aboutsummaryrefslogtreecommitdiffstats
path: root/python/sandcrawler
diff options
context:
space:
mode:
Diffstat (limited to 'python/sandcrawler')
-rw-r--r--python/sandcrawler/grobid.py14
-rw-r--r--python/sandcrawler/html.py73
-rw-r--r--python/sandcrawler/ia.py88
-rw-r--r--python/sandcrawler/ingest.py150
-rw-r--r--python/sandcrawler/misc.py24
5 files changed, 334 insertions, 15 deletions
diff --git a/python/sandcrawler/grobid.py b/python/sandcrawler/grobid.py
index f157241..d83fedc 100644
--- a/python/sandcrawler/grobid.py
+++ b/python/sandcrawler/grobid.py
@@ -2,6 +2,7 @@
import requests
from collections import Counter
+from grobid2json import teixml2json
from .workers import SandcrawlerWorker
from .misc import gen_file_metadata
from .ia import WaybackClient, WaybackError
@@ -49,6 +50,19 @@ class GrobidClient(object):
info['error_msg'] = grobid_response.text[:10000]
return info
+ def metadata(self, result):
+ if result['status'] != 'success':
+ return None
+ tei_json = teixml2json(result['tei_xml'], encumbered=False)
+ meta = dict()
+ biblio = dict()
+ for k in ('title', 'authors', 'journal', 'date', 'doi', ):
+ biblio[k] = tei_json.get(k)
+ meta['biblio'] = biblio
+ for k in ('grobid_version', 'grobid_timestamp', 'fatcat_release', 'language_code'):
+ meta[k] = tei_json.get(k)
+ return meta
+
class GrobidWorker(SandcrawlerWorker):
def __init__(self, grobid_client, wayback_client=None, sink=None, **kwargs):
diff --git a/python/sandcrawler/html.py b/python/sandcrawler/html.py
new file mode 100644
index 0000000..3191b66
--- /dev/null
+++ b/python/sandcrawler/html.py
@@ -0,0 +1,73 @@
+
+import re
+import sys
+import urllib.parse
+
+from bs4 import BeautifulSoup
+
+RESEARCHSQUARE_REGEX = re.compile(r'"url":"(https://assets.researchsquare.com/files/.{1,50}/v\d+/Manuscript.pdf)"')
+
+def extract_fulltext_url(html_url, html_body):
+ """
+ Takes an HTML document (and URL), assumed to be a landing page, and tries
+ to find a fulltext PDF url.
+ """
+
+ host_prefix = '/'.join(html_url.split('/')[:3])
+ soup = BeautifulSoup(html_body, 'html.parser')
+
+ ### General Tricks ###
+
+ # highwire-style meta tag
+ meta = soup.find('meta', attrs={"name":"citation_pdf_url"})
+ if not meta:
+ meta = soup.find('meta', attrs={"name":"bepress_citation_pdf_url"})
+ if meta:
+ url = meta['content'].strip()
+ if url.startswith('http'):
+ return dict(pdf_url=url, technique='citation_pdf_url')
+ else:
+ sys.stderr.write("malformed citation_pdf_url? {}\n".format(url))
+
+ # ACS (and probably others) like:
+ # https://pubs.acs.org/doi/10.1021/acs.estlett.9b00379
+ # <a href="/doi/pdf/10.1021/acs.estlett.9b00379" title="PDF" target="_blank" class="button_primary"><i class="icon-file-pdf-o"></i><span>PDF (1 MB)</span></a>
+ href = soup.find('a', attrs={"title":"PDF"})
+ if href:
+ url = href['href'].strip()
+ if url.startswith('http'):
+ return dict(pdf_url=url, technique='href_title')
+ elif url.startswith('/'):
+ return dict(pdf_url=host_prefix+url, technique='href_title')
+
+ ### Publisher/Platform Specific ###
+
+ # eLife (elifesciences.org)
+ if '://elifesciences.org/articles/' in html_url:
+ anchor = soup.find("a", attrs={"data-download-type": "pdf-article"})
+ if anchor:
+ url = anchor['href'].strip()
+ assert '.pdf' in url
+ return dict(pdf_url=url)
+
+ # research square (researchsquare.com)
+ if 'researchsquare.com/article/' in html_url:
+ # JSON in body with a field like:
+ # "url":"https://assets.researchsquare.com/files/4a57970e-b002-4608-b507-b95967649483/v2/Manuscript.pdf"
+ m = RESEARCHSQUARE_REGEX.search(html_body.decode('utf-8'))
+ if m:
+ url = m.group(1)
+ assert len(url) < 1024
+ return dict(release_stage="manuscript", pdf_url=url)
+
+ # ehp.niehs.nih.gov
+ # <a href="/doi/pdf/10.1289/EHP3950">
+ if '://linkinghub.elsevier.com/retrieve/pii/' in html_url:
+ redirect = soup.find("input", attrs={"name": "redirectURL"})
+ if redirect:
+ url = redirect['value'].strip()
+ if 'sciencedirect.com' in url:
+ url = urllib.parse.unquote(url)
+ return dict(next_url=url)
+
+ return dict()
diff --git a/python/sandcrawler/ia.py b/python/sandcrawler/ia.py
index 365cf82..a772bd4 100644
--- a/python/sandcrawler/ia.py
+++ b/python/sandcrawler/ia.py
@@ -3,7 +3,7 @@
# in `wayback` library. Means we can't run pylint.
# pylint: skip-file
-import os, sys
+import os, sys, time
import requests
import wayback.exception
@@ -11,6 +11,8 @@ from http.client import IncompleteRead
from wayback.resourcestore import ResourceStore
from gwb.loader import CDXLoaderFactory
+from .misc import b32_hex, requests_retry_session
+
class CdxApiError(Exception):
pass
@@ -19,7 +21,7 @@ class CdxApiClient:
def __init__(self, host_url="https://web.archive.org/cdx/search/cdx"):
self.host_url = host_url
- def lookup_latest(self, url):
+ def lookup_latest(self, url, follow_redirects=False):
"""
Looks up most recent HTTP 200 record for the given URL.
@@ -28,15 +30,20 @@ class CdxApiClient:
XXX: should do authorized lookup using cookie to get all fields
"""
- resp = requests.get(self.host_url, params={
+ params = {
'url': url,
'matchType': 'exact',
'limit': -1,
- 'filter': 'statuscode:200',
'output': 'json',
- })
- if resp.status_code != 200:
- raise CDXApiError(resp.text)
+ }
+ if not follow_redirects:
+ params['filter'] = 'statuscode:200'
+ resp = requests.get(self.host_url, params=params)
+ if follow_redirects:
+ raise NotImplementedError
+ else:
+ if resp.status_code != 200:
+ raise CdxApiError(resp.text)
rj = resp.json()
if len(rj) <= 1:
return None
@@ -113,23 +120,74 @@ class SavePageNowError(Exception):
class SavePageNowClient:
- def __init__(self, cdx_client=None, endpoint="https://web.archive.org/save/"):
+ def __init__(self, cdx_client=None,
+ v1endpoint="https://web.archive.org/save/",
+ v2endpoint="https://web.archive.org/save"):
if cdx_client:
self.cdx_client = cdx_client
else:
self.cdx_client = CdxApiClient()
- self.endpoint = endpoint
+ self.ia_access_key = os.environ.get('IA_ACCESS_KEY')
+ self.ia_secret_key = os.environ.get('IA_SECRET_KEY')
+ self.v1endpoint = v1endpoint
+ self.v2endpoint = v2endpoint
+ self.http_session = requests_retry_session(retries=5, backoff_factor=3)
+ self.http_session.headers.update({
+ 'User-Agent': 'Mozilla/5.0 sandcrawler.SavePageNowClient',
+ })
+ self.v2_session = requests_retry_session(retries=5, backoff_factor=3)
+ self.v2_session.headers.update({
+ 'User-Agent': 'Mozilla/5.0 sandcrawler.SavePageNowClient',
+ 'Accept': 'application/json',
+ 'Authorization': 'LOW {}:{}'.format(self.ia_access_key, self.ia_secret_key),
+ })
- def save_url_now(self, url):
+ def save_url_now_v1(self, url):
"""
- Returns a tuple (cdx, blob) on success, or raises an error on non-success.
-
- XXX: handle redirects?
+ Returns a tuple (cdx, blob) on success of single fetch, or raises an
+ error on non-success.
"""
- resp = requests.get(self.endpoint + url)
+ resp = self.http_session.get(self.v1endpoint + url)
if resp.status_code != 200:
raise SavePageNowError("HTTP status: {}, url: {}".format(resp.status_code, url))
+ terminal_url = '/'.join(resp.url.split('/')[5:])
body = resp.content
- cdx = self.cdx_client.lookup_latest(url)
+ cdx = self.cdx_client.lookup_latest(terminal_url)
+ if not cdx:
+ raise SavePageNowError("SPN was successful, but CDX lookup then failed")
return (cdx, body)
+ def save_url_now_v2(self, url):
+ """
+ Returns a list of cdx objects, or raises an error on non-success.
+ """
+ if not (self.ia_access_key and self.ia_secret_key):
+ raise Exception("SPNv2 requires authentication (IA_ACCESS_KEY/IA_SECRET_KEY)")
+ resp = self.v2_session.post(
+ self.v2endpoint,
+ data={
+ 'url': url,
+ 'capture_all': 1,
+ 'if_not_archived_within': '1d',
+ },
+ )
+ if resp.status_code != 200:
+ raise SavePageNowError("HTTP status: {}, url: {}".format(resp.status_code, url))
+ resp_json = resp.json()
+ assert resp_json
+
+ # poll until complete
+ for i in range(90):
+ resp = self.v2_session.get("{}/status/{}".format(self.v2endpoint, resp_json['job_id']))
+ resp.raise_for_status()
+ status = resp.json()['status']
+ if status == 'success':
+ resp = resp.json()
+ break
+ elif status == 'pending':
+ time.sleep(1.0)
+ else:
+ raise SavePageNowError("SPN2 status:{} url:{}".format(status, url))
+
+ return resp['resources']
+
diff --git a/python/sandcrawler/ingest.py b/python/sandcrawler/ingest.py
new file mode 100644
index 0000000..2469df6
--- /dev/null
+++ b/python/sandcrawler/ingest.py
@@ -0,0 +1,150 @@
+
+import sys
+import json
+import base64
+import requests
+from http.server import BaseHTTPRequestHandler, HTTPServer
+
+from sandcrawler.ia import SavePageNowClient, CdxApiClient, WaybackClient
+from sandcrawler.grobid import GrobidClient
+from sandcrawler.misc import gen_file_metadata
+from sandcrawler.html import extract_fulltext_url
+
+class FileIngester:
+
+ def __init__(self, **kwargs):
+
+ self.spn_client = kwargs.get('spn_client',
+ SavePageNowClient())
+ self.wayback_client = kwargs.get('wayback_client',
+ WaybackClient())
+ self.cdx_client = kwargs.get('cdx_client',
+ CdxApiClient())
+ self.grobid_client = kwargs.get('grobid_client',
+ GrobidClient())
+
+
+ def get_cdx_and_body(self, url):
+ """
+ Returns a CDX dict and body as a tuple.
+
+ If there isn't an existing wayback capture, take one now. Raises an
+ exception if can't capture, or if CDX API not available.
+
+ Raises an exception if can't find/fetch.
+
+ TODO:
+ - doesn't handle redirects (at CDX layer). could allow 3xx status codes and follow recursively
+ """
+
+ WAYBACK_ENDPOINT = "https://web.archive.org/web/"
+
+ cdx = self.cdx_client.lookup_latest(url)
+ if not cdx:
+ # sciencedirect.com (Elsevier) requires browser crawling (SPNv2)
+ if ('sciencedirect.com' in url and '.pdf' in url):
+ cdx_list = self.spn_client.save_url_now_v2(url)
+ for cdx_url in cdx_list:
+ if 'pdf.sciencedirectassets.com' in cdx_url and '.pdf' in cdx_url:
+ cdx = self.cdx_client.lookup_latest(cdx_url)
+ break
+ if 'osapublishing.org' in cdx_url and 'abstract.cfm' in cdx_url:
+ cdx = self.cdx_client.lookup_latest(cdx_url)
+ break
+ if not cdx:
+ raise Exception("Failed to crawl sciencedirect.com PDF URL")
+ else:
+ return self.spn_client.save_url_now_v1(url)
+
+ resp = requests.get(WAYBACK_ENDPOINT + cdx['datetime'] + "id_/" + cdx['url'])
+ if resp.status_code != 200:
+ raise WaybackError(resp.text)
+ body = resp.content
+ return (cdx, body)
+
+ def ingest_file(self, request):
+ """
+ 1. check sandcrawler-db for base_url
+ -> if found, populate terminal+wayback fields
+ 2. check CDX for base_url (only 200, past year)
+ -> if found, populate terminal+wayback fields
+ 3. if we have wayback, fetch that. otherwise do recursive SPN crawl
+ -> populate terminal+wayback
+ 4. calculate file_meta
+ -> populate file_meta
+ 5. check sandcrawler-db for GROBID XML
+ 6. run GROBID if we didn't already
+ -> push results to minio+sandcrawler-db
+ 7. decide if this was a hit
+
+ In all cases, print JSON status, and maybe push to sandcrawler-db
+ """
+
+ response = dict(request=request)
+ url = request['base_url']
+ while url:
+ (cdx_dict, body) = self.get_cdx_and_body(url)
+ sys.stderr.write("CDX hit: {}\n".format(cdx_dict))
+
+ response['cdx'] = cdx_dict
+ response['terminal'] = dict()
+ file_meta = gen_file_metadata(body)
+ mimetype = cdx_dict['mimetype']
+ if mimetype in ('warc/revisit', 'binary/octet-stream', 'application/octet-stream'):
+ mimetype = file_meta['mimetype']
+ if 'html' in mimetype:
+ page_metadata = extract_fulltext_url(response['cdx']['url'], body)
+ if page_metadata and page_metadata.get('pdf_url'):
+ url = page_metadata.get('pdf_url')
+ continue
+ elif page_metadata and page_metadata.get('next_url'):
+ url = page_metadata.get('next_url')
+ continue
+ else:
+ response['terminal']['html'] = page_metadata
+ response['status'] = 'no-pdf-link'
+ return response
+ elif 'pdf' in mimetype:
+ response['file_meta'] = file_meta
+ break
+ else:
+ response['status'] = 'other-mimetype'
+ return response
+
+ # if we got here, we have a PDF
+ sha1hex = response['file_meta']['sha1hex']
+
+ # do GROBID
+ response['grobid'] = self.grobid_client.process_fulltext(body)
+ sys.stderr.write("GROBID status: {}\n".format(response['grobid']['status']))
+
+ # TODO: optionally publish to Kafka here, but continue on failure (but
+ # send a sentry exception?)
+
+ # parse metadata, but drop fulltext from ingest response
+ if response['grobid']['status'] == 'success':
+ grobid_metadata = self.grobid_client.metadata(response['grobid'])
+ if grobid_metadata:
+ response['grobid'].update(grobid_metadata)
+ response['grobid'].pop('tei_xml')
+
+ # Ok, now what?
+ sys.stderr.write("GOT TO END\n")
+ response['status'] = "success"
+ response['hit'] = True
+ return response
+
+class IngestFileRequestHandler(BaseHTTPRequestHandler):
+ def do_POST(self):
+ if self.path != "/ingest":
+ self.send_response(404)
+ self.end_headers()
+ self.wfile.write("404: Not Found")
+ return
+ length = int(self.headers.get('content-length'))
+ request = json.loads(self.rfile.read(length).decode('utf-8'))
+ print("Got request: {}".format(request))
+ result = ingest_file(request)
+ self.send_response(200)
+ self.end_headers()
+ self.wfile.write(json.dumps(result))
diff --git a/python/sandcrawler/misc.py b/python/sandcrawler/misc.py
index 4ffc5d7..5713199 100644
--- a/python/sandcrawler/misc.py
+++ b/python/sandcrawler/misc.py
@@ -3,6 +3,10 @@ import base64
import magic
import hashlib
import datetime
+import requests
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error
+
def gen_file_metadata(blob):
"""
@@ -131,3 +135,23 @@ def parse_cdx_datetime(dt_str):
return datetime.strptime(dt_str, "%Y%m%d%H%M%S")
except Exception:
return None
+
+
+def requests_retry_session(retries=10, backoff_factor=3,
+ status_forcelist=(500, 502, 504), session=None):
+ """
+ From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests
+ """
+ session = session or requests.Session()
+ retry = Retry(
+ total=retries,
+ read=retries,
+ connect=retries,
+ backoff_factor=backoff_factor,
+ status_forcelist=status_forcelist,
+ )
+ adapter = HTTPAdapter(max_retries=retry)
+ session.mount('http://', adapter)
+ session.mount('https://', adapter)
+ return session
+
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-29 04:06:41 +0000