1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/d44244ed570a/
changeset: r5353:d44244ed570a
user: natefoo
date: 2011-04-06 18:44:58
summary: Disable eagerloading of a job's datasets. This results in more queries but does away with a join that was returning a far bigger result than it should've.
affected #: 1 file (36 bytes)
--- a/lib/galaxy/model/mapping.py Wed Apr 06 12:40:20 2011 -0400
+++ b/lib/galaxy/model/mapping.py Wed Apr 06 12:44:58 2011 -0400
@@ -1392,10 +1392,10 @@
history=relation( History ),
library_folder=relation( LibraryFolder ),
parameters=relation( JobParameter, lazy=False ),
- input_datasets=relation( JobToInputDatasetAssociation, lazy=False ),
- output_datasets=relation( JobToOutputDatasetAssociation, lazy=False ),
+ input_datasets=relation( JobToInputDatasetAssociation ),
+ output_datasets=relation( JobToOutputDatasetAssociation ),
post_job_actions=relation( PostJobActionAssociation, lazy=False ),
- output_library_datasets=relation( JobToOutputLibraryDatasetAssociation, lazy=False ),
+ output_library_datasets=relation( JobToOutputLibraryDatasetAssociation ),
external_output_metadata = relation( JobExternalOutputMetadata, lazy = False ) ) )
assign_mapper( context, Task, Task.table,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/cd2aff5b117c/
changeset: r5350:cd2aff5b117c
user: kellyv
date: 2011-04-06 16:16:30
summary: Corrected typo in manual build name
affected #: 1 file (0 bytes)
--- a/tool-data/shared/ucsc/manual_builds.txt Tue Apr 05 17:59:43 2011 -0400
+++ b/tool-data/shared/ucsc/manual_builds.txt Wed Apr 06 10:16:30 2011 -0400
@@ -692,7 +692,7 @@
eschColi_TW14359 Escherichia coli TW14359 chr=5528136,plasmid_pO157=94601
pUC18 pUC18 Plasmid plasmid=2686
nomLeu1 Gibbon chr1=245538060,chr10=135320619,chr10_random=51011,chr11=134551115,chr12=132397767,chr12_random=336702,chr13=114140689,chr14=106383727,chr15=100373758,chr15_random=814500,chr16=88836341,chr16_random=121782,chr17=78641643,chr17_random=2617017,chr18=76124575,chr19=63791437,chr19_random=297341,chr1_random=3502083,chr2=242756806,chr20=62432189,chr21=47019833,chr22=49520868,chr22_random=31530,chr2_random=335351,chr3=199337376,chr3_random=950829,chr4=191633586,chr4_random=923474,chr5=180612635,chr5_random=150620,chr6=170839170,chr6_random=1837487,chr7=158619002,chr7_random=805938,chr8=146283503,chr8_random=649034,chr9=138402467,chr9_random=1315712,chrUn=217400297,chrX=154793867,chrX_random=1690203,chrY=57470892
-Saccharomcyes_cerevisiae_S288C_SGD2010 S. cerevisae str. S288C chr1=230218,chr2=813184,chr3=316620,chr4=1531933,chr5=576874,chr6=270161,chr7=1090940,chr8=562643,chr9=439888,chr10=745751,chr11=666816,chr12=1078177,chr13=924431,chr14=784333,chr15=1091291,chr16=948066,chrM=85779
+Saccharomyces_cerevisiae_S288C_SGD2010 S. cerevisae str. S288C chr1=230218,chr2=813184,chr3=316620,chr4=1531933,chr5=576874,chr6=270161,chr7=1090940,chr8=562643,chr9=439888,chr10=745751,chr11=666816,chr12=1078177,chr13=924431,chr14=784333,chr15=1091291,chr16=948066,chrM=85779
Spur_v2.6 Purple Sea Urchin (Strongylocentrotus purpuratus) v2.6
Ptrichocarpa_156 Poplar (Populus trichocarpa)
Hydra_JCVI Hydra magnipapillata str. 105
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/dd604de40ac4/
changeset: r5349:dd604de40ac4
user: jgoecks
date: 2011-04-05 23:59:43
summary: Trackster: ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px.
affected #: 1 file (317 bytes)
--- a/static/scripts/trackster.js Tue Apr 05 14:16:26 2011 -0400
+++ b/static/scripts/trackster.js Tue Apr 05 17:59:43 2011 -0400
@@ -1126,10 +1126,9 @@
/**
* Tiles for TiledTracks.
*/
-var Tile = function(track, canvas, histo_max) {
+var Tile = function(track, canvas) {
this.track = track;
this.canvas = canvas;
- this.histo_max = histo_max;
};
/**
@@ -2192,7 +2191,7 @@
// Start dealing with row-by-row tracks
- // If working with a mode where slotting is neccesary, update the incremental slotting
+ // If working with a mode where slotting is necessary, update the incremental slotting
var slots, slots_required = 1;
if ( mode === "no_detail" || mode === "Squish" || mode === "Pack" ) {
slots_required = this.incremental_slots(w_scale, result.data, mode);
@@ -3164,6 +3163,14 @@
var seq_start = feature_start + base_offset,
s_start = Math.floor( Math.max(0, (seq_start - tile_low) * w_scale) ),
s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low) * w_scale) );
+
+ // Make sure that read is drawn even if it too small to be rendered officially; in this case,
+ // read is drawn at 1px.
+ // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting
+ // and drawing.
+ if (s_start === s_end) {
+ s_end += 1;
+ }
switch (cig_op) {
case "H": // Hard clipping.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b53f0963bffc/
changeset: r5339:b53f0963bffc
user: james_taylor
date: 2011-04-05 05:27:25
summary: trackster: draw lines to indicate when line tracks overflow the visible region
affected #: 1 file (1.4 KB)
--- a/static/scripts/trackster.js Mon Apr 04 13:40:09 2011 -0400
+++ b/static/scripts/trackster.js Mon Apr 04 23:27:25 2011 -0400
@@ -2668,6 +2668,7 @@
this.max_value = max_value;
this.color = color;
this.mode = mode;
+ this.overflow_color = "#F66";
}
LinePainter.prototype.draw = function( ctx, width, height ) {
@@ -2690,14 +2691,6 @@
// Line at 0.0
if ( mode !== "Intensity" ) {
- /*
- ctx.beginPath();
- ctx.moveTo( 0, y_zero );
- ctx.lineTo( width, y_zero );
- // ctx.lineWidth = 0.5;
- ctx.fillStyle = "#aaa";
- ctx.stroke();
- */
ctx.fillStyle = "#aaa";
ctx.fillRect( 0, y_zero, width, 1 );
}
@@ -2761,6 +2754,37 @@
ctx.stroke();
}
+ // Draw lines at bounderies if overflowing min or max
+ var overflow_min_start = -1,
+ overflow_max_start = -1;
+ ctx.fillStyle = this.overflow_color;
+ for (var i = 0, len = data.length; i < len; i++) {
+ y = data[i][1];
+ x_scaled = Math.round((data[i][0] - view_start) * w_scale);
+ x_minus_scaled = Math.round((data[i][0] - 1 - view_start) * w_scale);
+
+ // If we are in a min/max run, check if it should be ended
+ if ( overflow_max_start >= 0 && ( y === null || y < max_value ) ) {
+ // Value does not exist or is in valid range, any overflow ends
+ ctx.fillRect( overflow_max_start, 0, x_minus_scaled - overflow_max_start + 1, 2 );
+ overflow_max_start = -1;
+ } else if ( overflow_min_start >= 0 && ( y === null || y > min_value ) ) {
+ // Draw bottom overflow bar
+ ctx.fillRect( overflow_min_start, height - 2, x_minus_scaled - overflow_min_start + 1, 2 );
+ overflow_min_start = -1;
+ }
+
+ // Now check if we should start a new one (this may happen on the same
+ // base as above if switching between min/max)
+ if ( y !== null && y > max_value && overflow_max_start < 0 ) {
+ // Top overflows and we are not already in a run of overflow
+ overflow_max_start = x_scaled;
+ } else if ( y !== null && y < min_value && overflow_min_start < 0 ) {
+ // Bottom overflows and we are not already in a run
+ overflow_min_start = x_scaled;
+ }
+ }
+
ctx.restore();
}
@@ -2806,7 +2830,7 @@
// Slot valid only if features are slotted and this feature is slotted;
// feature may not be due to lack of space.
slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid] : null);
-
+
// Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes).
if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null)) {
this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale,
@@ -3146,7 +3170,7 @@
seq_offset = 0,
gap = 0
ref_seq = this.ref_seq,
- char_width_px = ctx.canvas.manager.char_width_px;
+ char_width_px = ctx.canvas.manager.char_width_px;
// Keep list of items that need to be drawn on top of initial drawing layer.
var draw_last = [];
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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