1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/58a0529c0a06/
Changeset: 58a0529c0a06
User: dan
Date: 2013-05-08 19:22:02
Summary: Allow dataset owners and admins to view deleted datasets.
Affected #: 1 file
diff -r daa7c3397ae946dc039ddab0bb4bece9b0a53557 -r 58a0529c0a0654db9751f6021bb14fb5a36093ad lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -290,7 +290,7 @@
raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( hda_id ) )
if not self._can_access_dataset( trans, data ):
return trans.show_error_message( "You are not allowed to access this dataset" )
- if data.deleted:
+ if data.deleted and not ( trans.user_is_admin() or ( data.history and trans.get_user() == data.history.user ) ):
return trans.show_error_message( "The dataset you are attempting to view has been deleted." )
if data.state == trans.model.Dataset.states.UPLOAD:
return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." )
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/2b92273f24b1/
Changeset: 2b92273f24b1
User: dan
Date: 2013-05-07 22:46:47
Summary: Fix for refreshing current history when copying datasets.
Affected #: 1 file
diff -r 6c462a5a566db9923a344b2bc8a89a797679aaa3 -r 2b92273f24b12372c77e8bf49bb59bda1def09d9 lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -1034,8 +1034,9 @@
user = trans.get_user()
if source_history is not None:
history = self.get_history(trans, source_history)
+ current_history = trans.get_history()
else:
- history = trans.get_history()
+ history = current_history = trans.get_history()
refresh_frames = []
if source_dataset_ids:
if not isinstance( source_dataset_ids, list ):
@@ -1083,7 +1084,7 @@
else:
for hist in target_histories:
hist.add_dataset( hda.copy( copy_children = True ) )
- if history in target_histories:
+ if current_history in target_histories:
refresh_frames = ['history']
trans.sa_session.flush()
hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' %
@@ -1100,7 +1101,7 @@
target_histories = user.active_histories
return trans.fill_template( "/dataset/copy_view.mako",
source_history = history,
- current_history = trans.get_history(),
+ current_history = current_history,
source_dataset_ids = source_dataset_ids,
target_history_id = target_history_id,
target_history_ids = target_history_ids,
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/3790a81856bf/
Changeset: 3790a81856bf
User: inithello
Date: 2013-05-06 22:57:57
Summary: Fix mismatch between tool id and test id when deleting tests/uninstalling tested repositories.
Affected #: 1 file
diff -r bcb6e71eda61f77426af60cbc854231b00ecabc3 -r 3790a81856bf4a8b1fc6b6075c467ce813155b2a test/install_and_test_tool_shed_repositories/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -196,6 +196,7 @@
name = str( repository.name )
owner = str( repository.owner )
changeset_revision = str( repository.installed_changeset_revision )
+ log.debug( 'Changeset revision %s of repository %s queued for uninstallation.' % ( changeset_revision, name ) )
repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision )
# Generate a test method to uninstall this repository through the embedded Galaxy application's web interface.
test_install_repositories.generate_uninstall_method( repository_dict )
@@ -321,6 +322,7 @@
# and try to re-run the tests after uninstalling the repository, which will cause false failure reports,
# since the test data has been deleted from disk by now.
tests_to_delete = []
+ tools_to_delete = []
global test_toolbox
for key in test_toolbox.__dict__:
if key.startswith( 'TestForTool_' ):
@@ -328,12 +330,14 @@
# We can't delete this test just yet, we're still iterating over __dict__.
tests_to_delete.append( key )
tool_id = key.replace( 'TestForTool_', '' )
- if tool_id in app.toolbox.tools_by_id:
- # But we can remove the relevant tool from app.toolbox.tools_by_id.
- del app.toolbox.tools_by_id[ tool_id ]
+ for tool in app.toolbox.tools_by_id:
+ if tool.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ):
+ tools_to_delete.append( tool )
for key in tests_to_delete:
# Now delete the tests found in the previous loop.
del test_toolbox.__dict__[ key ]
+ for tool in tools_to_delete:
+ del app.toolbox.tools_by_id[ tool ]
def run_tests( test_config ):
loader = nose.loader.TestLoader( config=test_config )
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/bcb6e71eda61/
Changeset: bcb6e71eda61
User: dannon
Date: 2013-05-06 21:49:37
Summary: Update worfklow_run to use the same styles as the tool pane 'Execute' button.
Affected #: 1 file
diff -r f10bc351f2ca97577a3a823dc4113f965164cbd5 -r bcb6e71eda61f77426af60cbc854231b00ecabc3 templates/webapps/galaxy/workflow/run.mako
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -504,6 +504,6 @@
<span id="new_history_input">named: <input type='text' name='new_history_name' value='${h.to_unicode( workflow.name )}'/></span></p>
%endif
-<input type="submit" name="run_workflow" value="Run workflow" />
+<input type="submit" class="btn btn-primary" name="run_workflow" value="Run workflow" /></form>
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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