def run(self):
common.shell_cmd('mkdir -p %s', self.local_dir)
soup = BeautifulSoup(urlopen(CAERS_DOWNLOAD_PAGE_URL).read(), 'lxml')
for a in soup.find_all(title=re.compile('CAERS ASCII.*')):
if 'Download CAERS ASCII' in re.sub(r'\s', ' ', a.text):
fileURL = urljoin('https://www.fda.gov', a['href'])
common.download(fileURL, join(self.output().path, a.attrs['title']+'.csv'))
def run(self):
logging.basicConfig(level=logging.INFO)
output_dir = TOBACCO_RAW_DIR
os.system('mkdir -p %s' % output_dir)
# Download all csv source files (current year and archived years).
soup = BeautifulSoup(
urlopen(TOBACCO_PROBLEM_DOWNLOAD_PAGE).read(), 'lxml')
for a in soup.find_all(title=re.compile('\d{4}.*tppr', re.IGNORECASE)):
file_name = a['title'] if '.csv' in a['title'] else (a['title'] +
'.csv')
common.download(urljoin('https://www.fda.gov', a['href']),
join(output_dir, file_name))
# Combine CSV files into a single json.
all_csv_files = [
i for i in glob.glob((output_dir + '/*.{}').format('csv'))
]
logging.info("Reading csv files: %s", (all_csv_files))
os.system('mkdir -p %s' % dirname(self.output().path))
df = pd.concat(
pd.read_csv(f, encoding='cp1252', skiprows=3)
for f in all_csv_files)
df.to_json(self.output().path, orient='records')
with open(self.output().path, "w") as f:
for row in df.iterrows():
row[1].to_json(f)
f.write("\n")
def run(self):
fileURL = None
soup = BeautifulSoup(urlopen(SUBSTANCE_DATA_DOWNLOAD_PAGE_URL).read(), 'lxml')
for a in soup.find_all(href=re.compile('.*.gsrs')):
if 'Full Public Data Dump' in a.text:
fileURL = urljoin(GINAS_ROOT_URL, a['href'])
common.download(fileURL, self.output().path)
def run(self):
common.shell_cmd('mkdir -p %s', self.local_dir)
soup = BeautifulSoup(urllib2.urlopen(DAILY_MED_DOWNLOADS_PAGE).read(), 'lxml')
for a in soup.find_all(href=re.compile('.*.zip')):
if '_human_' in a.text:
try:
common.download(a['href'], join(self.local_dir, a['href'].split('/')[-1]))
except ProcessException as e:
logging.error("Could not download a DailyMed SPL archive: {0}: {1}".format(a['href'], e))
def run(self):
soup = BeautifulSoup(
urllib2.urlopen(CLEARED_DEVICE_URL).read(), 'lxml')
for a in soup.find_all(href=re.compile('.*.zip')):
if a.text.startswith('PMN') and a.text != 'PMNLSTMN.ZIP':
fileURL = a['href']
common.download(
fileURL, join(self.output().path,
a['href'].split('/')[-1]))
def run(self):
zip_urls = []
soup = BeautifulSoup(urlopen(DEVICE_REG_PAGE).read())
for a in soup.find_all(href=re.compile('.*.zip')):
zip_urls.append(a['href'])
if not zip_urls:
logging.info('No Registration Zip Files Found At %s' % DEVICE_REG_PAGE)
for zip_url in zip_urls:
filename = zip_url.split('/')[-1]
common.download(zip_url, join(self.output().path, filename))
def _run(self):
zip_urls = []
soup = BeautifulSoup(urllib2.urlopen(DEVICE_DOWNLOAD_PAGE).read())
for a in soup.find_all(href=re.compile('.*.zip')):
zip_urls.append(a['href'])
if not zip_urls:
logging.fatal('No MAUDE Zip Files Found At %s' % DEVICE_CLASS_DOWNLOAD)
for zip_url in zip_urls:
filename = zip_url.split('/')[-1]
common.download(zip_url, join(self.output().path, filename))
def run(self):
zip_urls = []
soup = BeautifulSoup(urllib2.urlopen(DEVICE_REG_PAGE).read())
for a in soup.find_all(href=re.compile(".*.zip")):
zip_urls.append(a["href"])
if not zip_urls:
logging.info("No Registration Zip Files Found At %s" % DEVICE_REG_PAGE)
for zip_url in zip_urls:
filename = zip_url.split("/")[-1]
common.download(zip_url, join(self.output().path, filename))
def _run(self):
zip_urls = []
soup = BeautifulSoup(urllib2.urlopen(DEVICE_DOWNLOAD_PAGE).read())
for a in soup.find_all(href=re.compile('.*.zip')):
zip_urls.append(a['href'])
if not zip_urls:
logging.fatal('No MAUDE Zip Files Found At %s' % DEVICE_CLASS_DOWNLOAD)
for zip_url in zip_urls:
filename = zip_url.split('/')[-1]
common.download(zip_url, join(self.output().path, filename))
def run(self):
zip_url = None
soup = BeautifulSoup(urllib2.urlopen(NDC_DOWNLOAD_PAGE).read(), 'lxml')
for a in soup.find_all(href=re.compile('.*.zip')):
if 'NDC Database File' in a.text:
zip_url = urlparse.urljoin('http://www.fda.gov', a['href'])
break
if not zip_url:
logging.fatal('NDC database file not found!')
common.download(zip_url, self.output().path)
def run(self):
zip_url = None
soup = BeautifulSoup(urllib2.urlopen(NDC_DOWNLOAD_PAGE).read(), 'lxml')
for a in soup.find_all(href=re.compile('.*.zip')):
if 'NDC Database File' in a.text:
zip_url = urlparse.urljoin('http://www.fda.gov', a['href'])
break
if not zip_url:
logging.fatal('NDC database file not found!')
common.download(zip_url, self.output().path)
def run(self):
# TODO(hansnelsen): copied from the FAERS pipeline, consider refactoring
# into a generalized approach
zip_urls = []
soup = BeautifulSoup(urllib2.urlopen(DEVICE_DOWNLOAD_PAGE).read())
for a in soup.find_all(href=re.compile('.*.zip')):
zip_urls.append(a['href'])
if not zip_urls:
logging.fatal('No MAUDE Zip Files Found At %s' % DEVICE_CLASS_DOWNLOAD)
for zip_url in zip_urls:
filename = zip_url.split('/')[-1]
common.download(zip_url, join(self.output().path, filename))
def run(self):
# TODO(hansnelsen): copied from the FAERS pipeline, consider refactoring
# into a generalized approach
zip_urls = []
soup = BeautifulSoup(urllib2.urlopen(DEVICE_DOWNLOAD_PAGE).read())
for a in soup.find_all(href=re.compile('.*.zip')):
zip_urls.append(a['href'])
if not zip_urls:
logging.fatal('No MAUDE Zip Files Found At %s' %
DEVICE_CLASS_DOWNLOAD)
for zip_url in zip_urls:
filename = zip_url.split('/')[-1]
common.download(zip_url, join(self.output().path, filename))
def _download_with_retry(self, url, target_name):
if os.path.exists(target_name):
return
for i in range(10):
try:
logging.info('Downloading: ' + url)
common.download(url, target_name)
subprocess.check_call('unzip -t %s' % target_name, shell=True)
return
except:
logging.info(
'Problem while unzipping[download URL:%s, zip file:%s], retrying...',
url, target_name)
logging.fatal(
'Zip File: %s from URL :%s is not valid, stop all processing',
target_name, url)
def run(self):
finished_ndc_url = None
unfinished_ndc_url = None
soup = BeautifulSoup(urlopen(NDC_DOWNLOAD_PAGE).read(), 'lxml')
for a in soup.find_all(href=re.compile('.*.zip')):
if 'NDC Database File' in a.text and 'text' in a['href']:
finished_ndc_url = urljoin('https://www.fda.gov', a['href'])
if 'NDC Unfinished' in a.text and 'unfinished.zip' in a['href']:
unfinished_ndc_url = urljoin('https://www.fda.gov', a['href'])
if not finished_ndc_url:
logging.fatal('NDC finished database file not found!')
if not unfinished_ndc_url:
logging.fatal('NDC unfinished drugs database file not found!')
common.download(finished_ndc_url, join(RAW_DIR, 'finished.zip'))
common.download(unfinished_ndc_url, join(RAW_DIR, 'unfinished.zip'))
def run(self):
logging.basicConfig(level=logging.INFO)
zip_filename = config.data_dir('nsde/raw/nsde.zip')
output_dir = config.data_dir('nsde/raw')
os.system('mkdir -p %s' % output_dir)
common.download(NSDE_DOWNLOAD, zip_filename)
os.system('unzip -o %(zip_filename)s -d %(output_dir)s' % locals())
csv_file = join(output_dir, self.csv_file_name)
logging.info("Reading csv file: %s", (csv_file))
os.system('mkdir -p %s' % dirname(self.output().path))
df = pd.read_csv(csv_file, encoding='utf-8-sig')
df.to_json(self.output().path, orient='records')
with open(self.output().path, "w") as f:
for row in df.iterrows():
row[1].to_json(f)
f.write("\n")
def run(self): common.download(self.url, os.path.join(self.local_dir, 'registration_listing.txt'))
def run(self):
output_filename = join(self.output().path, DEVICE_PMA_ZIP.split('/')[-1])
common.download(DEVICE_PMA_ZIP, output_filename)
def run(self):
for url in SPL_DOWNLOADS:
filename = join(self.output().path, url.split('/')[-1])
common.download(url, filename)
def run(self):
output_dir = self.output().path
for zip_url in CLEARED_DEV_ZIPS:
output_filename = join(output_dir, zip_url.split('/')[-1])
common.download(zip_url, output_filename)
def run(self):
output_dir = dirname(self.output().path)
zip_filename = join(output_dir, 'nsde.zip')
common.download(NSDE_DOWNLOAD, zip_filename)
os.system('unzip -o %(zip_filename)s -d %(output_dir)s' % locals())
os.rename(glob.glob(join(output_dir, '*.csv'))[0], self.output().path)
def run(self):
output_filename = join(self.output().path,
DEVICE_PMA_ZIP.split('/')[-1])
common.download(DEVICE_PMA_ZIP, output_filename)
def run(self): common.download(PHARM_CLASS_DOWNLOAD, self.output().path)
def run(self): common.download(RXNORM_DOWNLOAD, self.output().path)
def run(self):
output_dir = self.output().path
for zip_url in CLEARED_DEV_ZIPS:
output_filename = join(output_dir, zip_url.split('/')[-1])
common.download(zip_url, output_filename)
def run(self):
common.download(RXNORM_DOWNLOAD, self.output().path)
def run(self):
common.download(PHARM_CLASS_DOWNLOAD, self.output().path)
def run(self):
common.download(DOWNLOAD_FILE, RAW_DATA_FILE)