galaxy-commits January 2014

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280 discussions

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 31 Jan '14

31 Jan '14

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 31 Jan '14

31 Jan '14

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%" 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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

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" 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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 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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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Grids: Remove url generation from js template
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/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: guerler: Grids: Fix pages
by commits-noreply＠bitbucket.org 31 Jan '14

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 30 Jan '14

30 Jan '14

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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Improved jobs testing.
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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits January 2014