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Handle tool versions with job reruns.

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This commit is contained in:
Greg Von Kuster
2012-03-12 10:20:56 -04:00
parent 2ebe0eb774
commit 1f75e767db
3 changed files with 85 additions and 11 deletions
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lib/galaxy/tools/__init__.py
+7 -1
View File
@@ -241,7 +241,7 @@ class ToolBox( object ):
os.close( fd )
shutil.move( filename, os.path.abspath( self.integrated_tool_panel_config ) )
os.chmod( self.integrated_tool_panel_config, 0644 )
def get_tool( self, tool_id, tool_version=None ):
def get_tool( self, tool_id, tool_version=None, get_all_versions=False ):
"""Attempt to locate a tool in the tool box."""
if tool_id in self.tools_by_id:
tool = self.tools_by_id[ tool_id ]
@@ -252,6 +252,12 @@ class ToolBox( object ):
tv = self.__get_tool_version( tool_id )
if tv:
tool_version_ids = tv.get_version_ids( self.app )
if get_all_versions:
available_tool_versions = []
for tool_version_id in tool_version_ids:
if tool_version_id in self.tools_by_id:
available_tool_versions.append( self.tools_by_id[ tool_version_id ] )
return available_tool_versions
for tool_version_id in tool_version_ids:
if tool_version_id in self.tools_by_id:
tool = self.tools_by_id[ tool_version_id ]
lib/galaxy/web/controllers/tool_runner.py
+61 -6
View File
@@ -109,16 +109,49 @@ class ToolRunner( BaseUIController ):
raise Exception("Failed to get job information for dataset hid %d" % data.hid)
# Get the tool object
tool_id = job.tool_id
tool_version = job.tool_version
try:
# Load the tool
toolbox = self.get_toolbox()
tool = toolbox.get_tool( tool_id )
tools = toolbox.get_tool( tool_id, tool_version=tool_version, get_all_versions=True )
if len( tools ) > 1:
tool_id_select_field = self.build_tool_id_select_field( tools, tool_id )
for tool in tools:
if tool.id == tool_id:
break
else:
tool = tools[ 0 ]
tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", and multiple derivations ' % ( job.tool_id, job.tool_version )
tool_id_version_message += 'of this tool are available. Rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_select_field = None
tool = tools[ 0 ]
if tool.id == job.tool_id and tool.version == job.tool_version:
tool_id_version_message = ''
elif tool.id == job.tool_id:
if job.tool_version == None:
# For some reason jobs don't always keep track of the tool version.
tool_id_version_message = ''
else:
if len( tools ) > 1:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.'
else:
if len( tools ) > 1:
tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version
tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.'
else:
tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % ( job.tool_id, job.tool_version )
tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.'
assert tool is not None, 'Requested tool has not been loaded.'
except:
#this is expected, so not an exception
# This is expected so not an exception.
tool_id_version_message = ''
error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id )
# Can't rerun upload, external data sources, et cetera. Workflow
# compatible will proxy this for now
# Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now
if not tool.is_workflow_compatible:
error( "The '%s' tool does not currently support rerunning." % tool.name )
# Get the job's parameters
@@ -163,7 +196,30 @@ class ToolRunner( BaseUIController ):
if from_noframe is not None:
add_frame.wiki_url = trans.app.config.wiki_url
add_frame.from_noframe = True
return trans.fill_template( "tool_form.mako", history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars )
return trans.fill_template( "tool_form.mako",
history=history,
toolbox=toolbox,
tool_id_select_field=tool_id_select_field,
tool=tool,
util=util,
add_frame=add_frame,
tool_id_version_message=tool_id_version_message,
**vars )
def build_tool_id_select_field( self, tools, selected_tool_id ):
"""Build a SelectField whose options are the ids for the received list of tools."""
options = []
refresh_on_change_values = []
for tool in tools:
options.append( ( tool.id, tool.id ) )
refresh_on_change_values.append( tool.id )
select_field = SelectField( name='tool_id', refresh_on_change=True, refresh_on_change_values=refresh_on_change_values )
for option_tup in options:
selected = option_tup[0] == selected_tool_id
if selected:
select_field.add_option( option_tup[0], option_tup[1], selected=True )
else:
select_field.add_option( option_tup[0], option_tup[1] )
return select_field
@web.expose
def redirect( self, trans, redirect_url=None, **kwd ):
if not redirect_url:
@@ -251,7 +307,6 @@ class ToolRunner( BaseUIController ):
datasets.append( create_dataset( 'Pasted Entry' ) )
break
return [ d.id for d in datasets ]
@web.expose
def upload_async_message( self, trans, **kwd ):
# might be more appropriate in a different controller
templates/tool_form.mako
+17 -4
View File
@@ -1,4 +1,5 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/base_panels.mako" import="overlay" />
<%def name="stylesheets()">
@@ -274,10 +275,11 @@
assert len(tool.action) == 2
tool_url = tool.action[0] + h.url_for(tool.action[1])
%>
%if message:
<div class="errormessage">${message}</div>
<br/>
%if tool_id_version_message:
${render_msg( tool_id_version_message, 'error' )}
%endif
<div class="toolForm" id="${tool.id}">
%if tool.has_multiple_pages:
<div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div>
@@ -286,7 +288,18 @@
%endif
<div class="toolFormBody">
<form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
<input type="hidden" name="tool_id" value="${tool.id}">
%if tool_id_select_field:
<div class="form-row">
<label>Tool id:</label>
${tool_id_select_field.get_html()}
<div class="toolParamHelp" style="clear: both;">
Select a different derivation of this tool to rerun the job.
</div>
</div>
<div style="clear: both"></div>
%else:
<input type="hidden" name="tool_id" value="${tool.id}">
%endif
<input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
%if tool.display_by_page[tool_state.page]:
${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}