1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/eea034b7cc62/
changeset: eea034b7cc62
user: greg
date: 2012-11-24 16:21:48
summary: Fix the tool migration process that was broken due to the recent changes in
the imports to various Galaxy framework files, mostly the Galaxy model.
affected #: 4 files
diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r
eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/tool_shed/__init__.py
--- a/lib/galaxy/tool_shed/__init__.py
+++ b/lib/galaxy/tool_shed/__init__.py
@@ -2,7 +2,7 @@
Classes encapsulating the management of repositories installed from Galaxy tool sheds.
"""
import os
-import galaxy.util.shed_util
+from galaxy.util.shed_util import *
from galaxy.model.orm import *
from galaxy import eggs
@@ -27,7 +27,7 @@
ElementInclude.include( root )
tool_path = root.get( 'tool_path', None )
if tool_path:
- tool_shed = galaxy.util.shed_util.clean_tool_shed_url(
tool_shed_repository.tool_shed )
+ tool_shed = clean_tool_shed_url( tool_shed_repository.tool_shed )
relative_path = os.path.join( tool_path,
tool_shed,
'repos',
@@ -44,13 +44,13 @@
.order_by(
self.model.ToolShedRepository.table.c.id ):
relative_install_dir = self.get_repository_install_dir( tool_shed_repository
)
if relative_install_dir:
- installed_repository_dict =
galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository,
relative_install_dir )
+ installed_repository_dict = load_installed_datatypes( self.app,
tool_shed_repository, relative_install_dir )
if installed_repository_dict:
self.installed_repository_dicts.append( installed_repository_dict )
def load_proprietary_converters_and_display_applications( self, deactivate=False ):
for installed_repository_dict in self.installed_repository_dicts:
if installed_repository_dict[ 'converter_path' ]:
- galaxy.util.shed_util.load_installed_datatype_converters( self.app,
installed_repository_dict, deactivate=deactivate )
+ load_installed_datatype_converters( self.app, installed_repository_dict,
deactivate=deactivate )
if installed_repository_dict[ 'display_path' ]:
- galaxy.util.shed_util.load_installed_display_applications( self.app,
installed_repository_dict, deactivate=deactivate )
+ load_installed_display_applications( self.app, installed_repository_dict,
deactivate=deactivate )
\ No newline at end of file
diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r
eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/tool_shed/migrate/common.py
--- a/lib/galaxy/tool_shed/migrate/common.py
+++ b/lib/galaxy/tool_shed/migrate/common.py
@@ -2,6 +2,7 @@
import galaxy.config
import galaxy.datatypes.registry
from galaxy import tools
+from galaxy.tools.data import *
import galaxy.model.mapping
import galaxy.tools.search
from galaxy.objectstore import build_object_store_from_config
@@ -42,8 +43,8 @@
# Load the data types in the Galaxy distribution, which are defined in
self.config.datatypes_config.
self.datatypes_registry.load_datatypes( self.config.root,
self.config.datatypes_config )
# Initialize tool data tables using the config defined by
self.config.tool_data_table_config_path.
- self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
tool_data_path=self.config.tool_data_path,
-
config_filename=self.config.tool_data_table_config_path )
+ self.tool_data_tables = ToolDataTableManager(
tool_data_path=self.config.tool_data_path,
+
config_filename=self.config.tool_data_table_config_path )
# Load additional entries defined by self.config.shed_tool_data_table_config into
tool data tables.
self.tool_data_tables.load_from_config_file(
config_filename=self.config.shed_tool_data_table_config,
tool_data_path=self.tool_data_tables.tool_data_path,
diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r
eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -1,7 +1,6 @@
import os, tempfile, shutil, logging, urllib2
from galaxy import util
from galaxy.datatypes.checkers import *
-from galaxy.datatypes.sniff import is_column_based
from galaxy.util.json import *
from galaxy.util.shed_util_common import *
from galaxy.tools.search import ToolBoxSearch
@@ -475,13 +474,6 @@
else:
tool_section = None
return tool_section
-def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ):
- """Update the received metadata_dict with changes that have been
applied to the received exported_workflow_dict."""
- if 'workflows' in metadata_dict:
- metadata_dict[ 'workflows' ].append( ( relative_path,
exported_workflow_dict ) )
- else:
- metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict
) ]
- return metadata_dict
def get_config( config_file, repo, ctx, dir ):
"""Return the latest version of config_filename from the repository
manifest."""
config_file = strip_path( config_file )
@@ -817,6 +809,24 @@
parent_id=tool_version_using_parent_id.id )
sa_session.add( tool_version_association )
sa_session.flush()
+def is_column_based( fname, sep='\t', skip=0, is_multi_byte=False ):
+ """See if the file is column based with respect to a
separator."""
+ headers = get_headers( fname, sep, is_multi_byte=is_multi_byte )
+ count = 0
+ if not headers:
+ return False
+ for hdr in headers[ skip: ]:
+ if hdr and hdr[ 0 ] and not hdr[ 0 ].startswith( '#' ):
+ if len( hdr ) > 1:
+ count = len( hdr )
+ break
+ if count < 2:
+ return False
+ for hdr in headers[ skip: ]:
+ if hdr and hdr[ 0 ] and not hdr[ 0 ].startswith( '#' ):
+ if len( hdr ) != count:
+ return False
+ return True
def is_data_index_sample_file( file_path ):
"""
Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when
a tool shed repository is being installed
diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r
eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -2,6 +2,7 @@
from galaxy import util
from galaxy.tools import parameters
from galaxy.util import inflector
+from galaxy.util.json import *
from galaxy.web import url_for
from galaxy.web.form_builder import SelectField
from galaxy.datatypes.checkers import *
@@ -724,6 +725,13 @@
else:
metadata_dict[ 'tools' ] = [ tool_dict ]
return metadata_dict
+def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ):
+ """Update the received metadata_dict with changes that have been
applied to the received exported_workflow_dict."""
+ if 'workflows' in metadata_dict:
+ metadata_dict[ 'workflows' ].append( ( relative_path,
exported_workflow_dict ) )
+ else:
+ metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict
) ]
+ return metadata_dict
def get_changectx_for_changeset( repo, changeset_revision, **kwd ):
"""Retrieve a specified changectx from a repository"""
for changeset in repo.changelog:
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