Mercurial > repos > gga > apollo_delete_organism
view fetch_organism_jbrowse.py @ 2:720f372226eb draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 33ce5bd0cce35a12725b9ef9aed0683f3c41fbf9
author | gga |
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date | Wed, 20 Sep 2017 09:09:05 -0400 |
parents | dc738069b5ac |
children | 0af4179e6758 |
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#!/usr/bin/env python from __future__ import print_function import argparse import filecmp import logging import os import subprocess import sys import time from webapollo import GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) def are_dir_trees_equal(dir1, dir2): """ Compare two directories recursively. Files in each directory are assumed to be equal if their names and contents are equal. @param dir1: First directory path @param dir2: Second directory path @return: True if the directory trees are the same and there were no errors while accessing the directories or files, False otherwise. # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395 """ dirs_cmp = filecmp.dircmp(dir1, dir2) if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \ len(dirs_cmp.funny_files) > 0: print(('LEFT', dirs_cmp.left_only)) print(('RIGHT', dirs_cmp.right_only)) print(('FUNNY', dirs_cmp.funny_files)) return False (_, mismatch, errors) = filecmp.cmpfiles( dir1, dir2, dirs_cmp.common_files, shallow=False) if len(mismatch) > 0 or len(errors) > 0: print(mismatch) print(errors) return False for common_dir in dirs_cmp.common_dirs: new_dir1 = os.path.join(dir1, common_dir) new_dir2 = os.path.join(dir2, common_dir) if not are_dir_trees_equal(new_dir1, new_dir2): return False return True if __name__ == '__main__': parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') WAAuth(parser) OrgOrGuess(parser) parser.add_argument('target_dir', help='Target directory') args = parser.parse_args() wa = WebApolloInstance(args.apollo, args.username, args.password) # User must have an account org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] org = wa.organisms.findOrganismByCn(org_cn) if not os.path.exists(args.target_dir): os.makedirs(args.target_dir) if not os.path.exists(os.path.join(org['directory'], 'seq')): sys.stderr.write("Missing seq directory BEFORE copy") sys.exit(1) cmd = [ 'rsync', '-avr', org['directory'].rstrip('/') + '/', os.path.join(args.target_dir, 'data', '') ] # We run this OBSESSIVELY because my org had a hiccup where the origin # (silent) cp -R failed at one point. This caused MANY HEADACHES. # # Our response is to run this 3 times (in case the issue is temporary), # with delays in between. And ensure that we have the correct number of # files / folders before and after. sys.stderr.write(' '.join(cmd)) sys.stderr.write('\n') sys.stderr.write(subprocess.check_output(cmd)) if not are_dir_trees_equal( os.path.join(org['directory'].rstrip('/')), os.path.join(args.target_dir, 'data') ): # Not good time.sleep(5) sys.stderr.write('\n') sys.stderr.write(' '.join(cmd)) sys.stderr.write('\n') sys.stderr.write(subprocess.check_output(cmd)) if not are_dir_trees_equal( os.path.join(org['directory'].rstrip('/'), 'data'), os.path.join(args.target_dir, 'data') ): time.sleep(5) sys.stderr.write('\n') sys.stderr.write(' '.join(cmd)) sys.stderr.write('\n') sys.stderr.write(subprocess.check_output(cmd)) if not are_dir_trees_equal( os.path.join(org['directory'].rstrip('/'), 'data'), os.path.join(args.target_dir, 'data') ): sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.') sys.exit(2)