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authorMartin Czygan <martin@archive.org>2020-11-19 22:36:55 +0000
committerMartin Czygan <martin@archive.org>2020-11-19 22:36:55 +0000
commit03eadfc7e2bee4213345f6464378e87b8f741d20 (patch)
tree3e5b13af8ba46b240f9ae53d5f522fb7ee02c219
parent5afde4690a4653db53fe4962af5da3eb9188d9a2 (diff)
parenta73b73c2944b3df2a62886c4e6b69c93f5e74222 (diff)
downloadfatcat-03eadfc7e2bee4213345f6464378e87b8f741d20.tar.gz
fatcat-03eadfc7e2bee4213345f6464378e87b8f741d20.zip
Merge branch 'bnewbold-xml-html-ingest' into 'master'
HTML webcapture ingest (and XML file ingest) See merge request webgroup/fatcat!88
-rwxr-xr-xpython/fatcat_import.py48
-rwxr-xr-xpython/fatcat_ingest.py4
-rw-r--r--python/fatcat_tools/importers/__init__.py2
-rw-r--r--python/fatcat_tools/importers/datacite.py8
-rw-r--r--python/fatcat_tools/importers/ingest.py329
-rw-r--r--python/fatcat_tools/transforms/ingest.py12
-rw-r--r--python/tests/files/example_ingest.json2
-rw-r--r--python/tests/files/example_ingest_html.json1
-rw-r--r--python/tests/files/example_ingest_xml.json1
-rw-r--r--python/tests/import_ingest.py68
10 files changed, 409 insertions, 66 deletions
diff --git a/python/fatcat_import.py b/python/fatcat_import.py
index e92b3106..19cf43ec 100755
--- a/python/fatcat_import.py
+++ b/python/fatcat_import.py
@@ -126,7 +126,7 @@ def run_arabesque_match(args):
def run_ingest_file(args):
ifri = IngestFileResultImporter(args.api,
editgroup_description=args.editgroup_description_override,
- skip_source_whitelist=args.skip_source_whitelist,
+ skip_source_allowlist=args.skip_source_allowlist,
do_updates=args.do_updates,
default_link_rel=args.default_link_rel,
require_grobid=(not args.no_require_grobid),
@@ -144,6 +144,26 @@ def run_ingest_file(args):
else:
JsonLinePusher(ifri, args.json_file).run()
+def run_ingest_web(args):
+ iwri = IngestWebResultImporter(args.api,
+ editgroup_description=args.editgroup_description_override,
+ skip_source_allowlist=args.skip_source_allowlist,
+ do_updates=args.do_updates,
+ default_link_rel=args.default_link_rel,
+ edit_batch_size=args.batch_size)
+ if args.kafka_mode:
+ KafkaJsonPusher(
+ iwri,
+ args.kafka_hosts,
+ args.kafka_env,
+ "ingest-file-results",
+ "fatcat-{}-ingest-web-result".format(args.kafka_env),
+ kafka_namespace="sandcrawler",
+ consume_batch_size=args.batch_size,
+ ).run()
+ else:
+ JsonLinePusher(iwri, args.json_file).run()
+
def run_savepapernow_file(args):
ifri = SavePaperNowFileImporter(args.api,
editgroup_description=args.editgroup_description_override,
@@ -442,9 +462,9 @@ def main():
sub_ingest_file.add_argument('json_file',
help="ingest_file JSON file to import from",
default=sys.stdin, type=argparse.FileType('r'))
- sub_ingest_file.add_argument('--skip-source-whitelist',
+ sub_ingest_file.add_argument('--skip-source-allowlist',
action='store_true',
- help="don't filter import based on request source whitelist")
+ help="don't filter import based on request source allowlist")
sub_ingest_file.add_argument('--kafka-mode',
action='store_true',
help="consume from kafka topic (not stdin)")
@@ -458,6 +478,28 @@ def main():
default="web",
help="default URL rel for matches (eg, 'publisher', 'web')")
+ sub_ingest_web = subparsers.add_parser('ingest-web-results',
+ help="add/update web entities linked to releases based on sandcrawler ingest results")
+ sub_ingest_web.set_defaults(
+ func=run_ingest_web,
+ auth_var="FATCAT_AUTH_WORKER_CRAWL",
+ )
+ sub_ingest_web.add_argument('json_file',
+ help="ingest_web JSON file to import from",
+ default=sys.stdin, type=argparse.FileType('r'))
+ sub_ingest_web.add_argument('--skip-source-allowlist',
+ action='store_true',
+ help="don't filter import based on request source allowlist")
+ sub_ingest_web.add_argument('--kafka-mode',
+ action='store_true',
+ help="consume from kafka topic (not stdin)")
+ sub_ingest_web.add_argument('--do-updates',
+ action='store_true',
+ help="update pre-existing web entities if new match (instead of skipping)")
+ sub_ingest_web.add_argument('--default-link-rel',
+ default="web",
+ help="default URL rel for matches (eg, 'publisher', 'web')")
+
sub_savepapernow_file = subparsers.add_parser('savepapernow-file-results',
help="add file entities crawled due to async Save Paper Now request")
sub_savepapernow_file.set_defaults(
diff --git a/python/fatcat_ingest.py b/python/fatcat_ingest.py
index 68676ad2..b9d71a7c 100755
--- a/python/fatcat_ingest.py
+++ b/python/fatcat_ingest.py
@@ -87,6 +87,7 @@ def _run_search_dump(args, search):
ingest_request = release_ingest_request(
release,
ingest_request_source="fatcat-ingest",
+ ingest_type=args.ingest_type,
)
if not ingest_request:
continue
@@ -214,6 +215,9 @@ def main():
parser.add_argument('--force-recrawl',
action='store_true',
help="Tell ingest worker to skip GWB history lookup and do SPNv2 crawl")
+ parser.add_argument('--ingest-type',
+ default="pdf",
+ help="What medium to ingest (pdf, xml, html)")
subparsers = parser.add_subparsers()
sub_container = subparsers.add_parser('container',
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index b82eb11a..c08e04c2 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -27,6 +27,6 @@ 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
diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py
index 86740e80..5cdc5577 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", []):
@@ -819,7 +819,7 @@ 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 +861,7 @@ 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/ingest.py b/python/fatcat_tools/importers/ingest.py
index 4b1d3702..4fbd19f1 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 file hash
+ for other in self._entity_queue:
+ if other.sha1 == wc.sha1:
+ 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
+
+ # TODO: for now, never update
+ self.counts['skip-update-disabled'] += 1
+ return False
+
+ 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))
diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py
index 2f4e2271..59831017 100644
--- a/python/fatcat_tools/transforms/ingest.py
+++ b/python/fatcat_tools/transforms/ingest.py
@@ -15,15 +15,19 @@ def release_ingest_request(release, ingest_request_source='fatcat', ingest_type=
if release.state != 'active':
return None
+ # TODO: infer ingest type based on release_type or container metadata?
+ if not ingest_type:
+ ingest_type = 'pdf'
+
# generate a URL where we expect to find fulltext
url = None
link_source = None
link_source_id = None
- if release.ext_ids.arxiv:
+ if release.ext_ids.arxiv and ingest_type == "pdf":
url = "https://arxiv.org/pdf/{}.pdf".format(release.ext_ids.arxiv)
link_source = "arxiv"
link_source_id = release.ext_ids.arxiv
- elif release.ext_ids.pmcid:
+ elif release.ext_ids.pmcid and ingest_type == "pdf":
# TODO: how to tell if an author manuscript in PMC vs. published?
#url = "https://www.ncbi.nlm.nih.gov/pmc/articles/{}/pdf/".format(release.ext_ids.pmcid)
url = "http://europepmc.org/backend/ptpmcrender.fcgi?accid={}&blobtype=pdf".format(release.ext_ids.pmcid)
@@ -40,10 +44,6 @@ def release_ingest_request(release, ingest_request_source='fatcat', ingest_type=
ext_ids = release.ext_ids.to_dict()
ext_ids = dict([(k, v) for (k, v) in ext_ids.items() if v])
- # TODO: infer ingest type based on release_type or container metadata?
- if not ingest_type:
- ingest_type = 'pdf'
-
ingest_request = {
'ingest_type': ingest_type,
'ingest_request_source': ingest_request_source,
diff --git a/python/tests/files/example_ingest.json b/python/tests/files/example_ingest.json
index cea67fa7..a9791587 100644
--- a/python/tests/files/example_ingest.json
+++ b/python/tests/files/example_ingest.json
@@ -1,2 +1,2 @@
-{"file_meta": {"sha1hex": "00242a192acc258bdfdb151943419437f440c313", "md5hex": "f4de91152c7ab9fdc2a128f962faebff", "sha256hex": "ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362", "size_bytes": 255629, "mimetype": "application/pdf"}, "request": {"ingest_request_source": "fatcat-changelog", "link_source": "doi", "link_source_id":"10.123/abc","ext_ids": {"doi": "10.123/abc"}}, "terminal": {"terminal_url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable", "terminal_dt": "20170227164644", "terminal_sha1hex": "00242a192acc258bdfdb151943419437f440c313"}, "cdx": { "datetime": "20170227164644", "url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable" }, "grobid": {"status_code": 200 }, "hit": true, "status": "success"}
+{"file_meta": {"sha1hex": "00242a192acc258bdfdb151943419437f440c313", "md5hex": "f4de91152c7ab9fdc2a128f962faebff", "sha256hex": "ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362", "size_bytes": 255629, "mimetype": "application/pdf"}, "request": {"ingest_type": "pdf", "ingest_request_source": "fatcat-changelog", "link_source": "doi", "link_source_id":"10.123/abc","ext_ids": {"doi": "10.123/abc"}}, "terminal": {"terminal_url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable", "terminal_dt": "20170227164644", "terminal_sha1hex": "00242a192acc258bdfdb151943419437f440c313"}, "cdx": { "datetime": "20170227164644", "url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable" }, "grobid": {"status_code": 200 }, "hit": true, "status": "success"}
{"request":{"ingest_type":"pdf","ingest_request_source":"fatcat-changelog","base_url":"https://doi.org/10.3917/popav.748.0017","release_stage":"published","fatcat":{"release_ident":"weeqjkvsx5abze2bhithyrx6wu","work_ident":"ujatsk25yrdw5gofubw7nogzgq"},"ext_ids":{"doi":"10.3917/popav.748.0017"},"link_source":"doi","link_source_id":"10.3917/popav.748.0017"},"hit":false,"hops":["https://doi.org/10.3917/popav.748.0017"],"status":"wayback-error","error_message":"replay fetch didn't return X-Archive-Src in headers"}
diff --git a/python/tests/files/example_ingest_html.json b/python/tests/files/example_ingest_html.json
new file mode 100644
index 00000000..6c646814
--- /dev/null
+++ b/python/tests/files/example_ingest_html.json
@@ -0,0 +1 @@
+{"cdx": {"datetime": "20200708025309", "mimetype": "text/html", "sha1b32": "THJFFZJR2VYN2FAR7X7LHFGRU2X5IC2U", "sha1hex": "99d252e531d570dd1411fdfeb394d1a6afd40b54", "status_code": 200, "surt": "py,una,iics,scielo)/scielo.php?lng=en&nrm=iso&pid=s1683-98032015000200002&script=sci_arttext&tlng=es", "url": "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es", "warc_csize": 13123, "warc_offset": 77579308, "warc_path": "SCIELO-CRAWL-2020-07-20200707211940442-00279-00347-wbgrp-svc206/SCIELO-CRAWL-2020-07-20200708024511243-00332-13069~wbgrp-svc206.us.archive.org~8443.warc.gz"}, "file_meta": {"md5hex": "515a61845a2f898438e3986e4506da8f", "mimetype": "text/html", "sha1hex": "99d252e531d570dd1411fdfeb394d1a6afd40b54", "sha256hex": "c4559d548476a325891461b71c796beee717e820d6a00cb8411176ce83a0f23f", "size_bytes": 47442}, "hit": true, "hops": ["http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es"], "html_biblio": {"container_issn": "1683-9803", "container_name": "Pediatr\u00eda (Asunci\u00f3n)", "contrib_names": ["Ruiz Valiente, Syntia Carolina", "Ruiz Ca\u00f1ete, Manuel", "Cohene Velazquez, Bartola"], "doi": "10.18004/ped.2015.agosto.102-107", "first_page": "102", "html_fulltext_url": "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es", "issue": "2", "last_page": "107", "pdf_fulltext_url": "http://scielo.iics.una.py/pdf/ped/v42n2/v42n2a02.pdf", "publisher": "Sociedad Paraguaya de Pediatr\u00eda", "release_date": "2015-08-06", "title": "Prevalence of malnutrition and eating habits in children under 5 years of age in indigenous communities in Azote'y and Yby Yau, 2011", "volume": "42", "xml_fulltext_url": "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en"}, "html_body": {"agent": "trafilatura/0.5.1", "status": "success", "word_count": 3500}, "html_resources": [{"mimetype": "image/gif", "resource_type": "image", "sha1hex": "4991aa771874daf8cba79be38d18d534f946b5d6", "sha256hex": "5e76fad755b873a439dd5e775684696c547008d45cc901606132e9a1ed970757", "size": 220, "status_code": 200, "surt": "py,una,iics,scielo)/img/en/alpha.gif", "timestamp": "2020-10-31T14:07:30", "url": "http://scielo.iics.una.py/img/en/alpha.gif"}, {"mimetype": "text/plain", "resource_type": "script", "sha1hex": "fd28e342fa1b40b84cc17dc66d22df3bf260170b", "sha256hex": "9cf2e81dd65d5a64200970bbd1cd9497b46b2af232e2fbfb79fef95b070f23d1", "size": 3653, "status_code": 200, "surt": "py,una,iics,scielo)/applications/scielo-org/js/toolbox.js", "timestamp": "2020-10-31T20:14:35", "url": "http://scielo.iics.una.py/applications/scielo-org/js/toolbox.js"}, {"mimetype": "image/gif", 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"ingest_request_source": "fatcat-changelog", "base_url": "http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "ext_ids": {"doi": "10.123/abc"}, "fatcat": {"release_ident": null}, "ingest_type": "html"}, "scope": "article-fulltext", "status": "success", "terminal": {"terminal_dt": "20200708025309", "terminal_sha1hex": "99d252e531d570dd1411fdfeb394d1a6afd40b54", "terminal_status_code": 200, "terminal_url": "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es"}}
diff --git a/python/tests/files/example_ingest_xml.json b/python/tests/files/example_ingest_xml.json
new file mode 100644
index 00000000..2f525998
--- /dev/null
+++ b/python/tests/files/example_ingest_xml.json
@@ -0,0 +1 @@
+{"cdx": {"datetime": "20200710091403", "mimetype": "text/xml", "sha1b32": "PWMQ2L4RHPJ3NVWC66GIJC36L5FXPOM6", "sha1hex": "7d990d2f913bd3b6d6c2f78c848b7e5f4b77b99e", "status_code": 200, "surt": "py,una,iics,scielo)/scieloorg/php/articlexml.php?lang=en&pid=s1683-98032015000200002", "url": "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en", "warc_csize": 12108, "warc_offset": 94730348, "warc_path": "SCIELO-CRAWL-2020-07-20200710082036515-00773-00843-wbgrp-svc206/SCIELO-CRAWL-2020-07-20200710085423121-00779-13069~wbgrp-svc206.us.archive.org~8443.warc.gz"}, "file_meta": {"md5hex": "cda133a706ce02a07fae8bd8d2694a2a", "mimetype": "application/jats+xml", "sha1hex": "7d990d2f913bd3b6d6c2f78c848b7e5f4b77b99e", "sha256hex": "be982ca211e4debb3f93f36d9f9dc1c80f99a8809eb4c41569b2b9503c27e751", "size_bytes": 49242}, "hit": true, "hops": ["http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en"], "request": {"link_source": "doi", "ingest_request_source": "fatcat-changelog","base_url": "http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "ext_ids": {"doi": "10.123/abc"}, "fatcat": {"release_ident": null}, "ingest_type": "xml"}, "status": "success", "terminal": {"terminal_dt": "20200710091403", "terminal_sha1hex": "7d990d2f913bd3b6d6c2f78c848b7e5f4b77b99e", "terminal_status_code": 200, "terminal_url": "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en"}, "xml_meta": {"status": "success"}}
diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py
index 4a46232a..92539f1a 100644
--- a/python/tests/import_ingest.py
+++ b/python/tests/import_ingest.py
@@ -2,7 +2,7 @@
import json
import pytest
-from fatcat_tools.importers import IngestFileResultImporter, JsonLinePusher
+from fatcat_tools.importers import IngestFileResultImporter, IngestWebResultImporter, JsonLinePusher
from fixtures import *
@@ -10,6 +10,10 @@ from fixtures import *
def ingest_importer(api):
yield IngestFileResultImporter(api)
+@pytest.fixture(scope="function")
+def ingest_web_importer(api):
+ yield IngestWebResultImporter(api)
+
# TODO: use API to check that entities actually created...
def test_ingest_importer_basic(ingest_importer):
with open('tests/files/example_ingest.json', 'r') as f:
@@ -41,6 +45,60 @@ def test_ingest_importer(ingest_importer):
assert counts['exists'] == 1
assert counts['skip'] == 1
+def test_ingest_importer_xml(ingest_importer):
+ last_index = ingest_importer.api.get_changelog(limit=1)[0].index
+ with open('tests/files/example_ingest_xml.json', 'r') as f:
+ ingest_importer.bezerk_mode = True
+ counts = JsonLinePusher(ingest_importer, f).run()
+ print(counts)
+ assert counts['insert'] == 1
+ assert counts['exists'] == 0
+ assert counts['skip'] == 0
+
+ # fetch most recent editgroup
+ change = ingest_importer.api.get_changelog_entry(index=last_index+1)
+ eg = change.editgroup
+ assert eg.description
+ assert "crawled from web" in eg.description.lower()
+ assert eg.extra['git_rev']
+ assert "fatcat_tools.IngestFileResultImporter" in eg.extra['agent']
+
+ # re-import should skip
+ with open('tests/files/example_ingest_xml.json', 'r') as f:
+ ingest_importer.reset()
+ ingest_importer.bezerk_mode = False
+ counts = JsonLinePusher(ingest_importer, f).run()
+ assert counts['insert'] == 0
+ assert counts['exists'] == 1
+ assert counts['skip'] == 0
+
+def test_ingest_importer_web(ingest_web_importer):
+ last_index = ingest_web_importer.api.get_changelog(limit=1)[0].index
+ with open('tests/files/example_ingest_html.json', 'r') as f:
+ ingest_web_importer.bezerk_mode = True
+ counts = JsonLinePusher(ingest_web_importer, f).run()
+ print(counts)
+ assert counts['insert'] == 1
+ assert counts['exists'] == 0
+ assert counts['skip'] == 0
+
+ # fetch most recent editgroup
+ change = ingest_web_importer.api.get_changelog_entry(index=last_index+1)
+ eg = change.editgroup
+ assert eg.description
+ assert "crawled from web" in eg.description.lower()
+ assert eg.extra['git_rev']
+ assert "fatcat_tools.IngestWebResultImporter" in eg.extra['agent']
+
+ # re-import should skip
+ with open('tests/files/example_ingest_html.json', 'r') as f:
+ ingest_web_importer.reset()
+ ingest_web_importer.bezerk_mode = False
+ counts = JsonLinePusher(ingest_web_importer, f).run()
+ assert counts['insert'] == 0
+ assert counts['exists'] == 1
+ assert counts['skip'] == 0
+
def test_ingest_importer_stage(ingest_importer, api):
"""
Tests that ingest importer correctly handles release stage matching
@@ -57,7 +115,7 @@ def test_ingest_importer_stage(ingest_importer, api):
with open('tests/files/example_ingest.json', 'r') as f:
raw = json.loads(f.readline())
for row in test_table:
- print(row)
+ #print(row)
# set dummy record stage
eg = quick_eg(api)
@@ -94,6 +152,12 @@ def test_ingest_dict_parse(ingest_importer):
def test_ingest_dict_parse_old(ingest_importer):
with open('tests/files/example_ingest.old.json', 'r') as f:
raw = json.loads(f.readline())
+
+ # ancient ingest requests had no type; skip them
+ f = ingest_importer.parse_record(raw)
+ assert f == None
+ raw['request']['ingest_type'] = 'pdf'
+
f = ingest_importer.parse_record(raw)
assert f.sha1 == "00242a192acc258bdfdb151943419437f440c313"
assert f.md5 == "f4de91152c7ab9fdc2a128f962faebff"