1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/28ffb6286b12/
changeset: 28ffb6286b12
user: greg
date: 2011-12-02 21:19:37
summary: Change column Uploaded By to be the Data type of the library dataset when browsing a data library. Fixes issue #597.
affected #: 1 file
diff -r 954f201a772e82039ec80802f9bca78d8903cd8a -r 28ffb6286b1226d8c7757e33bb7790eaa08ae29d templates/library/common/browse_library.mako
--- a/templates/library/common/browse_library.mako
+++ b/templates/library/common/browse_library.mako
@@ -218,10 +218,6 @@
is_admin = trans.user_is_admin() and cntrller == 'library_admin'
- if ldda.user:
- uploaded_by = ldda.user.email
- else:
- uploaded_by = 'anonymous'
if ldda == library_dataset.library_dataset_dataset_association:
current_version = True
if is_admin:
@@ -303,7 +299,7 @@
</td>
% if not simple:
<td id="libraryItemInfo">${render_library_item_info( ldda )}</td>
- <td>${uploaded_by}</td>
+ <td>${ldda.extension}</td>
% endif
<td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td><td>${ldda.get_size( nice_size=True )}</td>
@@ -579,10 +575,10 @@
</th>
% if not simple:
<th>Message</th>
- <th>Uploaded By</th>
+ <th>Data type</th>
% endif
- <th>Date</th>
- <th>File Size</th>
+ <th>Date uploaded</th>
+ <th>File size</th></tr></thead><% row_counter = RowCounter() %>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/87dc2336c189/
changeset: 87dc2336c189
user: jgoecks
date: 2011-12-02 20:20:29
summary: Trackster bug fix: add missing object reference.
affected #: 1 file
diff -r 107d3f0a59fae43ca9b62fe30453caed898993e6 -r 87dc2336c1892878b26a110bb1857722fd3f4903 static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -2355,6 +2355,7 @@
more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div);
// Set up actions for icons.
+ var tile = this;
more_down_icon.click(function() {
// Mark tile as stale, request more data, and redraw track.
tile.stale = true;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/107d3f0a59fa/
changeset: 107d3f0a59fa
user: jgoecks
date: 2011-12-02 19:56:45
summary: (1) Fail gracefully when visualization cannot be saved and (2) fix bug in setting modal's minimum width.
affected #: 2 files
diff -r 4a9d57a68f91b17fa47b8e5b73e54b6bdcbc912d -r 107d3f0a59fae43ca9b62fe30453caed898993e6 static/scripts/galaxy.panels.js
--- a/static/scripts/galaxy.panels.js
+++ b/static/scripts/galaxy.panels.js
@@ -211,7 +211,7 @@
}
var body_elt = $( ".dialog-box" ).find( ".body" );
// Clear min-width to allow for modal to take size of new body.
- body_elt.css("min-width", "");
+ body_elt.css("min-width", "0px");
$( ".dialog-box" ).find( ".body" ).html( body );
if ( ! $(".dialog-box-container").is( ":visible" ) ) {
$("#overlay").show();
diff -r 4a9d57a68f91b17fa47b8e5b73e54b6bdcbc912d -r 107d3f0a59fae43ca9b62fe30453caed898993e6 templates/tracks/browser.mako
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -230,7 +230,7 @@
$("#save-icon").click( function() {
// Show saving dialog box
- show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>");
+ show_modal("Saving...", "progress");
// Save bookmarks.
var bookmarks = [];
@@ -267,7 +267,10 @@
// Needed to set URL when first saving a visualization.
window.history.pushState({}, "", vis_info.url);
},
- error: function() { alert("Could not save visualization"); }
+ error: function() {
+ show_modal( "Could Not Save", "Could not save visualization. Please try again later.",
+ { "Close" : hide_modal } );
+ }
});
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4a9d57a68f91/
changeset: 4a9d57a68f91
user: jgoecks
date: 2011-12-02 18:32:14
summary: Trackster: default to datasets in current history when adding tracks.
affected #: 2 files
diff -r da1ccd08865963c99a55b621af481023b61e3b32 -r 4a9d57a68f91b17fa47b8e5b73e54b6bdcbc912d lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -735,6 +735,15 @@
return self.histories_grid( trans, **kwargs )
@web.expose
+ @web.require_login( "see current history's datasets that can added to this visualization" )
+ def list_current_history_datasets( self, trans, **kwargs ):
+ """ List a history's datasets that can be added to a visualization. """
+
+ kwargs[ 'f-history' ] = trans.security.encode_id( trans.get_history().id )
+ kwargs[ 'show_item_checkboxes' ] = 'True'
+ return self.list_history_datasets( trans, **kwargs )
+
+ @web.expose
@web.require_login( "see a history's datasets that can added to this visualization" )
def list_history_datasets( self, trans, **kwargs ):
"""List a history's datasets that can be added to a visualization."""
diff -r da1ccd08865963c99a55b621af481023b61e3b32 -r 4a9d57a68f91b17fa47b8e5b73e54b6bdcbc912d templates/tracks/browser.mako
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -63,7 +63,7 @@
*/
var add_tracks = function() {
$.ajax({
- url: "${h.url_for( action='list_histories' )}",
+ url: "${h.url_for( action='list_current_history_datasets' )}",
data: { "f-dbkey": view.dbkey },
error: function() { alert( "Grid failed" ); },
success: function(table_html) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/da1ccd088659/
changeset: da1ccd088659
user: jgoecks
date: 2011-12-02 17:10:04
summary: Trackster: interpret feature track data using 0-based, half-open coordinate system.
affected #: 1 file
diff -r 9eddcedc574e0a071fce78f51b9352d3efb7635c -r da1ccd08865963c99a55b621af481023b61e3b32 static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -4294,6 +4294,8 @@
/**
* Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work.
+ * Painter uses a 0-based, half-open coordinate system; start coordinate is closed--included--and the end is open.
+ * This coordinate system matches the BED format.
*/
var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
Painter.call(this, data, view_start, view_end, prefs, mode);
@@ -4419,7 +4421,8 @@
var
feature_uid = feature[0],
feature_start = feature[1],
- feature_end = feature[2],
+ // -1 because end is not included in feature; see FeaturePainter documentation for details.
+ feature_end = feature[2] - 1,
feature_name = feature[3],
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
@@ -4537,7 +4540,8 @@
for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
var block = feature_blocks[k],
block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
- block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ),
+ // -1 because end is not included in feature; see FeaturePainter documentation for details.
+ block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ),
last_block_start, last_block_end;
// Skip drawing if block not on tile.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9eddcedc574e/
changeset: 9eddcedc574e
user: jgoecks
date: 2011-12-01 21:01:28
summary: Trackster: fix bug in determining when to display filters.
affected #: 1 file
diff -r eb9d842f9faf3b7c13d40c387b528b256f29b31a -r 9eddcedc574e0a071fce78f51b9352d3efb7635c static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -3459,13 +3459,17 @@
}
// Determine if filters are available; this is based on the tiles' data.
+ // Criteria for filter to be available: (a) it is applicable to tile data and (b) filter min != filter max.
var filters_available = false,
- example_feature;
+ example_feature,
+ filter;
for (var i = 0; i < tiles.length; i++) {
if (tiles[i].data.length) {
example_feature = tiles[i].data[0];
for (var f = 0; f < filters.length; f++) {
- if (filters[f].applies_to(example_feature)) {
+ filter = filters[f];
+ if ( filter.applies_to(example_feature) &&
+ filter.min !== filter.max ) {
filters_available = true;
break;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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