Source code for galaxy.tool_shed.util.hg_util

import logging
import os
import subprocess

from galaxy.tool_shed.util import basic_util
from galaxy.util import unicodify

log = logging.getLogger(__name__)

INITIAL_CHANGELOG_HASH = '000000000000'


[docs]def clone_repository(repository_clone_url, repository_file_dir, ctx_rev=None): """ Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository. """ cmd = ['hg', 'clone'] if ctx_rev: cmd.extend(['-r', str(ctx_rev)]) cmd.extend([repository_clone_url, repository_file_dir]) # Make sure the destination path actually exists before attempting to clone if not os.path.exists(repository_file_dir): os.makedirs(repository_file_dir) try: subprocess.check_output(cmd, stderr=subprocess.STDOUT, stdin=subprocess.DEVNULL) return True, None except Exception as e: error_message = 'Error cloning repository: %s' % unicodify(e) if isinstance(e, subprocess.CalledProcessError): error_message += "\nOutput was:\n%s" % unicodify(e.output) log.error(error_message) return False, error_message
[docs]def copy_file_from_manifest(repo, changeset_revision, filename, dir): """ Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers. """ for changeset in reversed_upper_bounded_changelog(repo, changeset_revision): changeset_ctx = repo[changeset] fctx = get_file_context_from_ctx(changeset_ctx, filename) if fctx and fctx not in ['DELETED']: file_path = os.path.join(dir, filename) fh = open(file_path, 'wb') fh.write(fctx.data()) fh.close() return file_path return None
[docs]def get_changectx_for_changeset(repo, changeset_revision, **kwd): """Retrieve a specified changectx from a repository.""" for changeset in repo.changelog: ctx = repo[changeset] if str(ctx) == changeset_revision: return ctx return None
[docs]def get_config_from_disk(config_file, relative_install_dir): for root, dirs, files in os.walk(relative_install_dir): if root.find('.hg') < 0: for name in files: if name == config_file: return os.path.abspath(os.path.join(root, name)) return None
[docs]def get_ctx_file_path_from_manifest(filename, repo, changeset_revision): """ Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision. """ stripped_filename = basic_util.strip_path(filename) for changeset in reversed_upper_bounded_changelog(repo, changeset_revision): manifest_ctx = repo[changeset] for ctx_file in manifest_ctx.files(): ctx_file_name = basic_util.strip_path(unicodify(ctx_file)) if ctx_file_name == stripped_filename: return manifest_ctx, ctx_file return None, None
[docs]def get_file_context_from_ctx(ctx, filename): """Return the mercurial file context for a specified file.""" # We have to be careful in determining if we found the correct file because multiple files with # the same name may be in different directories within ctx if the files were moved within the change # set. For example, in the following ctx.files() list, the former may have been moved to the latter: # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. # Another scenario is that the file has been deleted. deleted = False filename = basic_util.strip_path(filename) for ctx_file in ctx.files(): ctx_file_name = basic_util.strip_path(unicodify(ctx_file)) if filename == ctx_file_name: try: # If the file was moved, its destination will be returned here. fctx = ctx[ctx_file] return fctx except LookupError: # Set deleted for now, and continue looking in case the file was moved instead of deleted. deleted = True if deleted: return 'DELETED' return None
[docs]def pull_repository(repo_path, repository_clone_url, ctx_rev): """Pull changes from a remote repository to a local one.""" try: subprocess.check_output(['hg', 'pull', '-r', ctx_rev, repository_clone_url], stderr=subprocess.STDOUT, cwd=repo_path) except Exception as e: error_message = "Error pulling revision '{}': {}".format(ctx_rev, unicodify(e)) if isinstance(e, subprocess.CalledProcessError): error_message += "\nOutput was:\n%s" % unicodify(e.output) raise Exception(error_message)
[docs]def reversed_lower_upper_bounded_changelog(repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision): """ Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and including the included_upper_bounds_changeset_revision. The value of excluded_lower_bounds_changeset_revision will be the value of INITIAL_CHANGELOG_HASH if no valid changesets exist before included_upper_bounds_changeset_revision. """ # To set excluded_lower_bounds_changeset_revision, calling methods should do the following, where the value # of changeset_revision is a downloadable changeset_revision. # excluded_lower_bounds_changeset_revision = \ # metadata_util.get_previous_metadata_changeset_revision(app, repository, changeset_revision, downloadable=?) if excluded_lower_bounds_changeset_revision == INITIAL_CHANGELOG_HASH: appending_started = True else: appending_started = False reversed_changelog = [] for changeset in repo.changelog: changeset_hash = str(repo[changeset]) if appending_started: reversed_changelog.insert(0, changeset) if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started: appending_started = True if changeset_hash == included_upper_bounds_changeset_revision: break return reversed_changelog
[docs]def reversed_upper_bounded_changelog(repo, included_upper_bounds_changeset_revision): """ Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision. """ return reversed_lower_upper_bounded_changelog(repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision)
[docs]def update_repository(repo_path, ctx_rev=None): """ Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. """ # TODO: We may have files on disk in the repo directory that aren't being tracked, so they must be removed. # The codes used to show the status of files are as follows. # M = modified # A = added # R = removed # C = clean # ! = deleted, but still tracked # ? = not tracked # I = ignored # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that # purging is not supported by the mercurial API. cmd = ['hg', 'update'] if ctx_rev: cmd.extend(['-r', ctx_rev]) try: subprocess.check_output(cmd, stderr=subprocess.STDOUT, cwd=repo_path) except Exception as e: error_message = 'Error updating repository: %s' % unicodify(e) if isinstance(e, subprocess.CalledProcessError): error_message += "\nOutput was:\n%s" % unicodify(e.output) raise Exception(error_message)
__all__ = ( 'clone_repository', 'copy_file_from_manifest', 'get_changectx_for_changeset', 'get_config_from_disk', 'get_ctx_file_path_from_manifest', 'get_file_context_from_ctx', 'pull_repository', 'reversed_lower_upper_bounded_changelog', 'reversed_upper_bounded_changelog', 'update_repository', )