deleted": obj.deleted,
+ "visible": obj.visible,
+ "file_name": obj.file_name,
+ "annotation": to_unicode( getattr( obj, 'annotation', '' ) ),
+ "tags": get_item_tag_dict( obj ),
}
if isinstance( obj, UnvalidatedValue ):
return obj.__str__()
@@ -347,15 +354,15 @@
# Write history attributes to file.
history = jeha.history
history_attrs = {
- "create_time" : history.create_time.__str__(),
- "update_time" : history.update_time.__str__(),
- "name" : to_unicode( history.name ),
- "hid_counter" : history.hid_counter,
- "genome_build" : history.genome_build,
- "annotation" : to_unicode( self.get_item_annotation_str( trans.sa_session, history.user, history ) ),
- "tags" : get_item_tag_dict( history ),
- "includes_hidden_datasets" : include_hidden,
- "includes_deleted_datasets" : include_deleted
+ "create_time": history.create_time.__str__(),
+ "update_time": history.update_time.__str__(),
+ "name": to_unicode( history.name ),
+ "hid_counter": history.hid_counter,
+ "genome_build": history.genome_build,
+ "annotation": to_unicode( self.get_item_annotation_str( trans.sa_session, history.user, history ) ),
+ "tags": get_item_tag_dict( history ),
+ "includes_hidden_datasets": include_hidden,
+ "includes_deleted_datasets": include_deleted
}
history_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name
history_attrs_out = open( history_attrs_filename, 'w' )
@@ -391,7 +398,7 @@
# Get the associated job, if any. If this hda was copied from another,
# we need to find the job that created the origial hda
job_hda = hda
- while job_hda.copied_from_history_dataset_association: #should this check library datasets as well?
+ while job_hda.copied_from_history_dataset_association: # should this check library datasets as well?
job_hda = job_hda.copied_from_history_dataset_association
if not job_hda.creating_job_associations:
# No viable HDA found.
@@ -472,4 +479,3 @@
shutil.rmtree( temp_dir )
except Exception, e:
log.debug( 'Error deleting directory containing attribute files (%s): %s' % ( temp_dir, e ) )
-
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
--- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
+++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
@@ -6,19 +6,25 @@
--[url|file] source type, either a URL or a file.
"""
-import sys, optparse, tarfile, tempfile, urllib2, math
+import sys
+import optparse
+import tarfile
+import tempfile
+import urllib2
+import math
# Set max size of archive/file that will be handled to be 100 GB. This is
# arbitrary and should be adjusted as needed.
MAX_SIZE = 100 * math.pow( 2, 30 )
+
def url_to_file( url, dest_file ):
"""
Transfer a file from a remote URL to a temporary file.
"""
try:
url_reader = urllib2.urlopen( url )
- CHUNK = 10 * 1024 # 10k
+ CHUNK = 10 * 1024 # 10k
total = 0
fp = open( dest_file, 'wb')
while True:
@@ -35,6 +41,7 @@
print "Exception getting file from URL: %s" % e, sys.stderr
return None
+
def unpack_archive( archive_file, dest_dir ):
"""
Unpack a tar and/or gzipped archive into a destination directory.
@@ -63,4 +70,4 @@
# Unpack archive.
unpack_archive( archive_file, dest_dir )
except Exception, e:
- print "Error unpacking tar/gz archive: %s" % e, sys.stderr
\ No newline at end of file
+ print "Error unpacking tar/gz archive: %s" % e, sys.stderr
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1653,7 +1653,7 @@
field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected )
# Also collect children via association object
dataset_collector( hda.children, hid )
- dataset_collector( history.active_datasets, None )
+ dataset_collector( history.active_datasets_children_and_roles, None )
some_data = bool( field.options )
if some_data:
if value is None or len( field.options ) == 1:
@@ -1693,11 +1693,6 @@
pass # no valid options
def dataset_collector( datasets ):
- def is_convertable( dataset ):
- target_ext, converted_dataset = dataset.find_conversion_destination( self.formats )
- if target_ext is not None:
- return True
- return False
for i, data in enumerate( datasets ):
if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]:
is_valid = False
@@ -1714,7 +1709,7 @@
most_recent_dataset.append(data)
# Also collect children via association object
dataset_collector( data.children )
- dataset_collector( history.datasets )
+ dataset_collector( history.active_datasets_children_and_roles )
most_recent_dataset.reverse()
if already_used is not None:
for val in most_recent_dataset:
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/parameters/grouping.py
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -361,6 +361,7 @@
'filename' : os.path.basename( ftp_file ) }
file_bunch = get_data_file_filename( ftp_data_file, override_name = name, override_info = info )
if file_bunch.path:
+ file_bunch.to_posix_lines = to_posix_lines
file_bunch.space_to_tab = space_to_tab
rval.append( file_bunch )
return rval
diff -r 8d408c81c6c4abafce7461cab6c5e4b677e238d5 -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 lib/galaxy/tools/util/hyphy_util.py
--- a/lib/galaxy/tools/util/hyphy_util.py
+++ /dev/null
@@ -1,1163 +0,0 @@
-#Dan Blankenberg
-#Contains file contents and helper methods for HYPHY configurations
-import tempfile, os
-
-def get_filled_temp_filename(contents):
- fh = tempfile.NamedTemporaryFile('w')
- filename = fh.name
- fh.close()
- fh = open(filename, 'w')
- fh.write(contents)
- fh.close()
- return filename
-
-NJ_tree_shared_ibf = """
-COUNT_GAPS_IN_FREQUENCIES = 0;
-methodIndex = 1;
-
-/*-----------------------------------------------------------------------------------------------------------------------------------------*/
-
-function InferTreeTopology(verbFlag)
-{
- distanceMatrix = {ds.species,ds.species};
-
- MESSAGE_LOGGING = 0;
- ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"chooseDistanceFormula.def");
- InitializeDistances (0);
-
- for (i = 0; i<ds.species; i=i+1)
- {
- for (j = i+1; j<ds.species; j = j+1)
- {
- distanceMatrix[i][j] = ComputeDistanceFormula (i,j);
- }
- }
-
- MESSAGE_LOGGING = 1;
- cladesMade = 1;
-
-
- if (ds.species == 2)
- {
- d1 = distanceMatrix[0][1]/2;
- treeNodes = {{0,1,d1__},
- {1,1,d1__},
- {2,0,0}};
-
- cladesInfo = {{2,0}};
- }
- else
- {
- if (ds.species == 3)
- {
- /* generate least squares estimates here */
-
- d1 = (distanceMatrix[0][1]+distanceMatrix[0][2]-distanceMatrix[1][2])/2;
- d2 = (distanceMatrix[0][1]-distanceMatrix[0][2]+distanceMatrix[1][2])/2;
- d3 = (distanceMatrix[1][2]+distanceMatrix[0][2]-distanceMatrix[0][1])/2;
-
- treeNodes = {{0,1,d1__},
- {1,1,d2__},
- {2,1,d3__}
- {3,0,0}};
-
- cladesInfo = {{3,0}};
- }
- else
- {
- njm = (distanceMatrix > methodIndex)>=ds.species;
-
- treeNodes = {2*(ds.species+1),3};
- cladesInfo = {ds.species-1,2};
-
- for (i=Rows(treeNodes)-1; i>=0; i=i-1)
- {
- treeNodes[i][0] = njm[i][0];
- treeNodes[i][1] = njm[i][1];
- treeNodes[i][2] = njm[i][2];
- }
-
- for (i=Rows(cladesInfo)-1; i>=0; i=i-1)
- {
- cladesInfo[i][0] = njm[i][3];
- cladesInfo[i][1] = njm[i][4];
- }
-
- njm = 0;
- }
- }
- return 1.0;
-}
-
-/*-----------------------------------------------------------------------------------------------------------------------------------------*/
-
-function TreeMatrix2TreeString (doLengths)
-{
- treeString = "";
- p = 0;
- k = 0;
- m = treeNodes[0][1];
- n = treeNodes[0][0];
- treeString*(Rows(treeNodes)*25);
-
- while (m)
- {
- if (m>p)
- {
- if (p)
- {
- treeString*",";
- }
- for (j=p;j<m;j=j+1)
- {
- treeString*"(";
- }
- }
- else
- {
- if (m<p)
- {
- for (j=m;j<p;j=j+1)
- {
- treeString*")";
- }
- }
- else
- {
- treeString*",";
- }
- }
- if (n<ds.species)
- {
- GetString (nodeName, ds, n);
- if (doLengths != 1)
- {
- treeString*nodeName;
- }
- else
- {
- treeString*taxonNameMap[nodeName];
- }
- }
- if (doLengths>.5)
- {
- nodeName = ":"+treeNodes[k][2];
- treeString*nodeName;
- }
- k=k+1;
- p=m;
- n=treeNodes[k][0];
- m=treeNodes[k][1];
- }
-
- for (j=m;j<p;j=j+1)
- {
- treeString*")";
- }
-
- treeString*0;
- return treeString;
-}
-"""
-
-def get_NJ_tree (filename):
- return """
-DISTANCE_PROMPTS = 1;
-ExecuteAFile ("%s");
-
-DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
-DataSetFilter filteredData = CreateFilter (ds,1);
-
-/* do sequence to branch map */
-
-taxonNameMap = {};
-
-for (k=0; k<ds.species; k=k+1)
-{
- GetString (thisName, ds,k);
- shortName = (thisName^{{"\\\\..+",""}})&&1;
- taxonNameMap[shortName] = thisName;
- SetParameter (ds,k,shortName);
-}
-
-DataSetFilter filteredData = CreateFilter (ds,1);
-InferTreeTopology (0);
-treeString = TreeMatrix2TreeString (1);
-
-fprintf (PROMPT_FOR_FILE, CLEAR_FILE, treeString);
-fscanf (stdin, "String", ps_file);
-
-if (Abs(ps_file))
-{
- treeString = TreeMatrix2TreeString (2);
- UseModel (USE_NO_MODEL);
- Tree givenTree = treeString;
- baseHeight = TipCount (givenTree)*28;
- TREE_OUTPUT_OPTIONS = {};
- TREE_OUTPUT_OPTIONS["__FONT_SIZE__"] = 14;
- baseWidth = 0;
- treeAVL = givenTree^0;
- drawLetter = "/drawletter {"+TREE_OUTPUT_OPTIONS["__FONT_SIZE__"]$4+" -"+TREE_OUTPUT_OPTIONS["__FONT_SIZE__"]$2+ " show} def\\n";
- for (k3 = 1; k3 < Abs(treeAVL); k3=k3+1)
- {
- nodeName = (treeAVL[k3])["Name"];
- if(Abs((treeAVL[k3])["Children"]) == 0)
- {
- mySpecs = {};
- mySpecs ["TREE_OUTPUT_BRANCH_LABEL"] = "(" + taxonNameMap[nodeName] + ") drawLetter";
- baseWidth = Max (baseWidth, (treeAVL[k3])["Depth"]);
- }
- }
- baseWidth = 40*baseWidth;
-
- fprintf (ps_file, CLEAR_FILE, drawLetter, PSTreeString (givenTree, "STRING_SUPPLIED_LENGTHS",{{baseWidth,baseHeight}}));
-}
-""" % (filename)
-
-def get_NJ_treeMF (filename):
- return """
-ExecuteAFile ("%s");
-
-VERBOSITY_LEVEL = -1;
-fscanf (PROMPT_FOR_FILE, "Lines", inLines);
-
-_linesIn = Columns (inLines);
-isomorphicTreesBySequenceCount = {};
-
-/*---------------------------------------------------------*/
-
-_currentGene = 1;
-_currentState = 0;
-geneSeqs = "";
-geneSeqs * 128;
-
-fprintf (PROMPT_FOR_FILE, CLEAR_FILE, KEEP_OPEN);
-treeOutFile = LAST_FILE_PATH;
-
-fscanf (stdin,"String", ps_file);
-if (Abs(ps_file))
-{
- fprintf (ps_file, CLEAR_FILE, KEEP_OPEN);
-}
-
-for (l=0; l<_linesIn; l=l+1)
-{
- if (Abs(inLines[l]) == 0)
- {
- if (_currentState == 1)
- {
- geneSeqs * 0;
- DataSet ds = ReadFromString (geneSeqs);
- _processAGene (_currentGene,treeOutFile,ps_file);
- geneSeqs * 128;
- _currentGene = _currentGene + 1;
- }
- }
- else
- {
- if (_currentState == 0)
- {
- _currentState = 1;
- }
- geneSeqs * inLines[l];
- geneSeqs * "\\n";
- }
-}
-
-
-if (_currentState == 1)
-{
- geneSeqs * 0;
- if (Abs(geneSeqs))
- {
- DataSet ds = ReadFromString (geneSeqs);
- _processAGene (_currentGene,treeOutFile,ps_file);
- }
-}
-
-fprintf (treeOutFile,CLOSE_FILE);
-if (Abs(ps_file))
-{
- fprintf (ps_file,CLOSE_FILE);
-}
-/*---------------------------------------------------------*/
-
-function _processAGene (_geneID, nwk_file, ps_file)
-{
- if (ds.species == 1)
- {
- fprintf (nwk_file, _geneID-1, "\\tNone \\tNone\\n");
- return 0;
-
- }
-
- DataSetFilter filteredData = CreateFilter (ds,1);
-
- /* do sequence to branch map */
-
- taxonNameMap = {};
-
- for (k=0; k<ds.species; k=k+1)
- {
- GetString (thisName, ds,k);
- shortName = (thisName^{{"\\\\..+",""}});
- taxonNameMap[shortName] = thisName;
- SetParameter (ds,k,shortName);
- }
-
- DataSetFilter filteredData = CreateFilter (ds,1);
- DISTANCE_PROMPTS = (_geneID==1);
-
- InferTreeTopology (0);
- baseTree = TreeMatrix2TreeString (0);
- UseModel (USE_NO_MODEL);
-
- Tree baseTop = baseTree;
-
- /* standardize this top */
-
- for (k=0; k<Abs(isomorphicTreesBySequenceCount[filteredData.species]); k=k+1)
- {
- testString = (isomorphicTreesBySequenceCount[filteredData.species])[k];
- Tree testTree = testString;
- if (testTree == baseTop)
- {
- baseTree = testString;
- break;
- }
- }
- if (k==Abs(isomorphicTreesBySequenceCount[filteredData.species]))
- {
- if (k==0)
- {
- isomorphicTreesBySequenceCount[filteredData.species] = {};
- }
- (isomorphicTreesBySequenceCount[filteredData.species])[k] = baseTree;
- }
-
- fprintf (nwk_file, _geneID-1, "\\t", baseTree, "\\t", TreeMatrix2TreeString (1), "\\n");
- if (Abs(ps_file))
- {
- treeString = TreeMatrix2TreeString (2);
- UseModel (USE_NO_MODEL);
- Tree givenTree = treeString;
- baseHeight = TipCount (givenTree)*28;
- TREE_OUTPUT_OPTIONS = {};
- TREE_OUTPUT_OPTIONS["__FONT_SIZE__"] = 14;
- baseWidth = 0;
- treeAVL = givenTree^0;
- drawLetter = "/drawletter {"+TREE_OUTPUT_OPTIONS["__FONT_SIZE__"]$4+" -"+TREE_OUTPUT_OPTIONS["__FONT_SIZE__"]$2+ " show} def\\n";
- for (k3 = 1; k3 < Abs(treeAVL); k3=k3+1)
- {
- nodeName = (treeAVL[k3])["Name"];
- if(Abs((treeAVL[k3])["Children"]) == 0)
- {
- mySpecs = {};
- mySpecs ["TREE_OUTPUT_BRANCH_LABEL"] = "(" + taxonNameMap[nodeName] + ") drawLetter";
- baseWidth = Max (baseWidth, (treeAVL[k3])["Depth"]);
- }
- }
- baseWidth = 40*baseWidth;
-
- fprintf (stdout, _geneID, ":", givenTree,"\\n");
- fprintf (ps_file, PSTreeString (givenTree, "STRING_SUPPLIED_LENGTHS",{{baseWidth,baseHeight}}));
- }
- return 0;
-}
-""" % (filename)
-
-BranchLengthsMF = """
-VERBOSITY_LEVEL = -1;
-
-fscanf (PROMPT_FOR_FILE, "Lines", inLines);
-
-
-
-_linesIn = Columns (inLines);
-
-
-
-/*---------------------------------------------------------*/
-
-
-
-_currentGene = 1;
-
-_currentState = 0;
-
-geneSeqs = "";
-
-geneSeqs * 128;
-
-
-
-for (l=0; l<_linesIn; l=l+1)
-
-{
-
- if (Abs(inLines[l]) == 0)
-
- {
-
- if (_currentState == 1)
-
- {
-
- geneSeqs * 0;
-
- DataSet ds = ReadFromString (geneSeqs);
-
- _processAGene (_currentGene);
-
- geneSeqs * 128;
-
- _currentGene = _currentGene + 1;
-
- }
-
- }
-
- else
-
- {
-
- if (_currentState == 0)
-
- {
-
- _currentState = 1;
-
- }
-
- geneSeqs * inLines[l];
-
- geneSeqs * "\\n";
-
- }
-
-}
-
-
-
-if (_currentState == 1)
-
-{
-
- geneSeqs * 0;
-
- if (Abs(geneSeqs))
-
- {
-
- DataSet ds = ReadFromString (geneSeqs);
-
- _processAGene (_currentGene);
-
- }
-
-}
-
-
-
-fprintf (resultFile,CLOSE_FILE);
-
-
-
-/*---------------------------------------------------------*/
-
-
-
-function _processAGene (_geneID)
-
-{
-
- DataSetFilter filteredData = CreateFilter (ds,1);
-
- if (_currentGene == 1)
-
- {
-
- SelectTemplateModel (filteredData);
-
-
-
- SetDialogPrompt ("Tree file");
-
- fscanf (PROMPT_FOR_FILE, "Tree", givenTree);
-
- fscanf (stdin, "String", resultFile);
-
-
-
- /* do sequence to branch map */
-
-
-
- validNames = {};
-
- taxonNameMap = {};
-
-
-
- for (k=0; k<TipCount(givenTree); k=k+1)
-
- {
-
- validNames[TipName(givenTree,k)&&1] = 1;
-
- }
-
-
-
- for (k=0; k<BranchCount(givenTree); k=k+1)
-
- {
-
- thisName = BranchName(givenTree,k);
-
- taxonNameMap[thisName&&1] = thisName;
-
- }
-
-
-
- storeValidNames = validNames;
-
- fprintf (resultFile,CLEAR_FILE,KEEP_OPEN,"Block\\tBranch\\tLength\\tLowerBound\\tUpperBound\\n");
-
- }
-
- else
-
- {
-
- HarvestFrequencies (vectorOfFrequencies, filteredData, 1,1,1);
-
- validNames = storeValidNames;
-
- }
-
-
-
- for (k=0; k<ds.species; k=k+1)
-
- {
-
- GetString (thisName, ds,k);
-
- shortName = (thisName^{{"\\\\..+",""}})&&1;
-
- if (validNames[shortName])
-
- {
-
- taxonNameMap[shortName] = thisName;
-
- validNames - (shortName);
-
- SetParameter (ds,k,shortName);
-
- }
-
- else
-
- {
-
- fprintf (resultFile,"ERROR:", thisName, " could not be matched to any of the leaves in tree ", givenTree,"\\n");
-
- return 0;
-
- }
-
- }
-
-
-
- /* */
-
-
-
- LikelihoodFunction lf = (filteredData,givenTree);
-
- Optimize (res,lf);
-
-
-
- timer = Time(0)-timer;
-
-
-
- branchNames = BranchName (givenTree,-1);
-
- branchLengths = BranchLength (givenTree,-1);
-
-
-
-
-
- for (k=0; k<Columns(branchNames)-1; k=k+1)
-
- {
-
- COVARIANCE_PARAMETER = "givenTree."+branchNames[k]+".t";
-
- COVARIANCE_PRECISION = 0.95;
-
- CovarianceMatrix (cmx,lf);
-
- if (k==0)
-
- {
-
- /* compute a scaling factor */
-
- ExecuteCommands ("givenTree."+branchNames[0]+".t=1");
-
- scaleFactor = BranchLength (givenTree,0);
-
- ExecuteCommands ("givenTree."+branchNames[0]+".t="+cmx[0][1]);
-
- }
-
- fprintf (resultFile,_geneID,"\\t",taxonNameMap[branchNames[k]&&1],"\\t",branchLengths[k],"\\t",scaleFactor*cmx[0][0],"\\t",scaleFactor*cmx[0][2],"\\n");
-
- }
-
-
-
- ttl = (branchLengths*(Transpose(branchLengths["1"])))[0];
-
- global treeScaler = 1;
-
- ReplicateConstraint ("this1.?.t:=treeScaler*this2.?.t__",givenTree,givenTree);
-
- COVARIANCE_PARAMETER = "treeScaler";
-
- COVARIANCE_PRECISION = 0.95;
-
- CovarianceMatrix (cmx,lf);
-
- fprintf (resultFile,_geneID,"\\tTotal Tree\\t",ttl,"\\t",ttl*cmx[0][0],"\\t",ttl*cmx[0][2],"\\n");
-
- ClearConstraints (givenTree);
-
- return 0;
-
-}
-"""
-
-BranchLengths = """
-DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
-DataSetFilter filteredData = CreateFilter (ds,1);
-
-SelectTemplateModel (filteredData);
-
-SetDialogPrompt ("Tree file");
-fscanf (PROMPT_FOR_FILE, "Tree", givenTree);
-fscanf (stdin, "String", resultFile);
-
-/* do sequence to branch map */
-
-validNames = {};
-taxonNameMap = {};
-
-for (k=0; k<TipCount(givenTree); k=k+1)
-{
- validNames[TipName(givenTree,k)&&1] = 1;
-}
-
-for (k=0; k<BranchCount(givenTree); k=k+1)
-{
- thisName = BranchName(givenTree,k);
- taxonNameMap[thisName&&1] = thisName;
-}
-
-for (k=0; k<ds.species; k=k+1)
-{
- GetString (thisName, ds,k);
- shortName = (thisName^{{"\\\\..+",""}})&&1;
- if (validNames[shortName])
- {
- taxonNameMap[shortName] = thisName;
- validNames - (shortName);
- SetParameter (ds,k,shortName);
- }
- else
- {
- fprintf (resultFile,CLEAR_FILE,"ERROR:", thisName, " could not be matched to any of the leaves in tree ", givenTree);
- return 0;
- }
-}
-
-/* */
-
-LikelihoodFunction lf = (filteredData,givenTree);
-
-Optimize (res,lf);
-
-timer = Time(0)-timer;
-
-branchNames = BranchName (givenTree,-1);
-branchLengths = BranchLength (givenTree,-1);
-
-fprintf (resultFile,CLEAR_FILE,KEEP_OPEN,"Branch\\tLength\\tLowerBound\\tUpperBound\\n");
-
-for (k=0; k<Columns(branchNames)-1; k=k+1)
-{
- COVARIANCE_PARAMETER = "givenTree."+branchNames[k]+".t";
- COVARIANCE_PRECISION = 0.95;
- CovarianceMatrix (cmx,lf);
- if (k==0)
- {
- /* compute a scaling factor */
- ExecuteCommands ("givenTree."+branchNames[0]+".t=1");
- scaleFactor = BranchLength (givenTree,0);
- ExecuteCommands ("givenTree."+branchNames[0]+".t="+cmx[0][1]);
- }
- fprintf (resultFile,taxonNameMap[branchNames[k]&&1],"\\t",branchLengths[k],"\\t",scaleFactor*cmx[0][0],"\\t",scaleFactor*cmx[0][2],"\\n");
-}
-
-ttl = (branchLengths*(Transpose(branchLengths["1"])))[0];
-global treeScaler = 1;
-ReplicateConstraint ("this1.?.t:=treeScaler*this2.?.t__",givenTree,givenTree);
-COVARIANCE_PARAMETER = "treeScaler";
-COVARIANCE_PRECISION = 0.95;
-CovarianceMatrix (cmx,lf);
-ClearConstraints (givenTree);
-fprintf (resultFile,"Total Tree\\t",ttl,"\\t",ttl*cmx[0][0],"\\t",ttl*cmx[0][2],"\\n");
-fprintf (resultFile,CLOSE_FILE);
-"""
-
-SimpleLocalFitter = """
-VERBOSITY_LEVEL = -1;
-COUNT_GAPS_IN_FREQUENCIES = 0;
-
-/*---------------------------------------------------------*/
-
-function returnResultHeaders (dummy)
-{
- _analysisHeaders = {};
- _analysisHeaders[0] = "BLOCK";
- _analysisHeaders[1] = "BP";
- _analysisHeaders[2] = "S_sites";
- _analysisHeaders[3] = "NS_sites";
- _analysisHeaders[4] = "Stop_codons";
- _analysisHeaders[5] = "LogL";
- _analysisHeaders[6] = "AC";
- _analysisHeaders[7] = "AT";
- _analysisHeaders[8] = "CG";
- _analysisHeaders[9] = "CT";
- _analysisHeaders[10] = "GT";
- _analysisHeaders[11] = "Tree";
-
- for (_biterator = 0; _biterator < treeBranchCount; _biterator = _biterator + 1)
- {
- branchName = treeBranchNames[_biterator];
-
- _analysisHeaders [Abs(_analysisHeaders)] = "length("+branchName+")";
- _analysisHeaders [Abs(_analysisHeaders)] = "dS("+branchName+")";
- _analysisHeaders [Abs(_analysisHeaders)] = "dN("+branchName+")";
- _analysisHeaders [Abs(_analysisHeaders)] = "omega("+branchName+")";
- }
-
- return _analysisHeaders;
-}
-
-/*---------------------------------------------------------*/
-
-function runAGeneFit (myID)
-{
- DataSetFilter filteredData = CreateFilter (ds,3,"","",GeneticCodeExclusions);
-
- if (_currentGene==1)
- {
- _MG94stdinOverload = {};
- _MG94stdinOverload ["0"] = "Local";
- _MG94stdinOverload ["1"] = modelSpecString;
-
- ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"MG94custom.mdl",
- _MG94stdinOverload);
-
- Tree codonTree = treeString;
- }
- else
- {
- HarvestFrequencies (observedFreq,filteredData,3,1,1);
- MULTIPLY_BY_FREQS = PopulateModelMatrix ("MG94custom", observedFreq);
- vectorOfFrequencies = BuildCodonFrequencies (observedFreq);
- Model MG94customModel = (MG94custom,vectorOfFrequencies,0);
-
- Tree codonTree = treeString;
- }
-
- LikelihoodFunction lf = (filteredData,codonTree);
-
- Optimize (res,lf);
-
- _snsAVL = _computeSNSSites ("filteredData", _Genetic_Code, vectorOfFrequencies, 0);
- _cL = ReturnVectorsOfCodonLengths (ComputeScalingStencils (0), "codonTree");
-
-
- _returnMe = {};
- _returnMe ["BLOCK"] = myID;
- _returnMe ["LogL"] = res[1][0];
- _returnMe ["BP"] = _snsAVL ["Sites"];
- _returnMe ["S_sites"] = _snsAVL ["SSites"];
- _returnMe ["NS_sites"] = _snsAVL ["NSSites"];
- _returnMe ["AC"] = AC;
- _returnMe ["AT"] = AT;
- _returnMe ["CG"] = CG;
- _returnMe ["CT"] = CT;
- _returnMe ["GT"] = GT;
- _returnMe ["Tree"] = Format(codonTree,0,1);
-
- for (_biterator = 0; _biterator < treeBranchCount; _biterator = _biterator + 1)
- {
- branchName = treeBranchNames[_biterator];
-
- _returnMe ["length("+branchName+")"] = (_cL["Total"])[_biterator];
- _returnMe ["dS("+branchName+")"] = (_cL["Syn"])[_biterator]*(_returnMe ["BP"]/_returnMe ["S_sites"]);
- _returnMe ["dN("+branchName+")"] = (_cL["NonSyn"])[_biterator]*(_returnMe ["BP"]/_returnMe ["NS_sites"]);
-
- ExecuteCommands ("_lom = _standardizeRatio(codonTree."+treeBranchNames[_biterator]+".nonSynRate,codonTree."+treeBranchNames[_biterator]+".synRate);");
- _returnMe ["omega("+branchName+")"] = _lom;
- }
-
- return _returnMe;
-}
-
-"""
-
-SimpleGlobalFitter = """
-VERBOSITY_LEVEL = -1;
-COUNT_GAPS_IN_FREQUENCIES = 0;
-
-/*---------------------------------------------------------*/
-
-function returnResultHeaders (dummy)
-{
- _analysisHeaders = {};
- _analysisHeaders[0] = "BLOCK";
- _analysisHeaders[1] = "BP";
- _analysisHeaders[2] = "S_sites";
- _analysisHeaders[3] = "NS_sites";
- _analysisHeaders[4] = "Stop_codons";
- _analysisHeaders[5] = "LogL";
- _analysisHeaders[6] = "omega";
- _analysisHeaders[7] = "omega_range";
- _analysisHeaders[8] = "AC";
- _analysisHeaders[9] = "AT";
- _analysisHeaders[10] = "CG";
- _analysisHeaders[11] = "CT";
- _analysisHeaders[12] = "GT";
- _analysisHeaders[13] = "Tree";
-
- return _analysisHeaders;
-}
-
-/*---------------------------------------------------------*/
-
-function runAGeneFit (myID)
-{
- fprintf (stdout, "[SimpleGlobalFitter.bf on GENE ", myID, "]\\n");
- taxonNameMap = {};
-
- for (k=0; k<ds.species; k=k+1)
- {
- GetString (thisName, ds,k);
- shortName = (thisName^{{"\\\\..+",""}})&&1;
- taxonNameMap[shortName] = thisName;
- SetParameter (ds,k,shortName);
- }
-
- DataSetFilter filteredData = CreateFilter (ds,1);
- _nucSites = filteredData.sites;
-
- if (Abs(treeString))
- {
- givenTreeString = treeString;
- }
- else
- {
- if (_currentGene==1)
- {
- ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"Utility"+DIRECTORY_SEPARATOR+"NJ.bf");
- }
- givenTreeString = InferTreeTopology (0);
- treeString = "";
- }
-
- DataSetFilter filteredData = CreateFilter (ds,3,"","",GeneticCodeExclusions);
-
- if (_currentGene==1)
- {
- _MG94stdinOverload = {};
- _MG94stdinOverload ["0"] = "Global";
- _MG94stdinOverload ["1"] = modelSpecString;
-
- ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"MG94custom.mdl",
- _MG94stdinOverload);
-
- Tree codonTree = givenTreeString;
- }
- else
- {
- HarvestFrequencies (observedFreq,filteredData,3,1,1);
- MULTIPLY_BY_FREQS = PopulateModelMatrix ("MG94custom", observedFreq);
- vectorOfFrequencies = BuildCodonFrequencies (observedFreq);
- Model MG94customModel = (MG94custom,vectorOfFrequencies,0);
-
- Tree codonTree = givenTreeString;
- }
-
- LikelihoodFunction lf = (filteredData,codonTree);
-
- Optimize (res,lf);
-
- _snsAVL = _computeSNSSites ("filteredData", _Genetic_Code, vectorOfFrequencies, 0);
- _cL = ReturnVectorsOfCodonLengths (ComputeScalingStencils (0), "codonTree");
-
-
- _returnMe = {};
- _returnMe ["BLOCK"] = myID;
- _returnMe ["LogL"] = res[1][0];
- _returnMe ["BP"] = _snsAVL ["Sites"];
- _returnMe ["S_sites"] = _snsAVL ["SSites"];
- _returnMe ["NS_sites"] = _snsAVL ["NSSites"];
- _returnMe ["Stop_codons"] = (_nucSites-filteredData.sites*3)$3;
- _returnMe ["AC"] = AC;
- _returnMe ["AT"] = AT;
- _returnMe ["CG"] = CG;
- _returnMe ["CT"] = CT;
- _returnMe ["GT"] = GT;
- _returnMe ["omega"] = R;
- COVARIANCE_PARAMETER = "R";
- COVARIANCE_PRECISION = 0.95;
- CovarianceMatrix (cmx,lf);
- _returnMe ["omega_range"] = ""+cmx[0]+"-"+cmx[2];
- _returnMe ["Tree"] = Format(codonTree,0,1);
-
-
- return _returnMe;
-}
-"""
-
-FastaReader = """
-fscanf (stdin, "String", _coreAnalysis);
-fscanf (stdin, "String", _outputDriver);
-
-ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def");
-ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"dSdNTreeTools.ibf");
-ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"Utility"+DIRECTORY_SEPARATOR+"CodonTools.bf");
-ExecuteAFile (HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"Utility"+DIRECTORY_SEPARATOR+"GrabBag.bf");
-
-SetDialogPrompt ("Tree file");
-fscanf (PROMPT_FOR_FILE, "Tree", givenTree);
-
-treeBranchNames = BranchName (givenTree,-1);
-treeBranchCount = Columns (treeBranchNames)-1;
-treeString = Format (givenTree,1,1);
-
-SetDialogPrompt ("Multiple gene FASTA file");
-fscanf (PROMPT_FOR_FILE, "Lines", inLines);
-fscanf (stdin, "String", modelSpecString);
-fscanf (stdin, "String", _outPath);
-
-ExecuteAFile (_outputDriver);
-ExecuteAFile (_coreAnalysis);
-
-/*---------------------------------------------------------*/
-
-_linesIn = Columns (inLines);
-_currentGene = 1;
- _currentState = 0;
-/* 0 - waiting for a non-empty line */
-/* 1 - reading files */
-
-geneSeqs = "";
-geneSeqs * 0;
-
-_prepareFileOutput (_outPath);
-
-for (l=0; l<_linesIn; l=l+1)
-{
- if (Abs(inLines[l]) == 0)
- {
- if (_currentState == 1)
- {
- geneSeqs * 0;
- DataSet ds = ReadFromString (geneSeqs);
- _processAGene (ds.species == treeBranchCount,_currentGene);
- geneSeqs * 128;
- _currentGene = _currentGene + 1;
- }
- }
- else
- {
- if (_currentState == 0)
- {
- _currentState = 1;
- }
- geneSeqs * inLines[l];
- geneSeqs * "\\n";
- }
-}
-
-if (_currentState == 1)
-{
- geneSeqs * 0;
- DataSet ds = ReadFromString (geneSeqs);
- _processAGene (ds.species == treeBranchCount,_currentGene);
-}
-
-_finishFileOutput (0);
-"""
-
-TabWriter = """
-/*---------------------------------------------------------*/
-function _prepareFileOutput (_outPath)
-{
- _outputFilePath = _outPath;
-
- _returnHeaders = returnResultHeaders(0);
-
- fprintf (_outputFilePath, CLEAR_FILE, KEEP_OPEN, _returnHeaders[0]);
- for (_biterator = 1; _biterator < Abs(_returnHeaders); _biterator = _biterator + 1)
- {
- fprintf (_outputFilePath,"\\t",_returnHeaders[_biterator]);
- }
-
-
-
- fprintf (_outputFilePath,"\\n");
- return 0;
-}
-
-/*---------------------------------------------------------*/
-
-function _processAGene (valid, _geneID)
-{
- if (valid)
- {
- returnValue = runAGeneFit (_geneID);
- fprintf (_outputFilePath, returnValue[_returnHeaders[0]]);
- for (_biterator = 1; _biterator < Abs(_returnHeaders); _biterator = _biterator + 1)
- {
- fprintf (_outputFilePath,"\\t",returnValue[_returnHeaders[_biterator]]);
- }
- fprintf (_outputFilePath, "\\n");
- }
- /*
- else
- {
- fprintf (_outputFilePath,
- _geneID, ", Incorrect number of sequences\\n");
- }
- */
- _currentState = 0;
- return 0;
-}
-
-/*---------------------------------------------------------*/
-function _finishFileOutput (dummy)
-{
- return 0;
-}
-"""
-
-def get_dnds_config_filename(Fitter_filename, TabWriter_filename, genetic_code, tree_filename, input_filename, nuc_model, output_filename, FastaReader_filename ):
- contents = """
-_genomeScreenOptions = {};
-
-/* all paths are either absolute or relative
-to the DATA READER */
-
-_genomeScreenOptions ["0"] = "%s";
- /* which analysis to run on each gene; */
-_genomeScreenOptions ["1"] = "%s";
- /* what output to produce; */
-_genomeScreenOptions ["2"] = "%s";
- /* genetic code */
-_genomeScreenOptions ["3"] = "%s";
- /* tree file */
-_genomeScreenOptions ["4"] = "%s";
- /* alignment file */
-_genomeScreenOptions ["5"] = "%s";
- /* nucleotide bias string; can define any of the 203 models */
-_genomeScreenOptions ["6"] = "%s";
- /* output csv file */
-
-ExecuteAFile ("%s", _genomeScreenOptions);
-""" % (Fitter_filename, TabWriter_filename, genetic_code, tree_filename, input_filename, nuc_model, output_filename, FastaReader_filename )
- return get_filled_temp_filename(contents)
-
-
-def get_branch_lengths_config_filename(input_filename, nuc_model, model_options, base_freq, tree_filename, output_filename, BranchLengths_filename):
- contents = """
-_genomeScreenOptions = {};
-
-/* all paths are either absolute or relative
-to the NucDataBranchLengths.bf */
-
-_genomeScreenOptions ["0"] = "%s";
- /* the file to analyze; */
-_genomeScreenOptions ["1"] = "CUSTOM";
- /* use an arbitrary nucleotide model */
-_genomeScreenOptions ["2"] = "%s";
- /* which model to use */
-_genomeScreenOptions ["3"] = "%s";
- /* model options */
-_genomeScreenOptions ["4"] = "Estimated";
- /* rate parameters */
-_genomeScreenOptions ["5"] = "%s";
- /* base frequencies */
-_genomeScreenOptions ["6"] = "%s";
- /* the tree to use; */
-_genomeScreenOptions ["7"] = "%s";
- /* write .csv output to; */
-
-ExecuteAFile ("%s", _genomeScreenOptions);
-""" % (input_filename, nuc_model, model_options, base_freq, tree_filename, output_filename, BranchLengths_filename)
- return get_filled_temp_filename(contents)
-
-
-def get_nj_tree_config_filename(input_filename, distance_metric, output_filename1, output_filename2, NJ_tree_filename):
- contents = """
-_genomeScreenOptions = {};
-
-/* all paths are either absolute or relative
-to the BuildNJTree.bf */
-
-_genomeScreenOptions ["0"] = "%s";
- /* the file to analyze; */
-_genomeScreenOptions ["1"] = "%s";
- /* pick which distance metric to use; TN93 is a good default */
-_genomeScreenOptions ["2"] = "%s";
- /* write Newick tree output to; */
-_genomeScreenOptions ["3"] = "%s";
- /* write a postscript tree file to this file; leave blank to not write a tree */
-
-ExecuteAFile ("%s", _genomeScreenOptions);
-""" % (input_filename, distance_metric, output_filename1, output_filename2, NJ_tree_filename)
- return get_filled_temp_filename(contents)
-
-
-def get_nj_treeMF_config_filename(input_filename, output_filename1, output_filename2, distance_metric, NJ_tree_filename):
- contents = """
-_genomeScreenOptions = {};
-
-/* all paths are either absolute or relative
-to the BuildNJTreeMF.bf */
-
-_genomeScreenOptions ["0"] = "%s";
- /* the multiple alignment file to analyze; */
-_genomeScreenOptions ["1"] = "%s";
- /* write Newick tree output to; */
-_genomeScreenOptions ["2"] = "%s";
- /* write a postscript tree file to this file; leave blank to not write a tree */
-_genomeScreenOptions ["3"] = "%s";
- /* pick which distance metric to use; TN93 is a good default */
-
-ExecuteAFile ("%s", _genomeScreenOptions);
-""" % (input_filename, output_filename1, output_filename2, distance_metric, NJ_tree_filename)
- return get_filled_temp_filename(contents)
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/e0e1dab49f16/
Changeset: e0e1dab49f16
Branch: job-search
User: Kyle Ellrott
Date: 2014-01-29 21:52:46
Summary: Fixing parameter finding for non-string parameters (ints/floats)
Affected #: 1 file
diff -r 7637cfbea32e2a5e4af28400fa88909cbb6bd058 -r e0e1dab49f16eacf6e43c7193129b8371866c2e8 lib/galaxy/webapps/galaxy/api/jobs.py
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -131,7 +131,7 @@
raise exceptions.ObjectNotFound( "Dataset %s not found" % ( v[ 'id' ] ) )
input_data[k] = dataset.dataset_id
else:
- input_param[k] = json.dumps( v )
+ input_param[k] = json.dumps( str(v) )
query = trans.sa_session.query( trans.app.model.Job ).filter(
trans.app.model.Job.tool_id == tool_id,
https://bitbucket.org/galaxy/galaxy-central/commits/be7ece945447/
Changeset: be7ece945447
User: jmchilton
Date: 2014-01-31 05:44:58
Summary: Merged in kellrott/galaxy-central/job-search (pull request #316)
Fixing non-string parameter selection for job searches
Affected #: 1 file
diff -r 24753d36e6a60bb446bd961d16cb4b59abf7b13b -r be7ece9454471d655668f3997c29b90c2f6c312d lib/galaxy/webapps/galaxy/api/jobs.py
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -131,7 +131,7 @@
raise exceptions.ObjectNotFound( "Dataset %s not found" % ( v[ 'id' ] ) )
input_data[k] = dataset.dataset_id
else:
- input_param[k] = json.dumps( v )
+ input_param[k] = json.dumps( str(v) )
query = trans.sa_session.query( trans.app.model.Job ).filter(
trans.app.model.Job.tool_id == tool_id,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Improved jobs testing.
by commits-noreply＠bitbucket.org 30 Jan '14
by commits-noreply＠bitbucket.org 30 Jan '14
30 Jan '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/24753d36e6a6/
Changeset: 24753d36e6a6
User: jmchilton
Date: 2014-01-31 05:44:10
Summary: Improved jobs testing.
Fix bug in buildbot related to differences between local handling of list/tuple parameters and requests handling (I mostly use requests locally, but buildbot doesn't have it available). Add test that fails without @kellrott's pull request #314 (and in turn verifies it fixes a problem).
Affected #: 2 files
diff -r 2ce1ba52c6a7b33676ffebb73053ab3f9e9baa21 -r 24753d36e6a60bb446bd961d16cb4b59abf7b13b test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -1,6 +1,7 @@
import os
from StringIO import StringIO
from galaxy.tools.parameters import grouping
+from galaxy.util import listify
from galaxy.util.odict import odict
import galaxy.model
from galaxy.model.orm import and_, desc
@@ -440,7 +441,16 @@
argsep = '&'
if '?' not in url:
argsep = '?'
- url = url + argsep + '&'.join( [ '%s=%s' % (k, v) for k, v in params.iteritems() ] )
+ param_pairs = []
+ for key, value in params.iteritems():
+ # Handle single parameters or lists and tuples of them.
+ if isinstance( value, tuple ):
+ value = list( value )
+ elif not isinstance( value, list ):
+ value = [ value ]
+ for val in value:
+ param_pairs.append( "%s=%s" % ( key, val ) )
+ url = url + argsep + '&'.join( param_pairs )
#req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' } )
try:
response = urllib2.urlopen( url )
diff -r 2ce1ba52c6a7b33676ffebb73053ab3f9e9baa21 -r 24753d36e6a60bb446bd961d16cb4b59abf7b13b test/functional/api/test_jobs.py
--- a/test/functional/api/test_jobs.py
+++ b/test/functional/api/test_jobs.py
@@ -82,8 +82,33 @@
self.__run_cat_tool( history_id, dataset_id )
self._wait_for_history( history_id, assert_ok=True )
+ self.__assert_one_search_result( search_payload )
+
+ def test_search_param( self ):
+ history_id, dataset_id = self.__history_with_ok_dataset()
+
+ inputs = json.dumps(
+ dict(
+ input=dict(
+ src='hda',
+ id=dataset_id,
+ ),
+ num_lines=1,
+ )
+ )
+ search_payload = dict(
+ tool_id="random_lines1",
+ inputs=inputs,
+ state="ok",
+ )
+
+ self.__run_randomlines_tool( 1, history_id, dataset_id )
+ self._wait_for_history( history_id, assert_ok=True )
+ self.__assert_one_search_result( search_payload )
+
+ def __assert_one_search_result( self, search_payload ):
search_response = self._post( "jobs/search", data=search_payload )
- self._assert_status_code_is( empty_search_response, 200 )
+ self._assert_status_code_is( search_response, 200 )
assert len( search_response.json() ) == 1, search_response.json()
def __run_cat_tool( self, history_id, dataset_id ):
@@ -100,6 +125,20 @@
)
self._post( "tools", data=payload )
+ def __run_randomlines_tool( self, lines, history_id, dataset_id ):
+ payload = self._run_tool_payload(
+ tool_id="random_lines1",
+ inputs=dict(
+ num_lines=lines,
+ input=dict(
+ src='hda',
+ id=dataset_id,
+ ),
+ ),
+ history_id=history_id,
+ )
+ self._post( "tools", data=payload )
+
def __uploads_with_state( self, *states ):
jobs_response = self._get( "jobs", data=dict( state=states ) )
self._assert_status_code_is( jobs_response, 200 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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