1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c25df9f3d31e/
Changeset: c25df9f3d31e
Branch: stable
User: natefoo
Date: 2015-01-06 14:00:16+00:00
Summary: Update tag latest_2014.10.06 for changeset ff6e36d7a238
Affected #: 1 file
diff -r ff6e36d7a2388214fe7636c43d30838c07246907 -r c25df9f3d31effd9c4abdbbffd40381f23fc6dc8 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-793d9cd5f9dec66ceafb36bc38f53453457056e6 latest_2014.10.06
+ff6e36d7a2388214fe7636c43d30838c07246907 latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ff6e36d7a238/
Changeset: ff6e36d7a238
Branch: stable
User: martenson
Date: 2015-01-05 21:53:57+00:00
Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #620)
[STABLE] Don't choke on tool versions switches with significant parameter changes.
Affected #: 1 file
diff -r dff4071c13f9b2908556583227766c65fcfb8a29 -r ff6e36d7a2388214fe7636c43d30838c07246907 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -80,14 +80,28 @@
message=message,
status=status,
redirect=redirect ) )
- params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
- #do param translation here, used by datasource tools
- if tool.input_translator:
- tool.input_translator.translate( params )
+
+ def _validated_params_for( kwd ):
+ params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers
+ #do param translation here, used by datasource tools
+ if tool.input_translator:
+ tool.input_translator.translate( params )
+ return params
+
+ params = _validated_params_for( kwd )
# We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
# so make sure to create a new history if we've never had one before.
history = tool.get_default_history_by_trans( trans, create=True )
- template, vars = tool.handle_input( trans, params.__dict__ )
+ try:
+ template, vars = tool.handle_input( trans, params.__dict__ )
+ except KeyError:
+ # This error indicates (or at least can indicate) there was a
+ # problem with the stored tool_state - it is incompatible with
+ # this variant of the tool - possibly because the tool changed
+ # or because the tool version changed.
+ del kwd[ "tool_state" ]
+ params = _validated_params_for( kwd )
+ template, vars = tool.handle_input( trans, params.__dict__ )
if len( params ) > 0:
trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id )
add_frame = AddFrameData()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/24c62137d466/
Changeset: 24c62137d466
Branch: stable
User: jmchilton
Date: 2014-12-18 14:47:08+00:00
Summary: Don't choke on tool versions switches with significant parameter changes.
Just regenerate the tool state from the supplied parameters instead - seems to still perserve parameters on the tool form that are common between the versions because they are coming in throuh kwd.
Affected #: 1 file
diff -r 7197e949d3ab990ceb76c193ebc940d90aa04cad -r 24c62137d46629f9200b43612485799cf39600d5 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -80,14 +80,28 @@
message=message,
status=status,
redirect=redirect ) )
- params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
- #do param translation here, used by datasource tools
- if tool.input_translator:
- tool.input_translator.translate( params )
+
+ def _validated_params_for( kwd ):
+ params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers
+ #do param translation here, used by datasource tools
+ if tool.input_translator:
+ tool.input_translator.translate( params )
+ return params
+
+ params = _validated_params_for( kwd )
# We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
# so make sure to create a new history if we've never had one before.
history = tool.get_default_history_by_trans( trans, create=True )
- template, vars = tool.handle_input( trans, params.__dict__ )
+ try:
+ template, vars = tool.handle_input( trans, params.__dict__ )
+ except KeyError:
+ # This error indicates (or at least can indicate) there was a
+ # problem with the stored tool_state - it is incompatible with
+ # this variant of the tool - possibly because the tool changed
+ # or because the tool version changed.
+ del kwd[ "tool_state" ]
+ params = _validated_params_for( kwd )
+ template, vars = tool.handle_input( trans, params.__dict__ )
if len( params ) > 0:
trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id )
add_frame = AddFrameData()
https://bitbucket.org/galaxy/galaxy-central/commits/ff6e36d7a238/
Changeset: ff6e36d7a238
Branch: stable
User: martenson
Date: 2015-01-05 21:53:57+00:00
Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #620)
[STABLE] Don't choke on tool versions switches with significant parameter changes.
Affected #: 1 file
diff -r dff4071c13f9b2908556583227766c65fcfb8a29 -r ff6e36d7a2388214fe7636c43d30838c07246907 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -80,14 +80,28 @@
message=message,
status=status,
redirect=redirect ) )
- params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers
- #do param translation here, used by datasource tools
- if tool.input_translator:
- tool.input_translator.translate( params )
+
+ def _validated_params_for( kwd ):
+ params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers
+ #do param translation here, used by datasource tools
+ if tool.input_translator:
+ tool.input_translator.translate( params )
+ return params
+
+ params = _validated_params_for( kwd )
# We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ),
# so make sure to create a new history if we've never had one before.
history = tool.get_default_history_by_trans( trans, create=True )
- template, vars = tool.handle_input( trans, params.__dict__ )
+ try:
+ template, vars = tool.handle_input( trans, params.__dict__ )
+ except KeyError:
+ # This error indicates (or at least can indicate) there was a
+ # problem with the stored tool_state - it is incompatible with
+ # this variant of the tool - possibly because the tool changed
+ # or because the tool version changed.
+ del kwd[ "tool_state" ]
+ params = _validated_params_for( kwd )
+ template, vars = tool.handle_input( trans, params.__dict__ )
if len( params ) > 0:
trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id )
add_frame = AddFrameData()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d50ee9520583/
Changeset: d50ee9520583
User: jmchilton
Date: 2015-01-05 21:09:45+00:00
Summary: Fix for Pull Request #614.
Affected #: 1 file
diff -r 2aa2f508c50864b3d309d384137e53f5750aed2d -r d50ee9520583c225e48c577ab977f18fd6cb7d6a config/datatypes_conf.xml.sample
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -299,7 +299,7 @@
<sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/><sniffer type="galaxy.datatypes.text:Obo"/>
- <sniffer type="galaxy.datatypes.text.Arff"/>
+ <sniffer type="galaxy.datatypes.text:Arff"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/><sniffer type="galaxy.datatypes.images:Jpg"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3fc8ce62285b/
Changeset: 3fc8ce62285b
User: jmchilton
Date: 2015-01-05 17:35:38+00:00
Summary: Another hack to fix 08f8850.
Need to figure out when tools are being loaded but don't have lineages defined.
Affected #: 1 file
diff -r 95189e44b9bfe5adac1841b72d621a99bff6c927 -r 3fc8ce62285bc3df5b934439e624f2d56cb062cf lib/galaxy/tools/toolbox/base.py
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -295,7 +295,10 @@
inserted = True
if not inserted:
# Check the tool's installed versions.
- for tool_lineage_version in tool.lineage.get_versions():
+ versions = []
+ if hasattr( tool, 'lineage' ):
+ versions = tool.lineage.get_versions()
+ for tool_lineage_version in versions:
lineage_id = tool_lineage_version.id
index = self._integrated_tool_panel.index_of_tool_id( lineage_id )
if index:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/95189e44b9bf/
Changeset: 95189e44b9bf
User: carlfeberhard
Date: 2015-01-05 15:34:05+00:00
Summary: Browser tests: remove console statements interferring with test json parsing
Affected #: 2 files
diff -r e34bf92384b6a6722657d83833fb52268865126d -r 95189e44b9bfe5adac1841b72d621a99bff6c927 test/casperjs/modules/api.js
--- a/test/casperjs/modules/api.js
+++ b/test/casperjs/modules/api.js
@@ -355,7 +355,6 @@
// have to attach like GET param - due to body loss in jq
url = utils.format( this.urlTpls.update, historyId, id );
if( purge ){
-console.debug( 'adding purge:' + purge );
url += '?purge=True';
}
return this.api._ajax( url, {
diff -r e34bf92384b6a6722657d83833fb52268865126d -r 95189e44b9bfe5adac1841b72d621a99bff6c927 test/casperjs/modules/historypanel.js
--- a/test/casperjs/modules/historypanel.js
+++ b/test/casperjs/modules/historypanel.js
@@ -139,9 +139,6 @@
var hdaOpacity = this.evaluate( function( name ){
// locate the hda by name and return its opacity
- console.debug( name );
- console.debug( $( '.name:contains("' + name + '")' ) );
- console.debug( $( '.name:contains("' + name + '")' ).parents( '.hda' ) );
return $( '.name:contains("' + name + '")' ).parents( '.dataset' ).css( 'opacity' );
}, hdaName );
//this.debug( 'fading in: ' + hdaOpacity );
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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