commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c4519bae84d3/
Changeset: c4519bae84d3
Branch: stable
User: guerler
Date: 2014-06-30 02:04:28
Summary: Fix popovers
Affected #: 2 files
diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r c4519bae84d32d638d8fe168c6fbcab40f4e8449 static/scripts/mvc/ui/ui-popover.js
--- a/static/scripts/mvc/ui/ui-popover.js
+++ b/static/scripts/mvc/ui/ui-popover.js
@@ -140,7 +140,7 @@
// template
_template: function(options) {
- var tmpl = '<div class="popover-view popover fade ' + options.placement + ' in">' +
+ var tmpl = '<div class="ui-popover popover fade ' + options.placement + ' in">' +
'<div class="arrow"></div>' +
'<div class="popover-title">' +
'<div class="popover-title-label">' +
diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r c4519bae84d32d638d8fe168c6fbcab40f4e8449 static/scripts/packed/mvc/ui/ui-popover.js
--- a/static/scripts/packed/mvc/ui/ui-popover.js
+++ b/static/scripts/packed/mvc/ui/ui-popover.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="popover-view popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{with_close:true,container:"body",title:null,placement:"top"},visible:false,initialize:function(d){var c=this;this.options=_.defaults(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.parent().append(this.$el);if(this.options.with_close){this.$el.find("#close").on("click",function(){c.hide()})}this.uuid=a.uuid();var c=this;$("body").on("mousedown."+this.uuid,function(f){c._hide(f)})},title:function(c){if(c!==undefined){this.$el.find(".popover-title-label").html(c)}},show:function(){this.$el.show();this.visible=true;var c=this._get_placement(this.options.placement);this.$el.css(c)},_get_placement:function(h){var d=this._get_width(this.$el);var j=this.$el.height();var k=this.options.container;var c=this._get_width(k);var f=this._get_height(k);var g=k.position();var i=0;var e=0;if(h=="top"||h=="bottom"){e=g.left-d+(c+d)/2;if(h=="top"){i=g.top-j-5}else{i=g.top+f+5}}return{top:i,left:e}},_get_width:function(c){return c.width()+parseInt(c.css("padding-left"))+parseInt(c.css("padding-right"))},_get_height:function(c){return c.height()+parseInt(c.css("padding-top"))+parseInt(c.css("padding-bottom"))},hide:function(){this.$el.hide();this.visible=false},append:function(c){this.$el.find(".popover-content").append(c)},empty:function(c){this.$el.find(".popover-content").empty()},remove:function(){$("body").off("mousedown."+this.uuid);this.$el.remove()},_hide:function(c){if(!$(this.options.container).is(c.target)&&!$(this.el).is(c.target)&&$(this.el).has(c.target).length===0){this.hide()}},_template:function(d){var c='<div class="ui-popover popover fade '+d.placement+' in"><div class="arrow"></div><div class="popover-title"><div class="popover-title-label">'+d.title+"</div>";if(d.with_close){c+='<div id="close" class="popover-close fa fa-times-circle"></div>'}c+='</div><div class="popover-content"></div></div>';return c}});return{View:b}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/2e1de0fc5a3c/
Changeset: 2e1de0fc5a3c
User: guerler
Date: 2014-06-30 02:05:17
Summary: Merge
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 7 months
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6487537fba23/
Changeset: 6487537fba23
Branch: daniel_blanchard/update-drmaa-python-version-in-eggsini-t-1402925026891
User: daniel_blanchard
Date: 2014-06-16 15:27:38
Summary: Update DRMAA Python version in eggs.ini to 0.7.6.
This version has better string handling and supports Python 3.
Affected #: 1 file
diff -r d3a0b4b9da32927b5aab806f1a991594285475f7 -r 6487537fba23263b041b46ec6268c7c9cd3a8aa9 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -38,7 +38,7 @@
boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
-drmaa = 0.6
+drmaa = 0.7.6
elementtree = 1.2.6_20050316
Fabric = 1.7.0
GeneTrack = 2.0.0_beta_1
https://bitbucket.org/galaxy/galaxy-central/commits/dd77a9684c7b/
Changeset: dd77a9684c7b
User: natefoo
Date: 2014-06-29 22:03:46
Summary: Merged in daniel_blanchard/galaxy-central/daniel_blanchard/update-drmaa-python-version-in-eggsini-t-1402925026891 (pull request #421)
Update DRMAA Python version in eggs.ini to 0.7.6.
Affected #: 1 file
diff -r 4de240e5a7819c768b8267c19e477530dab54370 -r dd77a9684c7b7430db1275c2e9bf30ab743cdc9f eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -38,7 +38,7 @@
boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
-drmaa = 0.6
+drmaa = 0.7.6
elementtree = 1.2.6_20050316
Fabric = 1.7.0
GeneTrack = 2.0.0_beta_1
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 7 months
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7094bb55cc8a/
Changeset: 7094bb55cc8a
User: jmchilton
Date: 2014-06-29 20:31:33
Summary: Spelling fix in method name.
Affected #: 2 files
diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2931,7 +2931,7 @@
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
"""
- return output_collect.collect_primary_datatasets( self, output, job_working_directory )
+ return output_collect.collect_primary_datasets( self, output, job_working_directory )
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -14,7 +14,7 @@
DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
-def collect_primary_datatasets( tool, output, job_working_directory ):
+def collect_primary_datasets( tool, output, job_working_directory ):
app = tool.app
sa_session = tool.sa_session
new_primary_datasets = {}
https://bitbucket.org/galaxy/galaxy-central/commits/4de240e5a781/
Changeset: 4de240e5a781
User: jmchilton
Date: 2014-06-29 20:31:33
Summary: Allow discovered datasets to use input data format in 'ext' definition.
Affected #: 4 files
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1181,6 +1181,13 @@
out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] )
+ input_ext = 'data'
+ for _, data in inp_data.items():
+ # For loop odd, but sort simulating behavior in galaxy.tools.actions
+ if not data:
+ continue
+ input_ext = data.ext
+
param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows
param_dict = self.tool.params_from_strings( param_dict, self.app )
# Check for and move associated_files
@@ -1191,7 +1198,7 @@
# Create generated output children and primary datasets and add to param_dict
collected_datasets = {
'children': self.tool.collect_child_datasets(out_data, self.working_directory),
- 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory)
+ 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext)
}
param_dict.update({'__collected_datasets__': collected_datasets})
# Certain tools require tasks to be completed after job execution
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2926,12 +2926,12 @@
self.sa_session.flush()
return children
- def collect_primary_datasets( self, output, job_working_directory ):
+ def collect_primary_datasets( self, output, job_working_directory, input_ext ):
"""
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
"""
- return output_collect.collect_primary_datasets( self, output, job_working_directory )
+ return output_collect.collect_primary_datasets( self, output, job_working_directory, input_ext )
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -14,7 +14,7 @@
DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
-def collect_primary_datasets( tool, output, job_working_directory ):
+def collect_primary_datasets( tool, output, job_working_directory, input_ext ):
app = tool.app
sa_session = tool.sa_session
new_primary_datasets = {}
@@ -66,6 +66,8 @@
designation = fields_match.designation
visible = fields_match.visible
ext = fields_match.ext
+ if ext == "input":
+ ext = input_ext
dbkey = fields_match.dbkey
# Create new primary dataset
primary_data = app.model.HistoryDatasetAssociation( extension=ext,
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r 4de240e5a7819c768b8267c19e477530dab54370 test/functional/tools/multi_output_configured.xml
--- a/test/functional/tools/multi_output_configured.xml
+++ b/test/functional/tools/multi_output_configured.xml
@@ -8,19 +8,24 @@
echo "1" > subdir2/CUSTOM_1.txt;
echo "2" > subdir2/CUSTOM_2.tabular;
echo "3" > subdir2/CUSTOM_3.txt;
+ mkdir subdir3;
+ echo "Foo" > subdir3/Foo;
</command><inputs>
- <param name="input" type="integer" value="7" />
+ <param name="num_param" type="integer" value="7" />
+ <param name="input" type="data" /></inputs><outputs><data format="txt" name="report"><discover_datasets pattern="__designation_and_ext__" directory="subdir1" /><discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" />
+ <discover_datasets pattern="__designation__" directory="subdir3" ext="input" /></data></outputs><tests><test>
- <param name="input" value="7" />
+ <param name="num_param" value="7" />
+ <param name="input" ftype="txt" value="simple_line.txt"/><output name="report"><assert_contents><has_line line="Hello" />
@@ -37,6 +42,9 @@
<discovered_dataset designation="2" ftype="tabular"><assert_contents><has_line line="2" /></assert_contents></discovered_dataset>
+ <discovered_dataset designation="Foo" ftype="txt">
+ <assert_contents><has_line line="Foo" /></assert_contents>
+ </discovered_dataset></output></test></tests>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 7 months
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/21b53ebad211/
Changeset: 21b53ebad211
Branch: stable
User: jmchilton
Date: 2014-06-29 20:24:32
Summary: Spelling fix in method name.
Affected #: 2 files
diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r 21b53ebad2119dd9968c72f67b53d069ebc17902 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2874,7 +2874,7 @@
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
"""
- return output_collect.collect_primary_datatasets( self, output, job_working_directory )
+ return output_collect.collect_primary_datasets( self, output, job_working_directory )
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
diff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 -r 21b53ebad2119dd9968c72f67b53d069ebc17902 lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -14,7 +14,7 @@
DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
-def collect_primary_datatasets( tool, output, job_working_directory ):
+def collect_primary_datasets( tool, output, job_working_directory ):
app = tool.app
sa_session = tool.sa_session
new_primary_datasets = {}
https://bitbucket.org/galaxy/galaxy-central/commits/c14bdcb9ae96/
Changeset: c14bdcb9ae96
Branch: stable
User: jmchilton
Date: 2014-06-29 20:24:32
Summary: Allow discovered datasets to use input data format in 'ext' definition.
Affected #: 4 files
diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1065,6 +1065,13 @@
out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] )
+ input_ext = 'data'
+ for _, data in inp_data.items():
+ # For loop odd, but sort simulating behavior in galaxy.tools.actions
+ if not data:
+ continue
+ input_ext = data.ext
+
param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows
param_dict = self.tool.params_from_strings( param_dict, self.app )
# Check for and move associated_files
@@ -1075,7 +1082,7 @@
# Create generated output children and primary datasets and add to param_dict
collected_datasets = {
'children': self.tool.collect_child_datasets(out_data, self.working_directory),
- 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory)
+ 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext)
}
param_dict.update({'__collected_datasets__': collected_datasets})
# Certain tools require tasks to be completed after job execution
diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2869,12 +2869,12 @@
self.sa_session.flush()
return children
- def collect_primary_datasets( self, output, job_working_directory ):
+ def collect_primary_datasets( self, output, job_working_directory, input_ext ):
"""
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
"""
- return output_collect.collect_primary_datasets( self, output, job_working_directory )
+ return output_collect.collect_primary_datasets( self, output, job_working_directory, input_ext )
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -14,7 +14,7 @@
DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
-def collect_primary_datasets( tool, output, job_working_directory ):
+def collect_primary_datasets( tool, output, job_working_directory, input_ext ):
app = tool.app
sa_session = tool.sa_session
new_primary_datasets = {}
@@ -66,6 +66,8 @@
designation = fields_match.designation
visible = fields_match.visible
ext = fields_match.ext
+ if ext == "input":
+ ext = input_ext
dbkey = fields_match.dbkey
# Create new primary dataset
primary_data = app.model.HistoryDatasetAssociation( extension=ext,
diff -r 21b53ebad2119dd9968c72f67b53d069ebc17902 -r c14bdcb9ae9643525c0797090f293030ea899948 test/functional/tools/multi_output_configured.xml
--- a/test/functional/tools/multi_output_configured.xml
+++ b/test/functional/tools/multi_output_configured.xml
@@ -8,19 +8,24 @@
echo "1" > subdir2/CUSTOM_1.txt;
echo "2" > subdir2/CUSTOM_2.tabular;
echo "3" > subdir2/CUSTOM_3.txt;
+ mkdir subdir3;
+ echo "Foo" > subdir3/Foo;
</command><inputs>
- <param name="input" type="integer" value="7" />
+ <param name="num_param" type="integer" value="7" />
+ <param name="input" type="data" /></inputs><outputs><data format="txt" name="report"><discover_datasets pattern="__designation_and_ext__" directory="subdir1" /><discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" />
+ <discover_datasets pattern="__designation__" directory="subdir3" ext="input" /></data></outputs><tests><test>
- <param name="input" value="7" />
+ <param name="num_param" value="7" />
+ <param name="input" ftype="txt" value="simple_line.txt"/><output name="report"><assert_contents><has_line line="Hello" />
@@ -37,6 +42,9 @@
<discovered_dataset designation="2" ftype="tabular"><assert_contents><has_line line="2" /></assert_contents></discovered_dataset>
+ <discovered_dataset designation="Foo" ftype="txt">
+ <assert_contents><has_line line="Foo" /></assert_contents>
+ </discovered_dataset></output></test></tests>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Merged in BjoernGruening/galaxy-central-2/BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 (pull request #430)
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/381a36069c14/
Changeset: 381a36069c14
User: davebgx
Date: 2014-06-29 16:30:21
Summary: Merged in BjoernGruening/galaxy-central-2/BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 (pull request #430)
Fix some spelling mistake and hopefully all of the install_*_environments.
Affected #: 1 file
diff -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 -r 381a36069c14bf20c98955c01ab00e7838257943 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -44,8 +44,8 @@
def __init__( self, app ):
self.app = app
- self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet',
- 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ]
+ self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment',
+ 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ]
def format_traceback( self ):
ex_type, ex, tb = sys.exc_info()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 7 months
commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5606d3b0cbc7/
Changeset: 5606d3b0cbc7
Branch: BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740
User: BjoernGruening
Date: 2014-06-29 16:25:44
Summary: Fix some spelling mistake and hopefully all of the install_*_environments.
Affected #: 1 file
diff -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 -r 5606d3b0cbc768cff6581a5fd79d561a81d0dc36 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -44,8 +44,8 @@
def __init__( self, app ):
self.app = app
- self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet',
- 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ]
+ self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment',
+ 'setup_r_environment', 'setup_ruby_environent', 'shell_command' ]
def format_traceback( self ):
ex_type, ex, tb = sys.exc_info()
https://bitbucket.org/galaxy/galaxy-central/commits/a78c3f818c01/
Changeset: a78c3f818c01
Branch: BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740
User: BjoernGruening
Date: 2014-06-29 16:28:13
Summary: Fix some spelling mistake and hopefully all of the install_*_environments.
Affected #: 1 file
diff -r 5606d3b0cbc768cff6581a5fd79d561a81d0dc36 -r a78c3f818c01fbc9bd217c599052f9e6486c1fcf lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -45,7 +45,7 @@
def __init__( self, app ):
self.app = app
self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment',
- 'setup_r_environment', 'setup_ruby_environent', 'shell_command' ]
+ 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ]
def format_traceback( self ):
ex_type, ex, tb = sys.exc_info()
https://bitbucket.org/galaxy/galaxy-central/commits/381a36069c14/
Changeset: 381a36069c14
User: davebgx
Date: 2014-06-29 16:30:21
Summary: Merged in BjoernGruening/galaxy-central-2/BjoernGruening/fix-some-spelling-mistake-and-hopefully--1404051898740 (pull request #430)
Fix some spelling mistake and hopefully all of the install_*_environments.
Affected #: 1 file
diff -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 -r 381a36069c14bf20c98955c01ab00e7838257943 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -44,8 +44,8 @@
def __init__( self, app ):
self.app = app
- self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environmnet',
- 'setup_r_environmnet', 'setup_ruby_environmnet', 'shell_command' ]
+ self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment',
+ 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ]
def format_traceback( self ):
ex_type, ex, tb = sys.exc_info()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: hackdna: Enable stopping jobs when history is deleted via the API.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7b02c61a6c21/
Changeset: 7b02c61a6c21
User: hackdna
Date: 2014-06-28 23:57:06
Summary: Enable stopping jobs when history is deleted via the API.
Affected #: 1 file
diff -r 2577b386dbbe421e80c816abf7683359ab64fe1f -r 7b02c61a6c21d0ffe8b7160ba51a27ab1bbf2b01 lib/galaxy/webapps/galaxy/api/histories.py
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -235,6 +235,10 @@
for hda in history.datasets:
if hda.purged:
continue
+ if hda.creating_job_associations:
+ job = hda.creating_job_associations[0].job
+ job.mark_deleted( self.app.config.track_jobs_in_database )
+ self.app.job_manager.job_stop_queue.put( job.id )
hda.purged = True
trans.sa_session.add( hda )
trans.sa_session.flush()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 7 months
commit/galaxy-central: dan: Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/65e5e5b72893/
Changeset: 65e5e5b72893
Branch: stable
User: dan
Date: 2014-06-27 20:44:55
Summary: Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.
Affected #: 9 files
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -7,7 +7,12 @@
<tool file="data_source/ebi_sra.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/gramene_mart.xml" />
+ <tool file="data_source/flymine.xml" /><tool file="data_source/fly_modencode.xml" />
+ <tool file="data_source/modmine.xml" />
+ <tool file="data_source/mousemine.xml" />
+ <tool file="data_source/ratmine.xml" />
+ <tool file="data_source/yeastmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" />
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -12,6 +12,13 @@
<tool file="data_source/cbi_rice_mart.xml" /><tool file="data_source/gramene_mart.xml" /><tool file="data_source/fly_modencode.xml" />
+ <tool file="data_source/flymine.xml" />
+ <tool file="data_source/flymine_test.xml" />
+ <tool file="data_source/modmine.xml" />
+ <tool file="data_source/mousemine.xml" />
+ <tool file="data_source/ratmine.xml" />
+ <tool file="data_source/yeastmine.xml" />
+ <tool file="data_source/metabolicmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/wormbase_test.xml" />
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/flymine.xml
--- /dev/null
+++ b/tools/data_source/flymine.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<!--
+ If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+ the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
+ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="Flymine" id="flymine" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://www.flymine.org" check_values="false" method="get">
+ <display>go to Flymine server $GALAXY_URL</display>
+ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
+ </inputs>
+ <request_param_translation>
+ <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+ <request_param galaxy_name="URL" remote_name="URL" missing="" />
+ <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
+ <request_param galaxy_name="organism" remote_name="organism" missing="" />
+ <request_param galaxy_name="table" remote_name="table" missing="" />
+ <request_param galaxy_name="description" remote_name="description" missing="" />
+ <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
+ <request_param galaxy_name="info" remote_name="info" missing="" />
+ <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+ <value_translation>
+ <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect -->
+ </value_translation>
+ </request_param>
+ </request_param_translation>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
+
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/flymine_test.xml
--- /dev/null
+++ b/tools/data_source/flymine_test.xml
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<!--
+ If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+ the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
+ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="Flymine test" id="flymine_test" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get">
+ <display>go to Flymine server $GALAXY_URL</display>
+ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
+ </inputs>
+ <request_param_translation>
+ <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+ <request_param galaxy_name="URL" remote_name="URL" missing="" />
+ <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
+ <request_param galaxy_name="organism" remote_name="organism" missing="" />
+ <request_param galaxy_name="table" remote_name="table" missing="" />
+ <request_param galaxy_name="description" remote_name="description" missing="" />
+ <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
+ <request_param galaxy_name="info" remote_name="info" missing="" />
+ <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
+ </request_param_translation>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
+
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/metabolicmine.xml
--- /dev/null
+++ b/tools/data_source/metabolicmine.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tool name="metabolicMine" id="metabolicmine" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get">
+ <display>go to metabolicMine server $GALAXY_URL</display>
+ </inputs>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/modmine.xml
--- /dev/null
+++ b/tools/data_source/modmine.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<!--
+ If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+ the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
+ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="modENCODE modMine" id="modmine" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://intermine.modencode.org/" check_values="false" method="get">
+ <display>go to modENCODE modMine server $GALAXY_URL</display>
+ </inputs>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
+
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/mousemine.xml
--- /dev/null
+++ b/tools/data_source/mousemine.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<!--
+ If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+ the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
+ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="MouseMine" id="mousemine" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get">
+ <display>go to MouseMine server $GALAXY_URL</display>
+ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" />
+ </inputs>
+ <request_param_translation>
+ <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+ <request_param galaxy_name="URL" remote_name="URL" missing="" />
+ <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
+ <request_param galaxy_name="organism" remote_name="organism" missing="" />
+ <request_param galaxy_name="table" remote_name="table" missing="" />
+ <request_param galaxy_name="description" remote_name="description" missing="" />
+ <request_param galaxy_name="name" remote_name="name" missing="MouseMine query" />
+ <request_param galaxy_name="info" remote_name="info" missing="" />
+ <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+ <value_translation>
+ <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect -->
+ </value_translation>
+ </request_param>
+ </request_param_translation>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
+
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/ratmine.xml
--- /dev/null
+++ b/tools/data_source/ratmine.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<!--
+ If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+ the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
+ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="Ratmine" id="ratmine" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get">
+ <display>go to Ratmine server $GALAXY_URL</display>
+ <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
+ </inputs>
+ <request_param_translation>
+ <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+ <request_param galaxy_name="URL" remote_name="URL" missing="" />
+ <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
+ <request_param galaxy_name="organism" remote_name="organism" missing="" />
+ <request_param galaxy_name="table" remote_name="table" missing="" />
+ <request_param galaxy_name="description" remote_name="description" missing="" />
+ <request_param galaxy_name="name" remote_name="name" missing="Ratmine query" />
+ <request_param galaxy_name="info" remote_name="info" missing="" />
+ <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+ <value_translation>
+ <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect -->
+ </value_translation>
+ </request_param>
+ </request_param_translation>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
diff -r 22bf162cd32a30d0962cf8a095104e088cc540ff -r 65e5e5b72893445eef5c4d2f43350df72e89b436 tools/data_source/yeastmine.xml
--- /dev/null
+++ b/tools/data_source/yeastmine.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<tool name="YeastMine" id="yeastmine" tool_type="data_source">
+ <description>server</description>
+ <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+ <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get">
+ <display>go to yeastMine server $GALAXY_URL</display>
+ </inputs>
+ <request_param_translation>
+ <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+ <value_translation>
+ <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect -->
+ </value_translation>
+ </request_param>
+ </request_param_translation>
+ <uihints minwidth="800"/>
+ <outputs>
+ <data name="output" format="txt" />
+ </outputs>
+ <options sanitize="False" refresh="True"/>
+</tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 7 months