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Merged next-stable

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This commit is contained in:
Greg Von Kuster
2014-04-03 17:41:18 -04:00
parent e630fb10c8 2abe24b292
commit 399f5508f6
6 changed files with 48 additions and 28 deletions
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lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+12 -9
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@@ -137,8 +137,8 @@ class AdminToolshed( AdminGalaxy ):
action='reselect_tool_panel_section',
**kwd ) )
else:
message = "Unable to get latest revision for repository <b>%s</b> from the tool shed, so repository " % str( repository.name )
message += "reinstallation is not possible at this time."
message = "Unable to get latest revision for repository <b>%s</b> from " % str( repository.name )
message += "the Tool Shed, so repository reinstallation is not possible at this time."
status = "error"
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='browse_repositories',
@@ -986,12 +986,15 @@ class AdminToolshed( AdminGalaxy ):
# The Tool Shed cannot handle the get_repository_id request, so the code must be older than the
# 04/2014 Galaxy release when it was introduced. It will be safest to error out and let the
# Tool Shed admin update the Tool Shed to a later release.
err_msg = 'The Tool Shed %s is running a code revision that does not ' % str( tool_shed_url)
err_msg += 'allow updating an installed repository where the updates include newly defined repository '
err_msg += 'or tool dependency definitions, so the repository %s cannot ' % str( repository.name )
err_msg += 'be updated at this time. Contact the Tool Shed administrator if possible and'
err_msg += 'ask if they can update the Tool Shed code to the latest release.'
return trans.show_error_message( err_msg )
message = 'The updates available for the repository <b>%s</b> ' % str( repository.name )
message += 'include newly defined repository or tool dependency definitions, and attempting '
message += 'to update the repository resulted in the following error. Contact the Tool Shed '
message += 'administrator if necessary.<br/>%s' % str( e )
status = 'error'
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='browse_repositories',
message=message,
status=status ) )
changeset_revisions = updating_to_changeset_revision
else:
changeset_revisions = kwd.get( 'changeset_revisions', None )
@@ -1811,7 +1814,7 @@ class AdminToolshed( AdminGalaxy ):
"""Update a cloned repository to the latest revision possible."""
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
tool_shed_url = kwd[ 'tool_shed_url' ]
tool_shed_url = kwd.get( 'tool_shed_url', None )
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
lib/galaxy/webapps/tool_shed/controllers/repository.py
+4 -3
View File
@@ -2535,18 +2535,19 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
metadata = repository_metadata.metadata
# Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
repository_dependencies = \
repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans,
repository=repository,
repository_metadata=repository_metadata,
toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
toolshed_base_url=toolshed_base_url,
key_rd_dicts_to_be_processed=None,
all_repository_dependencies=None,
handled_key_rd_dicts=None )
if metadata:
if 'repository_dependencies' in metadata and not repository_dependencies:
# See if we have an invalid repository dependency definition or if the repository dependency is required only for compiling the
# repository's tool dependency.
# See if we have an invalid repository dependency definition or if the repository dependency is required
# only for compiling the repository's tool dependency.
invalid = False
repository_dependencies_dict = metadata[ 'repository_dependencies' ]
rd_tups = repository_dependencies_dict.get( 'repository_dependencies', [] )
lib/tool_shed/util/commit_util.py
+10 -8
View File
@@ -138,8 +138,8 @@ def handle_bz2( repository, uploaded_file_name ):
def handle_complex_repository_dependency_elem( trans, elem, sub_elem_index, sub_elem, sub_elem_altered, altered, unpopulate=False ):
"""
Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines a complex repository
dependency.
Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines
a complex repository dependency.
"""
# The received sub_elem looks something like the following:
# <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" />
@@ -153,15 +153,16 @@ def handle_complex_repository_dependency_elem( trans, elem, sub_elem_index, sub_
altered = True
return altered, sub_elem_altered, elem, error_message
def handle_directory_changes( trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message,
undesirable_dirs_removed, undesirable_files_removed ):
def handle_directory_changes( trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert,
commit_message, undesirable_dirs_removed, undesirable_files_removed ):
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
content_alert_str = ''
files_to_remove = []
filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ]
if remove_repo_files_not_in_tar and not repository.is_new( trans.app ):
# We have a repository that is not new (it contains files), so discover those files that are in the repository, but not in the uploaded archive.
# We have a repository that is not new (it contains files), so discover those files that are in the
# repository, but not in the uploaded archive.
for root, dirs, files in os.walk( full_path ):
if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
for undesirable_dir in UNDESIRABLE_DIRS:
@@ -413,9 +414,10 @@ def handle_tool_dependencies_definition( trans, tool_dependencies_config, unpopu
# <install version="1.0">
for actions_index, actions_elem in enumerate( package_elem ):
if actions_elem.tag == 'actions_group':
# Inspect all entries in the <actions_group> tag set, skipping <actions> tag sets that define os and architecture
# attributes. We want to inspect only the last <actions> tag set contained within the <actions_group> tag set to
# see if a complex repository dependency is defined.
# Inspect all entries in the <actions_group> tag set, skipping <actions>
# tag sets that define os and architecture attributes. We want to inspect
# only the last <actions> tag set contained within the <actions_group> tag
# set to see if a complex repository dependency is defined.
for actions_group_index, actions_group_elem in enumerate( actions_elem ):
if actions_group_elem.tag == 'actions':
# Skip all actions tags that include os or architecture attributes.
lib/tool_shed/util/export_util.py
+2 -1
View File
@@ -228,11 +228,12 @@ def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision
repository = suc.get_repository_in_tool_shed( trans, repository_id )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
# Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
repository_dependencies = \
repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans,
repository=repository,
repository_metadata=repository_metadata,
toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
toolshed_base_url=toolshed_base_url,
key_rd_dicts_to_be_processed=None,
all_repository_dependencies=None,
handled_key_rd_dicts=None )
lib/tool_shed/util/repository_dependency_util.py
+7 -4
View File
@@ -106,6 +106,8 @@ def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_
only those items contained in the received repo_info_dicts list will be processed.
"""
log.debug( "Creating repository dependency objects..." )
# Handle secure and insecure protocol since it may change over time.
tool_shed_url = suc.handle_tool_shed_url_protocol( trans.app, tool_shed_url )
# The following list will be maintained within this method to contain all created or updated tool shed repositories,
# including repository dependencies that may not be installed.
all_created_or_updated_tool_shed_repositories = []
@@ -293,8 +295,8 @@ def get_prior_installation_required_and_only_if_compiling_contained_td( trans, t
def get_repository_dependencies_for_installed_tool_shed_repository( trans, repository ):
"""
Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined for the received repository which is
installed into Galaxy. This method is called only from Galaxy.
Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined
for the received repository which is installed into Galaxy. This method is called only from Galaxy.
"""
tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
url = suc.url_join( tool_shed_url,
@@ -565,12 +567,13 @@ def handle_key_rd_dicts_for_repository( trans, current_repository_key, repositor
key_rd_dicts_to_be_processed = remove_from_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed )
else:
# The repository is in a different tool shed, so build an url and send a request.
error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition "
error_message = "Repository dependencies are currently supported only within the same Tool Shed. Ignoring repository dependency definition "
error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision )
log.debug( error_message )
return toolshed, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts
def handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ):
def handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts,
circular_repository_dependencies ):
next_repository_key_rd_dict = key_rd_dicts_to_be_processed.pop( 0 )
next_repository_key_rd_dicts = [ next_repository_key_rd_dict ]
next_repository_key = next_repository_key_rd_dict.keys()[ 0 ]
lib/tool_shed/util/shed_util_common.py
+13 -3
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@@ -1341,9 +1341,7 @@ def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_sh
"""
# This method is used only in Galaxy, not the tool shed.
repository_query = __repository_query( app )
if tool_shed.find( '//' ) > 0:
tool_shed = tool_shed.split( '//' )[1]
tool_shed = tool_shed.rstrip( '/' )
tool_shed = remove_protocol_from_tool_shed_url( tool_shed )
return repository_query \
.filter( and_( app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
app.install_model.ToolShedRepository.table.c.name == name,
@@ -1597,6 +1595,12 @@ def handle_galaxy_url( trans, **kwd ):
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
return galaxy_url
def handle_tool_shed_url_protocol( app, tool_shed_url ):
"""Handle secure and insecure HTTP protocol since they may change over time."""
tool_shed_url = remove_protocol_from_tool_shed_url( tool_shed_url )
tool_shed_url = get_url_from_tool_shed( app, tool_shed_url )
return tool_shed_url
def have_shed_tool_conf_for_install( trans ):
if not trans.app.toolbox.shed_tool_confs:
return False
@@ -1653,6 +1657,12 @@ def remove_file( file_name ):
except:
pass
def remove_protocol_from_tool_shed_url( tool_shed_url ):
if tool_shed_url.find( '//' ) > 0:
tool_shed_url = tool_shed_url.split( '//' )[1]
tool_shed_url = tool_shed_url.rstrip( '/' )
return tool_shed_url
def __repository_query( app ):
if app.name == "galaxy":
query = app.install_model.context.query( app.install_model.ToolShedRepository )