def test_copy(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
local_file = 'biomaj_tests.py'
files_to_copy = [ {'root': from_dir, 'name': local_file}]
to_dir = self.utils.data_dir
Utils.copy_files(files_to_copy, to_dir)
self.assertTrue(os.path.exists(to_dir+'/biomaj_tests.py'))
def test_copy(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
local_file = "biomaj_tests.py"
files_to_copy = [{"root": from_dir, "name": local_file}]
to_dir = self.utils.data_dir
Utils.copy_files(files_to_copy, to_dir)
self.assertTrue(os.path.exists(to_dir + "/biomaj_tests.py"))
def test_uncompress(self):
from_file = {"root": os.path.dirname(os.path.realpath(__file__)), "name": "bank/test.fasta.gz"}
to_dir = self.utils.data_dir
Utils.copy_files([from_file], to_dir)
Utils.uncompress(os.path.join(to_dir, from_file["name"]))
self.assertTrue(os.path.exists(to_dir + "/bank/test.fasta"))
def test_copy(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
local_file = 'biomaj_tests.py'
files_to_copy = [{'root': from_dir, 'name': local_file}]
to_dir = self.utils.data_dir
Utils.copy_files(files_to_copy, to_dir)
self.assertTrue(os.path.exists(to_dir + '/biomaj_tests.py'))
def test_uncompress(self):
from_file = { 'root': os.path.dirname(os.path.realpath(__file__)),
'name': 'bank/test.fasta.gz'
}
to_dir = self.utils.data_dir
Utils.copy_files([from_file], to_dir)
Utils.uncompress(os.path.join(to_dir, from_file['name']))
self.assertTrue(os.path.exists(to_dir+'/bank/test.fasta'))
def test_uncompress(self):
from_file = {
'root': os.path.dirname(os.path.realpath(__file__)),
'name': 'bank/test.fasta.gz'
}
to_dir = self.utils.data_dir
Utils.copy_files([from_file], to_dir)
Utils.uncompress(os.path.join(to_dir, from_file['name']))
self.assertTrue(os.path.exists(to_dir + '/bank/test.fasta'))
def wf_uncompress(self):
'''
Uncompress files if archives and no.extract = false
'''
logging.info('Workflow:wf_uncompress')
no_extract = self.session.config.get('no.extract')
if no_extract is None or no_extract == 'false':
for file in self.downloaded_files:
if 'save_as' not in file:
file['save_as'] = file['name']
Utils.uncompress(self.session.get_offline_directory() + '/' + file['save_as'])
return True
def download(self, local_dir):
'''
Copy local files to local_dir
:param local_dir: Directory where files should be copied
:type local_dir: str
:return: list of downloaded files
'''
logging.debug('Local:Download')
Utils.copy_files(self.files_to_download, local_dir, lock=self.mkdir_lock)
return self.files_to_download
def download(self, local_dir):
'''
Copy local files to local_dir
:param local_dir: Directory where files should be copied
:type local_dir: str
:return: list of downloaded files
'''
logging.debug('Local:Download')
Utils.copy_files(self.files_to_download,
local_dir,
lock=self.mkdir_lock)
return self.files_to_download
def test_get_more_recent_file(self):
files = [{
'name': '/test1',
'year': '2013',
'month': '11',
'day': '10',
'size': 10
}, {
'name': '/test2',
'year': '2013',
'month': '11',
'day': '12',
'size': 10
}, {
'name': '/test/test1',
'year': '1988',
'month': '11',
'day': '10',
'size': 10
}, {
'name': '/test/test11',
'year': '2013',
'month': '9',
'day': '23',
'size': 10
}]
release = Utils.get_more_recent_file(files)
self.assertTrue(release['year'] == '2013')
self.assertTrue(release['month'] == '11')
self.assertTrue(release['day'] == '12')
def test_get_more_recent_file(self):
files = [
{"name": "/test1", "year": "2013", "month": "11", "day": "10", "size": 10},
{"name": "/test2", "year": "2013", "month": "11", "day": "12", "size": 10},
{"name": "/test/test1", "year": "1988", "month": "11", "day": "10", "size": 10},
{"name": "/test/test11", "year": "2013", "month": "9", "day": "23", "size": 10},
]
release = Utils.get_more_recent_file(files)
self.assertTrue(release["year"] == "2013")
self.assertTrue(release["month"] == "11")
self.assertTrue(release["day"] == "12")
def test_get_more_recent_file(self):
files = [
{'name':'/test1', 'year': '2013', 'month': '11', 'day': '10', 'size': 10},
{'name':'/test2', 'year': '2013', 'month': '11', 'day': '12', 'size': 10},
{'name':'/test/test1', 'year': '1988', 'month': '11', 'day': '10', 'size': 10},
{'name':'/test/test11', 'year': '2013', 'month': '9', 'day': '23', 'size': 10}
]
release = Utils.get_more_recent_file(files)
self.assertTrue(release['year']=='2013')
self.assertTrue(release['month']=='11')
self.assertTrue(release['day']=='12')
def wf_stats(self):
'''
Get some stats from current release data dir
'''
logging.info('Workflow:wf_stats')
do_stats = self.bank.config.get('data.stats')
if do_stats is None or do_stats == '0':
self.session.set('fullsize', 0)
return True
prod_dir = self.session.get_full_release_directory()
dir_size = Utils.get_folder_size(prod_dir)
self.session.set('fullsize', dir_size)
return True
def wf_stats(self):
"""
Get some stats from current release data dir
"""
logging.info("Workflow:wf_stats")
do_stats = self.bank.config.get("data.stats")
if do_stats is None or do_stats == "0":
self.session.set("fullsize", 0)
return True
prod_dir = self.session.get_full_release_directory()
dir_size = Utils.get_folder_size(prod_dir)
self.session.set("fullsize", dir_size)
return True
def wf_copy(self):
'''
Copy files from offline directory to release directory
'''
logging.info('Workflow:wf_copy')
from_dir = os.path.join(self.session.config.get('data.dir'),
self.session.config.get('offline.dir.name'))
regexp = self.session.config.get('local.files').split()
to_dir = os.path.join(self.session.config.get('data.dir'),
self.session.config.get('dir.version'),
self.session.get_release_directory(), 'flat')
local_files = Utils.copy_files_with_regexp(from_dir,to_dir,regexp, True)
self.session._session['files'] = local_files
if len(self.session._session['files']) == 0:
logging.error('Workflow:wf_copy:No file match in offline dir')
return False
return True
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-s',
'--scan',
dest="directory",
help="Directory to scan")
parser.add_argument('--type', dest="ftype", help="Files type")
parser.add_argument(
'--tags',
dest="tags",
action="append",
default=[],
help="tags, format key:value, can be repeated multiple times")
args = parser.parse_args()
if not os.path.exists(args.directory):
sys.exit(1)
res = {}
for (path, dirs, files) in os.walk(args.directory):
for file in files:
filename = os.path.join(path, file)
(file_format, mime) = Utils.detect_format(filename)
if file_format is not None:
file_format = file_format.replace('application/', '')
filename = filename.replace(args.directory + '/', '')
if file_format is not None:
if file_format not in res:
res[file_format] = [filename]
else:
res[file_format].append(filename)
f_type = ''
if args.ftype:
f_type = args.ftype
tags = ''
if args.tags:
tags = ','.join(args.tags)
for fformat in res.keys():
print '##BIOMAJ#' + fformat + '#' + f_type + '#' + tags + '#' + ','.join(
res[fformat])
def wf_copy(self):
"""
Copy files from offline directory to release directory
"""
logging.info("Workflow:wf_copy")
from_dir = os.path.join(self.session.config.get("data.dir"), self.session.config.get("offline.dir.name"))
regexp = self.session.config.get("local.files").split()
to_dir = os.path.join(
self.session.config.get("data.dir"),
self.session.config.get("dir.version"),
self.session.get_release_directory(),
"flat",
)
local_files = Utils.copy_files_with_regexp(from_dir, to_dir, regexp, True)
self.session._session["files"] = local_files
if len(self.session._session["files"]) == 0:
logging.error("Workflow:wf_copy:No file match in offline dir")
return False
return True
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-s", "--scan", dest="directory", help="Directory to scan")
parser.add_argument("--type", dest="ftype", help="Files type")
parser.add_argument(
"--tags",
dest="tags",
action="append",
default=[],
help="tags, format key:value, can be repeated multiple times",
)
args = parser.parse_args()
if not os.path.exists(args.directory):
sys.exit(1)
res = {}
for (path, dirs, files) in os.walk(args.directory):
for file in files:
filename = os.path.join(path, file)
(file_format, mime) = Utils.detect_format(filename)
if file_format is not None:
file_format = file_format.replace("application/", "")
filename = filename.replace(args.directory + "/", "")
if file_format is not None:
if file_format not in res:
res[file_format] = [filename]
else:
res[file_format].append(filename)
f_type = ""
if args.ftype:
f_type = args.ftype
tags = ""
if args.tags:
tags = ",".join(args.tags)
for fformat in res.keys():
print "##BIOMAJ#" + fformat + "#" + f_type + "#" + tags + "#" + ",".join(res[fformat])
def wf_uncompress(self):
"""
Uncompress files if archives and no.extract = false
"""
logging.info("Workflow:wf_uncompress")
no_extract = self.session.config.get("no.extract")
if no_extract is None or no_extract == "false":
for file in self.downloaded_files:
if "save_as" not in file:
file["save_as"] = file["name"]
nb_try = 1
not_ok = True
while nb_try < 3 and not_ok:
status = Utils.uncompress(self.session.get_offline_directory() + "/" + file["save_as"])
if status:
not_ok = False
else:
logging.warn("Workflow:wf_uncompress:Failure:" + file["name"] + ":" + str(nb_try))
nb_try += 1
if not_ok:
logging.error("Workflow:wf_uncompress:Failure:" + file["name"])
return False
return True
def test_mimes(self):
fasta_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),'bank/test2.fasta')
(mime, encoding) = Utils.detect_format(fasta_file)
self.assertTrue('application/fasta' == mime)
def test_mimes(self):
fasta_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'bank/test2.fasta')
(mime, encoding) = Utils.detect_format(fasta_file)
self.assertTrue('application/fasta' == mime)
def list(self, directory=''):
'''
List FTP directory
:return: tuple of file and dirs in current directory with details
'''
logging.debug('Download:List:' + self.url + self.rootdir + directory)
#self.crl.setopt(pycurl.URL, self.url+self.rootdir+directory)
try:
self.crl.setopt(pycurl.URL, self.url + self.rootdir + directory)
except Exception as a:
self.crl.setopt(pycurl.URL,
(self.url + self.rootdir + directory).encode(
'ascii', 'ignore'))
if self.proxy is not None:
self.crl.setopt(pycurl.PROXY, self.proxy)
if self.proxy_auth is not None:
self.crl.setopt(pycurl.PROXYUSERPWD, self.proxy_auth)
if self.credentials is not None:
self.crl.setopt(pycurl.USERPWD, self.credentials)
output = BytesIO()
# lets assign this buffer to pycurl object
self.crl.setopt(pycurl.WRITEFUNCTION, output.write)
self.crl.setopt(pycurl.HEADERFUNCTION, self.header_function)
self.crl.setopt(pycurl.CONNECTTIMEOUT, 300)
# Download should not take more than 5minutes
self.crl.setopt(pycurl.TIMEOUT, self.timeout)
self.crl.setopt(pycurl.NOSIGNAL, 1)
try:
self.crl.perform()
except Exception as e:
logging.error('Could not get errcode:' + str(e))
# Figure out what encoding was sent with the response, if any.
# Check against lowercased header name.
encoding = None
if 'content-type' in self.headers:
content_type = self.headers['content-type'].lower()
match = re.search('charset=(\S+)', content_type)
if match:
encoding = match.group(1)
if encoding is None:
# Default encoding for HTML is iso-8859-1.
# Other content types may have different default encoding,
# or in case of binary data, may have no encoding at all.
encoding = 'iso-8859-1'
# lets get the output in a string
result = output.getvalue().decode(encoding)
# FTP LIST output is separated by \r\n
# lets split the output in lines
#lines = result.split(r'[\r\n]+')
lines = re.split(r'[\n\r]+', result)
# lets walk through each line
rfiles = []
rdirs = []
for line in lines:
rfile = {}
# lets print each part separately
parts = line.split()
# the individual fields in this list of parts
if not parts: continue
rfile['permissions'] = parts[0]
rfile['group'] = parts[2]
rfile['user'] = parts[3]
rfile['size'] = parts[4]
rfile['month'] = Utils.month_to_num(parts[5])
rfile['day'] = parts[6]
rfile['hash'] = hashlib.md5(line.encode('utf-8')).hexdigest()
try:
rfile['year'] = int(parts[7])
except Exception as e:
# specific ftp case issues at getting date info
curdate = datetime.now()
rfile['year'] = curdate.year
# Year not precised, month feater than current means previous year
if rfile['month'] > curdate.month:
rfile['year'] = curdate.year - 1
# Same month but later day => previous year
if rfile['month'] == curdate.month and int(
rfile['day']) > curdate.day:
rfile['year'] = curdate.year - 1
rfile['name'] = parts[8]
if len(parts) >= 10 and parts[9] == '->':
# Symlink, add to files AND dirs as we don't know the type of the link
rdirs.append(rfile)
is_dir = False
if re.match('^d', rfile['permissions']):
is_dir = True
if not is_dir:
rfiles.append(rfile)
else:
rdirs.append(rfile)
return (rfiles, rdirs)
def list(self, directory=''):
'''
Try to get file headers to get last_modification and size
'''
for file in self.files_to_download:
self.crl.setopt(pycurl.HEADER, True)
if self.credentials is not None:
self.crl.setopt(pycurl.USERPWD, self.credentials)
if self.proxy is not None:
self.crl.setopt(pycurl.PROXY, self.proxy)
if self.proxy_auth is not None:
curl.setopt(pycurl.PROXYUSERPWD, self.proxy_auth)
self.crl.setopt(pycurl.NOBODY, True)
try:
self.crl.setopt(pycurl.URL, self.url+self.rootdir+file['name'])
except Exception as a:
self.crl.setopt(pycurl.URL, (self.url+self.rootdir+file['name']).encode('ascii','ignore'))
#self.crl.setopt(pycurl.URL, self.url+self.rootdir+file['name'])
output = BytesIO()
# lets assign this buffer to pycurl object
self.crl.setopt(pycurl.WRITEFUNCTION, output.write)
self.crl.setopt(pycurl.HEADERFUNCTION, self.header_function)
self.crl.perform()
# Figure out what encoding was sent with the response, if any.
# Check against lowercased header name.
encoding = None
if 'content-type' in self.headers:
content_type = self.headers['content-type'].lower()
match = re.search('charset=(\S+)', content_type)
if match:
encoding = match.group(1)
if encoding is None:
# Default encoding for HTML is iso-8859-1.
# Other content types may have different default encoding,
# or in case of binary data, may have no encoding at all.
encoding = 'iso-8859-1'
# lets get the output in a string
result = output.getvalue().decode(encoding)
lines = re.split(r'[\n\r]+', result)
for line in lines:
parts = line.split(':')
if parts[0].strip() == 'Content-Length':
file['size'] = parts[1].strip()
if parts[0].strip() == 'Last-Modified':
# Sun, 06 Nov 1994
res = re.match('(\w+),\s+(\d+)\s+(\w+)\s+(\d+)', parts[1].strip())
if res:
file['day'] = res.group(2)
file['month'] = Utils.month_to_num(res.group(3))
file['year'] = res.group(4)
continue
#Sunday, 06-Nov-94
res = re.match('(\w+),\s+(\d+)-(\w+)-(\d+)', parts[1].strip())
if res:
file['day'] = res.group(2)
file['month'] = Utils.month_to_num(res.group(3))
file['year'] = str(2000 + int(res.group(4)))
continue
#Sun Nov 6 08:49:37 1994
res = re.match('(\w+)\s+(\w+)\s+(\d+)\s+\d{2}:\d{2}:\d{2}\s+(\d+)', parts[1].strip())
if res:
file['day'] = res.group(3)
file['month'] = Utils.month_to_num(res.group(2))
file['year'] = res.group(4)
continue
return (self.files_to_download,[])
def test_copy_with_regexp(self): from_dir = os.path.dirname(os.path.realpath(__file__)) to_dir = self.utils.data_dir Utils.copy_files_with_regexp(from_dir, to_dir, ['.*\.py']) self.assertTrue(os.path.exists(to_dir+'/biomaj_tests.py'))
def test_copy_with_regexp(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
to_dir = self.utils.data_dir
Utils.copy_files_with_regexp(from_dir, to_dir, ['.*\.py'])
self.assertTrue(os.path.exists(to_dir + '/biomaj_tests.py'))
def list(self, directory=''):
'''
List FTP directory
:return: tuple of file and dirs in current directory with details
'''
logging.debug('Download:List:'+self.url+self.rootdir+directory)
#self.crl.setopt(pycurl.URL, self.url+self.rootdir+directory)
try:
self.crl.setopt(pycurl.URL, self.url+self.rootdir+directory)
except Exception as a:
self.crl.setopt(pycurl.URL, (self.url+self.rootdir+directory).encode('ascii','ignore'))
if self.proxy is not None:
self.crl.setopt(pycurl.PROXY, self.proxy)
if self.proxy_auth is not None:
curl.setopt(pycurl.PROXYUSERPWD, self.proxy_auth)
if self.credentials is not None:
self.crl.setopt(pycurl.USERPWD, self.credentials)
output = BytesIO()
# lets assign this buffer to pycurl object
self.crl.setopt(pycurl.WRITEFUNCTION, output.write)
self.crl.setopt(pycurl.HEADERFUNCTION, self.header_function)
self.crl.perform()
# Figure out what encoding was sent with the response, if any.
# Check against lowercased header name.
encoding = None
if 'content-type' in self.headers:
content_type = self.headers['content-type'].lower()
match = re.search('charset=(\S+)', content_type)
if match:
encoding = match.group(1)
if encoding is None:
# Default encoding for HTML is iso-8859-1.
# Other content types may have different default encoding,
# or in case of binary data, may have no encoding at all.
encoding = 'iso-8859-1'
# lets get the output in a string
result = output.getvalue().decode(encoding)
'''
'http.parse.dir.line': r'<a[\s]+href="([\S]+)/".*alt="\[DIR\]">.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})',
'http.parse.file.line': r'<a[\s]+href="([\S]+)".*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})[\s]+([\d\.]+[MKG]{0,1})',
'http.group.dir.name': 1,
'http.group.dir.date': 2,
'http.group.file.name': 1,
'http.group.file.date': 2,
'http.group.file.size': 3,
'''
rfiles = []
rdirs = []
dirs = re.findall(self.config.get('http.parse.dir.line'), result)
if dirs is not None and len(dirs)>0:
for dir in dirs:
rfile = {}
rfile['permissions'] = ''
rfile['group'] = ''
rfile['user'] = ''
rfile['size'] = '0'
date = dir[int(self.config.get('http.group.dir.date'))-1]
dirdate = date.split()
parts = dirdate[0].split('-')
#19-Jul-2014 13:02
rfile['month'] = Utils.month_to_num(parts[1])
rfile['day'] = parts[0]
rfile['year'] = parts[2]
rfile['name'] = dir[int(self.config.get('http.group.dir.name'))-1]
rdirs.append(rfile)
files = re.findall(self.config.get('http.parse.file.line'), result)
if files is not None and len(files)>0:
for file in files:
rfile = {}
rfile['permissions'] = ''
rfile['group'] = ''
rfile['user'] = ''
rfile['size'] = file[int(self.config.get('http.group.file.size'))-1]
date = file[int(self.config.get('http.group.file.date'))-1]
dirdate = date.split()
parts = dirdate[0].split('-')
#19-Jul-2014 13:02
rfile['month'] = Utils.month_to_num(parts[1])
rfile['day'] = parts[0]
rfile['year'] = parts[2]
rfile['name'] = file[int(self.config.get('http.group.file.name'))-1]
rfiles.append(rfile)
return (rfiles, rdirs)
def list(self, directory=''):
'''
List FTP directory
:return: tuple of file and dirs in current directory with details
'''
logging.debug('Download:List:'+self.url+self.rootdir+directory)
#self.crl.setopt(pycurl.URL, self.url+self.rootdir+directory)
try:
self.crl.setopt(pycurl.URL, self.url+self.rootdir+directory)
except Exception as a:
self.crl.setopt(pycurl.URL, (self.url+self.rootdir+directory).encode('ascii', 'ignore'))
if self.proxy is not None:
self.crl.setopt(pycurl.PROXY, self.proxy)
if self.proxy_auth is not None:
self.crl.setopt(pycurl.PROXYUSERPWD, self.proxy_auth)
if self.credentials is not None:
self.crl.setopt(pycurl.USERPWD, self.credentials)
output = BytesIO()
# lets assign this buffer to pycurl object
self.crl.setopt(pycurl.WRITEFUNCTION, output.write)
self.crl.setopt(pycurl.HEADERFUNCTION, self.header_function)
self.crl.perform()
# Figure out what encoding was sent with the response, if any.
# Check against lowercased header name.
encoding = None
if 'content-type' in self.headers:
content_type = self.headers['content-type'].lower()
match = re.search('charset=(\S+)', content_type)
if match:
encoding = match.group(1)
if encoding is None:
# Default encoding for HTML is iso-8859-1.
# Other content types may have different default encoding,
# or in case of binary data, may have no encoding at all.
encoding = 'iso-8859-1'
# lets get the output in a string
result = output.getvalue().decode(encoding)
# FTP LIST output is separated by \r\n
# lets split the output in lines
#lines = result.split(r'[\r\n]+')
lines = re.split(r'[\n\r]+', result)
# lets walk through each line
rfiles = []
rdirs = []
for line in lines:
rfile = {}
# lets print each part separately
parts = line.split()
# the individual fields in this list of parts
if not parts: continue
rfile['permissions'] = parts[0]
rfile['group'] = parts[2]
rfile['user'] = parts[3]
rfile['size'] = parts[4]
rfile['month'] = Utils.month_to_num(parts[5])
rfile['day'] = parts[6]
try:
rfile['year'] = int(parts[7])
except Exception as e:
# specific ftp case issues at getting date info
curdate = datetime.now()
rfile['year'] = curdate.year
# Year not precised, month feater than current means previous year
if rfile['month'] > curdate.month:
rfile['year'] = curdate.year - 1
# Same month but later day => previous year
if rfile['month'] == curdate.month and int(rfile['day']) > curdate.day:
rfile['year'] = curdate.year - 1
rfile['name'] = parts[8]
if len(parts) >= 10 and parts[9] == '->':
# Symlink, add to files AND dirs as we don't know the type of the link
rdirs.append(rfile)
is_dir = False
if re.match('^d', rfile['permissions']):
is_dir = True
if not is_dir:
rfiles.append(rfile)
else:
rdirs.append(rfile)
return (rfiles, rdirs)
def wf_download(self):
"""
Download remote files or use an available local copy from last production directory if possible.
"""
logging.info("Workflow:wf_download")
flow = self.get_flow(Workflow.FLOW_DOWNLOAD)
downloader = None
cf = self.session.config
self.session.previous_release = self.session.get("previous_release")
if cf.get("protocol") == "multi":
"""
Search for:
protocol = multi
remote.file.0.protocol = directftp
remote.file.0.server = ftp.ncbi.org
remote.file.0.path = /musmusculus/chr1/chr1.fa
=> http://ftp2.fr.debian.org/debian/README.html?key1=value&key2=value2
remote.file.1.protocol = directhttp
remote.file.1.server = ftp2.fr.debian.org
remote.file.1.path = debian/README.html
remote.file.1.method = GET
remote.file.1.params.keys = key1,key2
remote.file.1.params.key1 = value1
remote.file.1.params.key2 = value2
=> http://ftp2.fr.debian.org/debian/README.html
#POST PARAMS:
key1=value
key2=value2
remote.file.1.protocol = directhttp
remote.file.1.server = ftp2.fr.debian.org
remote.file.1.path = debian/README.html
remote.file.1.method = POST
remote.file.1.params.keys = key1,key2
remote.file.1.params.key1 = value1
remote.file.1.params.key2 = value2
......
"""
downloader = MultiDownload()
downloaders = []
# Creates multiple downloaders
i = 0
rfile = cf.get("remote.file." + str(i) + ".path")
while rfile is not None:
if cf.get("remote.file." + str(i) + ".protocol") is not None:
protocol = cf.get("remote.file." + str(i) + ".protocol")
else:
protocol = cf.get("protocol")
if cf.get("remote.file." + str(i) + ".server") is not None:
server = cf.get("remote.file." + str(i) + ".server")
else:
server = cf.get("server")
subdownloader = self.get_handler(protocol, server, "", [cf.get("remote.file." + str(i) + ".path")])
if cf.get("remote.file." + str(i) + ".credentials") is not None:
credentials = cf.get("remote.file." + str(i) + ".credentials")
else:
credentials = cf.get("server.credentials")
if credentials is not None:
subdownloader.set_credentials(credentials)
if protocol == "directhttp":
subdownloader.method = cf.get("remote.file." + str(i) + ".method")
if subdownloader.method is None:
subdownloader.method = "GET"
if cf.get("remote.file." + str(i) + ".name"):
subdownloader.save_as = cf.get("remote.file." + str(i) + ".name")
else:
subdownloader.save_as = cf.get("remote.file." + str(i) + ".path")
if cf.get("remote.file." + str(i) + ".method"):
subdownloader.method = cf.get("remote.file." + str(i) + ".method").strip().upper()
subdownloader.params = {}
keys = cf.get("remote.file." + str(i) + ".params.keys")
if keys is not None:
keys = keys.split(",")
for key in keys:
param = cf.get("remote.file." + str(i) + ".params." + key.strip())
subdownloader.param[key.strip()] = param.strip()
downloaders.append(subdownloader)
i += 1
rfile = cf.get("remote.file." + str(i) + ".path")
downloader.add_downloaders(downloaders)
else:
"""
Simple case, one downloader with regexp
"""
protocol = cf.get("protocol")
if protocol == "directhttp" or protocol == "directftp":
downloader = self.get_handler(cf.get("protocol"), cf.get("server"), "/", [cf.get("remote.dir")[:-1]])
downloader.method = cf.get("url.method")
if downloader.method is None:
downloader.method = "GET"
downloader.save_as = cf.get("target.name")
keys = cf.get("url.params")
if keys is not None:
keys = keys.split(",")
for key in keys:
param = cf.get(key.strip() + ".value")
downloader.param[key.strip()] = param.strip()
else:
downloader = self.get_handler(cf.get("protocol"), cf.get("server"), cf.get("remote.dir"))
if downloader is None:
logging.error("Protocol " + cf.get("protocol") + " not supported")
return False
(file_list, dir_list) = downloader.list()
downloader.match(cf.get("remote.files").split(), file_list, dir_list)
for f in downloader.files_to_download:
f["save_as"] = f["name"]
for p in cf.get("remote.files").split():
res = re.match("/" + p, f["name"])
if res is not None and res.groups() is not None and len(res.groups()) >= 1:
f["save_as"] = "/".join(res.groups())
break
self.session.set("download_files", downloader.files_to_download)
if self.session.get("release") is None:
# Not defined, or could not get it ealier
# Set release to most recent file to download
release_dict = Utils.get_more_recent_file(downloader.files_to_download)
if release_dict is None:
today = datetime.datetime.now()
release_dict = {"year": today.year, "month": today.month, "day": today.day}
release = str(release_dict["year"]) + "-" + str(release_dict["month"]) + "-" + str(release_dict["day"])
self.session.set("release", release)
self.session.set("remoterelease", release)
# We restart from scratch, check if directory with this release already exists
if self.options.get_option(Options.FROMSCRATCH):
index = 0
# Release directory exits, set index to 1
if os.path.exists(self.session.get_full_release_directory()):
index = 1
for x in range(1, 100):
if os.path.exists(self.session.get_full_release_directory() + "__" + str(x)):
index = x + 1
# while os.path.exists(self.session.get_full_release_directory()+'__'+str(index)):
# index += 1
# If we found a directory for this release: XX or XX__Y
if index > 0:
self.session.set("release", release + "__" + str(index))
release = release + "__" + str(index)
logging.info("Workflow:wf_download:release:remoterelease:" + self.session.get("remoterelease"))
logging.info("Workflow:wf_download:release:release:" + release)
MongoConnector.banks.update({"name": self.bank.name}, {"$set": {"status.release.progress": str(release)}})
self.download_go_ahead = False
if self.options.get_option(Options.FROM_TASK) == "download":
# We want to download again in same release, that's fine, we do not care it is the same release
self.download_go_ahead = True
if not self.download_go_ahead and self.session.previous_release == self.session.get("remoterelease"):
logging.info("Workflow:wf_release:same_as_previous_session")
return self.no_need_to_update()
self.banks = MongoConnector.banks
self.bank.bank = self.banks.find_one({"name": self.name})
nb_prod_dir = len(self.bank.bank["production"])
offline_dir = self.session.get_offline_directory()
copied_files = []
# Check if already in offlinedir
keep_files = []
if os.path.exists(offline_dir):
for file_to_download in downloader.files_to_download:
# If file is in offline dir and has same date and size, do not download again
if os.path.exists(offline_dir + "/" + file_to_download["name"]):
try:
file_stat = os.stat(offline_dir + "/" + file_to_download["name"])
f_stat = datetime.datetime.fromtimestamp(
os.path.getmtime(offline_dir + "/" + file_to_download["name"])
)
year = str(f_stat.year)
month = str(f_stat.month)
day = str(f_stat.day)
if (
str(file_stat.st_size) != str(file_to_download["size"])
or str(year) != str(file_to_download["year"])
or str(month) != str(file_to_download["month"])
or str(day) != str(file_to_download["day"])
):
logging.debug("Workflow:wf_download:different_from_offline:" + file_to_download["name"])
keep_files.append(file_to_download)
else:
logging.debug("Workflow:wf_download:offline:" + file_to_download["name"])
except Exception as e:
# Could not get stats on file
os.remove(offline_dir + "/" + file_to_download["name"])
keep_files.append(file_to_download)
else:
keep_files.append(file_to_download)
downloader.files_to_download = keep_files
self.download_go_ahead = False
if self.options.get_option(Options.FROM_TASK) == "download":
# We want to download again in same release, that's fine, we do not care it is the same release
self.download_go_ahead = True
if not self.options.get_option(Options.FROMSCRATCH) and not self.download_go_ahead and nb_prod_dir > 0:
# for prod in self.bank.bank['production']:
# if self.session.get('release') == prod['release']:
# logging.info('Workflow:wf_release:same_as_previous_production_dir')
# return self.no_need_to_update()
# Get last production
last_production = self.bank.bank["production"][nb_prod_dir - 1]
# Get session corresponding to production directory
last_production_session = self.banks.find_one(
{"name": self.name, "sessions.id": last_production["session"]}, {"sessions.$": 1}
)
last_production_dir = os.path.join(
last_production["data_dir"], cf.get("dir.version"), last_production["release"]
)
# Checks if some files can be copied instead of downloaded
downloader.download_or_copy(last_production_session["sessions"][0]["files"], last_production_dir)
if len(downloader.files_to_download) == 0:
return self.no_need_to_update()
# release_dir = os.path.join(self.session.config.get('data.dir'),
# self.session.config.get('dir.version'),
# self.session.get_release_directory())
logging.debug("Workflow:wf_download:Copy files from " + last_production_dir)
copied_files = downloader.files_to_copy
Utils.copy_files(downloader.files_to_copy, offline_dir)
downloader.close()
DownloadThread.NB_THREAD = int(self.session.config.get("files.num.threads"))
if cf.get("protocol") == "multi":
thlist = DownloadThread.get_threads_multi(downloader.downloaders, offline_dir)
else:
thlist = DownloadThread.get_threads(downloader, offline_dir)
running_th = []
for th in thlist:
running_th.append(th)
th.start()
while len(running_th) > 0:
try:
# Join all threads using a timeout so it doesn't block
# Filter out threads which have been joined or are None
running_th = [t.join(1000) for t in running_th if t is not None and t.isAlive()]
logging.debug("Workflow:wf_download:Download:Threads:" + str(running_th))
except KeyboardInterrupt:
logging.warn("Ctrl-c received! Sending kill to threads...")
logging.warn("Running tasks will continue and process will stop.")
for t in running_th:
t.downloader.kill_received = True
logging.info("Workflow:wf_download:Download:Threads:Over")
# for th in thlist:
# th.join()
is_error = False
for th in thlist:
if th.error:
is_error = True
downloader.error = True
break
self.downloaded_files = downloader.files_to_download + copied_files
# self.downloaded_files = downloader.download(offline_dir) + copied_files
# downloader.close()
if downloader.error:
logging.error("An error occured during download")
return False
return True
def list(self, directory=''):
'''
List FTP directory
:return: tuple of file and dirs in current directory with details
'''
logging.debug('Download:List:' + self.url + self.rootdir + directory)
#self.crl.setopt(pycurl.URL, self.url+self.rootdir+directory)
try:
self.crl.setopt(pycurl.URL, self.url + self.rootdir + directory)
except Exception as a:
self.crl.setopt(pycurl.URL,
(self.url + self.rootdir + directory).encode(
'ascii', 'ignore'))
if self.proxy is not None:
self.crl.setopt(pycurl.PROXY, self.proxy)
if self.proxy_auth is not None:
self.crl.setopt(pycurl.PROXYUSERPWD, self.proxy_auth)
if self.credentials is not None:
self.crl.setopt(pycurl.USERPWD, self.credentials)
output = BytesIO()
# lets assign this buffer to pycurl object
self.crl.setopt(pycurl.WRITEFUNCTION, output.write)
self.crl.setopt(pycurl.HEADERFUNCTION, self.header_function)
self.crl.perform()
# Figure out what encoding was sent with the response, if any.
# Check against lowercased header name.
encoding = None
if 'content-type' in self.headers:
content_type = self.headers['content-type'].lower()
match = re.search('charset=(\S+)', content_type)
if match:
encoding = match.group(1)
if encoding is None:
# Default encoding for HTML is iso-8859-1.
# Other content types may have different default encoding,
# or in case of binary data, may have no encoding at all.
encoding = 'iso-8859-1'
# lets get the output in a string
result = output.getvalue().decode(encoding)
'''
'http.parse.dir.line': r'<a[\s]+href="([\S]+)/".*alt="\[DIR\]">.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})',
'http.parse.file.line': r'<a[\s]+href="([\S]+)".*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})[\s]+([\d\.]+[MKG]{0,1})',
'http.group.dir.name': 1,
'http.group.dir.date': 2,
'http.group.file.name': 1,
'http.group.file.date': 2,
'http.group.file.size': 3,
'''
rfiles = []
rdirs = []
dirs = re.findall(self.config.get('http.parse.dir.line'), result)
if dirs is not None and len(dirs) > 0:
for founddir in dirs:
rfile = {}
rfile['permissions'] = ''
rfile['group'] = ''
rfile['user'] = ''
rfile['size'] = '0'
date = founddir[int(self.config.get('http.group.dir.date')) -
1]
dirdate = date.split()
parts = dirdate[0].split('-')
#19-Jul-2014 13:02
rfile['month'] = Utils.month_to_num(parts[1])
rfile['day'] = parts[0]
rfile['year'] = parts[2]
rfile['name'] = founddir[
int(self.config.get('http.group.dir.name')) - 1]
rdirs.append(rfile)
files = re.findall(self.config.get('http.parse.file.line'), result)
if files is not None and len(files) > 0:
for foundfile in files:
rfile = {}
rfile['permissions'] = ''
rfile['group'] = ''
rfile['user'] = ''
rfile['size'] = foundfile[
int(self.config.get('http.group.file.size')) - 1]
date = foundfile[int(self.config.get('http.group.file.date')) -
1]
if self.config.get('http.parse.file.date.format'):
date_object = datetime.datetime.strptime(
date,
self.config.get('http.parse.file.date.format').replace(
'%%', '%'))
rfile['month'] = date_object.month
rfile['day'] = date_object.day
rfile['year'] = date_object.year
else:
dirdate = date.split()
parts = dirdate[0].split('-')
#19-Jul-2014 13:02
rfile['month'] = Utils.month_to_num(parts[1])
rfile['day'] = parts[0]
rfile['year'] = parts[2]
rfile['name'] = foundfile[
int(self.config.get('http.group.file.name')) - 1]
filehash = (rfile['name'] + str(date) +
str(rfile['size'])).encode('utf-8')
rfile['hash'] = hashlib.md5(filehash).hexdigest()
rfiles.append(rfile)
print("###OSALLOU " + str(rfile))
return (rfiles, rdirs)
def list(self, directory=''):
'''
Try to get file headers to get last_modification and size
'''
for file in self.files_to_download:
self.crl.setopt(pycurl.HEADER, True)
if self.credentials is not None:
self.crl.setopt(pycurl.USERPWD, self.credentials)
if self.proxy is not None:
self.crl.setopt(pycurl.PROXY, self.proxy)
if self.proxy_auth is not None:
self.crl.setopt(pycurl.PROXYUSERPWD, self.proxy_auth)
self.crl.setopt(pycurl.NOBODY, True)
try:
self.crl.setopt(pycurl.URL, self.url+self.rootdir+file['name'])
except Exception as a:
self.crl.setopt(pycurl.URL, (self.url+self.rootdir+file['name']).encode('ascii', 'ignore'))
#self.crl.setopt(pycurl.URL, self.url+self.rootdir+file['name'])
output = BytesIO()
# lets assign this buffer to pycurl object
self.crl.setopt(pycurl.WRITEFUNCTION, output.write)
self.crl.setopt(pycurl.HEADERFUNCTION, self.header_function)
self.crl.perform()
# Figure out what encoding was sent with the response, if any.
# Check against lowercased header name.
encoding = None
if 'content-type' in self.headers:
content_type = self.headers['content-type'].lower()
match = re.search('charset=(\S+)', content_type)
if match:
encoding = match.group(1)
if encoding is None:
# Default encoding for HTML is iso-8859-1.
# Other content types may have different default encoding,
# or in case of binary data, may have no encoding at all.
encoding = 'iso-8859-1'
# lets get the output in a string
result = output.getvalue().decode(encoding)
lines = re.split(r'[\n\r]+', result)
for line in lines:
parts = line.split(':')
if parts[0].strip() == 'Content-Length':
file['size'] = parts[1].strip()
if parts[0].strip() == 'Last-Modified':
# Sun, 06 Nov 1994
res = re.match('(\w+),\s+(\d+)\s+(\w+)\s+(\d+)', parts[1].strip())
if res:
file['hash'] = hashlib.md5(str(res.group(0)).encode('utf-8')).hexdigest()
file['day'] = res.group(2)
file['month'] = Utils.month_to_num(res.group(3))
file['year'] = res.group(4)
continue
#Sunday, 06-Nov-94
res = re.match('(\w+),\s+(\d+)-(\w+)-(\d+)', parts[1].strip())
if res:
file['hash'] = hashlib.md5(str(res.group(0)).encode('utf-8')).hexdigest()
file['day'] = res.group(2)
file['month'] = Utils.month_to_num(res.group(3))
file['year'] = str(2000 + int(res.group(4)))
continue
#Sun Nov 6 08:49:37 1994
res = re.match('(\w+)\s+(\w+)\s+(\d+)\s+\d{2}:\d{2}:\d{2}\s+(\d+)', parts[1].strip())
if res:
file['hash'] = hashlib.md5(str(res.group(0)).encode('utf-8')).hexdigest()
file['day'] = res.group(3)
file['month'] = Utils.month_to_num(res.group(2))
file['year'] = res.group(4)
continue
return (self.files_to_download, [])
