much progress on file ingest path

1 files changed, 4 insertions, 320 deletions

diff --git a/python/ingest_file.py b/python/ingest_file.py
index 4daa472..40eee4d 100755
--- a/python/ingest_file.py
+++ b/python/ingest_file.py
@@ -1,314 +1,12 @@
 #!/usr/bin/env python3
 
-"""
-IngestRequest
-  - ingest_type
-  - base_url
-  - release_stage
-  - release_id
-  - ext_ids
-    - doi
-    - pmcid
-    - ...
-  - expect_mimetypes
-  - project/source (?)
-  - expect_sha1
-
-FileIngestResult
-  - request (object)
-  - terminal
-    - url
-    - status_code
-  - wayback
-    - datetime
-    - archive_url
-  - file_meta
-    - size_bytes
-    - md5
-    - sha1
-    - sha256
-    - mimetype
-  - grobid
-    - version
-    - status_code
-    - xml_url
-    - release_id
-  - status (slug)
-  - hit (boolean)
-
-Simplified process, assuming totally new URL and PDF file:
-
-- crawl via SPN (including redirects, extraction)
-    => terminal
-    => wayback
-- calculate file metadata
-    => file_meta
-- run GROBID
-    => grobid
-
-Optimizations:
-
-- sandcrawler-db lookup of base_url: terminal+wayback
-- GWB CDX lookup of base_url: terminal+wayback
-- sandcrawler-db lookup of GROBID: grobid
-
-New "ingest" table?
-- base_url (indexed)
-- datetime
-- terminal_status
-- terminal_url
-- terminal_sha1
-- hit
-
-"""
-
 import sys
 import json
-import base64
-import hashlib
 import argparse
-import datetime
-import requests
-from http.server import BaseHTTPRequestHandler, HTTPServer
-
-from grobid2json import teixml2json
-
-
-GROBID_ENDPOINT = "http://grobid.qa.fatcat.wiki"
-
-class CDXApiError(Exception):
-    pass
-
-class WaybackError(Exception):
-    pass
-
-class SavePageNowError(Exception):
-    pass
-
-class SandcrawlerDB:
-
-    def __init__(self, **kwargs):
-        self.api_uri = kwargs.get('api_url',
-            "http://aitio.us.archive.org:3030")
-
-    def get_cdx(self, url):
-        resp = requests.get(self.api_url + "/cdx", params=dict(url='eq.'+url))
-        resp.raise_for_status()
-        return resp.json() or None
-
-    def get_grobid(self, sha1):
-        resp = requests.get(self.api_url + "/grobid", params=dict(sha1hex='eq.'+sha1))
-        resp.raise_for_status()
-        resp = resp.json()
-        if resp:
-            return resp[0]
-        else:
-            return None
-
-    def get_file_meta(self, sha1):
-        resp = requests.get(self.api_url + "/file_meta", params=dict(sha1hex='eq.'+sha1))
-        resp.raise_for_status()
-        resp = resp.json()
-        if resp:
-            return resp[0]
-        else:
-            return None
-
-def b32_hex(s):
-    s = s.strip().split()[0].lower()
-    if s.startswith("sha1:"):
-        s = s[5:]
-    if len(s) != 32:
-        return s
-    return base64.b16encode(base64.b32decode(s.upper())).lower().decode('utf-8')
-
-
-def cdx_api_lookup(url):
-    """
-    Returns a CDX dict, or None if not found.
-    """
-    CDX_API_ENDPOINT = "https://web.archive.org/cdx/search/cdx"
-
-    resp = requests.get(CDX_API_ENDPOINT, params={
-        'url': url,
-        'matchType': 'exact',
-        'limit': -1,
-        'filter': 'statuscode:200',
-        'output': 'json',
-    })
-    if resp.status_code != 200:
-        raise CDXApiError(resp.text)
-    rj = resp.json()
-    if len(rj) <= 1:
-        return None
-    cdx = rj[1]
-    assert len(cdx) == 7    # JSON is short
-    cdx = dict(
-        surt=cdx[0],
-        datetime=cdx[1],
-        url=cdx[2],
-        mimetype=cdx[3],
-        status_code=int(cdx[4]),
-        sha1b32=cdx[5],
-        sha1hex=b32_hex(cdx[5]),
-    )
-    return cdx
-
-def parse_html(body):
-    raise NotImplementedError()
 
-def save_url_now(url):
-    """
-    Tries to "save page now"
-    """
+from http.server import HTTPServer
+from sandcrawler.ingest import IngestFileRequestHandler, FileIngester
 
-    SPN_ENDPOINT = "https://web.archive.org/save/"
-    resp = requests.get(SPN_ENDPOINT + url)
-    if resp.status_code != 200:
-        raise SavePageNowError("HTTP status: {}, url: {}".format(resp.status_code, url))
-    cdx = cdx_api_lookup(url)
-    body = resp.content
-    return (cdx, body)
-
-def get_cdx_and_body(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 = cdx_api_lookup(url)
-    if not cdx:
-        return save_url_now(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 file_metadata(blob):
-    """
-    Returns a dict: size_bytes, md5, sha1, sha256
-    """
-    hashes = [
-        hashlib.sha1(),
-        hashlib.sha256(),
-        hashlib.md5(),
-    ]
-    for h in hashes:
-        h.update(blob)
-    return dict(
-        size_bytes=len(blob),
-        sha1=hashes[0].hexdigest(),
-        sha256=hashes[1].hexdigest(),
-        md5=hashes[2].hexdigest(),
-    )
-
-
-def do_grobid(sha1hex, blob):
-    grobid_response = requests.post(
-        GROBID_ENDPOINT + "/api/processFulltextDocument",
-        files={'input': blob, 'consolidateHeader': '2'},
-    )
-
-    info = dict(
-        sha1hex=sha1hex,
-        status_code=grobid_response.status_code,
-    )
-    # 4 MByte XML size limit; don't record GROBID status on this path
-    if len(grobid_response.content) > 4000000:
-        info['status'] = 'oversize'
-        return info
-    if grobid_response.status_code != 200:
-        # response.text is .content decoded as utf-8
-        info['status'] = 'error'
-        info['error_msg'] = grobid_response.text[:10000]
-        dict(status='error', description=grobid_response.text)
-        return info, dict(status="error", reason="non-200 GROBID HTTP status",
-            extra=grobid_response.text)
-    else:
-        info['status'] = 'success'
-
-    metadata = teixml2json(grobid_response.text, encumbered=False)
-    year = None
-    mdate = metadata.get('date')
-    if mdate and len(mdate) >= 4:
-        year = int(mdate[0:4])
-    info['metadata'] = dict(
-        title=metadata.get('title'),
-        authors=metadata.get('authors'),
-        journal=metadata.get('journal'),
-        year=metadata.get('year'),
-        # TODO: any other biblio-glutton fields? first-page, volume
-    )
-    info['version'] = metadata.get('grobid_version')
-    info['timestamp'] = metadata.get('grobid_timestamp')
-    info['glutton_fatcat'] = metadata.get('fatcat_release')
-    # TODO: push to kafka
-    return info
-
-def ingest_file(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) = get_cdx_and_body(url)
-        sys.stderr.write("CDX hit: {}\n".format(cdx_dict))
-
-        response['cdx'] = cdx_dict
-        response['terminal'] = dict()
-        if 'html' in cdx_dict['mimetype']:
-            page_metadata = parse_html(body)
-            if page_metadata.get('pdf_url'):
-                url = page_metadata.get('pdf_url')
-                continue
-            response['terminal']['html'] = page_metadata
-            response['status'] = 'no-pdf-link'
-            return response
-        elif 'pdf' in cdx_dict['mimetype']:
-            break
-        else:
-            response['status'] = 'other-mimetype'
-            return response
-
-    # if we got here, we have a PDF
-    response['file_meta'] = file_metadata(body)
-    sha1hex = response['file_meta']['sha1']
-
-    # do GROBID
-    response['grobid'] = do_grobid(sha1hex, body)
-    sys.stderr.write("GROBID status: {}\n".format(response['grobid']['status']))
-
-    # Ok, now what?
-    sys.stderr.write("GOT TO END\n")
-    response['status'] = "success"
-    response['hit'] = True
-    return response
 
 def run_single_ingest(args):
     request = dict(
@@ -316,7 +14,8 @@ def run_single_ingest(args):
         ext_ids=dict(doi=args.doi),
         release_id=args.release_id,
     )
-    result = ingest_file(request)
+    ingester = FileIngester()
+    result = ingester.ingest_file(request)
     print(json.dumps(result))
     return result
 
@@ -326,21 +25,6 @@ def run_requests(args):
         result = ingest_file(request)
         print(json.dumps(result))
 
-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))
-
 def run_api(args):
     port = 8083
     print("Listening on localhost:{}".format(port))