Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/galaxy/tool_util/verify/test_data.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
---|---|
date | Mon, 22 Mar 2021 18:12:50 +0000 |
parents | |
children |
line wrap: on
line source
import hashlib import os import re import subprocess from string import Template from galaxy.util import ( asbool, in_directory, smart_str ) 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(r"\s*,\s*") class TestDataResolver: def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ): if file_dirs is None: file_dirs = environ.get(env_var, None) if file_dirs is None: file_dirs = "test-data,https://github.com/galaxyproject/galaxy-test-data.git" if file_dirs: self.resolvers = [build_resolver(u, environ) for u in LIST_SEP.split(file_dirs)] else: self.resolvers = [] def get_filename(self, name): for resolver in self.resolvers or []: if not resolver.exists(name): continue filename = resolver.path(name) if filename: return os.path.abspath(filename) def get_filecontent(self, name): filename = self.get_filename(name=name) with open(filename, mode='rb') as f: return f.read() def get_directory(self, name): return self.get_filename(name=name) def build_resolver(uri, environ): if uri.startswith("http") and uri.endswith(".git"): return GitDataResolver(uri, environ) else: return FileDataResolver(uri) class FileDataResolver: def __init__(self, file_dir): self.file_dir = file_dir def exists(self, filename): path = os.path.abspath(self.path(filename)) return os.path.exists(path) and in_directory(path, self.file_dir) 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(smart_str(repository)) repo_path = os.path.join(repo_cache, m.hexdigest()) super().__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().exists(filename) if exists_now or not self.fetch_data or self.updated: return exists_now self.update_repository() return super().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(f"git clone '{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))