1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ef39a1112100/
changeset: ef39a1112100
user: richard_burhans
date: 2011-10-31 22:13:24
summary: I had an older tabular.py, fixed one line that got changed by mistake
affected #: 1 file
diff -r 69602a4fb17b3aa775c970580de8979c428b9b68 -r ef39a111210018fb50282a352182b298c23be8f7 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -481,4 +481,4 @@
return out
def get_track_type( self ):
- return "FeatureTrack", {"data": "tabix", "index": "summary_tree"}
+ return "VcfTrack", {"data": "tabix", "index": "summary_tree"}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/309f2650b4f4/
changeset: 309f2650b4f4
user: greg
date: 2011-10-28 22:13:21
summary: Fixes for finding tools installed from a tool shed when building workflows from the current history or running workflows, and the workflow in question references tools using the old tool_id.
affected #: 1 file
diff -r 2369a117e49772b9074dab996ef1601969f007dc -r 309f2650b4f46c4cd75ca252b215dae1799732ee lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1296,7 +1296,16 @@
for job_id in job_ids:
assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
job = jobs_by_id[ job_id ]
- tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
+ try:
+ tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
+ except KeyError, e:
+ # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
+ # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id
+ # attribute should contain what we're looking for.
+ for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+ if job.tool_id == available_tool.old_id:
+ tool = available_tool
+ break
param_values = job.get_param_values( trans.app )
associations = cleanup_param_values( tool.inputs, param_values )
# Doing it this way breaks dynamic parameters, backed out temporarily.
@@ -1463,7 +1472,16 @@
# Execute module
job = None
if step.type == 'tool' or step.type is None:
- tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+ try:
+ tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
+ except KeyError, e:
+ # Handle the case where the workflow requires a tool not available in the local Galaxy instance.
+ # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id
+ # attribute should contain what we're looking for.
+ for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+ if step.tool_id == available_tool.old_id:
+ tool = available_tool
+ break
input_values = step.state.inputs
# Connect up
def callback( input, value, prefixed_name, prefixed_label ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/2369a117e497/
changeset: 2369a117e497
user: greg
date: 2011-10-28 21:19:09
summary: Don't display the "User Info" select field when registering as a new user of editing your information as an existing user unless there are existing form definitions that provide options for selection.
affected #: 2 files
diff -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 -r 2369a117e49772b9074dab996ef1601969f007dc templates/user/register.mako
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -65,7 +65,7 @@
${subscribe_check_box.get_html()}
</div>
%endif
- %if user_type_fd_id_select_field:
+ %if len( user_type_fd_id_select_field.options ) > 1:
<div class="form-row"><label>User type</label>
${user_type_fd_id_select_field.get_html()}
diff -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 -r 2369a117e49772b9074dab996ef1601969f007dc templates/webapps/galaxy/user/info.mako
--- a/templates/webapps/galaxy/user/info.mako
+++ b/templates/webapps/galaxy/user/info.mako
@@ -13,7 +13,7 @@
<div class="toolForm"><form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" ><div class="toolFormTitle">User information</div>
- %if user_type_fd_id_select_field:
+ %if len( user_type_fd_id_select_field.options ) > 1:
<div class="form-row"><label>User type:</label>
${user_type_fd_id_select_field.get_html()}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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