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import datetime
import fatcat_openapi_client
from .common import EntityImporter, make_rel_url
class IngestFileResultImporter(EntityImporter):
def __init__(self, api, require_grobid=True, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled from web using sandcrawler ingest tool"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileResultImporter')
kwargs['do_updates'] = kwargs.get("do_updates", False)
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.use_glutton_match = False
self.default_link_rel = kwargs.get("default_link_rel", "web")
assert self.default_link_rel
self.require_grobid = require_grobid
if self.require_grobid:
print("Requiring GROBID status == 200 (for PDFs)")
else:
print("NOT checking GROBID success")
self.ingest_request_source_allowlist = [
'fatcat-changelog',
'fatcat-ingest-container',
'fatcat-ingest',
'arabesque',
#'mag-corpus',
#'mag',
'unpaywall-corpus',
'unpaywall',
#'s2-corpus',
#'s2',
'doaj',
'dblp',
]
if kwargs.get('skip_source_allowlist', False):
self.ingest_request_source_allowlist = []
def want_file(self, row) -> bool:
"""
File-specific part of want(). Generic across general ingest and save-paper-now.
"""
if not row.get('file_meta'):
self.counts['skip-file-meta'] += 1
return False
# 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
return False
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
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 row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2', 'doaj', 'dblp'):
self.counts['skip-link-source'] += 1
return False
if source.startswith('savepapernow'):
# never process async savepapernow requests
self.counts['skip-savepapernow'] += 1
return False
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_ingest(row):
return False
if not self.want_file(row):
return False
return True
def parse_ingest_release_ident(self, row):
request = row['request']
fatcat = request.get('fatcat')
release_ident = None
if fatcat and fatcat.get('release_ident'):
release_ident = fatcat.get('release_ident')
elif request.get('ext_ids'):
# if no fatcat ident, try extids
for extid_type in ('doi', 'pmid', 'pmcid', 'arxiv', 'doaj', 'dblp'):
extid = request['ext_ids'].get(extid_type)
if not extid:
continue
if extid_type == 'doi':
extid = extid.lower()
try:
release = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status == 404:
continue
elif err.status == 400:
self.counts['warn-extid-invalid'] += 1
continue
raise err
# verify release_stage
if request.get('release_stage') and release.release_stage:
if request['release_stage'] != release.release_stage:
self.counts['skip-release-stage'] += 1
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
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:
return None
else:
terminal = {
'terminal_url': cdx['url'],
'terminal_dt': cdx['datetime'],
'terminal_status_code': cdx.get('status_code') or cdx.get('http_status'),
}
# work around old schema
if not 'terminal_url' in terminal:
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':
default_rel = 'publisher'
default_rel = request.get('rel', default_rel)
url = make_rel_url(terminal['terminal_url'], default_rel)
if not url:
self.counts['skip-url'] += 1
return None
wayback = "https://web.archive.org/web/{}/{}".format(
terminal['terminal_dt'],
terminal['terminal_url'])
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']
if edit_extra['link_source'] == 'doi':
edit_extra['link_source_id'] = edit_extra['link_source_id'].lower()
# GROBID metadata, for SPN requests (when there might not be 'success')
if request.get('ingest_type') == 'pdf':
if row.get('grobid') and row['grobid'].get('status') != 'success':
edit_extra['grobid_status_code'] = row['grobid']['status_code']
edit_extra['grobid_version'] = row['grobid'].get('grobid_version')
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'],
sha1=file_meta['sha1hex'],
sha256=file_meta['sha256hex'],
size=file_meta['size_bytes'],
mimetype=file_meta['mimetype'],
release_ids=[release_ident],
urls=urls,
)
edit_extra = self.parse_edit_extra(row)
if edit_extra:
fe.edit_extra = edit_extra
return fe
def try_update(self, fe):
# lookup sha1, or create new entity
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
# check for existing edits-in-progress with same file hash
for other in self._entity_queue:
if other.sha1 == fe.sha1:
self.counts['skip-in-queue'] += 1
return False
if not existing:
return True
# NOTE: the following checks all assume there is an existing item
if (fe.release_ids[0] in existing.release_ids) and existing.urls:
# TODO: could still, in theory update with the new URL?
self.counts['exists'] += 1
return False
if not self.do_updates:
self.counts['skip-update-disabled'] += 1
return False
# TODO: for now, never update
self.counts['skip-update-disabled'] += 1
return False
def insert_batch(self, batch):
if self.submit_mode:
eg = self.api.create_editgroup(fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra))
for fe in batch:
self.api.create_file(eg.editgroup_id, fe)
self.api.update_editgroup(eg.editgroup_id, eg, submit=True)
else:
self.api.create_file_auto_batch(fatcat_openapi_client.FileAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
class SavePaperNowFileImporter(IngestFileResultImporter):
"""
This worker ingests from the same feed as IngestFileResultImporter, but
only imports files from anonymous save-paper-now requests, and "submits"
them for further human review (as opposed to accepting by default).
"""
def __init__(self, api, submit_mode=True, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled after a public 'Save Paper Now' request"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.SavePaperNowFileImporter')
kwargs['submit_mode'] = submit_mode
kwargs['require_grobid'] = False
kwargs['do_updates'] = False
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
def want(self, row):
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
if not source.startswith('savepapernow'):
self.counts['skip-not-savepapernow'] += 1
return False
if row.get('hit') != True:
self.counts['skip-hit'] += 1
return False
if not self.want_file(row):
return False
return True
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
# webcapture-specific filters
if row['request'].get('ingest_type') != 'html':
self.counts['skip-ingest-type'] += 1
return False
if not row.get('file_meta'):
self.counts['skip-file-meta'] += 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']
if terminal_cdx['url'] != terminal['terminal_url']:
self.counts['skip-terminal-url-mismatch'] += 1
return None
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):
if self.submit_mode:
eg = self.api.create_editgroup(fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra))
for fe in batch:
self.api.create_webcapture(eg.editgroup_id, fe)
self.api.update_editgroup(eg.editgroup_id, eg, submit=True)
else:
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))
class SavePaperNowWebImporter(IngestWebResultImporter):
"""
Like SavePaperNowFileImporter, but for webcapture (HTML) ingest.
"""
def __init__(self, api, submit_mode=True, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Webcaptures crawled after a public 'Save Paper Now' request"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.SavePaperNowWebImporter')
kwargs['submit_mode'] = submit_mode
kwargs['do_updates'] = False
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
def want(self, row):
"""
Relatively custom want() here, a synthesis of other filters.
We do currently allow unknown-scope through for this specific code
path, which means allowing hit=false.
"""
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
if not source.startswith('savepapernow'):
self.counts['skip-not-savepapernow'] += 1
return False
# webcapture-specific filters
if row['request'].get('ingest_type') != 'html':
self.counts['skip-ingest-type'] += 1
return False
if not row.get('file_meta'):
self.counts['skip-file-meta'] += 1
return False
if row['file_meta'].get('mimetype') not in ("text/html", "application/xhtml+xml"):
self.counts['skip-mimetype'] += 1
return False
if row.get('status') not in ['success', 'unknown-scope']:
self.counts['skip-hit'] += 1
return False
return True
class IngestFilesetResultImporter(IngestFileResultImporter):
"""
Variant of IngestFileResultImporter for processing, eg, dataset ingest
results into fileset objects.
"""
def __init__(self, api, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Filesets crawled from web using sandcrawler ingest tool"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFilesetResultImporter')
kwargs['do_updates'] = False
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.max_file_count = 300
def want_fileset(self, row):
if not row.get('manifest') or len(row.get('manifest')) == 0:
self.counts['skip-empty-manifest'] += 1
return False
if len(row.get('manifest')) > self.max_file_count:
self.counts['skip-too-many-files'] += 1
return False
return True
def want(self, row):
if not self.want_ingest(row):
return False
# fileset-specific filters
if row['request'].get('ingest_type') not in ['dataset',]:
self.counts['skip-ingest-type'] += 1
return False
if not self.want_fileset(row):
return False
return True
def parse_fileset_urls(self, row):
# XXX: create URLs and rel for dataset ingest
if not row.get('strategy'):
return []
urls = []
if row['strategy'] == 'archiveorg-fileset' and row.get('archiveorg_item_name'):
urls.append(fatcat_openapi_client.FilesetUrl(
url=f"https://archive.org/download/{row['archiveorg_item_name']}/",
rel="archive",
))
elif row['strategy'] == 'archiveorg-file-hundle' and row.get('archiveorg_item_name'):
# XXX: what is the filename of bundle?
urls.append(fatcat_openapi_client.FilesetUrl(
url=f"https://archive.org/download/{row['archiveorg_item_name']}/",
rel="archive",
))
elif row['strategy'].startswith('web') and row.get('platform_base_url'):
urls.append(fatcat_openapi_client.FilesetUrl(
url=f"https://web.archive.org/web/{row['web_base_url_dt']}/{row['web_base_url']}",
rel="webarchive",
))
elif row['strategy'] == 'web-file-bundle' and row.get('platform_bundle_url'):
urls.append(fatcat_openapi_client.FilesetUrl(
url=f"https://web.archive.org/web/{row['web_bundle_url_dt']}/{row['web_bundle_url']}",
rel="webarchive",
))
else:
# if no archival URLs, bail out
return []
# add any additional / platform URLs here
if row.get('platform_bundle_url'):
urls.append(fatcat_openapi_client.FilesetUrl(
url=row['platform_bundle_url'],
rel="repository-bundle",
))
if row.get('platform_base_url'):
urls.append(fatcat_openapi_client.FilesetUrl(
url=row['platform_bundle_url'],
rel="repository",
))
return urls
def parse_record(self, row):
request = row['request']
# double check that want() filtered request correctly
if request.get('ingest_type') not in ["dataset",]:
self.counts['skip-ingest-type'] += 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
entity_extra = dict()
edit_extra = self.parse_edit_extra(row)
edit_extra['ingest_strategy'] = row['ingest_strategy']
if row.get('platform'):
edit_extra['platform'] = row['platform']
if row.get('platform_id'):
edit_extra['platform_id'] = row['platform_id']
entity_urls = self.parse_fileset_urls(row)
if not entity_urls:
self.counts['skip-no-access-url'] += 1
return None
assert row['file_count'] == len(row['manifest'])
if row['file_count'] > self.max_file_count:
self.counts['skip-too-many-manifest-files'] += 1
return None
manifest = []
for ingest_file in row['manifest']:
fsf = fatcat_openapi_client.FilesetFile(
path=ingest_file['path'],
size=ingest_file['size'],
md5=ingest_file['md5'],
sha1=ingest_file['sha1'],
sha256=ingest_file.get('sha256'),
extra=dict(
mimetype=ingest_file['mimetype'],
),
)
if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size):
self.counts['skip-partial-file-info'] += 1
return None
if ingest_file.get('platform_url'):
# XXX: should we include this?
fsf.extra['original_url'] = ingest_file['platform_url']
if ingest_file.get('terminal_url') and ingest_file.get('terminal_dt'):
fsf.extra['wayback_url'] = f"https://web.archive.org/web/{ingest_file['terminal_dt']}/{ingest_file['terminal_url']}"
manifest.append(fsf)
fe = fatcat_openapi_client.FilesetEntity(
manifest=manifest,
urls=entity_urls,
release_ids=[release_ident],
)
if entity_extra:
fe.extra = entity_extra
if edit_extra:
fe.edit_extra = edit_extra
return fe
def try_update(self, wc):
# check for existing edits-in-progress with same URL
for other in self._entity_queue:
# XXX: how to duplicate check?
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
# NOTE: in lieu of existing checks (by lookup), only allow one fileset per release
release = self.api.get_release(wc.release_ids[0], expand="filesets")
if release.filesets:
# XXX: how to duplicate check filesets?
# check if this is an existing match, or just a similar hit
for other in release.filesets:
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-fileset'] += 1
return False
return True
def insert_batch(self, batch):
if self.submit_mode:
eg = self.api.create_editgroup(fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra))
for fe in batch:
self.api.create_fileset(eg.editgroup_id, fe)
self.api.update_editgroup(eg.editgroup_id, eg, submit=True)
else:
self.api.create_fileset_auto_batch(fatcat_openapi_client.FilesetAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
class SavePaperNowFilesetImporter(IngestFilesetResultImporter):
"""
Like SavePaperNowFileImporter, but for fileset/dataset ingest.
"""
def __init__(self, api, submit_mode=True, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Fileset crawled after a public 'Save Paper Now' request"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.SavePaperNowFilesetImporter')
kwargs['submit_mode'] = submit_mode
kwargs['do_updates'] = False
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
def want(self, row):
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
if not source.startswith('savepapernow'):
self.counts['skip-not-savepapernow'] += 1
return False
if row.get('hit') != True:
self.counts['skip-hit'] += 1
return False
if not self.want_fileset(row):
return False
return True
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