|
| 1 | +from __future__ import print_function |
| 2 | +import re |
| 3 | +import os |
| 4 | +import sys |
| 5 | +import tempfile |
| 6 | +import subprocess |
| 7 | +import multiprocessing |
| 8 | +import multiprocessing.pool |
| 9 | + |
| 10 | +import dxpy |
| 11 | + |
| 12 | +def normalize_timedelta(timedelta): |
| 13 | + """ |
| 14 | + Given a string like "1w" or "5d", convert it to an integer in seconds. |
| 15 | + Integers without a suffix are interpreted as seconds. |
| 16 | + Note: not related to the datetime timedelta class. |
| 17 | + """ |
| 18 | + try: |
| 19 | + return int(timedelta) |
| 20 | + except ValueError as e: |
| 21 | + suffix_multipliers = {'s': 1, 'm': 60, 'h': 60*60, 'd': 60*60*24, 'w': 60*60*24*7, |
| 22 | + 'M': 60*60*24*30, 'y': 60*60*24*365} |
| 23 | + |
| 24 | + re_match = re.match('([0-9]+)([\s]*)([a-zA-Z]*)', timedelta) |
| 25 | + if re_match is None: |
| 26 | + msg = 'Could not parse time delta {0}'.format(timedelta) |
| 27 | + raise dxpy.AppInternalError(msg) |
| 28 | + |
| 29 | + t, space, suffix = re_match.groups() |
| 30 | + |
| 31 | + if suffix in suffix_multipliers: |
| 32 | + normalized_time = int(t) * suffix_multipliers[suffix] |
| 33 | + elif suffix not in suffix_multipliers and len(suffix) > 1 and suffix[0] in suffix_multipliers: |
| 34 | + old_suffix = suffix |
| 35 | + suffix = suffix[0] |
| 36 | + print('Not familiar with suffix {0}. Assuming you meant {1}.'.format(old_suffix, suffix), file=sys.stderr) |
| 37 | + normalized_time = int(t) * suffix_multipliers[suffix] |
| 38 | + else: |
| 39 | + msg = 'Valid suffixes for time duration are {0}.'.format(str(suffix_multipliers.keys())) |
| 40 | + raise dxpy.AppInternalError(msg) |
| 41 | + |
| 42 | + return normalized_time |
| 43 | + |
| 44 | + |
| 45 | +def _eap_wrapper(func, q, *args, **kwargs): |
| 46 | + try: |
| 47 | + result = func(*args, **kwargs) |
| 48 | + except Exception as e: |
| 49 | + q.put(e.__str__()) |
| 50 | + pass |
| 51 | + |
| 52 | + return result |
| 53 | + |
| 54 | + |
| 55 | +def get_project(project_name): |
| 56 | + '''Try to find the project with the given name or id.''' |
| 57 | + |
| 58 | + # First, see if the project is a project-id. |
| 59 | + try: |
| 60 | + project = dxpy.DXProject(project_name) |
| 61 | + return project |
| 62 | + except dxpy.DXError: |
| 63 | + pass |
| 64 | + |
| 65 | + project = dxpy.find_projects(name=project_name, name_mode='glob', return_handler=True, level="VIEW") |
| 66 | + project = [p for p in project] |
| 67 | + if len(project) < 1: |
| 68 | + print('Did not find project {0}.'.format(project_name), file=sys.stderr) |
| 69 | + sys.exit(1) |
| 70 | + elif len(project) > 1: |
| 71 | + print('Found more than 1 project matching {0}.'.format(project_name), file=sys.stderr) |
| 72 | + sys.exit(1) |
| 73 | + else: |
| 74 | + project = project[0] |
| 75 | + |
| 76 | + return project |
| 77 | + |
| 78 | + |
| 79 | +class ExceptionAwarePool(multiprocessing.pool.Pool): |
| 80 | + def __init__(self, *args, **kwargs): |
| 81 | + super(ExceptionAwarePool, self).__init__(*args, **kwargs) |
| 82 | + self.manager = multiprocessing.Manager() |
| 83 | + self.q = self.manager.Queue() |
| 84 | + |
| 85 | + def apply_async(self, func, args=(), kwds={}, callback=None): |
| 86 | + return super(ExceptionAwarePool, self).apply_async(_eap_wrapper, args=(func, self.q) + args, kwds=kwds, callback=callback) |
| 87 | + |
| 88 | + def join(self): |
| 89 | + super(ExceptionAwarePool, self).join() |
| 90 | + if self.q.qsize() > 0: |
| 91 | + raise Exception('\n'.join([self.q.get() for i in xrange(self.q.qsize())])) |
| 92 | + |
| 93 | + |
| 94 | +def get_memory(suffix='M'): |
| 95 | + if suffix == 'K': |
| 96 | + shift = 1 |
| 97 | + elif suffix == 'M': |
| 98 | + shift = 1 << 10 |
| 99 | + elif suffix == 'G': |
| 100 | + shift = 1 << 20 |
| 101 | + else: |
| 102 | + raise dxpy.DXError('Unknown memory suffix {0}. Please choose from K, M, or G.'.format(suffix)) |
| 103 | + |
| 104 | + # Calc amount of memory available for gatk and Picard. |
| 105 | + total_mem = re.findall('^MemTotal:[\s]*([0-9]*) kB', |
| 106 | + open('/proc/meminfo').read()) |
| 107 | + if(len(total_mem) != 1): |
| 108 | + raise dxpy.DXError('Problem reading system memory from /proc/meminfo') |
| 109 | + return float(total_mem[0]) / shift |
| 110 | + |
| 111 | + |
| 112 | +def run_cmd(cmd, returnOutput=False): |
| 113 | + if type(cmd) is list: |
| 114 | + shell=False |
| 115 | + executable = None |
| 116 | + print(subprocess.list2cmdline(cmd), file=sys.stderr) |
| 117 | + else: |
| 118 | + shell=True |
| 119 | + executable = '/bin/bash' |
| 120 | + print(cmd, file=sys.stderr) |
| 121 | + |
| 122 | + if returnOutput: |
| 123 | + output = subprocess.check_output(cmd, shell=shell, executable=executable).strip() |
| 124 | + print(output) |
| 125 | + return output |
| 126 | + else: |
| 127 | + subprocess.check_call(cmd, shell=shell, executable=executable) |
| 128 | + |
| 129 | + |
| 130 | +class cd: |
| 131 | + '''From: http://stackoverflow.com/questions/431684/how-do-i-cd-in-python |
| 132 | + Context manager for changing the current working directory''' |
| 133 | + def __init__(self, newPath=None, tempDir=None): |
| 134 | + if newPath is not None: |
| 135 | + self.newPath = newPath |
| 136 | + self.removeFolder = False |
| 137 | + else: |
| 138 | + self.newPath = tempfile.mkdtemp(dir=tempDir) |
| 139 | + self.removeFolder = True |
| 140 | + |
| 141 | + def __enter__(self): |
| 142 | + self.savedPath = os.getcwd() |
| 143 | + os.chdir(self.newPath) |
| 144 | + |
| 145 | + def __exit__(self, etype, value, traceback): |
| 146 | + os.chdir(self.savedPath) |
| 147 | + if self.removeFolder: |
| 148 | + subprocess.check_call('rm -rf {0}'.format(self.newPath), shell=True) |
| 149 | + |
| 150 | + |
| 151 | +def schedule_lpt(jobs, num_bins): |
| 152 | + '''This function implements the Longest Processing Time algorithm to get |
| 153 | + a good division of labor for the multiprocessor scheduling problem.''' |
| 154 | + |
| 155 | + def _index_min(values): |
| 156 | + # Efficient index of min from stackoverflow.com/questions/2474015 |
| 157 | + return min(xrange(len(values)), key=values.__getitem__) |
| 158 | + |
| 159 | + # We expect a list of tuples, with the first value the name of the |
| 160 | + # job and the second value the weight. If we are given a dict |
| 161 | + # then convert keys to job names and values to weights. |
| 162 | + if(type(jobs) == dict): |
| 163 | + jobs = zip(jobs.keys(), jobs.values()) |
| 164 | + |
| 165 | + num_bins = min(num_bins, len(jobs)) |
| 166 | + jobs.sort(key=lambda j: j[1], reverse=True) |
| 167 | + partition = {'groups': [[] for i in xrange(num_bins)], |
| 168 | + 'size': [0 for i in xrange(num_bins)]} |
| 169 | + |
| 170 | + for job in jobs: |
| 171 | + idx = _index_min(partition['size']) |
| 172 | + partition['groups'][idx] += [job[0]] |
| 173 | + partition['size'][idx] += job[1] |
| 174 | + |
| 175 | + return partition['groups'] |
| 176 | + |
| 177 | + |
| 178 | +def gzip_and_upload(fn, rfn=None): |
| 179 | + if rfn is None: |
| 180 | + rfn = os.path.split(fn)[-1] |
| 181 | + cmd = 'gzip --fast -c {0} | dx upload --brief --path {1}.gz -'.format(fn, rfn) |
| 182 | + print(cmd) |
| 183 | + fid = subprocess.check_output(cmd, shell=True).strip() |
| 184 | + |
| 185 | + return dxpy.dxlink(fid) |
| 186 | + |
| 187 | + |
| 188 | +def tar_files_and_upload(filenames, prefix): |
| 189 | + with tempfile.NamedTemporaryFile(delete=False) as fh: |
| 190 | + fh.write('\n'.join(filenames)) |
| 191 | + |
| 192 | + ofn = '{0}.tar.gz'.format(prefix) |
| 193 | + cmd = 'tar cvf - --files-from {0} | gzip --fast | dx upload --brief --destination "{1}" - '.format(fh.name, ofn) |
| 194 | + fid = run_cmd(cmd, returnOutput=True) |
| 195 | + cmd = ['rm', fh.name] |
| 196 | + run_cmd(cmd) |
| 197 | + |
| 198 | + return dxpy.dxlink(fid) |
| 199 | + |
| 200 | +def remove_special_chars(string): |
| 201 | + '''function that replaces any characters in a string that are not |
| 202 | + alphanumeric or _ or . so that they do not cause issues in commands''' |
| 203 | + string = "".join( |
| 204 | + char for char in string if char.isalnum() or char in ['_', '.']) |
| 205 | + |
| 206 | + return string |
| 207 | + |
| 208 | +def download_and_gunzip_file(input_file, skip_decompress=False, additional_pipe=None, create_named_pipe=False, input_filename=None): |
| 209 | + input_file = dxpy.DXFile(input_file) |
| 210 | + if input_filename is None: |
| 211 | + input_filename = input_file.describe()['name'] |
| 212 | + ofn = remove_special_chars(input_filename) |
| 213 | + |
| 214 | + cmd = 'dx download ' + input_file.get_id() + ' -o - ' |
| 215 | + if input_filename.endswith('.tar.gz'): |
| 216 | + ofn = 'tar_output_{0}'.format(ofn.replace('.tar.gz', '')) |
| 217 | + cmd += '| tar -zxvf - ' |
| 218 | + elif input_filename.endswith('.tar.bz2'): |
| 219 | + ofn = 'tar_output_{0}'.format(ofn.replace('.tar.bz2', '')) |
| 220 | + cmd += '| tar -jxvf - ' |
| 221 | + elif input_filename.endswith('.tar'): |
| 222 | + ofn = 'tar_output_{0}'.format(ofn.replace('.tar', '')) |
| 223 | + cmd += '| tar -xvf - ' |
| 224 | + elif (os.path.splitext(input_filename)[-1] == '.gz') and not skip_decompress: |
| 225 | + cmd += '| gunzip ' |
| 226 | + ofn = os.path.splitext(ofn)[0] |
| 227 | + if additional_pipe is not None: |
| 228 | + cmd += '| ' + additional_pipe |
| 229 | + cmd += ' > "{0}"'.format(ofn) |
| 230 | + |
| 231 | + if create_named_pipe: |
| 232 | + named_pipe_cmd = 'mkfifo {0}'.format(ofn) |
| 233 | + run_cmd(named_pipe_cmd) |
| 234 | + cmd += '&' |
| 235 | + |
| 236 | + run_cmd(cmd) |
| 237 | + |
| 238 | + return ofn |
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