def harvest(self, start_date=None, end_date=None):
start_date = (start_date or date.today() -
timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
if self.timezone_granularity:
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
url = furl(self.base_url)
url.args['verb'] = 'ListRecords'
url.args['metadataPrefix'] = 'oai_dc'
url.args['from'] = start_date
url.args['until'] = end_date
records = self.get_records(url.url, start_date, end_date)
rawdoc_list = []
for record in records:
doc_id = record.xpath('ns0:header/ns0:identifier',
namespaces=self.namespaces)[0].text
record = etree.tostring(record, encoding=self.record_encoding)
rawdoc_list.append(
RawDocument({
'doc': record,
'source': util.copy_to_unicode(self.short_name),
'docID': util.copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return rawdoc_list
def harvest(self, start_date=None, end_date=None):
start_date = (start_date or date.today() - timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
if self.timezone_granularity:
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
url = furl(self.base_url)
url.args['verb'] = 'ListRecords'
url.args['metadataPrefix'] = 'oai_dc'
url.args['from'] = start_date
url.args['until'] = end_date
records = self.get_records(url.url, start_date, end_date)
rawdoc_list = []
for record in records:
doc_id = record.xpath(
'ns0:header/ns0:identifier', namespaces=self.namespaces)[0].text
record = etree.tostring(record, encoding=self.record_encoding)
rawdoc_list.append(RawDocument({
'doc': record,
'source': util.copy_to_unicode(self.short_name),
'docID': util.copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return rawdoc_list
def process_raw(self, raw_doc):
self.send_to_database(source=copy_to_unicode(raw_doc['source']),
docID=copy_to_unicode(raw_doc['docID']),
doc=six.text_type(
raw_doc['doc']).encode('utf-8'),
filetype=copy_to_unicode(raw_doc['filetype']),
timestamps=raw_doc.get('timestamps', {})).save()
def harvest(self, start_date=None, end_date=None):
start_date = (start_date or date.today() - timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
if self.timezone_granularity:
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
records_url = self.base_url + self.RECORDS_URL
request_url = records_url + self.META_PREFIX_DATE.format(start_date, end_date)
records = self.get_records(request_url, start_date, end_date)
rawdoc_list = []
for record in records:
doc_id = record.xpath(
'ns0:header/ns0:identifier', namespaces=self.namespaces)[0].text
record = etree.tostring(record, encoding=self.record_encoding)
rawdoc_list.append(RawDocument({
'doc': record,
'source': util.copy_to_unicode(self.short_name),
'docID': util.copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return rawdoc_list
def harvest(self, start_date=None, end_date=None):
start_date = (start_date or date.today() -
timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
if self.timezone_granularity:
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
records_url = self.base_url + self.RECORDS_URL
request_url = records_url + self.META_PREFIX_DATE.format(
start_date, end_date)
records = self.get_records(request_url, start_date, end_date)
rawdoc_list = []
for record in records:
doc_id = record.xpath('ns0:header/ns0:identifier',
namespaces=self.namespaces)[0].text
record = etree.tostring(record, encoding=self.record_encoding)
rawdoc_list.append(
RawDocument({
'doc': record,
'source': util.copy_to_unicode(self.short_name),
'docID': util.copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return rawdoc_list
def process_raw(self, raw_doc):
self.send_to_database(
source=copy_to_unicode(raw_doc['source']),
docID=copy_to_unicode(raw_doc['docID']),
doc=six.text_type(raw_doc['doc']).encode('utf-8'),
filetype=copy_to_unicode(raw_doc['filetype']),
timestamps=raw_doc.get('timestamps', {})
).save()
def harvest(self, start_date=None, end_date=None):
start_date = (start_date or date.today() -
timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
base_url = 'https://www.earthsystemgrid.org/oai/repository?verb=ListRecords&metadataPrefix=dif&from={}&until={}'
url = base_url.format(start_date, end_date)
data = requests.get(url)
doc = etree.XML(data.content)
records = doc.xpath('//OAI-PMH:record', namespaces=self.namespaces)
xml_list = []
for record in records:
doc_id = record.xpath('//OAI-PMH:header/OAI-PMH:identifier/node()',
namespaces=self.namespaces)[0]
record = etree.tostring(record)
xml_list.append(
RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
base_url = 'http://www.osti.gov/pages/pagesxml?nrows={0}&EntryDateFrom={1}&EntryDateTo={2}'
url = base_url.format('1', format_date_with_slashes(start_date), format_date_with_slashes(end_date))
initial_data = requests.get(url)
record_encoding = initial_data.encoding
initial_doc = etree.XML(initial_data.content)
num_results = int(initial_doc.xpath('//records/@count', namespaces=self.namespaces)[0])
url = base_url.format(num_results, start_date, end_date)
data = requests.get(url)
doc = etree.XML(data.content)
records = doc.xpath('records/record')
xml_list = []
for record in records:
doc_id = record.xpath('dc:ostiId/node()', namespaces=self.namespaces)[0]
record = etree.tostring(record, encoding=record_encoding)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
records = self.get_records(start_date, end_date)
xml_list = []
for record in records:
# This ID is unique per data package, but won't unify multiple packages for the same project
doc_id = record.xpath("str[@name='id']")[0].text
format_type = record.xpath("str[@name='formatType']")[0].text
record = ElementTree.tostring(record,
encoding=self.record_encoding)
if format_type.lower() != 'metadata':
logger.info(
'Not normalizing record with ID {}, type {}'.format(
doc_id, format_type))
else:
xml_list.append(
RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
"""
Return a list of RawDocuments
"""
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
base_url = 'http://exporter.nih.gov/'
table_url = 'http://exporter.nih.gov/ExPORTER_Catalog.aspx/'
# get ExPORTER page html and rows storing records
html = requests.get(table_url).content
soup = BeautifulSoup(html, 'lxml')
table = soup.find('table', id="ContentPlaceHolder1_ProjectData_dgProjectData")
rows = table.find_all('tr', class_="row_bg")
urls = [i for i in construct_urls(base_url, start_date, end_date, rows)]
return [
RawDocument({
'doc': etree.tostring(record, encoding=self.DEFAULT_ENCODING),
'source': self.short_name,
'docID': copy_to_unicode(record.xpath('.//APPLICATION_ID/node()', namespaces=self.namespaces)[0]),
'filetype': 'xml'
}) for record in xml_records(get_xml_files(urls))
]
def harvest(self, start_date=None, end_date=None):
"""
Return a list of RawDocuments
"""
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
base_url = 'http://exporter.nih.gov/'
table_url = 'http://exporter.nih.gov/ExPORTER_Catalog.aspx/'
# get ExPORTER page html and rows storing records
html = requests.get(table_url).content
soup = BeautifulSoup(html, 'lxml')
table = soup.find('table',
id="ContentPlaceHolder1_ProjectData_dgProjectData")
rows = table.find_all('tr', class_="row_bg")
urls = [
i for i in construct_urls(base_url, start_date, end_date, rows)
]
return [
RawDocument({
'doc':
etree.tostring(record, encoding=self.DEFAULT_ENCODING),
'source':
self.short_name,
'docID':
copy_to_unicode(
record.xpath('.//APPLICATION_ID/node()',
namespaces=self.namespaces)[0]),
'filetype':
'xml'
}) for record in xml_records(get_xml_files(urls))
]
def harvest(self, start_date=None, end_date=None):
''' First, get a list of all recently updated study urls,
then get the xml one by one and save it into a list
of docs including other information '''
start_date = (start_date or date.today() - timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
# grab each of those urls for full content
xml_list = []
xml_base_url = self.canonical_base_url + '&view=xml'
for dataset_id in self.query_by_date(start_date, end_date):
try:
item_url = str(xml_base_url).format(dataset_id)
content = requests.get(item_url, throttle=2)
except exceptions.ConnectionError as e:
logger.info('Connection error: {}, wait a bit...'.format(e))
time.sleep(30)
content = requests.get(item_url)
doc = etree.XML(content.content)
record = etree.tostring(doc, encoding=self.DEFAULT_ENCODING)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(dataset_id),
'filetype': 'xml',
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
''' First, get a list of all recently updated study urls,
then get the xml one by one and save it into a list
of docs including other information '''
start_date = (start_date or date.today() -
timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
# grab each of those urls for full content
xml_list = []
xml_base_url = self.canonical_base_url + '&view=xml'
for dataset_id in self.query_by_date(start_date, end_date):
try:
item_url = str(xml_base_url).format(dataset_id)
content = requests.get(item_url, throttle=2)
except exceptions.ConnectionError as e:
logger.info('Connection error: {}, wait a bit...'.format(e))
time.sleep(30)
content = requests.get(item_url)
doc = etree.XML(content.content)
record = etree.tostring(doc, encoding=self.DEFAULT_ENCODING)
xml_list.append(
RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(dataset_id),
'filetype': 'xml',
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
start_date = (start_date or date.today() - timedelta(settings.DAYS_BACK)).isoformat()
end_date = (end_date or date.today()).isoformat()
start_date += 'T00:00:00Z'
end_date += 'T00:00:00Z'
base_url = 'https://www.earthsystemgrid.org/oai/repository?verb=ListRecords&metadataPrefix=dif&from={}&until={}'
url = base_url.format(start_date, end_date)
data = requests.get(url)
doc = etree.XML(data.content)
records = doc.xpath('//OAI-PMH:record', namespaces=self.namespaces)
xml_list = []
for record in records:
doc_id = record.xpath('//OAI-PMH:header/OAI-PMH:identifier/node()', namespaces=self.namespaces)[0]
record = etree.tostring(record)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, days_back=1):
today = date.today()
start_date = today - timedelta(days_back)
base_url = 'http://www.osti.gov/pages/pagesxml?nrows={0}&EntryDateFrom={1}&EntryDateTo={2}'
url = base_url.format('1', start_date.strftime('%m/%d/%Y'), today.strftime('%m/%d/%Y'))
initial_data = requests.get(url)
record_encoding = initial_data.encoding
initial_doc = etree.XML(initial_data.content)
num_results = int(initial_doc.xpath('//records/@count', namespaces=self.namespaces)[0])
url = base_url.format(num_results, start_date.strftime('%m/%d/%Y'), today.strftime('%m/%d/%Y'))
data = requests.get(url)
doc = etree.XML(data.content)
records = doc.xpath('records/record')
xml_list = []
for record in records:
doc_id = record.xpath('dc:ostiId/node()', namespaces=self.namespaces)[0]
record = etree.tostring(record, encoding=record_encoding)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, days_back=1):
records = self.get_records(days_back)
xml_list = []
for record in records:
doc_id = record.xpath("str[@name='id']")[0].text
record = ElementTree.tostring(record, encoding=self.record_encoding)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def get_ids(self, result, doc):
"""
Gather the DOI and url from identifiers, if possible.
Tries to save the DOI alone without a url extension.
Tries to save a link to the original content at the source,
instead of direct to a PDF, which is usually linked with viewcontent.cgi?
in the url field
"""
serviceID = doc.get('docID')
url = 'http://core.tdar.org/document/' + serviceID.replace('oai:tdar.org:Resource:', '')
return {
'serviceID': serviceID,
'url': util.copy_to_unicode(url),
'doi': ''
}
def harvest(self, start_date=None, end_date=None):
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
records = self.get_records(start_date, end_date)
xml_list = []
for record in records:
doc_id = record.xpath("str[@name='id']")[0].text
record = ElementTree.tostring(record, encoding=self.record_encoding)
xml_list.append(
RawDocument(
{"doc": record, "source": self.short_name, "docID": copy_to_unicode(doc_id), "filetype": "xml"}
)
)
return xml_list
def harvest(self, start_date=None, end_date=None):
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
records = self.get_records(start_date, end_date)
xml_list = []
for record in records:
# This ID is unique per data package, but won't unify multiple packages for the smae project
doc_id = record.xpath("str[@name='id']")[0].text
record = ElementTree.tostring(record, encoding=self.record_encoding)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
url = 'http://dailyssrn.com/rss/rss-all-2.0.xml'
data = requests.get(url)
doc = etree.XML(data.content)
records = doc.xpath('channel/item')
xml_list = []
for record in records:
doc_id = parse_id_from_url(record.xpath('link/node()'))
record = etree.tostring(record)
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
records = self.get_records(start_date, end_date)
xml_list = []
for record in records:
doc_id = record.xpath("str[@name='id']")[0].text
record = ElementTree.tostring(record,
encoding=self.record_encoding)
xml_list.append(
RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
url = 'http://dailyssrn.com/rss/rss-all-2.0.xml'
data = requests.get(url, force=True)
doc = etree.XML(data.content)
records = doc.xpath('channel/item')
xml_list = []
for record in records:
doc_id = parse_id_from_url(record.xpath('link/node()'))
record = etree.tostring(record)
xml_list.append(
RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def harvest(self, start_date=None, end_date=None):
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
records = self.get_records(start_date, end_date)
xml_list = []
for record in records:
# This ID is unique per data package, but won't unify multiple packages for the same project
doc_id = record.xpath("str[@name='id']")[0].text
format_type = record.xpath("str[@name='formatType']")[0].text
record = ElementTree.tostring(record, encoding=self.record_encoding)
if format_type.lower() != 'metadata':
logger.info('Not normalizing record with ID {}, type {}'.format(doc_id, format_type))
else:
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml'
}))
return xml_list
def process_normalized(self, raw_doc, normalized):
self.send_to_database(
source=copy_to_unicode(raw_doc['source']),
docID=copy_to_unicode(raw_doc['docID']),
contributors=copy_to_unicode(json.dumps(normalized['contributors'])),
description=copy_to_unicode(normalized.get('description')),
uris=copy_to_unicode(json.dumps(normalized['uris'])),
providerUpdatedDateTime=parse(normalized['providerUpdatedDateTime']).replace(tzinfo=None),
freeToRead=copy_to_unicode(json.dumps(normalized.get('freeToRead', {}))),
languages=normalized.get('language'),
licenses=copy_to_unicode(json.dumps(normalized.get('licenseRef', []))),
publisher=copy_to_unicode(json.dumps(normalized.get('publisher', {}))),
sponsorships=copy_to_unicode(json.dumps(normalized.get('sponsorship', []))),
title=copy_to_unicode(normalized['title']),
version=copy_to_unicode(json.dumps(normalized.get('version'), {})),
otherProperties=copy_to_unicode(json.dumps(normalized.get('otherProperties', {}))),
shareProperties=copy_to_unicode(json.dumps(normalized['shareProperties']))
).save()
def process_normalized(self, raw_doc, normalized):
self.send_to_database(
source=copy_to_unicode(raw_doc['source']),
docID=copy_to_unicode(raw_doc['docID']),
contributors=copy_to_unicode(json.dumps(normalized['contributors'])),
description=copy_to_unicode(normalized.get('description')),
uris=copy_to_unicode(json.dumps(normalized['uris'])),
providerUpdatedDateTime=parse(normalized['providerUpdatedDateTime']).replace(tzinfo=None),
freeToRead=copy_to_unicode(json.dumps(normalized.get('freeToRead', {}))),
languages=normalized.get('language'),
licenses=copy_to_unicode(json.dumps(normalized.get('licenseRef', []))),
publisher=copy_to_unicode(json.dumps(normalized.get('publisher', {}))),
sponsorships=copy_to_unicode(json.dumps(normalized.get('sponsorship', []))),
title=copy_to_unicode(normalized['title']),
version=copy_to_unicode(json.dumps(normalized.get('version'), {})),
otherProperties=copy_to_unicode(json.dumps(normalized.get('otherProperties', {}))),
shareProperties=copy_to_unicode(json.dumps(normalized['shareProperties']))
).save()
def harvest(self, start_date=None, end_date=None):
""" First, get a list of all recently updated study urls,
then get the xml one by one and save it into a list
of docs including other information """
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
end_month = end_date.strftime('%m')
end_day = end_date.strftime('%d')
end_year = end_date.strftime('%Y')
start_month = start_date.strftime('%m')
start_day = start_date.strftime('%d')
start_year = start_date.strftime('%Y')
base_url = 'http://clinicaltrials.gov/ct2/results?lup_s='
url_end = '{}%2F{}%2F{}&lup_e={}%2F{}%2F{}&displayxml=true'.\
format(start_month, start_day, start_year, end_month, end_day, end_year)
url = base_url + url_end
# grab the total number of studies
initial_request = requests.get(url)
record_encoding = initial_request.encoding
initial_request_xml = etree.XML(initial_request.content)
count = int(initial_request_xml.xpath('//search_results/@count')[0])
xml_list = []
if int(count) > 0:
# get a new url with all results in it
url = url + '&count=' + str(count)
total_requests = requests.get(url)
initial_doc = etree.XML(total_requests.content)
# make a list of urls from that full list of studies
study_urls = []
for study in initial_doc.xpath('//clinical_study'):
study_urls.append(
study.xpath('url/node()')[0] + '?displayxml=true')
# grab each of those urls for full content
logger.info("There are {} urls to harvest - be patient...".format(
len(study_urls)))
count = 0
official_count = 0
for study_url in study_urls:
try:
content = requests.get(study_url)
except requests.exceptions.ConnectionError as e:
logger.info(
'Connection error: {}, wait a bit...'.format(e))
time.sleep(30)
continue
doc = etree.XML(content.content)
record = etree.tostring(doc, encoding=record_encoding)
doc_id = doc.xpath('//nct_id/node()')[0]
xml_list.append(
RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml',
}))
official_count += 1
count += 1
if count % 100 == 0:
logger.info(
"You've requested {} studies, keep going!".format(
official_count))
count = 0
return xml_list
def harvest(self, start_date=None, end_date=None):
""" First, get a list of all recently updated study urls,
then get the xml one by one and save it into a list
of docs including other information """
start_date = start_date or date.today() - timedelta(settings.DAYS_BACK)
end_date = end_date or date.today()
end_month = end_date.strftime('%m')
end_day = end_date.strftime('%d')
end_year = end_date.strftime('%Y')
start_month = start_date.strftime('%m')
start_day = start_date.strftime('%d')
start_year = start_date.strftime('%Y')
base_url = 'http://clinicaltrials.gov/ct2/results?lup_s='
url_end = '{}%2F{}%2F{}%2F&lup_e={}%2F{}%2F{}&displayxml=true'.\
format(start_month, start_day, start_year, end_month, end_day, end_year)
url = base_url + url_end
# grab the total number of studies
initial_request = requests.get(url)
record_encoding = initial_request.encoding
initial_request_xml = etree.XML(initial_request.content)
count = int(initial_request_xml.xpath('//search_results/@count')[0])
xml_list = []
if int(count) > 0:
# get a new url with all results in it
url = url + '&count=' + str(count)
total_requests = requests.get(url)
initial_doc = etree.XML(total_requests.content)
# make a list of urls from that full list of studies
study_urls = []
for study in initial_doc.xpath('//clinical_study'):
study_urls.append(study.xpath('url/node()')[0] + '?displayxml=true')
# grab each of those urls for full content
logger.info("There are {} urls to harvest - be patient...".format(len(study_urls)))
count = 0
official_count = 0
for study_url in study_urls:
try:
content = requests.get(study_url)
except requests.exceptions.ConnectionError as e:
logger.info('Connection error: {}, wait a bit...'.format(e))
time.sleep(30)
continue
doc = etree.XML(content.content)
record = etree.tostring(doc, encoding=record_encoding)
doc_id = doc.xpath('//nct_id/node()')[0]
xml_list.append(RawDocument({
'doc': record,
'source': self.short_name,
'docID': copy_to_unicode(doc_id),
'filetype': 'xml',
}))
official_count += 1
count += 1
if count % 100 == 0:
logger.info("You've requested {} studies, keep going!".format(official_count))
count = 0
return xml_list
def test_copy_to_unicode(self):
converted = util.copy_to_unicode('test')
assert converted == u'test'
assert isinstance(converted, unicode)
