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Fixes for complext repository dependency definitions that do not include a changeset_revision attribute. A fix for indenting the updates XML file is also included.

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This commit is contained in:
Greg Von Kuster
2013-05-21 12:26:55 -04:00
parent 730a15657f
commit 4d781de114
2 changed files with 16 additions and 11 deletions
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lib/galaxy/webapps/tool_shed/controllers/upload.py
+6 -6
View File
@@ -131,7 +131,7 @@ class UploadController( BaseUIController ):
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
tmp_filename = commit_util.create_and_write_tmp_file( root )
shutil.move( tmp_filename, full_path )
else:
shutil.move( uploaded_file_name, full_path )
@@ -140,7 +140,7 @@ class UploadController( BaseUIController ):
# are missing and if so, set them appropriately.
altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
tmp_filename = commit_util.create_and_write_tmp_file( root )
shutil.move( tmp_filename, full_path )
else:
shutil.move( uploaded_file_name, full_path )
@@ -268,13 +268,13 @@ class UploadController( BaseUIController ):
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
tmp_filename = commit_util.create_and_write_tmp_file( root )
shutil.move( tmp_filename, uploaded_file_name )
elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml':
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
tmp_filename = commit_util.create_and_write_tmp_file( root )
shutil.move( tmp_filename, uploaded_file_name )
if ok:
repo_path = os.path.join( full_path, relative_path )
@@ -330,13 +330,13 @@ class UploadController( BaseUIController ):
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
tmp_filename = commit_util.create_and_write_tmp_file( root )
shutil.move( tmp_filename, uploaded_file_name )
elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml':
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
tmp_filename = commit_util.create_and_write_tmp_file( root )
shutil.move( tmp_filename, uploaded_file_name )
return commit_util.handle_directory_changes( trans,
repository,
lib/tool_shed/util/commit_util.py
+10 -5
View File
@@ -1,5 +1,6 @@
import logging
import os
import pkg_resources
import shutil
import tempfile
from galaxy import util
@@ -9,11 +10,15 @@ import tool_shed.util.shed_util_common as suc
from tool_shed.util import tool_util
from galaxy import eggs
eggs.require( 'mercurial' )
from mercurial import commands
from mercurial import hg
from mercurial import ui
pkg_resources.require( 'elementtree' )
from elementtree.ElementTree import tostring
log = logging.getLogger( __name__ )
UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ]
@@ -57,13 +62,13 @@ def check_file_content_for_html_and_images( file_path ):
message = 'The file "%s" contains image content.\n' % str( file_path )
return message
def create_and_write_tmp_file( text ):
def create_and_write_tmp_file( root ):
fh = tempfile.NamedTemporaryFile( 'wb' )
tmp_filename = fh.name
fh.close()
fh = open( tmp_filename, 'wb' )
fh.write( '<?xml version="1.0"?>\n' )
fh.write( text )
fh.write( tostring( root, 'utf-8' ) )
fh.close()
return tmp_filename
@@ -255,7 +260,6 @@ def handle_tool_dependencies_definition( trans, tool_dependencies_config ):
package_altered = True
if not altered:
altered = True
elif package_elem.tag == 'install':
# <install version="1.0">
for actions_index, actions_elem in enumerate( package_elem ):
@@ -277,8 +281,9 @@ def handle_tool_dependencies_definition( trans, tool_dependencies_config ):
if package_altered:
actions_elem[ action_index ] = action_elem
if package_altered:
root_elem[ actions_index ] = actions_elem
package_elem[ actions_index ] = actions_elem
if package_altered:
root_elem[ package_index ] = package_elem
if package_altered:
root[ root_index ] = root_elem
return altered, root