1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8483f0ef8288/
Changeset: 8483f0ef8288
User: dan
Date: 2013-05-14 22:52:58
Summary: Fix for determining Data Manager Tool Filename.
Affected #: 1 file
diff -r 6d72b2db32c0d84032ee40f2cd86b7b09485c441 -r 8483f0ef8288b6eecf65a556c75b65e944a00bb0 lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -362,7 +362,7 @@
data_tables.append( data_table_name )
if bad_data_table:
continue
- data_manager_metadata_tool_file = os.path.join( relative_data_manager_dir, tool_file )
+ data_manager_metadata_tool_file = os.path.normpath( os.path.join( relative_data_manager_dir, tool_file ) )
tool_metadata_tool_file = os.path.join( repo_files_directory, data_manager_metadata_tool_file )
tool = tools.get( tool_metadata_tool_file, None )
if tool is None:
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/c1f961549cca/
Changeset: c1f961549cca
User: dan
Date: 2013-05-14 21:54:33
Summary: Fix for detecting job error in data manager tools; needed as a result of recent job flow changes.
Affected #: 1 file
diff -r 4573880b2d9b7a76abcbe2ccac824ab9338df802 -r c1f961549cca546214ff4430dd6a01c42cfeaa63 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -3157,6 +3157,10 @@
#process results of tool
if job and job.state == job.states.ERROR:
return
+ #Job state may now be 'running' instead of previous 'error', but datasets are still set to e.g. error
+ for dataset in out_data.itervalues():
+ if dataset.state != dataset.states.OK:
+ return
data_manager_id = job.data_manager_association.data_manager_id
data_manager = self.app.data_managers.get_manager( data_manager_id, None )
assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_id )
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/1a4b56a78124/
Changeset: 1a4b56a78124
User: greg
Date: 2013-05-14 20:30:08
Summary: Display the Reset all metadata on repository option in the Resporitory Actions popup menu in more pages in the tool shed than the Manage repsitory page.
Affected #: 2 files
diff -r 1cabd9fd107c14caa379e591ff3fea66c3cc5ce4 -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d templates/webapps/tool_shed/common/repository_actions_menu.mako
--- a/templates/webapps/tool_shed/common/repository_actions_menu.mako
+++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako
@@ -1,6 +1,6 @@
<%inherit file="/base.mako"/>
-<%def name="render_tool_shed_repository_actions( repository, repo=None, metadata=None, changeset_revision=None )">
+<%def name="render_tool_shed_repository_actions( repository, metadata=None, changeset_revision=None )"><%
from tool_shed.util.review_util import can_browse_repository_reviews, changeset_revision_reviewed_by_user, get_review_by_repository_id_changeset_revision_user_id
from tool_shed.util.shed_util_common import changeset_is_malicious
@@ -54,11 +54,8 @@
else:
can_download = False
- if not is_deprecated:
- if repo and len( repo ) > 0:
- can_reset_all_metadata = True
- else:
- can_reset_all_metadata = False
+ if ( is_admin or ( trans.user and trans.user == repository.user ) ) and not repository.deleted and not repository.deprecated and not is_new:
+ can_reset_all_metadata = True
else:
can_reset_all_metadata = False
diff -r 1cabd9fd107c14caa379e591ff3fea66c3cc5ce4 -r 1a4b56a78124b26103c61f8e6e736b088e65aa6d templates/webapps/tool_shed/repository/manage_repository.mako
--- a/templates/webapps/tool_shed/repository/manage_repository.mako
+++ b/templates/webapps/tool_shed/repository/manage_repository.mako
@@ -88,7 +88,7 @@
${container_javascripts()}
</%def>
-${render_tool_shed_repository_actions( repository, repo=repo, metadata=metadata, changeset_revision=changeset_revision )}
+${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )}
%if message:
${render_msg( message, status )}
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/842a78530fcd/
Changeset: 842a78530fcd
User: greg
Date: 2013-05-14 19:45:08
Summary: Allow tool shed repository dependency definition tags to not include a toolshed attribute. If missing, the toolshed value will default to the current tool shed. The following example shows what was required before this changeset:
<repository toolshed="http://localhost:9009/" name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
Now the following is also valid:
<repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
Affected #: 1 file
diff -r d3be8f8f8096ad723644019bd742904046df54ba -r 842a78530fcd87670198d55d96d9adbdfc53483e lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -9,6 +9,7 @@
from galaxy.tools.data_manager.manager import DataManager
from galaxy.util import inflector
from galaxy.util import json
+from galaxy.web import url_for
from galaxy.webapps.tool_shed.util import container_util
import tool_shed.util.shed_util_common as suc
from tool_shed.util import common_util
@@ -1050,6 +1051,9 @@
is_valid = True
error_message = ''
toolshed = repository_elem.get( 'toolshed' )
+ if not toolshed:
+ # Default to the current tool shed.
+ toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' )
name = repository_elem.get( 'name' )
owner = repository_elem.get( 'owner' )
changeset_revision = repository_elem.get( 'changeset_revision' )
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/6fac39a6786e/
Changeset: 6fac39a6786e
Branch: stable
User: dan
Date: 2013-05-14 19:13:21
Summary: Have datatypes.checkers.check_binary call util.is_binary. Fixes unicode file upload under certain conditions.
Affected #: 1 file
diff -r 7cf2f256b3d9c32f76567f49a0935b0ca9da9f7e -r 6fac39a6786e555c5bd57f98b4601c9949aae37d lib/galaxy/datatypes/checkers.py
--- a/lib/galaxy/datatypes/checkers.py
+++ b/lib/galaxy/datatypes/checkers.py
@@ -58,7 +58,7 @@
for chars in temp:
for char in chars:
chars_read += 1
- if ord( char ) > 128:
+ if util.is_binary( char ):
is_binary = True
break
if chars_read > 100:
https://bitbucket.org/galaxy/galaxy-central/commits/686170571216/
Changeset: 686170571216
Branch: stable
User: dan
Date: 2013-05-14 19:13:21
Summary: Use util.unicodify when generating dataset peeks.
Affected #: 1 file
diff -r 6fac39a6786e555c5bd57f98b4601c9949aae37d -r 6861705712161c545398e6db1a7cdadda931fc7a lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -860,7 +860,7 @@
text = "%s file" % file_type
else:
try:
- text = unicode( '\n'.join( lines ), 'utf-8' )
+ text = util.unicodify( '\n'.join( lines ) )
except UnicodeDecodeError:
text = "binary/unknown file"
return text
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/3667a65b86a9/
Changeset: 3667a65b86a9
User: dan
Date: 2013-05-14 19:13:21
Summary: Have datatypes.checkers.check_binary call util.is_binary. Fixes unicode file upload under certain conditions.
Affected #: 1 file
diff -r 8882e45504a37ab9f87f2872df2a6749673bd741 -r 3667a65b86a9418bc67c89ce0fdfd0dfc55a0021 lib/galaxy/datatypes/checkers.py
--- a/lib/galaxy/datatypes/checkers.py
+++ b/lib/galaxy/datatypes/checkers.py
@@ -58,7 +58,7 @@
for chars in temp:
for char in chars:
chars_read += 1
- if ord( char ) > 128:
+ if util.is_binary( char ):
is_binary = True
break
if chars_read > 100:
https://bitbucket.org/galaxy/galaxy-central/commits/d3be8f8f8096/
Changeset: d3be8f8f8096
User: dan
Date: 2013-05-14 19:13:21
Summary: Use util.unicodify when generating dataset peeks.
Affected #: 1 file
diff -r 3667a65b86a9418bc67c89ce0fdfd0dfc55a0021 -r d3be8f8f8096ad723644019bd742904046df54ba lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -865,7 +865,7 @@
text = "%s file" % file_type
else:
try:
- text = unicode( '\n'.join( lines ), 'utf-8' )
+ text = util.unicodify( '\n'.join( lines ) )
except UnicodeDecodeError:
text = "binary/unknown file"
return text
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/8882e45504a3/
Changeset: 8882e45504a3
User: jgoecks
Date: 2013-05-14 17:54:00
Summary: Add annotation when importing workflow.
Affected #: 1 file
diff -r c842439a245cf97137a819aaae9907240f47e6d9 -r 8882e45504a37ab9f87f2872df2a6749673bd741 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1855,14 +1855,19 @@
conn.output_name = conn_dict['output_name']
conn.output_step = steps_by_external_id[ conn_dict['id'] ]
del step.temp_input_connections
+
# Order the steps if possible
attach_ordered_steps( workflow, steps )
+
# Connect up
stored = model.StoredWorkflow()
stored.name = workflow.name
workflow.stored_workflow = stored
stored.latest_workflow = workflow
stored.user = trans.user
+ if data[ 'annotation' ]:
+ self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] )
+
# Persist
trans.sa_session.add( stored )
trans.sa_session.flush()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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