mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
120 lines
4.0 KiB
Python
120 lines
4.0 KiB
Python
from __future__ import print_function
|
|
import hashlib
|
|
import os
|
|
import re
|
|
from string import Template
|
|
import subprocess
|
|
|
|
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*")
|
|
|
|
|
|
class TestDataResolver(object):
|
|
|
|
def __init__(self, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ):
|
|
file_dirs = environ.get(env_var, None)
|
|
if file_dirs:
|
|
self.resolvers = map(lambda u: build_resolver(u, environ), LIST_SEP.split(file_dirs))
|
|
else:
|
|
self.resolvers = []
|
|
|
|
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)
|
|
|
|
|
|
def build_resolver(uri, environ):
|
|
if uri.startswith("http") and uri.endswith(".git"):
|
|
return GitDataResolver(uri, environ)
|
|
else:
|
|
return FileDataResolver(uri)
|
|
|
|
|
|
class FileDataResolver(object):
|
|
|
|
def __init__(self, file_dir):
|
|
self.file_dir = file_dir
|
|
|
|
def exists(self, filename):
|
|
return os.path.exists(self.path(filename))
|
|
|
|
def path(self, filename):
|
|
return os.path.join(self.file_dir, filename)
|
|
|
|
|
|
class GitDataResolver(FileDataResolver):
|
|
|
|
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"))
|
|
|
|
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)
|
|
|
|
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)
|
|
|
|
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))
|