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commit/galaxy-central: carlfeberhard: fix imports
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48dad8860ee1/ changeset: 48dad8860ee1 user: carlfeberhard date: 2013-03-06 21:34:25 summary: fix imports affected #: 1 file diff -r dc10f9430b6aaaf85c67a998d4ce666a5b66b600 -r 48dad8860ee1b1196a1f242c9dd18d218e6db573 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -19,6 +19,9 @@ eggs.require( "simplejson" ) eggs.require( "MarkupSafe" ) #MarkupSafe must load before mako eggs.require( "Mako" ) +eggs.require( "elementtree" ) +eggs.require( "Paste" ) +eggs.require( "SQLAlchemy >= 0.4" ) import simplejson from cgi import FieldStorage Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc10f9430b6a/ changeset: dc10f9430b6a user: dan date: 2013-03-06 19:47:00 summary: Fix display bug for DrillDown Fields and parameters. affected #: 2 files diff -r d1b435e7200d4543fe3060ba9c362220d73d615b -r dc10f9430b6aaaf85c67a998d4ce666a5b66b600 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1075,9 +1075,9 @@ >>> print p.get_html() <div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span><input type="checkbox" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="some_name" value="option1" >Option 1 </div> @@ -1085,9 +1085,9 @@ <input type="checkbox" name="some_name" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span><input type="checkbox" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="some_name" value="option3" >Option 3 </div> @@ -1121,9 +1121,9 @@ >>> print p.get_html() <div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span><input type="radio" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="some_name" value="option1" >Option 1 </div> @@ -1131,9 +1131,9 @@ <input type="radio" name="some_name" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span><input type="radio" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="some_name" value="option3" >Option 3 </div> diff -r d1b435e7200d4543fe3060ba9c362220d73d615b -r dc10f9430b6aaaf85c67a998d4ce666a5b66b600 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -396,9 +396,9 @@ >>> print t.get_html() <div class="form-row drilldown-container" id="drilldown--666f6f"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span><input type="checkbox" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="foo" value="option1" >Option 1 </div> @@ -406,9 +406,9 @@ <input type="checkbox" name="foo" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span><input type="checkbox" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="foo" value="option3" >Option 3 </div> @@ -427,9 +427,9 @@ >>> print t.get_html() <div class="form-row drilldown-container" id="drilldown--666f6f"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span><input type="radio" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="foo" value="option1" >Option 1 </div> @@ -437,9 +437,9 @@ <input type="radio" name="foo" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span><input type="radio" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="foo" value="option3" >Option 3 </div> @@ -501,10 +501,10 @@ html.append( '<div class="form-row-input">') drilldown_group_id = "%s-%s" % ( base_id, hexlify( option['value'] ) ) if option['options']: - html.append( '<span class="%s" id="%s-click"></span>' % ( span_class, drilldown_group_id ) ) + html.append( '<div><span class="%s" id="%s-click"></span>' % ( span_class, drilldown_group_id ) ) html.append( '<input type="%s" name="%s%s" value="%s" %s>%s' % ( self.display, prefix, self.name, escaped_option_value, selected, option['name']) ) if option['options']: - html.append( '<div class="form-row" id="%s-container" style="float: left; margin-left: 1em;">' % ( drilldown_group_id ) ) + html.append( '</div><div class="form-row" id="%s-container" style="float: left; margin-left: 1em;">' % ( drilldown_group_id ) ) recurse_options( html, option['options'], drilldown_group_id, expanded_options ) html.append( '</div>') html.append( '</div>') https://bitbucket.org/galaxy/galaxy-central/commits/779b54139013/ changeset: 779b54139013 branch: stable user: dan date: 2013-03-06 19:47:00 summary: Fix display bug for DrillDown Fields and parameters. affected #: 2 files diff -r b65ed2831d234ef9fc78b8c15d9dfcf40f879c4f -r 779b54139013946613772d02a3fbb61e067f3267 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1072,9 +1072,9 @@ >>> print p.get_html() <div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span><input type="checkbox" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="some_name" value="option1" >Option 1 </div> @@ -1082,9 +1082,9 @@ <input type="checkbox" name="some_name" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span><input type="checkbox" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="some_name" value="option3" >Option 3 </div> @@ -1118,9 +1118,9 @@ >>> print p.get_html() <div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span><input type="radio" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="some_name" value="option1" >Option 1 </div> @@ -1128,9 +1128,9 @@ <input type="radio" name="some_name" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span><input type="radio" name="some_name" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="some_name" value="option3" >Option 3 </div> diff -r b65ed2831d234ef9fc78b8c15d9dfcf40f879c4f -r 779b54139013946613772d02a3fbb61e067f3267 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -396,9 +396,9 @@ >>> print t.get_html() <div class="form-row drilldown-container" id="drilldown--666f6f"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span><input type="checkbox" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="foo" value="option1" >Option 1 </div> @@ -406,9 +406,9 @@ <input type="checkbox" name="foo" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span><input type="checkbox" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="checkbox" name="foo" value="option3" >Option 3 </div> @@ -427,9 +427,9 @@ >>> print t.get_html() <div class="form-row drilldown-container" id="drilldown--666f6f"><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span><input type="radio" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="foo" value="option1" >Option 1 </div> @@ -437,9 +437,9 @@ <input type="radio" name="foo" value="option2" >Option 2 </div><div class="form-row-input"> - <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span> + <div><span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span><input type="radio" name="foo" value="heading1" >Heading 1 - <div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + </div><div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"><div class="form-row-input"><input type="radio" name="foo" value="option3" >Option 3 </div> @@ -501,10 +501,10 @@ html.append( '<div class="form-row-input">') drilldown_group_id = "%s-%s" % ( base_id, hexlify( option['value'] ) ) if option['options']: - html.append( '<span class="%s" id="%s-click"></span>' % ( span_class, drilldown_group_id ) ) + html.append( '<div><span class="%s" id="%s-click"></span>' % ( span_class, drilldown_group_id ) ) html.append( '<input type="%s" name="%s%s" value="%s" %s>%s' % ( self.display, prefix, self.name, escaped_option_value, selected, option['name']) ) if option['options']: - html.append( '<div class="form-row" id="%s-container" style="float: left; margin-left: 1em;">' % ( drilldown_group_id ) ) + html.append( '</div><div class="form-row" id="%s-container" style="float: left; margin-left: 1em;">' % ( drilldown_group_id ) ) recurse_options( html, option['options'], drilldown_group_id, expanded_options ) html.append( '</div>') html.append( '</div>') Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Re-add secondary workflow api download route to support applications already using it.
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1b435e7200d/ changeset: d1b435e7200d user: dannon date: 2013-03-06 19:09:35 summary: Re-add secondary workflow api download route to support applications already using it. affected #: 1 file diff -r 47480f11d5d5c99dfe67710cc4a7ecbaeebebb4a -r d1b435e7200d4543fe3060ba9c362220d73d615b lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -153,6 +153,8 @@ # Defines a named route "import_workflow". webapp.api_mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"])) webapp.api_mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + # Preserve the following download route for now for dependent applications -- deprecate at some point + webapp.api_mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Connect logger from app if app.trace_logger: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47480f11d5d5/ changeset: 47480f11d5d5 user: natefoo date: 2013-03-06 18:40:31 summary: Make maf-to-bed object-store aware affected #: 1 file diff -r 3ec030c42b9e59234d4c005e6a7f1de6e0e1e736 -r 47480f11d5d5c99dfe67710cc4a7ecbaeebebb4a tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py +++ b/tools/maf/maf_to_bed_code.py @@ -1,3 +1,4 @@ +import os import pkg_resources; pkg_resources.require( "bx-python" ) from bx.align import maf from galaxy import datatypes, config, jobs @@ -38,7 +39,8 @@ app.model.context.add( history ) app.model.context.flush() try: - move(filepath,newdata.file_name) + app.object_store.update_from_file( newdata.dataset, file_name=filepath, create=True ) + os.unlink( filepath ) newdata.info = newdata.name newdata.state = newdata.states.OK except: https://bitbucket.org/galaxy/galaxy-central/commits/b65ed2831d23/ changeset: b65ed2831d23 branch: stable user: natefoo date: 2013-03-06 18:40:31 summary: Make maf-to-bed object-store aware affected #: 1 file diff -r c177960e4ed61925a8b6c858e1f3f8d54c93cb37 -r b65ed2831d234ef9fc78b8c15d9dfcf40f879c4f tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py +++ b/tools/maf/maf_to_bed_code.py @@ -1,3 +1,4 @@ +import os import pkg_resources; pkg_resources.require( "bx-python" ) from bx.align import maf from galaxy import datatypes, config, jobs @@ -38,7 +39,8 @@ app.model.context.add( history ) app.model.context.flush() try: - move(filepath,newdata.file_name) + app.object_store.update_from_file( newdata.dataset, file_name=filepath, create=True ) + os.unlink( filepath ) newdata.info = newdata.name newdata.state = newdata.states.OK except: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Remove unused import in objectstore.
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ec030c42b9e/ changeset: 3ec030c42b9e user: dannon date: 2013-03-06 18:38:48 summary: Remove unused import in objectstore. affected #: 1 file diff -r 3bdfcb0a7e9722ce4074c52528a4c0324f2fb83a -r 3ec030c42b9e59234d4c005e6a7f1de6e0e1e736 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -9,7 +9,6 @@ import time import random import shutil -import statvfs import logging import threading import subprocess Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix incorrect workflow download path via the API. Now is is correctly set to /api/workflows/<id>/download
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3bdfcb0a7e97/ changeset: 3bdfcb0a7e97 user: dannon date: 2013-03-06 17:50:53 summary: Fix incorrect workflow download path via the API. Now is is correctly set to /api/workflows/<id>/download affected #: 2 files diff -r f97ebc1cf57d20019b785106221964931b122bb7 -r 3bdfcb0a7e9722ce4074c52528a4c0324f2fb83a lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -258,24 +258,16 @@ trans.sa_session.flush() return rval - # ---------------------------------------------------------------------------------------------- # - # ---------------------------------------------------------------------------------------------- # - # ---- RPARK EDITS ---- # - # ---------------------------------------------------------------------------------------------- # - # ---------------------------------------------------------------------------------------------- # @web.expose_api - #(a)web.json def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) except Exception,e: return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: diff -r f97ebc1cf57d20019b785106221964931b122bb7 -r 3bdfcb0a7e9722ce4074c52528a4c0324f2fb83a lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -152,7 +152,7 @@ # "POST /api/workflows/import" => ``workflows.import_workflow()``. # Defines a named route "import_workflow". webapp.api_mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"])) - webapp.api_mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + webapp.api_mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Connect logger from app if app.trace_logger: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Workflow controller import refactoring to eliminate import *'s.
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f97ebc1cf57d/ changeset: f97ebc1cf57d user: dannon date: 2013-03-06 17:40:39 summary: Workflow controller import refactoring to eliminate import *'s. affected #: 1 file diff -r 7eda7f4b555eb13e8382e34b9739a38af6072849 -r f97ebc1cf57d20019b785106221964931b122bb7 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1,28 +1,41 @@ -from galaxy.web.base.controller import * - import pkg_resources pkg_resources.require( "simplejson" ) pkg_resources.require( "SVGFig" ) + +import base64 +import httplib +import math +import os +import sgmllib import simplejson -import base64, httplib, urllib2, sgmllib, svgfig, urllib, urllib2 -import math -from galaxy.web.framework.helpers import time_ago, grids -from galaxy.tools.parameters import * -from galaxy.tools import DefaultToolState -from galaxy.tools.parameters.grouping import Repeat, Conditional +import svgfig +import urllib2 + +from sqlalchemy import and_ +from tool_shed.util import encoding_util + +from galaxy import model +from galaxy import util +from galaxy import web from galaxy.datatypes.data import Data +from galaxy.jobs.actions.post import ActionBox +from galaxy.model.mapping import desc +from galaxy.tools.parameters import RuntimeValue, visit_input_values +from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue +from galaxy.tools.parameters.grouping import Conditional, Repeat +from galaxy.util.json import from_json_string from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html -from galaxy.util.topsort import topsort, topsort_levels, CycleError -from tool_shed.util import encoding_util -from galaxy.workflow.modules import * -from galaxy import model -from galaxy import util -from galaxy.model.mapping import desc -from galaxy.model.orm import * -from galaxy.model.item_attrs import * +from galaxy.util.topsort import CycleError, topsort, topsort_levels +from galaxy.web import error, url_for +from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin +from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings +from galaxy.web.framework import form +from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.framework.helpers import to_unicode -from galaxy.jobs.actions.post import ActionBox +from galaxy.workflow.modules import module_factory, ToolModule + + class StoredWorkflowListGrid( grids.Grid ): class StepsColumn( grids.GridColumn ): @@ -1813,7 +1826,7 @@ # Unpack and add post-job actions. post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], + pja = model.PostJobAction( pja_dict[ 'action_type' ], step, pja_dict[ 'output_name' ], pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history panel and api: if hda.peek is 'no peek' do not send peek through api and do not render peek in expanded hda
by commits-noreply＠bitbucket.org 06 Mar '13

06 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7eda7f4b555e/ changeset: 7eda7f4b555e user: carlfeberhard date: 2013-03-06 16:02:24 summary: history panel and api: if hda.peek is 'no peek' do not send peek through api and do not render peek in expanded hda affected #: 3 files diff -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 -r 7eda7f4b555eb13e8382e34b9739a38af6072849 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -221,7 +221,8 @@ hda_dict[ 'display_types' ] = get_old_display_applications( trans, hda ) hda_dict[ 'visualizations' ] = hda.get_visualizations() - hda_dict[ 'peek' ] = to_unicode( hda.display_peek() ) + if hda.peek and hda.peek != 'no peek': + hda_dict[ 'peek' ] = to_unicode( hda.display_peek() ) if hda.creating_job and hda.creating_job.tool_id: tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) diff -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 -r 7eda7f4b555eb13e8382e34b9739a38af6072849 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -319,12 +319,13 @@ */ //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible _render_peek : function(){ - if( !this.model.get( 'peek' ) ){ return null; } + var peek = this.model.get( 'peek' ); + if( !peek ){ return null; } return $( '<div/>' ).append( $( '<pre/>' ) .attr( 'id', 'peek' + this.model.get( 'id' ) ) .addClass( 'peek' ) - .append( this.model.get( 'peek' ) ) + .append( peek ) ); }, diff -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 -r 7eda7f4b555eb13e8382e34b9739a38af6072849 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Enhance the display of functional test results in the tol shed for tests run against contained tools when the repository is installed into Galaxy.
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a3eab0b0adb/ changeset: 3a3eab0b0adb user: greg date: 2013-03-05 22:37:51 summary: Enhance the display of functional test results in the tol shed for tests run against contained tools when the repository is installed into Galaxy. affected #: 4 files diff -r 26006e793a32a35328d941f6cea573b0108faab7 -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2452,7 +2452,6 @@ revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: - repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, @@ -2468,7 +2467,6 @@ message += orphan_message status = 'warning' else: - repository_metadata_id = None metadata = None is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) if is_malicious: @@ -2492,7 +2490,7 @@ return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, - repository_metadata_id=repository_metadata_id, + repository_metadata=repository_metadata, metadata=metadata, containers_dict=containers_dict, avg_rating=avg_rating, diff -r 26006e793a32a35328d941f6cea573b0108faab7 -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako --- a/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako +++ b/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako @@ -5,6 +5,7 @@ <% from galaxy.web.framework.helpers import time_ago + from tool_shed.util.shed_util_common import to_safe_string changeset_revision = repository_metadata.changeset_revision has_metadata = repository.metadata_revisions @@ -157,23 +158,61 @@ <div class="form-row"><table class="grid"> %for test_results_dict in test_errors: + <% + test_id = test_results_dict.get( 'test_id', 'unknown' ) + if test_id != 'unknown': + # The test_id looks something like: + # test_tool_000003 (functional.test_toolbox.TestForTool_localhost:9009/repos/test/bwa_mappers/bwa_color_wrapper/1.0.2) + # Highlight the tool id and version. + test_id_items = test_id.split( '/' ) + tool_id = test_id_items[ -2 ] + tool_id = '<b>%s</b>' % tool_id + test_id_items[ -2 ] = tool_id + tool_version = test_id_items[ -1 ] + tool_version = '<b>%s</b>' % ( tool_version.rstrip( ')' ) ) + tool_version = '%s)' % tool_version + test_id_items[ -1 ] = tool_version + test_id = '/'.join( test_id_items ) + test_id_items = test_id.split( ' ' ) + test_num = test_id_items[ 0 ] + test_num = '<b>%s</b>' % test_num + test_id_items[ 0 ] = test_num + test_id = ' '.join( test_id_items ) + + test_status = '<font color="green">Test passed</font>' + stdout = test_results_dict.get( 'stdout', '' ) + if stdout: + stdout = to_safe_string( stdout, to_html=True ) + stderr = test_results_dict.get( 'stderr', '' ) + if stderr: + stderr = to_safe_string( stderr, to_html=True ) + test_status = '<font color="red">Test failed</font>' + traceback = test_results_dict.get( 'traceback', '' ) + if traceback: + traceback = to_safe_string( traceback, to_html=True ) + test_status = '<font color="red">Test failed</font>' + %><tr><td bgcolor="#FFFFCC"><b>Test id</b></td> - <td bgcolor="#FFFFCC">${test_results_dict.get( 'test_id', 'unknown' )}</td> + <td bgcolor="#FFFFCC">${test_id}</td> + </tr> + <tr> + <td><b>Status</b></td> + <td>${test_status}</td></tr> %if repository_metadata.tools_functionally_correct: <tr><td><b>Stdout</b></td> - <td>${test_results_dict.get( 'stdout', '' )}</td> + <td>${stdout}</td></tr> %else: <tr><td><b>Stderr</b></td> - <td>${test_results_dict.get( 'stderr', '' )}</td> + <td>${stderr}</td></tr><tr><td><b>Traceback</b></td> - <td>${test_results_dict.get( 'traceback', '' )}</td> + <td>${traceback}</td></tr> %endif %endfor diff -r 26006e793a32a35328d941f6cea573b0108faab7 -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -88,6 +88,9 @@ %if can_browse_repository_reviews: <a class="action-button" href="${h.url_for( controller='repository_review', action='manage_repository_reviews', id=trans.app.security.encode_id( repository.id ) )}">Browse reviews of this repository</a> %endif + %if can_display_tool_functional_test_results: + <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a> + %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif @@ -112,9 +115,6 @@ %if can_undeprecate: <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a> %endif - %if can_display_tool_functional_test_results: - <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a> - %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> diff -r 26006e793a32a35328d941f6cea573b0108faab7 -r 3a3eab0b0adbda30e72fdda0c5de899728bcd5e6 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -25,6 +25,14 @@ can_view_change_log = trans.webapp.name == 'tool_shed' and not is_new changeset_revision_is_repository_tip = changeset_revision == repository.tip( trans.app ) + if repository_metadata: + if repository_metadata.includes_tools and repository_metadata.tool_test_errors is not None: + can_display_tool_functional_test_results = True + else: + can_display_tool_functional_test_results = False + else: + can_display_tool_functional_test_results = False + if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -80,6 +88,9 @@ %if can_browse_repository_reviews: <a class="action-button" href="${h.url_for( controller='repository_review', action='manage_repository_reviews', id=trans.app.security.encode_id( repository.id ) )}">Browse reviews of this repository</a> %endif + %if can_display_tool_functional_test_results: + <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a> + %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1da2068fa58c/ changeset: 1da2068fa58c user: dannon date: 2013-03-05 22:15:54 summary: Fix workflow modules imports. affected #: 1 file diff -r f7904535003fdf8e56588fb78ebcdf9af913cc55 -r 1da2068fa58c5f1ac9d4bee510644a1dce20e814 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -1,13 +1,20 @@ +""" +Modules used in building workflows +""" + +import logging import re + from elementtree.ElementTree import Element + +import galaxy.tools from galaxy import web -from galaxy.tools.parameters import DataToolParameter, DummyDataset, RuntimeValue, check_param, visit_input_values -import galaxy.tools +from galaxy.jobs.actions.post import ActionBox +from galaxy.model import PostJobAction +from galaxy.tools.parameters import check_param, DataToolParameter, DummyDataset, RuntimeValue, visit_input_values from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string -from galaxy.jobs.actions.post import ActionBox -from galaxy.model import PostJobAction -import logging + log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/26006e793a32/ changeset: 26006e793a32 user: dannon date: 2013-03-05 22:18:16 summary: Workflow modules: Adjust spacing to new guidelines. affected #: 1 file diff -r 1da2068fa58c5f1ac9d4bee510644a1dce20e814 -r 26006e793a32a35328d941f6cea573b0108faab7 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -15,8 +15,8 @@ from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string +log = logging.getLogger( __name__ ) -log = logging.getLogger( __name__ ) class WorkflowModule( object ): @@ -31,6 +31,7 @@ Create a new instance of the module with default state """ return Class( trans ) + @classmethod def from_dict( Class, trans, d ): """ @@ -38,6 +39,7 @@ dictionary `d`. """ return Class( trans ) + @classmethod def from_workflow_step( Class, trans, step ): return Class( trans ) @@ -51,10 +53,13 @@ def get_type( self ): return self.type + def get_name( self ): return self.name + def get_tool_id( self ): return None + def get_tooltip( self, static_path='' ): return None @@ -62,14 +67,19 @@ def get_state( self ): return None + def get_errors( self ): return None + def get_data_inputs( self ): return [] + def get_data_outputs( self ): return [] + def update_state( self ): pass + def get_config_form( self ): raise TypeError( "Abstract method" ) @@ -84,18 +94,23 @@ def get_runtime_inputs( self ): raise TypeError( "Abstract method" ) + def get_runtime_state( self ): raise TypeError( "Abstract method" ) + def encode_runtime_state( self, trans, state ): raise TypeError( "Abstract method" ) + def decode_runtime_state( self, trans, string ): raise TypeError( "Abstract method" ) + def update_runtime_state( self, trans, state, values ): raise TypeError( "Abstract method" ) def execute( self, trans, state ): raise TypeError( "Abstract method" ) + class InputDataModule( WorkflowModule ): type = "data_input" name = "Input dataset" @@ -105,12 +120,14 @@ module = Class( trans ) module.state = dict( name="Input Dataset" ) return module + @classmethod def from_dict( Class, trans, d, secure=True ): module = Class( trans ) state = from_json_string( d["tool_state"] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) return module + @classmethod def from_workflow_step( Class, trans, step ): module = Class( trans ) @@ -172,6 +189,7 @@ def execute( self, trans, state ): return None, dict( output=state.inputs['input']) + class ToolModule( WorkflowModule ): type = "tool" @@ -286,6 +304,7 @@ def get_data_inputs( self ): data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): data_inputs.append( dict( @@ -293,6 +312,7 @@ label=prefixed_label, multiple=input.multiple, extensions=input.extensions ) ) + visit_input_values( self.tool.inputs, self.state.inputs, callback ) return data_inputs @@ -338,6 +358,7 @@ make_runtime_key = incoming.get( 'make_runtime', None ) make_buildtime_key = incoming.get( 'make_buildtime', None ) + def item_callback( trans, key, input, value, error, old_value, context ): # Dummy value for Data parameters if isinstance( input, DataToolParameter ): @@ -354,6 +375,7 @@ return value, None else: return value, error + # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) self.errors = errors or None @@ -370,6 +392,7 @@ input_connections_by_name = {} # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) + def callback( input, value, prefixed_name, prefixed_label ): replacement = None if isinstance( input, DataToolParameter ): @@ -379,9 +402,12 @@ else: replacement = DummyDataset() return replacement + visit_input_values( self.tool.inputs, self.state.inputs, callback ) + class WorkflowModuleFactory( object ): + def __init__( self, module_types ): self.module_types = module_types Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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