def __init__(self, url_list, brand_names=[]):
for i in url_list:
self.urls.append(check_url(i))
for i in brand_names:
self.brand_names.append(i)
user_agent = 'Mozilla/6.0 (compatible; MSIE 5.5; Windows NT)'
self.headers = { 'User-Agent' : user_agent }
self.log = get_file_logger('ju_report')
def __init__(self, url_list, brand_names=[]):
for i in url_list:
self.urls.append(check_url(i))
for i in brand_names:
self.brand_names.append(i)
user_agent = 'Mozilla/6.0 (compatible; MSIE 5.5; Windows NT)'
self.headers = {'User-Agent': user_agent}
self.log = get_file_logger('ju_report')
def main():
log = get_file_logger('ju_item_insert')
hostaddress = 'localhost'
database = 'ju_db'
user = MYSQL_USER
password = MYSQL_PASSWORD
db = torndb.Connection(hostaddress, database, user, password)
excel_handler = DealExcel(INPUT_FILE_PATH, 'Sheet1')
ju_brands = excel_handler.read_column_excel(1, 2)
ju_urls = excel_handler.read_column_excel(2, 2)
ju_pages = GetPageData(ju_urls, ju_brands)
result = []
for i, j in zip(ju_urls, ju_brands):
result.append(ju_pages.get_page(i, j))
# 在页面中抓取出floors
floors = []
for index, item in enumerate(result):
floors.append(GetJuFloor(item['data'], item['title']).get_floors())
values = []
time_start = time.strftime('%Y-%m-%d-%H:%M:%S',time.localtime(time.time()))
for item in floors:
row_big_item = []
row_small_item = []
row_big_item = GetJuItem(item.get('big'), item['brand_name']).get_big_items()
values.extend(row_big_item)
small_pages = GetPageData(item['small'].get('urls'), item['brand_name']).get_pages()
for i in small_pages:
row_small_item.extend(GetJuItem(i, item['brand_name']).get_small_items())
values.extend(row_small_item)
sql_item = "INSERT INTO ju_brand_item (id, name, description, created, price, orig_price, started, item_type, brand_name) \
VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s)"
sql_num = "INSERT INTO ju_brand_item_num (item_id, sold_num) VALUES (%s, %s)"
sql_item_detail = "INSERT INTO ju_brand_item_detail (item_id, img_src, detail_src) VALUES (%s, %s, %s)"
db_item = []
db_item_num = []
db_item_detail = []
for value in values:
try:
if value['str_people'] == u'\u4eba\u5df2\u4e70\n':
is_started = True
else:
is_started = False
item_id = string.atoi(re.findall(r'\d+', value['src_detail'])[0])
db_item.append([item_id, value['name'], value['desc'], value['date_time'], value['price'], value['orig_price'], is_started, value['item_type'], value['brand_name']])
db_item_num.append([item_id, value['sold_num']])
db_item_detail.append([item_id, value['img_src'], value['src_detail']])
except Exception, e:
log.error(str(value['name']))
continue
def set_logger(self):
created_dir = False
if not os.path.isdir(self.log_dir):
try:
os.makedirs(self.log_dir)
created_dir = True
except Exception:
raise AttributeError(
"Failed to create log output directory %s" % self.log_dir)
self.logger = get_file_logger(
name=self.title,
filestem=os.path.join(self.log_dir,
'%s.%s.log' % (self.title, self.now_str)))
if created_dir:
self.logger.info("Created log output directory %s.", self.log_dir)
class GetPageData(object):
'''
输入url抓取网页信息，并保存unicode格式的文本信息
'''
urls = []
brand_names = []
log = get_file_logger('get_page')
def __init__(self, url_list, brand_names=[]):
for i in url_list:
self.urls.append(check_url(i))
for i in brand_names:
self.brand_names.append(i)
user_agent = 'Mozilla/6.0 (compatible; MSIE 5.5; Windows NT)'
self.headers = {'User-Agent': user_agent}
def get_page(self, url='', page_title=u'', decode_str='gbk'):
"""
将url对应的界面数据以及名称打包成结果返回
"""
try:
page = ''
if not url.strip():
raise Exception('url is None')
req = urllib2.Request(url, headers=self.headers)
response = urllib2.urlopen(req)
html = response.read()
page = html.decode(decode_str)
except Exception, e:
self.log.error(e)
return None
result = {
'data': page,
'title': page_title,
}
return result
def __init__(self, page, brand_name):
self.unicode_page = check_page(page)
self.log = get_file_logger('ju_report')
self.brand_name = brand_name
def __init__(self, file_name, sheet_name):
self.file_name = file_name
self.sheet_name = sheet_name
self.log = get_file_logger('excel_handler')
def __init__(self, file_name, sheet_name):
self.file_name = file_name
self.sheet_name = sheet_name
self.log = get_file_logger('excel_handler')
def main():
log = get_file_logger('ju_item_insert')
hostaddress = 'localhost'
database = 'ju_db'
user = MYSQL_USER
password = MYSQL_PASSWORD
db = torndb.Connection(hostaddress, database, user, password)
excel_handler = DealExcel(INPUT_FILE_PATH, 'Sheet1')
ju_brands = excel_handler.read_column_excel(1, 2)
ju_urls = excel_handler.read_column_excel(2, 2)
ju_pages = GetPageData(ju_urls, ju_brands)
result = []
for i, j in zip(ju_urls, ju_brands):
result.append(ju_pages.get_page(i, j))
# 在页面中抓取出floors
floors = []
for index, item in enumerate(result):
floors.append(GetJuFloor(item['data'], item['title']).get_floors())
values = []
time_start = time.strftime('%Y-%m-%d-%H:%M:%S',
time.localtime(time.time()))
for item in floors:
row_big_item = []
row_small_item = []
row_big_item = GetJuItem(item.get('big'),
item['brand_name']).get_big_items()
values.extend(row_big_item)
small_pages = GetPageData(item['small'].get('urls'),
item['brand_name']).get_pages()
for i in small_pages:
row_small_item.extend(
GetJuItem(i, item['brand_name']).get_small_items())
values.extend(row_small_item)
sql_item = "INSERT INTO ju_brand_item (id, name, description, created, price, orig_price, started, item_type, brand_name) \
VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s)"
sql_num = "INSERT INTO ju_brand_item_num (item_id, sold_num) VALUES (%s, %s)"
sql_item_detail = "INSERT INTO ju_brand_item_detail (item_id, img_src, detail_src) VALUES (%s, %s, %s)"
db_item = []
db_item_num = []
db_item_detail = []
for value in values:
try:
if value['str_people'] == u'\u4eba\u5df2\u4e70\n':
is_started = True
else:
is_started = False
item_id = string.atoi(re.findall(r'\d+', value['src_detail'])[0])
db_item.append([
item_id, value['name'], value['desc'], value['date_time'],
value['price'], value['orig_price'], is_started,
value['item_type'], value['brand_name']
])
db_item_num.append([item_id, value['sold_num']])
db_item_detail.append(
[item_id, value['img_src'], value['src_detail']])
except Exception, e:
log.error(str(value['name']))
continue
def set_logger(self):
self.logger = get_file_logger(
name=self.title,
filestem=os.path.join(self.log_dir,
'%s.%s.log' % (self.title, self.now_str)))
def __init__(self, floor_data, brand_name):
self.log = get_file_logger('ju_report')
self.floor_data = floor_data
self.brand_name = brand_name
def __init__(self, page, brand_name):
self.unicode_page = check_page(page)
self.log = get_file_logger('ju_report')
self.brand_name = brand_name
def get_methylation_gene_expression_data(case_ids):
outdir = unique_output_dir("gdc-nih_gene_expr", reuse_empty=True)
logger = get_file_logger("nih_methylation_gene_counts",
os.path.join(outdir, "getter.log"))
# get relevant files for download
qry_case = {
"op": "in",
"content": {
"field": "cases.case_id",
"value": list(case_ids)
}
}
qry = {
"filters":
and_query(qry_primary, qry_case, or_query(qry_trans, qry_meth450)),
"format":
"json",
"fields":
','.join(FILE_FIELDS),
"size":
10000
}
response = requests.post(FILES_ENDPOINT, json=qry)
if response.status_code != 200:
logger.error("Initial query failed: %s", response.content)
raise ValueError("Query failed")
res = response.json()['data']['hits']
meta = {}
num_error = 0
num_files = 0
for r in res:
if len(r['cases']) > 1:
logger.error("File with ID %s has multiple case ID matches",
r['file_id'])
cid = r['cases'][0]['case_id']
fid = r['file_id']
fname = r['file_name']
meta.setdefault(cid, {})
if r['data_type'] == 'Gene Expression Quantification':
if 'FPKM-UQ' in fname:
continue
elif 'FPKM' in fname:
meta[cid]['fpkm'] = r
outfn = os.path.join(outdir, cid, 'fpkm.gz')
elif 'htseq.counts' in fname:
meta[cid]['counts'] = r
outfn = os.path.join(outdir, cid, 'counts.gz')
elif r['data_type'] == 'Methylation Beta Value':
meta[cid]['methylation'] = r
outfn = os.path.join(outdir, cid, 'methylation.txt')
try:
download_data(fid, outfn)
except Exception:
logger.exception("Failed to download %s for case id %s", fname,
cid)
num_error += 1
else:
logger.info("Downloaded case ID %s file ID %s to %s", cid, fid,
outfn)
num_files += 1
logger.info("Downloaded %d files. Encountered %d errors.", num_files,
num_error)
# run back through and write meta files
num_meta = 0
num_meta_errors = 0
# write meta files
for cid, d in meta.iteritems():
meta_fn = os.path.join(outdir, cid, 'meta.json')
if os.path.exists(meta_fn):
logger.error("Meta file already exists: %s", meta_fn)
num_meta_errors += 1
else:
with open(meta_fn, 'wb') as f:
json.dump(d, f)
num_meta += 1
logger.info("Create %d meta files. Encountered %d errors.", num_meta,
num_meta_errors)
def get_legacy_idat(case_ids):
outdir = unique_output_dir("gdc-nih_methylation", reuse_empty=True)
logger = get_file_logger("legacy_idats",
os.path.join(outdir, "getter.log"))
qry_case = in_query("cases.case_id", case_ids)
qry_idat = equal_query("files.data_format", "idat")
qry = {
"filters": and_query(qry_primary, qry_case, qry_idat, qry_meth450),
"format": "json",
"fields": ','.join(FILE_FIELDS),
"size": 10000
}
response = requests.post(LEGACY_FILES_ENDPOINT, json=qry)
if response.status_code != 200:
logger.error("Initial query failed: %s", response.content)
raise ValueError("Query failed")
res = response.json()['data']['hits']
logger.info("Found %d idat files.", len(res))
num_error = 0
num_files = 0
# we need to keep track of the files in order to write meta correctly
meta = {}
for r in res:
if len(r['cases']) > 1:
logger.error("File with ID %s has multiple case ID matches",
r['file_id'])
cid = r['cases'][0]['case_id']
fid = r['file_id']
fname = r['file_name']
outfn = os.path.join(outdir, cid, fname)
meta.setdefault(cid, [])
logger.info("Case %s. File ID %s. Output path %s.", cid, fid, outfn)
try:
download_data(fid, outfn, legacy=True)
except Exception:
logger.exception("Failed to download %s for case id %s", fname,
cid)
num_error += 1
else:
logger.info("Downloaded case ID %s file ID %s to %s", cid, fid,
outfn)
meta[cid].append(r)
num_files += 1
logger.info("Downloaded %d files. Encountered %d errors.", num_files,
num_error)
num_meta = 0
num_meta_errors = 0
# write meta files
for cid, arr in meta.iteritems():
meta_fn = os.path.join(outdir, cid, 'meta.json')
if os.path.exists(meta_fn):
logger.error("Meta file already exists: %s", meta_fn)
num_meta_errors += 1
else:
with open(meta_fn, 'wb') as f:
json.dump(arr, f)
num_meta += 1
logger.info("Create %d meta files. Encountered %d errors.", num_meta,
num_meta_errors)
def __init__(self, floor_data, brand_name):
self.log = get_file_logger('ju_report')
self.floor_data = floor_data
self.brand_name = brand_name
read_dir = sys.argv[1]
ref_fn = sys.argv[2]
out_dir = sys.argv[3]
qmap_args = sys.argv[4:]
# put global log output into the output directory
log_fn = os.path.join(out_dir, 'qualimap')
if not os.path.isdir(read_dir):
raise ValueError("Could not find specified read directory %s" %
read_dir)
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
logger = get_file_logger(__name__, log_fn)
# fastq.gz file discovery
rr = re.compile(r'\.bam$', flags=re.IGNORECASE)
flist = [t for t in os.listdir(read_dir) if re.search(rr, t)]
# check for existing output and identify files
fl = {}
for t in flist:
base = re.sub(r'\.bam$', '', t)
out_subdir = os.path.join(out_dir, base)
# if output folder exists, log warning and skip
if os.path.isdir(out_subdir):
logger.warn("Folder already exists: %s. Skipping.", out_subdir)
continue
else:
os.makedirs(out_subdir)
# {'base_dir': '2017-08-23',
# 'chipType': 'EPIC',
# 'sampleType': 'KRYO DNA'},
# {'base_dir': '2017-09-19',
# 'chipType': 'EPIC',
# 'sampleType': 'KRYO DNA'},
{'base_dir': 'GSE92462_450K',
'chipType': '450K',
'sampleType': 'KRYO DNA'},
]
# include_subdir = True
include_subdir = False
n_retry = 3
wait_between_retries = 5 # seconds
outdir = unique_output_dir('heidelberg_bulk_upload', reuse_empty=True)
flog = get_file_logger('heidelberg_bulk_upload', os.path.join(outdir, 'automated_upload.log'))
# include = [
# 'GBM018 P10 DNA 8/11/2016 CLEANED',
# 'GBM019 P4 DNA 8/11/2016 CLEANED',
# 'GBM024 P9 DNA 13/10/2016',
# 'GBM026 P8 DNA 24/10/2016',
# 'GBM031 P4 DNA 13/10/2016'
# ]
include = [
'GSC80',
'GSC164',
'GSC64',
'GSC76',
'GSC102',
'GSC6',
'GSC14',
