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Source code for galaxy.tools.verify.test_data

from __future__ import print_function

import hashlib
import os
import re
import subprocess

from string import Template

from galaxy.util import asbool

UPDATE_TEMPLATE = Template(
    "git --work-tree $dir --git-dir $dir/.git fetch && "
    "git --work-tree $dir --git-dir $dir/.git merge origin/master"
)

UPDATE_FAILED_TEMPLATE = Template(
    "Warning failed to update test repository $dir - "
    "update stdout was [$stdout] and stderr was [$stderr]."
)


LIST_SEP = re.compile("\s*,\s*")


[docs]class TestDataResolver(object):
[docs] def __init__(self, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ): file_dirs = environ.get(env_var, None) if file_dirs: self.resolvers = [build_resolver(u, environ) for u in LIST_SEP.split(file_dirs)] else: self.resolvers = []
[docs] def get_filename(self, name): if not self.resolvers: filename = None else: resolver = self.resolvers[0] filename = resolver.path(name) if not resolver.exists(filename): for resolver in self.resolvers[1:]: if resolver.exists(name): filename = resolver.path(name) else: # For backward compat. returning first path if none # exist - though I don't know if this function is ever # actually used in a context where one should return # a file even if it doesn't exist (e.g. a prefix or # or something) - I am pretty sure it is not used in # such a fashion in the context of tool tests. filename = resolver.path(name) return os.path.abspath(filename)
[docs]def build_resolver(uri, environ): if uri.startswith("http") and uri.endswith(".git"): return GitDataResolver(uri, environ) else: return FileDataResolver(uri)
[docs]class FileDataResolver(object):
[docs] def __init__(self, file_dir): self.file_dir = file_dir
[docs] def exists(self, filename): return os.path.exists(self.path(filename))
[docs] def path(self, filename): return os.path.join(self.file_dir, filename)
[docs]class GitDataResolver(FileDataResolver):
[docs] def __init__(self, repository, environ): self.repository = repository self.updated = False repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-cache") m = hashlib.md5() m.update(repository) repo_path = os.path.join(repo_cache, m.hexdigest()) super(GitDataResolver, self).__init__(repo_path) # My preference would be for this to be false, but for backward compat # will leave it as true for now. self.fetch_data = asbool(environ.get("GALAXY_TEST_FETCH_DATA", "true"))
[docs] def exists(self, filename): exists_now = super(GitDataResolver, self).exists(filename) if exists_now or not self.fetch_data or self.updated: return exists_now self.update_repository() return super(GitDataResolver, self).exists(filename)
[docs] def update_repository(self): self.updated = True if not os.path.exists(self.file_dir): parent_dir = os.path.dirname(self.file_dir) if not os.path.exists(parent_dir): os.makedirs(parent_dir) self.execute("git clone '%s' '%s'" % (self.repository, self.file_dir)) update_command = UPDATE_TEMPLATE.safe_substitute(dir=self.file_dir) self.execute(update_command)
[docs] def execute(self, cmd): subprocess_kwds = dict( shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, ) print("Executing %s" % cmd) p = subprocess.Popen(cmd, **subprocess_kwds) stdout, stderr = p.communicate() if p.returncode != 0: kwds = { 'dir': self.file_dir, 'stdout': stdout, 'stderr': stderr, } print(UPDATE_FAILED_TEMPLATE.substitute(**kwds))