1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f7e9759b27a0/
Changeset: f7e9759b27a0
User: dan
Date: 2014-12-03 17:18:38+00:00
Summary: Specify the third argument for HdaImplicitMatch.
Affected #: 1 file
diff -r 0273de7467e0f42a56ffa018c5fb9a53a6396e76 -r f7e9759b27a00e7e4a0d6c455dfa4e3744f484f9 lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -53,11 +53,12 @@
return False
target_ext, converted_dataset = hda.find_conversion_destination( formats )
if target_ext:
+ original_hda = hda
if converted_dataset:
hda = converted_dataset
if check_security and not self.__can_access_dataset( hda.dataset ):
return False
- rval = HdaImplicitMatch( hda, target_ext )
+ rval = HdaImplicitMatch( hda, target_ext, original_hda )
else:
return False
if self.filter( hda ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3808622909a6/
Changeset: 3808622909a6
Branch: next-stable
User: dan
Date: 2014-12-03 17:17:25+00:00
Summary: Specify the third argument for HdaImplicitMatch.
Affected #: 1 file
diff -r 172f91ec31ef89d0f0eaa162bab5cfdf90866c22 -r 3808622909a6bb561c46d2ff5a5675f1da589c8b lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -53,11 +53,12 @@
return False
target_ext, converted_dataset = hda.find_conversion_destination( formats )
if target_ext:
+ original_hda = hda
if converted_dataset:
hda = converted_dataset
if check_security and not self.__can_access_dataset( hda.dataset ):
return False
- rval = HdaImplicitMatch( hda, target_ext )
+ rval = HdaImplicitMatch( hda, target_ext, original_hda )
else:
return False
if self.filter( hda ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0273de7467e0/
Changeset: 0273de7467e0
User: dan
Date: 2014-12-03 16:35:35+00:00
Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format).
Affected #: 1 file
diff -r 87ef26ad1876d0d6162eb4b6e7c93c8d69fbc4d6 -r 0273de7467e0f42a56ffa018c5fb9a53a6396e76 lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -39,27 +39,30 @@
return state_valid and ( not check_security or self.__can_access_dataset( dataset ) )
def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ):
- """ Return False of this parameter can not be matched to a the supplied
+ """ Return False of this parameter can not be matched to the supplied
HDA, otherwise return a description of the match (either a
HdaDirectMatch describing a direct match or a HdaImplicitMatch
describing an implicit conversion.)
"""
+ rval = False
+ formats = self.param.formats
+ if hda.datatype.matches_any( formats ):
+ rval = HdaDirectMatch( hda )
+ else:
+ if not check_implicit_conversions:
+ return False
+ target_ext, converted_dataset = hda.find_conversion_destination( formats )
+ if target_ext:
+ if converted_dataset:
+ hda = converted_dataset
+ if check_security and not self.__can_access_dataset( hda.dataset ):
+ return False
+ rval = HdaImplicitMatch( hda, target_ext )
+ else:
+ return False
if self.filter( hda ):
return False
- formats = self.param.formats
- if hda.datatype.matches_any( formats ):
- return HdaDirectMatch( hda )
- if not check_implicit_conversions:
- return False
- target_ext, converted_dataset = hda.find_conversion_destination( formats )
- if target_ext:
- original_hda = hda
- if converted_dataset:
- hda = converted_dataset
- if check_security and not self.__can_access_dataset( hda.dataset ):
- return False
- return HdaImplicitMatch( hda, target_ext, original_hda )
- return False
+ return rval
def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ):
""" If HDA is accessible, return information about whether it could
https://bitbucket.org/galaxy/galaxy-central/commits/13d43b327511/
Changeset: 13d43b327511
Branch: next-stable
User: dan
Date: 2014-12-03 16:35:35+00:00
Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format).
Affected #: 1 file
diff -r f05ed31c16741b5c1a4a43c73697f7ca9a6919d8 -r 13d43b327511d46e836398fa09330722acccd419 lib/galaxy/tools/parameters/dataset_matcher.py
--- a/lib/galaxy/tools/parameters/dataset_matcher.py
+++ b/lib/galaxy/tools/parameters/dataset_matcher.py
@@ -39,27 +39,30 @@
return state_valid and ( not check_security or self.__can_access_dataset( dataset ) )
def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ):
- """ Return False of this parameter can not be matched to a the supplied
+ """ Return False of this parameter can not be matched to the supplied
HDA, otherwise return a description of the match (either a
HdaDirectMatch describing a direct match or a HdaImplicitMatch
describing an implicit conversion.)
"""
+ rval = False
+ formats = self.param.formats
+ if hda.datatype.matches_any( formats ):
+ rval = HdaDirectMatch( hda )
+ else:
+ if not check_implicit_conversions:
+ return False
+ target_ext, converted_dataset = hda.find_conversion_destination( formats )
+ if target_ext:
+ if converted_dataset:
+ hda = converted_dataset
+ if check_security and not self.__can_access_dataset( hda.dataset ):
+ return False
+ rval = HdaImplicitMatch( hda, target_ext )
+ else:
+ return False
if self.filter( hda ):
return False
- formats = self.param.formats
- if hda.datatype.matches_any( formats ):
- return HdaDirectMatch( hda )
- if not check_implicit_conversions:
- return False
- target_ext, converted_dataset = hda.find_conversion_destination( formats )
- if target_ext:
- original_hda = hda
- if converted_dataset:
- hda = converted_dataset
- if check_security and not self.__can_access_dataset( hda.dataset ):
- return False
- return HdaImplicitMatch( hda, target_ext, original_hda )
- return False
+ return rval
def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ):
""" If HDA is accessible, return information about whether it could
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a734cbf4bd36/
Changeset: a734cbf4bd36
User: jgoecks
Date: 2014-12-02 18:31:09+00:00
Summary: Merge next-stable to default
Affected #: 3 files
diff -r 447e69511115f2e2d5a13d8bbe2282cf0c94c5db -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 client/galaxy/scripts/viz/trackster/slotting.js
--- a/client/galaxy/scripts/viz/trackster/slotting.js
+++ b/client/galaxy/scripts/viz/trackster/slotting.js
@@ -138,7 +138,6 @@
// Feature is slotted; if feature now has larger start/end coordinates,
// update drawing coordinates.
if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) {
- console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature)));
// Feature has changed (e.g. a single read now has its pair), so recalculate its
// drawing coordinates.
var old_draw_coords = this._get_draw_coords(slotted_info.feature),
diff -r 447e69511115f2e2d5a13d8bbe2282cf0c94c5db -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 static/scripts/packed/viz/trackster/slotting.js
--- a/static/scripts/packed/viz/trackster/slotting.js
+++ b/static/scripts/packed/viz/trackster/slotting.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){console.log(x[3],g.slot,this._find_slot(this._get_draw_coords(x)));var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}});
\ No newline at end of file
+define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}});
\ No newline at end of file
diff -r 447e69511115f2e2d5a13d8bbe2282cf0c94c5db -r a734cbf4bd368198e2c813b5ea61e807f9a1af33 static/scripts/viz/trackster/slotting.js
--- a/static/scripts/viz/trackster/slotting.js
+++ b/static/scripts/viz/trackster/slotting.js
@@ -138,7 +138,6 @@
// Feature is slotted; if feature now has larger start/end coordinates,
// update drawing coordinates.
if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) {
- console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature)));
// Feature has changed (e.g. a single read now has its pair), so recalculate its
// drawing coordinates.
var old_draw_coords = this._get_draw_coords(slotted_info.feature),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/eb9d9ab34d23/
Changeset: eb9d9ab34d23
Branch: next-stable
User: jgoecks
Date: 2014-12-02 18:30:19+00:00
Summary: Remove debugging statement.
Affected #: 3 files
diff -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 -r eb9d9ab34d23456d58f291b782b42724a83f711e client/galaxy/scripts/viz/trackster/slotting.js
--- a/client/galaxy/scripts/viz/trackster/slotting.js
+++ b/client/galaxy/scripts/viz/trackster/slotting.js
@@ -138,7 +138,6 @@
// Feature is slotted; if feature now has larger start/end coordinates,
// update drawing coordinates.
if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) {
- console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature)));
// Feature has changed (e.g. a single read now has its pair), so recalculate its
// drawing coordinates.
var old_draw_coords = this._get_draw_coords(slotted_info.feature),
diff -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 -r eb9d9ab34d23456d58f291b782b42724a83f711e static/scripts/packed/viz/trackster/slotting.js
--- a/static/scripts/packed/viz/trackster/slotting.js
+++ b/static/scripts/packed/viz/trackster/slotting.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){console.log(x[3],g.slot,this._find_slot(this._get_draw_coords(x)));var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}});
\ No newline at end of file
+define(["libs/underscore"],function(c){var f=c.extend;var d=2,b=5;var a=function(h,g){this.slot=h;this.feature=g};var e=function(j,i,g,h){this.slots={};this.start_end_dct={};this.w_scale=j;this.mode=i;this.include_label=(i==="Pack");this.max_rows=g;this.measureText=h};f(e.prototype,{_get_draw_coords:function(j){var h=Math.floor(j[1]*this.w_scale),i=Math.ceil(j[2]*this.w_scale),g=j[3],k;if(g!==undefined&&this.include_label){var l=this.measureText(g).width+(d+b);if(h-l>=0){h-=l;k="left"}else{i+=l;k="right"}}return[h,i]},_find_slot:function(j){var o=j[0],n=j[1];for(var l=0;l<=this.max_rows;l++){var p=false,m=this.start_end_dct[l];if(m!==undefined){for(var g=0,h=m.length;g<h;g++){var i=m[g];if(n>i[0]&&o<i[1]){p=true;break}}}if(!p){return l}}return -1},slot_features:function(h){var q=this.start_end_dct,v=[],m=0,x,l;for(var o=0,t=h.length;o<t;o++){x=h[o];l=x[0];var g=this.slots[l];if(g){if(x[1]<g.feature[1]||g.feature[2]<x[2]){var s=this._get_draw_coords(g.feature),p=this._get_draw_coords(x),j=this.start_end_dct[g.slot];for(var n=0;n<j.length;n++){var w=j[n];if(w[0]===s[0]&&w[1]===s[1]){j[n]=p}}}m=Math.max(m,this.slots[l].slot)}else{v.push(o)}}for(var o=0,t=v.length;o<t;o++){x=h[v[o]];l=x[0];var r=this._get_draw_coords(x);var u=this._find_slot(r);if(u>=0){if(q[u]===undefined){q[u]=[]}q[u].push(r);this.slots[l]=new a(u,x);m=Math.max(m,u)}}return m+1}});return{FeatureSlotter:e}});
\ No newline at end of file
diff -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 -r eb9d9ab34d23456d58f291b782b42724a83f711e static/scripts/viz/trackster/slotting.js
--- a/static/scripts/viz/trackster/slotting.js
+++ b/static/scripts/viz/trackster/slotting.js
@@ -138,7 +138,6 @@
// Feature is slotted; if feature now has larger start/end coordinates,
// update drawing coordinates.
if (feature[1] < slotted_info.feature[1] || slotted_info.feature[2] < feature[2]) {
- console.log(feature[3], slotted_info.slot, this._find_slot(this._get_draw_coords(feature)));
// Feature has changed (e.g. a single read now has its pair), so recalculate its
// drawing coordinates.
var old_draw_coords = this._get_draw_coords(slotted_info.feature),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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