[galaxy-commits] [hg] galaxy 3668: User-custom dbkeys can now be set for datasets...

10 May 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/91b8f0abffc8
changeset: 3668:91b8f0abffc8
user:      Kanwei Li kanwei@gmail.com
date:      Mon Apr 19 16:03:24 2010 -0400
description:
User-custom dbkeys can now be set for datasets in Edit Attributes and upload
Always use autocomplete for dbkey entry (used to be >20)
diffstat:
lib/galaxy/web/controllers/tracks.py |  15 +++++++--------
 lib/galaxy/web/framework/__init__.py |  12 +++++++++---
 static/scripts/galaxy.base.js        |   8 ++++----
 static/scripts/packed/galaxy.base.js |   2 +-
 4 files changed, 21 insertions(+), 16 deletions(-)
diffs (104 lines):
diff -r 3c6ffa5362d2 -r 91b8f0abffc8 lib/galaxy/web/controllers/tracks.py

--- a/lib/galaxy/web/controllers/tracks.py	Mon Apr 19 14:09:07 2010 -0400
+++ b/lib/galaxy/web/controllers/tracks.py	Mon Apr 19 16:03:24 2010 -0400
@@ -21,7 +21,6 @@
 from galaxy.web.framework import simplejson
 from galaxy.web.framework.helpers import time_ago, grids
 from galaxy.util.bunch import Bunch
-from galaxy.util import dbnames
from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider
 from galaxy.visualization.tracks.data.interval_index import IntervalIndexDataProvider
@@ -79,7 +78,7 @@
     """
available_tracks = None
-    len_dbkeys = None
+    len_files = None
@web.expose
     @web.require_login()
@@ -91,17 +90,17 @@
     @web.expose
     @web.require_login()
     def new_browser( self, trans ):
-        if not self.len_dbkeys:
+        if not self.len_files:
             len_files = glob.glob(os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "*.len" ))
-            len_files = [ os.path.split(f)[1].split(".len")[0] for f in len_files ] # get xxx.len
-            loaded_dbkeys = dbnames
-            self.len_dbkeys = [ (k, v) for k, v in loaded_dbkeys if k in len_files ]
+            self.len_files = [ os.path.split(f)[1].split(".len")[0] for f in len_files ] # get xxx.len
-        user_keys = None
+        user_keys = {}
         user = trans.get_user()
         if 'dbkeys' in user.preferences:
             user_keys = from_json_string( user.preferences['dbkeys'] )
-        return trans.fill_template( "tracks/new_browser.mako", user_keys=user_keys, dbkeys=self.len_dbkeys )
+            
+        dbkeys = [ (k, v) for k, v in trans.db_builds if k in self.len_files or k in user_keys ]
+        return trans.fill_template( "tracks/new_browser.mako", dbkeys=dbkeys )
@web.json
     @web.require_login()
diff -r 3c6ffa5362d2 -r 91b8f0abffc8 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py	Mon Apr 19 14:09:07 2010 -0400
+++ b/lib/galaxy/web/framework/__init__.py	Mon Apr 19 16:03:24 2010 -0400
@@ -10,7 +10,7 @@
 import base
 import pickle
 from galaxy import util
-from galaxy.util.json import to_json_string
+from galaxy.util.json import to_json_string, from_json_string
pkg_resources.require( "simplejson" )
 import simplejson
@@ -657,10 +657,16 @@
         dbnames = list()
         datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \
                                   .filter_by( deleted=False, history_id=self.history.id, extension="len" )
-        if datasets.count() > 0:
-            dbnames.append( (util.dbnames.default_value, '--------- User Defined Builds ----------') )
+        
         for dataset in datasets:
             dbnames.append( (dataset.dbkey, dataset.name) )
+            
+        user = self.get_user()
+        if user and 'dbkeys' in user.preferences:
+            user_keys = from_json_string( user.preferences['dbkeys'] )
+            for key, chrom_dict in user_keys.iteritems():
+                dbnames.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key) ))
+                    
         dbnames.extend( util.dbnames )
         return dbnames
diff -r 3c6ffa5362d2 -r 91b8f0abffc8 static/scripts/galaxy.base.js
--- a/static/scripts/galaxy.base.js	Mon Apr 19 14:09:07 2010 -0400
+++ b/static/scripts/galaxy.base.js	Mon Apr 19 16:03:24 2010 -0400
@@ -144,13 +144,13 @@
     return 0;
 }
-// Replace any select box with 20+ options with a text input box + autocomplete.
+// Replace select box with a text input box + autocomplete.
 // TODO: make work with dynamic tool inputs and then can replace all big selects.
-function replace_big_select_inputs() {
+function replace_big_select_inputs(min_length) {
     $('select[name=dbkey]').each( function() {
         var select_elt = $(this);
-        // Skip if there are < 20 options.
-        if (select_elt.find('option').length < 20)
+        // Skip if # of options < threshold
+        if (min_length !== undefined && select_elt.find('option').length < min_length)
             return;
// Replace select with text + autocomplete.
diff -r 3c6ffa5362d2 -r 91b8f0abffc8 static/scripts/packed/galaxy.base.js
--- a/static/scripts/packed/galaxy.base.js	Mon Apr 19 14:09:07 2010 -0400
+++ b/static/scripts/packed/galaxy.base.js	Mon Apr 19 16:03:24 2010 -0400
@@ -1,1 +1,1 @@
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\ No newline at end of file
+$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen!
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\ No newline at end of file

    

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[galaxy-commits] [hg] galaxy 3668: User-custom dbkeys can now be set for datasets...