1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f720e8e003f7/
Changeset: f720e8e003f7
User: dannon
Date: 2013-06-18 20:24:33
Summary: Toolshed workflow import: add storedworkflowannotation in addition to just the step annotations (oops)
Affected #: 1 file
diff -r ff17100de392abf7fba9327949308ab2594d2d07 -r f720e8e003f750a8c1f9c4f72ac4acadae9e761d lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -420,7 +420,8 @@
repository_id=repository_id,
changeset_revision=changeset_revision )
# Save the workflow in the Galaxy database.
- stored_workflow = workflow_util.save_workflow( trans, workflow )
+ # Pass workflow_dict along to create annotation at this point
+ stored_workflow = workflow_util.save_workflow( trans, workflow, workflow_dict )
# Use the latest version of the saved workflow.
workflow = stored_workflow.latest_workflow
if workflow_name:
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/ff17100de392/
Changeset: ff17100de392
User: dannon
Date: 2013-06-18 20:04:21
Summary: Enable workflow step annotations for toolshed imported workflows.
Affected #: 1 file
diff -r 81a2bb351c1a0f545a1f69b5514a29d96eb4575a -r ff17100de392abf7fba9327949308ab2594d2d07 lib/tool_shed/util/workflow_util.py
--- a/lib/tool_shed/util/workflow_util.py
+++ b/lib/tool_shed/util/workflow_util.py
@@ -12,9 +12,7 @@
from tool_shed.util import metadata_util
from tool_shed.util import tool_util
-import pkg_resources
-
-pkg_resources.require( "SVGFig" )
+eggs.require( "SVGFig" )
import svgfig
log = logging.getLogger( __name__ )
@@ -386,6 +384,28 @@
workflow.has_errors = True
# Stick this in the step temporarily.
step.temp_input_connections = step_dict[ 'input_connections' ]
+
+ # This should be considered a *temporary* hack.
+ # Usually we'd use the UsesAnnotation mixin, but
+ # that's not possible here. This entire module
+ # needs to die and get replaced with the regular
+ # galaxy/workflow methods.
+ from galaxy.util.sanitize_html import sanitize_html
+ annotation = step_dict.get( 'annotation', '')
+ if annotation:
+ annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
+ new_step_annotation = trans.model.WorkflowStepAnnotationAssociation()
+ new_step_annotation.annotation = annotation
+ new_step_annotation.user = trans.user
+ step.annotations.append(new_step_annotation)
+ # Unpack and add post-job actions.
+ post_job_actions = step_dict.get( 'post_job_actions', {} )
+ for name, pja_dict in post_job_actions.items():
+ trans.model.PostJobAction( pja_dict[ 'action_type' ],
+ step, pja_dict[ 'output_name' ],
+ pja_dict[ 'action_arguments' ] )
+ # End temporary hack
+
steps.append( step )
steps_by_external_id[ step_dict[ 'id' ] ] = step
# Second pass to deal with connections between steps.
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/fcffbe5a0a4c/
Changeset: fcffbe5a0a4c
User: jgoecks
Date: 2013-06-18 18:43:38
Summary: Return empty string rather than None because Mako functions write by default; add comments as well.
Affected #: 1 file
diff -r d6d2f0287e6ff6d3dc2e4cf3ed4778b77e2abda9 -r fcffbe5a0a4c4e53d4f091df004118613abda807 templates/refresh_frames.mako
--- a/templates/refresh_frames.mako
+++ b/templates/refresh_frames.mako
@@ -1,9 +1,11 @@
## Include JavaScript code to refresh Galaxy application frames as needed.
<%def name="handle_refresh_frames()">
+ ## If no refresh frames, print nothing.
<%
- if not refresh_frames: return
+ if not refresh_frames: return ''
%>
+ ## Write JavaScript to refresh specified frames.
<script type="text/javascript">
%if 'everything' in refresh_frames:
parent.location.href="${h.url_for( controller='root' )}";
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/d6d2f0287e6f/
Changeset: d6d2f0287e6f
User: dannon
Date: 2013-06-18 18:20:18
Summary: Tools/Workflows: Handle loading saved tool states that may not have rerun_remap_job_id in state.
Affected #: 1 file
diff -r f3fed61f4575620827fbf992781ef230bb9042ba -r d6d2f0287e6ff6d3dc2e4cf3ed4778b77e2abda9 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -848,7 +848,10 @@
# Restore from string
values = json_fix( simplejson.loads( value ) )
self.page = values.pop( "__page__" )
- self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" )
+ if '__rerun_remap_job_id__' in values:
+ self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" )
+ else:
+ self.rerun_remap_job_id = None
self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True )
class ToolOutput( object ):
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/d20c3481acb6/
Changeset: d20c3481acb6
User: greg
Date: 2013-06-18 15:44:13
Summary: Fix for handing comments as the last element in a set_environment tag set in tool dependency definitions. Contributed by Adam Novak.
Affected #: 1 file
diff -r 7a6bc7485be9da1b07ac5bf8d9d62dcff327b5ba -r d20c3481acb6581b239b20a34078f927dcc2a3c2 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -431,7 +431,8 @@
if env_var_dict:
env_var_dicts.append( env_var_dict )
if env_var_dicts:
- action_dict[ env_elem.tag ] = env_var_dicts
+ # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'.
+ action_dict[ 'environment_variable' ] = env_var_dicts
else:
continue
elif action_type == 'set_environment_for_install':
https://bitbucket.org/galaxy/galaxy-central/commits/ddeb00845879/
Changeset: ddeb00845879
Branch: stable
User: greg
Date: 2013-06-18 15:44:13
Summary: Fix for handing comments as the last element in a set_environment tag set in tool dependency definitions. Contributed by Adam Novak.
Affected #: 1 file
diff -r f295092476c781987d5a31e44e7a19a372a461aa -r ddeb0084587994c3a0b9d1504950b4639ab7e7e8 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -431,7 +431,8 @@
if env_var_dict:
env_var_dicts.append( env_var_dict )
if env_var_dicts:
- action_dict[ env_elem.tag ] = env_var_dicts
+ # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'.
+ action_dict[ 'environment_variable' ] = env_var_dicts
else:
continue
elif action_type == 'set_environment_for_install':
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/564f28960281/
Changeset: 564f28960281
User: dannon
Date: 2013-06-18 14:59:17
Summary: Fix tool panel rendering user requirement logic.
Affected #: 1 file
diff -r d2d4b6ac2139f1623301990462a5e63b2952dcc1 -r 564f289602814adae34ec716c18a2d9ea0ebf1ff templates/webapps/galaxy/root/tool_menu.mako
--- a/templates/webapps/galaxy/root/tool_menu.mako
+++ b/templates/webapps/galaxy/root/tool_menu.mako
@@ -29,7 +29,7 @@
Galaxy.toolPanel = tool_panel;
## Populate tool panel if (a) anonymous use possible or (b) user is logged in.
- %if trans.app.config.require_login and trans.user:
+ %if trans.user or not trans.app.config.require_login:
tool_panel.reset( tool_panel.parse( ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )} ) );
%endif
@@ -90,4 +90,4 @@
</div></div>
-</%def>
\ No newline at end of file
+</%def>
https://bitbucket.org/galaxy/galaxy-central/commits/7a6bc7485be9/
Changeset: 7a6bc7485be9
User: dannon
Date: 2013-06-18 15:01:15
Summary: Merge
Affected #: 1 file
diff -r 564f289602814adae34ec716c18a2d9ea0ebf1ff -r 7a6bc7485be9da1b07ac5bf8d9d62dcff327b5ba templates/refresh_frames.mako
--- a/templates/refresh_frames.mako
+++ b/templates/refresh_frames.mako
@@ -1,9 +1,10 @@
## Include JavaScript code to refresh Galaxy application frames as needed.
<%def name="handle_refresh_frames()">
- <script type="text/javascript"><%
if not refresh_frames: return
%>
+
+ <script type="text/javascript">
%if 'everything' in refresh_frames:
parent.location.href="${h.url_for( controller='root' )}";
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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