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-rw-r--r--python/fatcat_tools/importers/__init__.py3
-rw-r--r--python/fatcat_tools/importers/common.py158
-rw-r--r--python/fatcat_tools/importers/crossref.py2
-rw-r--r--python/fatcat_tools/importers/datacite.py10
-rw-r--r--python/fatcat_tools/importers/doaj_article.py358
-rw-r--r--python/fatcat_tools/importers/ingest.py329
6 files changed, 648 insertions, 212 deletions
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index b82eb11a..d2928d09 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -27,6 +27,7 @@ from .orcid import OrcidImporter
from .arabesque import ArabesqueMatchImporter, ARABESQUE_MATCH_WHERE_CLAUSE
from .wayback_static import auto_wayback_static
from .cdl_dash_dat import auto_cdl_dash_dat
-from .ingest import IngestFileResultImporter, SavePaperNowFileImporter
+from .ingest import IngestFileResultImporter, SavePaperNowFileImporter, IngestWebResultImporter
from .shadow import ShadowLibraryImporter
from .file_meta import FileMetaImporter
+from .doaj_article import DoajArticleImporter
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 14415683..3c810391 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -3,12 +3,9 @@ import re
import sys
import csv
import json
-import ftfy
-import base64
import sqlite3
import datetime
import subprocess
-import unicodedata
from collections import Counter
from confluent_kafka import Consumer, KafkaException
import xml.etree.ElementTree as ET
@@ -18,162 +15,13 @@ from bs4 import BeautifulSoup
import fatcat_openapi_client
from fatcat_openapi_client.rest import ApiException
+# TODO: refactor so remove need for this (re-imports for backwards compatibility)
+from fatcat_tools.normal import (clean_str as clean, is_cjk, b32_hex, LANG_MAP_MARC) # noqa: F401
DATE_FMT = "%Y-%m-%d"
SANE_MAX_RELEASES = 200
SANE_MAX_URLS = 100
-# These are very close, but maybe not exactly 1-to-1 with 639-2? Some mix of
-# 2/T and 2/B?
-# PubMed/MEDLINE and JSTOR use these MARC codes
-# https://www.loc.gov/marc/languages/language_name.html
-LANG_MAP_MARC = {
- 'afr': 'af',
- 'alb': 'sq',
- 'amh': 'am',
- 'ara': 'ar',
- 'arm': 'hy',
- 'aze': 'az',
- 'ben': 'bn',
- 'bos': 'bs',
- 'bul': 'bg',
- 'cat': 'ca',
- 'chi': 'zh',
- 'cze': 'cs',
- 'dan': 'da',
- 'dut': 'nl',
- 'eng': 'en',
- 'epo': 'eo',
- 'est': 'et',
- 'fin': 'fi',
- 'fre': 'fr',
- 'geo': 'ka',
- 'ger': 'de',
- 'gla': 'gd',
- 'gre': 'el',
- 'heb': 'he',
- 'hin': 'hi',
- 'hrv': 'hr',
- 'hun': 'hu',
- 'ice': 'is',
- 'ind': 'id',
- 'ita': 'it',
- 'jpn': 'ja',
- 'kin': 'rw',
- 'kor': 'ko',
- 'lat': 'la',
- 'lav': 'lv',
- 'lit': 'lt',
- 'mac': 'mk',
- 'mal': 'ml',
- 'mao': 'mi',
- 'may': 'ms',
- 'nor': 'no',
- 'per': 'fa',
- 'per': 'fa',
- 'pol': 'pl',
- 'por': 'pt',
- 'pus': 'ps',
- 'rum': 'ro',
- 'rus': 'ru',
- 'san': 'sa',
- 'slo': 'sk',
- 'slv': 'sl',
- 'spa': 'es',
- 'srp': 'sr',
- 'swe': 'sv',
- 'tha': 'th',
- 'tur': 'tr',
- 'ukr': 'uk',
- 'urd': 'ur',
- 'vie': 'vi',
- 'wel': 'cy',
-
-# additions
- 'gle': 'ga', # "Irish" (Gaelic)
- 'jav': 'jv', # Javanese
- 'welsh': 'cy', # Welsh
- 'oci': 'oc', # Occitan
-
-# Don't have ISO 639-1 codes
- 'grc': 'el', # Ancient Greek; map to modern greek
- 'map': None, # Austronesian (collection)
- 'syr': None, # Syriac, Modern
- 'gem': None, # Old Saxon
- 'non': None, # Old Norse
- 'emg': None, # Eastern Meohang
- 'neg': None, # Negidal
- 'mul': None, # Multiple languages
- 'und': None, # Undetermined
-}
-
-
-def clean(thing, force_xml=False):
- """
- This function is appropriate to be called on any random, non-markup string,
- such as author names, titles, etc.
-
- It will try to clean up common unicode mangles, HTML characters, etc.
-
- This will detect XML/HTML and "do the right thing" (aka, not remove
- entities like '&amp' if there are tags in the string), unless you pass the
- 'force_xml' parameter, which might be appropriate for, eg, names and
- titles, which generally should be projected down to plain text.
-
- Also strips extra whitespace.
- """
- if not thing:
- return None
- fix_entities = 'auto'
- if force_xml:
- fix_entities = True
- fixed = ftfy.fix_text(thing, fix_entities=fix_entities).strip()
- if not fixed or len(fixed) <= 1:
- # wasn't zero-length before, but is now; return None
- return None
- return fixed
-
-def test_clean():
-
- assert clean(None) == None
- assert clean('') == None
- assert clean('1') == None
- assert clean('123') == '123'
- assert clean('a&amp;b') == 'a&b'
- assert clean('<b>a&amp;b</b>') == '<b>a&amp;b</b>'
- assert clean('<b>a&amp;b</b>', force_xml=True) == '<b>a&b</b>'
-
-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 is_cjk(s):
- if not s:
- return False
- for c in s:
- if c.isalpha():
- lang_prefix = unicodedata.name(c).split()[0]
- return lang_prefix in ('CJK', 'HIRAGANA', 'KATAKANA', 'HANGUL')
- return False
-
-def test_is_cjk():
- assert is_cjk(None) is False
- assert is_cjk('') is False
- assert is_cjk('blah') is False
- assert is_cjk('岡, 鹿, 梨, 阜, 埼') is True
- assert is_cjk('[岡, 鹿, 梨, 阜, 埼]') is True
- assert is_cjk('菊') is True
- assert is_cjk('岡, 鹿, 梨, 阜, 埼 with eng after') is True
- assert is_cjk('水道') is True
- assert is_cjk('オウ, イク') is True # kanji
- assert is_cjk('ひヒ') is True
- assert is_cjk('き゚ゅ') is True
- assert is_cjk('ㄴ, ㄹ, ㅁ, ㅂ, ㅅ') is True
-
DOMAIN_REL_MAP = {
"archive.org": "archive",
# LOCKSS, Portico, DuraSpace, etc would also be "archive"
@@ -444,6 +292,7 @@ class EntityImporter:
raise NotImplementedError
def is_orcid(self, orcid):
+ # TODO: replace with clean_orcid() from fatcat_tools.normal
return self._orcid_regex.match(orcid) is not None
def lookup_orcid(self, orcid):
@@ -464,6 +313,7 @@ class EntityImporter:
return creator_id
def is_doi(self, doi):
+ # TODO: replace with clean_doi() from fatcat_tools.normal
return doi.startswith("10.") and doi.count("/") >= 1
def lookup_doi(self, doi):
diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py
index 71f08952..e77fa65e 100644
--- a/python/fatcat_tools/importers/crossref.py
+++ b/python/fatcat_tools/importers/crossref.py
@@ -487,8 +487,6 @@ class CrossrefImporter(EntityImporter):
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
- # doesn't exist, need to update
- return True
# eventually we'll want to support "updates", but for now just skip if
# entity already exists
diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py
index 86740e80..70f8db86 100644
--- a/python/fatcat_tools/importers/datacite.py
+++ b/python/fatcat_tools/importers/datacite.py
@@ -151,7 +151,7 @@ UNKNOWN_MARKERS = set(DATACITE_UNKNOWN_MARKERS).union(set((
'Unknown',
)))
-# UNKNOWN_MARKERS_LOWER are lowercase version of UNKNOWN blacklist.
+# UNKNOWN_MARKERS_LOWER are lowercase version of UNKNOWN blocklist.
UNKNOWN_MARKERS_LOWER = set((v.lower() for v in UNKNOWN_MARKERS))
# Any "min" number of "tokens" will signal "spam", https://fatcat.wiki/release/rzcpjwukobd4pj36ipla22cnoi
@@ -346,7 +346,7 @@ class DataciteImporter(EntityImporter):
print('[{}] skipping record w/o title: {}'.format(doi, obj), file=sys.stderr)
return False
- # check for blacklisted "spam", e.g. "FULL MOVIE"
+ # check for blocklisted "spam", e.g. "FULL MOVIE"
for rule in DATACITE_TITLE_SPAM_WORDGROUPS:
seen = set()
for token in rule.get("tokens", []):
@@ -781,8 +781,6 @@ class DataciteImporter(EntityImporter):
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
- # doesn't exist, need to update
- return True
# eventually we'll want to support "updates", but for now just skip if
# entity already exists
@@ -819,7 +817,7 @@ class DataciteImporter(EntityImporter):
contribs = []
# Names, that should be ignored right away.
- name_blacklist = set(('Occdownload Gbif.Org',))
+ name_blocklist = set(('Occdownload Gbif.Org',))
i = 0
for c in creators:
@@ -861,7 +859,7 @@ class DataciteImporter(EntityImporter):
continue
if not name:
name = "{} {}".format(given_name or '', surname or '').strip()
- if name in name_blacklist:
+ if name in name_blocklist:
continue
if name.lower() in UNKNOWN_MARKERS_LOWER:
continue
diff --git a/python/fatcat_tools/importers/doaj_article.py b/python/fatcat_tools/importers/doaj_article.py
new file mode 100644
index 00000000..03752484
--- /dev/null
+++ b/python/fatcat_tools/importers/doaj_article.py
@@ -0,0 +1,358 @@
+"""
+Importer for DOAJ article-level metadata, schema v1.
+
+DOAJ API schema and docs: https://doaj.org/api/v1/docs
+"""
+
+import warnings
+import datetime
+from typing import List, Optional
+
+import fatcat_openapi_client
+from fatcat_tools.normal import (clean_doi, clean_str, parse_month,
+ clean_orcid, detect_text_lang, parse_lang_name, parse_country_name,
+ clean_pmid, clean_pmcid)
+from fatcat_tools.importers.common import EntityImporter
+
+# Cutoff length for abstracts.
+MAX_ABSTRACT_LENGTH = 2048
+
+
+class DoajArticleImporter(EntityImporter):
+
+ def __init__(self,
+ api,
+ issn_map_file,
+ **kwargs):
+
+ eg_desc = kwargs.get(
+ 'editgroup_description',
+ "Automated import of DOAJ article metadata, harvested from REST API or bulk dumps"
+ )
+ eg_extra = kwargs.get('editgroup_extra', dict())
+ eg_extra['agent'] = eg_extra.get('agent',
+ 'fatcat_tools.DoajArticleImporter')
+ # ensure default is to not do updates with this worker (override super() default)
+ kwargs['do_updates'] = kwargs.get("do_updates", False)
+ super().__init__(api,
+ issn_map_file=issn_map_file,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs)
+
+ self.this_year = datetime.datetime.now().year
+ self.read_issn_map_file(issn_map_file)
+
+ def want(self, obj):
+ return True
+
+ def parse_record(self, obj):
+ """
+ bibjson {
+ abstract (string, optional),
+ author (Array[bibjson.author], optional),
+ identifier (Array[bibjson.identifier]),
+ journal (bibjson.journal, optional),
+ keywords (Array[string], optional),
+ link (Array[bibjson.link], optional),
+ month (string, optional),
+ subject (Array[bibjson.subject], optional),
+ title (string),
+ year (string, optional)
+ }
+ bibjson.journal {
+ country (string, optional),
+ end_page (string, optional),
+ language (Array[string], optional),
+ license (Array[bibjson.journal.license], optional),
+ number (string, optional),
+ publisher (string, optional),
+ start_page (string, optional),
+ title (string, optional),
+ volume (string, optional)
+ }
+ """
+
+ if not obj or not isinstance(obj, dict) or not 'bibjson' in obj:
+ self.counts['skip-empty'] += 1
+ return None
+
+ bibjson = obj['bibjson']
+
+ title = clean_str(bibjson.get('title'), force_xml=True)
+ if not title:
+ self.counts['skip-title'] += 1
+ return False
+
+ container_name = clean_str(bibjson['journal']['title'])
+ container_id = None
+ # NOTE: 'issns' not documented in API schema
+ for issn in bibjson['journal']['issns']:
+ issnl = self.issn2issnl(issn)
+ if issnl:
+ container_id = self.lookup_issnl(self.issn2issnl(issn))
+ if container_id:
+ # don't store container_name when we have an exact match
+ container_name = None
+ break
+
+ volume = clean_str(bibjson['journal'].get('volume'))
+ # NOTE: this schema seems to use "number" as "issue number"
+ issue = clean_str(bibjson['journal'].get('number'))
+ publisher = clean_str(bibjson['journal'].get('publisher'))
+
+ try:
+ release_year = int(bibjson.get('year'))
+ except (TypeError, ValueError):
+ release_year = None
+ release_month = parse_month(clean_str(bibjson.get('month')))
+
+ # block bogus far-future years/dates
+ if release_year is not None and (release_year > (self.this_year + 5) or release_year < 1000):
+ release_month = None
+ release_year = None
+
+ license_slug = self.doaj_license_slug(bibjson['journal'].get('license'))
+ country = parse_country_name(bibjson['journal'].get('country'))
+ language = None
+ for raw in bibjson['journal'].get('language') or []:
+ language = parse_lang_name(raw)
+ if language:
+ break
+
+ # pages
+ # NOTE: error in API docs? seems like start_page not under 'journal' object
+ start_page = clean_str(bibjson['journal'].get('start_page')) or clean_str(bibjson.get('start_page'))
+ end_page = clean_str(bibjson['journal'].get('end_page')) or clean_str(bibjson.get('end_page'))
+ pages: Optional[str] = None
+ if start_page and end_page:
+ pages = f"{start_page}-{end_page}"
+ elif start_page:
+ pages = start_page
+
+ doaj_article_id = obj['id'].lower()
+ ext_ids = self.doaj_ext_ids(bibjson['identifier'], doaj_article_id)
+ abstracts = self.doaj_abstracts(bibjson)
+ contribs = self.doaj_contribs(bibjson.get('author') or [])
+
+ # DOAJ-specific extra
+ doaj_extra = dict()
+ if bibjson.get('subject'):
+ doaj_extra['subject'] = bibjson.get('subject')
+ if bibjson.get('keywords'):
+ doaj_extra['keywords'] = [k for k in [clean_str(s) for s in bibjson.get('keywords')] if k]
+
+ # generic extra
+ extra = dict()
+ if country:
+ extra['country'] = country
+ if not container_id and container_name:
+ extra['container_name'] = container_name
+ if release_year and release_month:
+ # TODO: schema migration
+ extra['release_month'] = release_month
+
+ if doaj_extra:
+ extra['doaj'] = doaj_extra
+ if not extra:
+ extra = None
+
+ re = fatcat_openapi_client.ReleaseEntity(
+ work_id=None,
+ container_id=container_id,
+ release_type='article-journal',
+ release_stage='published',
+ title=title,
+ release_year=release_year,
+ #release_date,
+ publisher=publisher,
+ ext_ids=ext_ids,
+ contribs=contribs,
+ volume=volume,
+ issue=issue,
+ pages=pages,
+ language=language,
+ abstracts=abstracts,
+ extra=extra,
+ license_slug=license_slug,
+ )
+ re = self.biblio_hacks(re)
+ return re
+
+ @staticmethod
+ def biblio_hacks(re):
+ """
+ This function handles known special cases. For example,
+ publisher-specific or platform-specific workarounds.
+ """
+ return re
+
+ def try_update(self, re):
+
+ # lookup existing release by DOAJ article id
+ existing = None
+ try:
+ existing = self.api.lookup_release(doaj=re.ext_ids.doaj)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+
+ # then try other ext_id lookups
+ if not existing:
+ for extid_type in ('doi', 'pmid', 'pmcid'):
+ extid_val = getattr(re.ext_ids, extid_type)
+ if not extid_val:
+ continue
+ #print(f" lookup release type: {extid_type} val: {extid_val}")
+ try:
+ existing = self.api.lookup_release(**{extid_type: extid_val})
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+ if existing:
+ if existing.ext_ids.doaj:
+ warn_str = f"unexpected DOAJ ext_id match after lookup failed doaj={re.ext_ids.doaj} ident={existing.ident}"
+ warnings.warn(warn_str)
+ self.counts["skip-doaj-id-mismatch"] += 1
+ return False
+ break
+
+ # TODO: in the future could do fuzzy match here, eg using elasticsearch
+
+ # create entity
+ if not existing:
+ return True
+
+ # other logic could go here about skipping updates
+ if not self.do_updates or existing.ext_ids.doaj:
+ self.counts['exists'] += 1
+ return False
+
+ # fields to copy over for update
+ existing.ext_ids.doaj = existing.ext_ids.doaj or re.ext_ids.doaj
+ existing.release_type = existing.release_type or re.release_type
+ existing.release_stage = existing.release_stage or re.release_stage
+ existing.container_id = existing.container_id or re.container_id
+ existing.abstracts = existing.abstracts or re.abstracts
+ existing.extra['doaj'] = re.extra['doaj']
+ existing.volume = existing.volume or re.volume
+ existing.issue = existing.issue or re.issue
+ existing.pages = existing.pages or re.pages
+ existing.language = existing.language or re.language
+
+ try:
+ self.api.update_release(self.get_editgroup_id(), existing.ident, existing)
+ self.counts['update'] += 1
+ except fatcat_openapi_client.rest.ApiException as err:
+ # there is a code path where we try to update the same release
+ # twice in a row; if that happens, just skip
+ # NOTE: API behavior might change in the future?
+ if "release_edit_editgroup_id_ident_id_key" in err.body:
+ self.counts['skip-update-conflict'] += 1
+ return False
+ else:
+ raise err
+
+ return False
+
+ def insert_batch(self, batch):
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
+ description=self.editgroup_description,
+ extra=self.editgroup_extra),
+ entity_list=batch))
+
+ def doaj_abstracts(self, bibjson: dict) -> List[fatcat_openapi_client.ReleaseAbstract]:
+ text = clean_str(bibjson.get('abstract'))
+ if not text or len(text) < 10:
+ return []
+ if len(text) > MAX_ABSTRACT_LENGTH:
+ text = text[:MAX_ABSTRACT_LENGTH] + " [...]"
+
+ lang = detect_text_lang(text)
+
+ abstract = fatcat_openapi_client.ReleaseAbstract(
+ mimetype="text/plain",
+ content=text,
+ lang=lang,
+ )
+
+ return [abstract,]
+
+ def doaj_contribs(self, authors: List[dict]) -> List[fatcat_openapi_client.ReleaseContrib]:
+ """
+ bibjson.author {
+ affiliation (string, optional),
+ name (string),
+ orcid_id (string, optional)
+ }
+ """
+ contribs = []
+ index = 0
+ for author in authors:
+ if not author.get('name'):
+ continue
+ creator_id = None
+ orcid = clean_orcid(author.get('orcid_id'))
+ if orcid:
+ creator_id = self.lookup_orcid(orcid)
+ contribs.append(fatcat_openapi_client.ReleaseContrib(
+ raw_name=author.get('name'),
+ role='author',
+ index=index,
+ creator_id=creator_id,
+ raw_affiliation=clean_str(author.get('affiliation')),
+ ))
+ index += 1
+ return contribs
+
+ def doaj_ext_ids(self, identifiers: List[dict], doaj_article_id: str) -> fatcat_openapi_client.ReleaseExtIds:
+ """
+ bibjson.identifier {
+ id (string),
+ type (string)
+ }
+ """
+
+ assert doaj_article_id.isalnum() and len(doaj_article_id) == 32
+
+ doi: Optional[str] = None
+ pmid: Optional[str] = None
+ pmcid: Optional[str] = None
+ for id_obj in identifiers:
+ if not id_obj.get('id'):
+ continue
+ if id_obj['type'].lower() == 'doi':
+ doi = clean_doi(id_obj['id'])
+ elif id_obj['type'].lower() == 'pmid':
+ pmid = clean_pmid(id_obj['id'])
+ elif id_obj['type'].lower() == 'pmcid':
+ pmcid = clean_pmcid(id_obj['id'])
+
+ return fatcat_openapi_client.ReleaseExtIds(
+ doaj=doaj_article_id,
+ doi=doi,
+ pmid=pmid,
+ pmcid=pmcid,
+ )
+
+ def doaj_license_slug(self, license_list: List[dict]) -> Optional[str]:
+ """
+ bibjson.journal.license {
+ open_access (boolean, optional),
+ title (string, optional),
+ type (string, optional),
+ url (string, optional),
+ version (string, optional)
+ }
+ """
+ if not license_list:
+ return None
+ for license in license_list:
+ if not license.get('open_access'):
+ continue
+ slug = license.get('type')
+ if slug.startswith('CC '):
+ slug = slug.replace('CC ', 'cc-').lower()
+ return slug
+ return None
diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py
index 4b1d3702..1e04e712 100644
--- a/python/fatcat_tools/importers/ingest.py
+++ b/python/fatcat_tools/importers/ingest.py
@@ -1,4 +1,6 @@
+import datetime
+
import fatcat_openapi_client
from .common import EntityImporter, make_rel_url
@@ -20,10 +22,10 @@ class IngestFileResultImporter(EntityImporter):
assert self.default_link_rel
self.require_grobid = require_grobid
if self.require_grobid:
- print("Requiring GROBID status == 200")
+ print("Requiring GROBID status == 200 (for PDFs)")
else:
print("NOT checking GROBID success")
- self.ingest_request_source_whitelist = [
+ self.ingest_request_source_allowlist = [
'fatcat-changelog',
'fatcat-ingest-container',
'fatcat-ingest',
@@ -35,23 +37,41 @@ class IngestFileResultImporter(EntityImporter):
's2-corpus',
's2',
]
- if kwargs.get('skip_source_whitelist', False):
- self.ingest_request_source_whitelist = []
+ if kwargs.get('skip_source_allowlist', False):
+ self.ingest_request_source_allowlist = []
- def want(self, row):
+ def want_file(self, row) -> bool:
+ """
+ File-specific part of want(). Generic across general ingest and save-paper-now.
"""
- Logic here probably needs work (TODO):
- - Direct ingests via DOI from fatcat-changelog should probably go
- through regardless of GROBID status
- - We should filter/block things like single-page PDFs here
- - public/anonymous submissions could require successful biblio-glutton
- match, or some other sanity check on the fatcat side (eg, fuzzy title
- match)
- - handle the case of release_stage not being 'published'; if pre-print,
- potentially create a new release.
+ if not row.get('file_meta'):
+ self.counts['skip-file-meta'] += 1
+ return False
- The current logic is intentionally conservative as a first step.
+ # type-specific filters
+ if row['request'].get('ingest_type') == 'pdf':
+ if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
+ self.counts['skip-grobid'] += 1
+ return False
+ if row['file_meta'].get('mimetype') not in ("application/pdf",):
+ self.counts['skip-mimetype'] += 1
+ return False
+ elif row['request'].get('ingest_type') == 'xml':
+ if row['file_meta'].get('mimetype') not in ("application/xml",
+ "application/jats+xml", "application/tei+xml", "text/xml"):
+ self.counts['skip-mimetype'] += 1
+ return False
+ else:
+ self.counts['skip-ingest-type'] += 1
+ return False
+
+ return True
+
+ def want_ingest(self, row) -> bool:
+ """
+ Sandcrawler ingest-specific part of want(). Generic across file and
+ webcapture ingest.
"""
if row.get('hit') != True:
self.counts['skip-hit'] += 1
@@ -60,33 +80,48 @@ class IngestFileResultImporter(EntityImporter):
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
- if self.ingest_request_source_whitelist and source not in self.ingest_request_source_whitelist:
+ if self.ingest_request_source_allowlist and source not in self.ingest_request_source_allowlist:
self.counts['skip-ingest_request_source'] += 1
return False
- if source.startswith('arabesque'):
- if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2'):
- self.counts['skip-arabesque-source'] += 1
- return False
+
+ if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2'):
+ self.counts['skip-link-source'] += 1
+ return False
+
if source.startswith('savepapernow'):
# never process async savepapernow requests
self.counts['skip-savepapernow'] += 1
return False
- if not row.get('file_meta'):
- self.counts['skip-file-meta'] += 1
+
+ return True
+
+ def want(self, row):
+ """
+ Overall logic here probably needs work (TODO):
+
+ - Direct ingests via DOI from fatcat-changelog should probably go
+ through regardless of GROBID status
+ - We should filter/block things like single-page PDFs here
+ - public/anonymous submissions could require successful biblio-glutton
+ match, or some other sanity check on the fatcat side (eg, fuzzy title
+ match)
+ - handle the case of release_stage not being 'published'; if pre-print,
+ potentially create a new release.
+
+ The current logic is intentionally conservative as a first step.
+ """
+ if not self.want_file(row):
return False
- if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
- self.counts['skip-grobid'] += 1
+ if not self.want_ingest(row):
return False
return True
- def parse_record(self, row):
+ def parse_ingest_release_ident(self, row):
request = row['request']
fatcat = request.get('fatcat')
- file_meta = row['file_meta']
- # identify release by fatcat ident, or extid lookup, or biblio-glutton match
release_ident = None
if fatcat and fatcat.get('release_ident'):
release_ident = fatcat.get('release_ident')
@@ -112,23 +147,21 @@ class IngestFileResultImporter(EntityImporter):
return None
release_ident = release.ident
break
+
if self.use_glutton_match and not release_ident and row.get('grobid'):
# try biblio-glutton extracted hit
if row['grobid'].get('fatcat_release'):
release_ident = row['grobid']['fatcat_release'].split('_')[-1]
self.counts['glutton-match'] += 1
- if not release_ident:
- self.counts['skip-release-not-found'] += 1
- return None
+ return release_ident
+ def parse_terminal(self, row):
terminal = row.get('terminal')
if not terminal:
# support old cdx-only ingest results
cdx = row.get('cdx')
if not cdx:
- # TODO: support archive.org hits?
- self.counts['skip-no-terminal'] += 1
return None
else:
terminal = {
@@ -142,7 +175,15 @@ class IngestFileResultImporter(EntityImporter):
terminal['terminal_url'] = terminal['url']
if not 'terminal_dt' in terminal:
terminal['terminal_dt'] = terminal['dt']
+
+ # convert CDX-style digits to ISO-style timestamp
assert len(terminal['terminal_dt']) == 14
+ terminal['terminal_timestamp'] = datetime.datetime.strptime(terminal['terminal_dt'], "%Y%m%d%H%M%S").isoformat() + "Z"
+ return terminal
+
+ def parse_urls(self, row, terminal):
+
+ request = row['request']
default_rel = self.default_link_rel
if request.get('link_source') == 'doi':
@@ -159,6 +200,55 @@ class IngestFileResultImporter(EntityImporter):
urls = [url, ("webarchive", wayback)]
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
+ return urls
+
+ def parse_edit_extra(self, row):
+
+ request = row['request']
+ edit_extra = dict()
+
+ if request.get('edit_extra'):
+ edit_extra = request['edit_extra']
+
+ if request.get('ingest_request_source'):
+ edit_extra['ingest_request_source'] = request['ingest_request_source']
+ if request.get('link_source') and request.get('link_source_id'):
+ edit_extra['link_source'] = request['link_source']
+ edit_extra['link_source_id'] = request['link_source_id']
+
+ return edit_extra
+
+ def parse_record(self, row):
+
+ request = row['request']
+ file_meta = row['file_meta']
+
+ # double check that want() filtered request correctly (eg, old requests)
+ if request.get('ingest_type') not in ('pdf', 'xml'):
+ self.counts['skip-ingest-type'] += 1
+ return None
+ assert (request['ingest_type'], file_meta['mimetype']) in [
+ ("pdf", "application/pdf"),
+ ("xml", "application/xml"),
+ ("xml", "application/jats+xml"),
+ ("xml", "application/tei+xml"),
+ ("xml", "text/xml"),
+ ]
+
+ # identify release by fatcat ident, or extid lookup, or biblio-glutton match
+ release_ident = self.parse_ingest_release_ident(row)
+
+ if not release_ident:
+ self.counts['skip-release-not-found'] += 1
+ return None
+
+ terminal = self.parse_terminal(row)
+ if not terminal:
+ # TODO: support archive.org hits?
+ self.counts['skip-no-terminal'] += 1
+ return None
+
+ urls = self.parse_urls(row, terminal)
fe = fatcat_openapi_client.FileEntity(
md5=file_meta['md5hex'],
@@ -169,17 +259,10 @@ class IngestFileResultImporter(EntityImporter):
release_ids=[release_ident],
urls=urls,
)
- if request.get('edit_extra'):
- fe.edit_extra = request['edit_extra']
- else:
- fe.edit_extra = dict()
- if request.get('ingest_request_source'):
- fe.edit_extra['ingest_request_source'] = request['ingest_request_source']
- if request.get('link_source') and request.get('link_source_id'):
- fe.edit_extra['link_source'] = request['link_source']
- fe.edit_extra['link_source_id'] = request['link_source_id']
- if not fe.edit_extra:
- fe.edit_extra = None
+
+ edit_extra = self.parse_edit_extra(row)
+ if edit_extra:
+ fe.edit_extra = edit_extra
return fe
def try_update(self, fe):
@@ -244,6 +327,9 @@ class SavePaperNowFileImporter(IngestFileResultImporter):
def want(self, row):
+ if not self.want_file(row):
+ return False
+
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
@@ -254,12 +340,6 @@ class SavePaperNowFileImporter(IngestFileResultImporter):
if row.get('hit') != True:
self.counts['skip-hit'] += 1
return False
- if not row.get('file_meta'):
- self.counts['skip-file-meta'] += 1
- return False
- if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
- self.counts['skip-grobid'] += 1
- return False
return True
@@ -280,3 +360,154 @@ class SavePaperNowFileImporter(IngestFileResultImporter):
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
+
+
+class IngestWebResultImporter(IngestFileResultImporter):
+ """
+ Variant of IngestFileResultImporter for processing HTML ingest requests
+ into webcapture objects.
+ """
+
+ def __init__(self, api, **kwargs):
+
+ eg_desc = kwargs.pop('editgroup_description', None) or "Webcaptures crawled from web using sandcrawler ingest tool"
+ eg_extra = kwargs.pop('editgroup_extra', dict())
+ eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestWebResultImporter')
+ kwargs['do_updates'] = False
+ super().__init__(api,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs)
+
+ def want(self, row):
+
+ if not self.want_ingest(row):
+ return False
+
+ if not row.get('file_meta'):
+ self.counts['skip-file-meta'] += 1
+ return False
+
+ # webcapture-specific filters
+ if row['request'].get('ingest_type') != 'html':
+ self.counts['skip-ingest-type'] += 1
+ return False
+ if row['file_meta'].get('mimetype') not in ("text/html", "application/xhtml+xml"):
+ self.counts['skip-mimetype'] += 1
+ return False
+
+ return True
+
+ def parse_record(self, row):
+
+ request = row['request']
+ file_meta = row['file_meta']
+
+ # double check that want() filtered request correctly (eg, old requests)
+ if request.get('ingest_type') != "html":
+ self.counts['skip-ingest-type'] += 1
+ return None
+ if file_meta['mimetype'] not in ("text/html", "application/xhtml+xml"):
+ self.counts['skip-mimetype'] += 1
+ return None
+
+ # identify release by fatcat ident, or extid lookup
+ release_ident = self.parse_ingest_release_ident(row)
+
+ if not release_ident:
+ self.counts['skip-release-not-found'] += 1
+ return None
+
+ terminal = self.parse_terminal(row)
+ if not terminal:
+ # TODO: support archive.org hits?
+ self.counts['skip-no-terminal'] += 1
+ return None
+
+ urls = self.parse_urls(row, terminal)
+ archive_urls = [u for u in urls if u.rel == 'webarchive']
+
+ if terminal['terminal_status_code'] != 200:
+ self.counts['skip-terminal-status-code'] += 1
+ return None
+
+ terminal_cdx = row['cdx']
+ if 'revisit_cdx' in row:
+ terminal_cdx = row['revisit_cdx']
+ assert terminal_cdx['surt']
+ assert terminal_cdx['url'] == terminal['terminal_url']
+
+ wc_cdx = []
+ # primary resource first
+ wc_cdx.append(fatcat_openapi_client.WebcaptureCdxLine(
+ surt=terminal_cdx['surt'],
+ timestamp=terminal['terminal_timestamp'],
+ url=terminal['terminal_url'],
+ mimetype=file_meta['mimetype'],
+ status_code=terminal['terminal_status_code'],
+ sha1=file_meta['sha1hex'],
+ sha256=file_meta['sha256hex'],
+ size=file_meta['size_bytes'],
+ ))
+
+ for resource in row.get('html_resources', []):
+ timestamp = resource['timestamp']
+ if not "+" in timestamp and not "Z" in timestamp:
+ timestamp += "Z"
+ wc_cdx.append(fatcat_openapi_client.WebcaptureCdxLine(
+ surt=resource['surt'],
+ timestamp=timestamp,
+ url=resource['url'],
+ mimetype=resource.get('mimetype'),
+ size=resource.get('size'),
+ sha1=resource.get('sha1hex'),
+ sha256=resource.get('sha256hex'),
+ ))
+
+ wc = fatcat_openapi_client.WebcaptureEntity(
+ cdx=wc_cdx,
+ archive_urls=archive_urls,
+ original_url=terminal['terminal_url'],
+ timestamp=terminal['terminal_timestamp'],
+ release_ids=[release_ident],
+ )
+
+ edit_extra = self.parse_edit_extra(row)
+
+ if edit_extra:
+ wc.edit_extra = edit_extra
+ return wc
+
+ def try_update(self, wc):
+
+ # check for existing edits-in-progress with same URL
+ for other in self._entity_queue:
+ if other.original_url == wc.original_url:
+ self.counts['skip-in-queue'] += 1
+ return False
+
+ # lookup sha1, or create new entity (TODO: API doesn't support this yet)
+ #existing = None
+
+ # TODO: currently only allow one release per webcapture
+ release = self.api.get_release(wc.release_ids[0], expand="webcaptures")
+ if release.webcaptures:
+ # check if this is an existing match, or just a similar hit
+ for other in release.webcaptures:
+ if wc.original_url == other.original_url:
+ # TODO: compare very similar timestamps of same time (different formats)
+ self.counts['exists'] += 1
+ return False
+ self.counts['skip-release-has-webcapture'] += 1
+ return False
+
+ # Ok, if we got here then no existing web capture for (first) release,
+ # so go ahead and insert!
+ return True
+
+ def insert_batch(self, batch):
+ self.api.create_webcapture_auto_batch(fatcat_openapi_client.WebcaptureAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
+ description=self.editgroup_description,
+ extra=self.editgroup_extra),
+ entity_list=batch))
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-01 07:02:55 +0000