def normalise_toolshed_url(toolshed):
"""
Return complete URL for a tool shed
Arguments:
toolshed (str): partial or full URL for a
toolshed server
Returns:
str: full URL for toolshed, including
leading protocol.
"""
if toolshed.startswith('http://') or \
toolshed.startswith('https://'):
return toolshed
return "https://%s" % toolshed
def installed_repositories(gi,name=None,
toolshed=None,
owner=None,
include_deleted=False,
only_updateable=False):
"""
Fetch a list of installed repository revisions
Arguments:
gi (bioblend.galaxy.GalaxyInstance): Galaxy instance
name (str): optional, only list tool repositiories
which match this string (can include wildcards)
toolshed (str): optional, only list tool
repositories from toolsheds that match this string
(can include wildcards)
owner (str): optional, only list tool repositiories
with owners who match this string (can include
wildcards)
list_tools (bool): if True then also list the tools
provided by the repository
include_deleted (bool): if True then also include
repository revisions that are marked as deleted
(default is to only show those which are not
deleted)
only_updateable (bool): if True then only report
repositories that have uninstalled updates or
upgrades available (default is to show all
repositories and revisions)
Returns:
List: a list of tuples consisting of three items
(repository,revision,tools), where
- 'repository' is a populated Repository instance
- 'revision' is a populated RepositoryRevision
- 'tools' is a list of Tool instances
"""
# Get the list of installed repos
installed_repos = []
repos = get_repositories(gi)
# Filter on name
if name:
name = name.lower()
repos = filter(lambda r: fnmatch.fnmatch(r.name.lower(),name),
repos)
# Filter on toolshed
if toolshed:
# Strip leading http(s)://
for protocol in ('https://','http://'):
if toolshed.startswith(protocol):
toolshed = toolshed[len(protocol):]
repos = filter(lambda r: fnmatch.fnmatch(r.tool_shed,toolshed),
repos)
# Filter on owner
if owner:
repos = filter(lambda r: fnmatch.fnmatch(r.owner,owner),repos)
# Get list of tools
tools = get_tools(gi)
for repo in repos:
# Check each revision
for revision in repo.revisions():
# Exclude deleted revisions
if not include_deleted and revision.deleted:
continue
# Exclude revisions that don't need updating
if only_updateable and \
(revision.newer_revision_installed() or \
revision.latest_revision):
continue
# Fetch tools associated with this revision
repo_tools = filter(lambda t:
t.tool_repo == repo.id and
t.tool_changeset ==
revision.installed_changeset_revision,
tools)
# Append to the list
installed_repos.append((repo,revision,repo_tools))
# Finished
return installed_repos
