diff options
Diffstat (limited to 'python')
21 files changed, 911 insertions, 292 deletions
diff --git a/python/Pipfile b/python/Pipfile index 1a19a145..a2ce14e1 100644 --- a/python/Pipfile +++ b/python/Pipfile @@ -30,6 +30,8 @@ Flask-Misaka = "*" flask-mwoauth = "*" WTForms = "*" loginpass = ">=0.4" +# loginpass 0.4 is not actually compatible with newer authlib +authlib = "<0.13" requests = ">=2" raven = {extras = ['flask'],version = "*"} pykafka = ">=2" @@ -51,6 +53,11 @@ dateparser = ">=0.7" langdetect = "*" pathlib2 = "*" pycountry = "*" +tldextract = "*" + +# this is only to lock to a python3.5-compatible version. needed by an +# importlib-metadata, under pytest +zipp = "<2.0.0" [requires] # Python 3.5 is the bundled (system) version of python for Ubuntu 16.04 diff --git a/python/Pipfile.lock b/python/Pipfile.lock index d813dd32..0b24eb88 100644 --- a/python/Pipfile.lock +++ b/python/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "edac46fb8a4b49aea89946621337abba881fff6f6768107d2529c752bcf702ac" + "sha256": "03588fffd1f322432b0e3d1197d0797a300b38f42aa84b4e1d5909e9a3d5a07a" }, "pipfile-spec": 6, "requires": { @@ -18,10 +18,11 @@ "default": { "authlib": { "hashes": [ - "sha256:401a4a184379a6551b79af30243ce1ad56da0a8da5b4925e0be260f07ee40009", - "sha256:e9a6a6c5748109bd9ce9f24e71d293156c43bd0d6595bc4e63dd8f5b9e809149" + "sha256:40728195efe915c96209a6a57ad6b5565a951bb469f01bd0c38ea13a0bac6c68", + "sha256:4b6a82217b376fe5e7a9e5348865591077c2e6e5d987f4741ac74975b75aa145" ], - "version": "==0.13" + "index": "pypi", + "version": "==0.12.1" }, "beautifulsoup4": { "hashes": [ @@ -53,41 +54,36 @@ }, "cffi": { "hashes": [ - "sha256:0b49274afc941c626b605fb59b59c3485c17dc776dc3cc7cc14aca74cc19cc42", - "sha256:0e3ea92942cb1168e38c05c1d56b0527ce31f1a370f6117f1d490b8dcd6b3a04", - "sha256:135f69aecbf4517d5b3d6429207b2dff49c876be724ac0c8bf8e1ea99df3d7e5", - "sha256:19db0cdd6e516f13329cba4903368bff9bb5a9331d3410b1b448daaadc495e54", - "sha256:2781e9ad0e9d47173c0093321bb5435a9dfae0ed6a762aabafa13108f5f7b2ba", - "sha256:291f7c42e21d72144bb1c1b2e825ec60f46d0a7468f5346841860454c7aa8f57", - "sha256:2c5e309ec482556397cb21ede0350c5e82f0eb2621de04b2633588d118da4396", - "sha256:2e9c80a8c3344a92cb04661115898a9129c074f7ab82011ef4b612f645939f12", - "sha256:32a262e2b90ffcfdd97c7a5e24a6012a43c61f1f5a57789ad80af1d26c6acd97", - "sha256:3c9fff570f13480b201e9ab69453108f6d98244a7f495e91b6c654a47486ba43", - "sha256:415bdc7ca8c1c634a6d7163d43fb0ea885a07e9618a64bda407e04b04333b7db", - "sha256:42194f54c11abc8583417a7cf4eaff544ce0de8187abaf5d29029c91b1725ad3", - "sha256:4424e42199e86b21fc4db83bd76909a6fc2a2aefb352cb5414833c030f6ed71b", - "sha256:4a43c91840bda5f55249413037b7a9b79c90b1184ed504883b72c4df70778579", - "sha256:599a1e8ff057ac530c9ad1778293c665cb81a791421f46922d80a86473c13346", - "sha256:5c4fae4e9cdd18c82ba3a134be256e98dc0596af1e7285a3d2602c97dcfa5159", - "sha256:5ecfa867dea6fabe2a58f03ac9186ea64da1386af2159196da51c4904e11d652", - "sha256:62f2578358d3a92e4ab2d830cd1c2049c9c0d0e6d3c58322993cc341bdeac22e", - "sha256:6471a82d5abea994e38d2c2abc77164b4f7fbaaf80261cb98394d5793f11b12a", - "sha256:6d4f18483d040e18546108eb13b1dfa1000a089bcf8529e30346116ea6240506", - "sha256:71a608532ab3bd26223c8d841dde43f3516aa5d2bf37b50ac410bb5e99053e8f", - "sha256:74a1d8c85fb6ff0b30fbfa8ad0ac23cd601a138f7509dc617ebc65ef305bb98d", - "sha256:7b93a885bb13073afb0aa73ad82059a4c41f4b7d8eb8368980448b52d4c7dc2c", - "sha256:7d4751da932caaec419d514eaa4215eaf14b612cff66398dd51129ac22680b20", - "sha256:7f627141a26b551bdebbc4855c1157feeef18241b4b8366ed22a5c7d672ef858", - "sha256:8169cf44dd8f9071b2b9248c35fc35e8677451c52f795daa2bb4643f32a540bc", - "sha256:aa00d66c0fab27373ae44ae26a66a9e43ff2a678bf63a9c7c1a9a4d61172827a", - "sha256:ccb032fda0873254380aa2bfad2582aedc2959186cce61e3a17abc1a55ff89c3", - "sha256:d754f39e0d1603b5b24a7f8484b22d2904fa551fe865fd0d4c3332f078d20d4e", - "sha256:d75c461e20e29afc0aee7172a0950157c704ff0dd51613506bd7d82b718e7410", - "sha256:dcd65317dd15bc0451f3e01c80da2216a31916bdcffd6221ca1202d96584aa25", - "sha256:e570d3ab32e2c2861c4ebe6ffcad6a8abf9347432a37608fe1fbd157b3f0036b", - "sha256:fd43a88e045cf992ed09fa724b5315b790525f2676883a6ea64e3263bae6549d" - ], - "version": "==1.13.2" + "sha256:001bf3242a1bb04d985d63e138230802c6c8d4db3668fb545fb5005ddf5bb5ff", + "sha256:00789914be39dffba161cfc5be31b55775de5ba2235fe49aa28c148236c4e06b", + "sha256:028a579fc9aed3af38f4892bdcc7390508adabc30c6af4a6e4f611b0c680e6ac", + "sha256:14491a910663bf9f13ddf2bc8f60562d6bc5315c1f09c704937ef17293fb85b0", + "sha256:1cae98a7054b5c9391eb3249b86e0e99ab1e02bb0cc0575da191aedadbdf4384", + "sha256:2089ed025da3919d2e75a4d963d008330c96751127dd6f73c8dc0c65041b4c26", + "sha256:2d384f4a127a15ba701207f7639d94106693b6cd64173d6c8988e2c25f3ac2b6", + "sha256:337d448e5a725bba2d8293c48d9353fc68d0e9e4088d62a9571def317797522b", + "sha256:399aed636c7d3749bbed55bc907c3288cb43c65c4389964ad5ff849b6370603e", + "sha256:3b911c2dbd4f423b4c4fcca138cadde747abdb20d196c4a48708b8a2d32b16dd", + "sha256:3d311bcc4a41408cf5854f06ef2c5cab88f9fded37a3b95936c9879c1640d4c2", + "sha256:62ae9af2d069ea2698bf536dcfe1e4eed9090211dbaafeeedf5cb6c41b352f66", + "sha256:66e41db66b47d0d8672d8ed2708ba91b2f2524ece3dee48b5dfb36be8c2f21dc", + "sha256:675686925a9fb403edba0114db74e741d8181683dcf216be697d208857e04ca8", + "sha256:7e63cbcf2429a8dbfe48dcc2322d5f2220b77b2e17b7ba023d6166d84655da55", + "sha256:8a6c688fefb4e1cd56feb6c511984a6c4f7ec7d2a1ff31a10254f3c817054ae4", + "sha256:8c0ffc886aea5df6a1762d0019e9cb05f825d0eec1f520c51be9d198701daee5", + "sha256:95cd16d3dee553f882540c1ffe331d085c9e629499ceadfbda4d4fde635f4b7d", + "sha256:99f748a7e71ff382613b4e1acc0ac83bf7ad167fb3802e35e90d9763daba4d78", + "sha256:b8c78301cefcf5fd914aad35d3c04c2b21ce8629b5e4f4e45ae6812e461910fa", + "sha256:c420917b188a5582a56d8b93bdd8e0f6eca08c84ff623a4c16e809152cd35793", + "sha256:c43866529f2f06fe0edc6246eb4faa34f03fe88b64a0a9a942561c8e22f4b71f", + "sha256:cab50b8c2250b46fe738c77dbd25ce017d5e6fb35d3407606e7a4180656a5a6a", + "sha256:cef128cb4d5e0b3493f058f10ce32365972c554572ff821e175dbc6f8ff6924f", + "sha256:cf16e3cf6c0a5fdd9bc10c21687e19d29ad1fe863372b5543deaec1039581a30", + "sha256:e56c744aa6ff427a607763346e4170629caf7e48ead6921745986db3692f987f", + "sha256:e577934fc5f8779c554639376beeaa5657d54349096ef24abe8c74c5d9c117c3", + "sha256:f2b0fa0c01d8a0c7483afd9f31d7ecf2d71760ca24499c8697aeb5ca37dc090c" + ], + "version": "==1.14.0" }, "chardet": { "hashes": [ @@ -98,11 +94,10 @@ }, "citeproc-py": { "hashes": [ - "sha256:ed513dbc76f782b5e98126d6bebbd1284841fcf199ec9dda552e2bce864adadf", - "sha256:ee1569e8b1f2c057c7893bbb067986bc362a6c861009d310700a12a1a0107b57" + "sha256:00f8919766fb07ddc6ace5e5b88282809ecae738b031bd32edeb762a31367113" ], "index": "pypi", - "version": "==0.4.0" + "version": "==0.5.0" }, "citeproc-py-styles": { "hashes": [ @@ -220,21 +215,23 @@ }, "flask-debugtoolbar": { "hashes": [ - "sha256:3d9657bc0c3633ace429e3ff451742bb59d1b7a7b95c9eb23a65ac9be2812959", - "sha256:ec810083123aae0632eb32ba11e1cb4cdace81e7ce6c5009dd06c5204afbce52" + "sha256:0e9a80d4c599233c68376e81cc99976200b5ac5248cfb24f18935cc5b69ac5b3", + "sha256:3c4e79d354ede014e6657c545a536d4fb273cc89e3fd6b4835b02e346dd3aab4" ], "index": "pypi", - "version": "==0.10.1" + "version": "==0.11.0" }, "flask-login": { "hashes": [ - "sha256:c815c1ac7b3e35e2081685e389a665f2c74d7e077cb93cecabaea352da4752ec" + "sha256:6d33aef15b5bcead780acc339464aae8a6e28f13c90d8b1cf9de8b549d1c0b4b", + "sha256:7451b5001e17837ba58945aead261ba425fdf7b4f0448777e597ddab39f4fba0" ], "index": "pypi", - "version": "==0.4.1" + "version": "==0.5.0" }, "flask-misaka": { "hashes": [ + "sha256:bcfdacc0803ccea75d377737e82c83489b2153d922c9d9f9eabc5148d216ed70", "sha256:d0cfb0efd9e5afacda76defd4a605a68390f4fb1bef283c71534fd3ce0d3efb5", "sha256:f423c3beb5502742a57330a272f81d53223f6f99d45cc45b03926e3a3034f589" ], @@ -257,18 +254,18 @@ }, "flask-wtf": { "hashes": [ - "sha256:5d14d55cfd35f613d99ee7cba0fc3fbbe63ba02f544d349158c14ca15561cc36", - "sha256:d9a9e366b32dcbb98ef17228e76be15702cd2600675668bca23f63a7947fd5ac" + "sha256:57b3faf6fe5d6168bda0c36b0df1d05770f8e205e18332d0376ddb954d17aef2", + "sha256:d417e3a0008b5ba583da1763e4db0f55a1269d9dd91dcc3eb3c026d3c5dbd720" ], "index": "pypi", - "version": "==0.14.2" + "version": "==0.14.3" }, "ftfy": { "hashes": [ - "sha256:6d7509c45e602dec890f0f6ee0623a8b5f50ec1188ac7ab9535e18e572c99bcc" + "sha256:67f9c8b33a4b742376a3eda11b0e3bd5c0cbe719d95ea0bfd3736a7bdd1c24c8" ], "index": "pypi", - "version": "==5.6" + "version": "==5.7" }, "future": { "hashes": [ @@ -278,10 +275,10 @@ }, "idna": { "hashes": [ - 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"version": "==1.4.0" + "version": "==1.4.1" }, "urllib3": { "hashes": [ - "sha256:a8a318824cc77d1fd4b2bec2ded92646630d7fe8619497b142c84a9e6f5a7293", - "sha256:f3c5fd51747d450d4dcf6f923c81f78f811aab8205fda64b0aba34a4e48b0745" + "sha256:2f3db8b19923a873b3e5256dc9c2dedfa883e33d87c690d9c7913e1f40673cdc", + "sha256:87716c2d2a7121198ebcb7ce7cccf6ce5e9ba539041cfbaeecfb641dc0bf6acc" ], - "version": "==1.25.7" + "version": "==1.25.8" }, "wcwidth": { "hashes": [ @@ -1044,10 +1069,11 @@ }, "zipp": { "hashes": [ - "sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e", - "sha256:f06903e9f1f43b12d371004b4ac7b06ab39a44adc747266928ae6debfa7b3335" + "sha256:c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1", + "sha256:e0d9e63797e483a30d27e09fffd308c59a700d365ec34e93cc100844168bf921" ], - "version": "==0.6.0" + "index": "pypi", + "version": "==1.2.0" } } } diff --git a/python/fatcat_import.py b/python/fatcat_import.py index bb715fb6..e1e06653 100755 --- a/python/fatcat_import.py +++ b/python/fatcat_import.py @@ -166,6 +166,11 @@ def run_grobid_metadata(args): bezerk_mode=args.bezerk_mode) LinePusher(fmi, args.tsv_file).run() +def run_shadow_lib(args): + fmi = ShadowLibraryImporter(args.api, + edit_batch_size=100) + JsonLinePusher(fmi, args.json_file).run() + def run_wayback_static(args): api = args.api @@ -475,6 +480,16 @@ def main(): action='store_true', help="don't lookup existing files, just insert (clobbers; only for fast bootstrap)") + sub_shadow_lib = subparsers.add_parser('shadow-lib', + help="create release and file entities based on GROBID PDF metadata extraction") + sub_shadow_lib.set_defaults( + func=run_shadow_lib, + auth_var="FATCAT_AUTH_WORKER_SHADOW", + ) + sub_shadow_lib.add_argument('json_file', + help="JSON file to import from (or stdin)", + default=sys.stdin, type=argparse.FileType('r')) + sub_wayback_static = subparsers.add_parser('wayback-static', help="crude crawl+ingest tool for single-page HTML docs from wayback") sub_wayback_static.set_defaults( diff --git a/python/fatcat_ingest.py b/python/fatcat_ingest.py index 6fda74c5..9ba95015 100755 --- a/python/fatcat_ingest.py +++ b/python/fatcat_ingest.py @@ -90,6 +90,8 @@ def _run_search_dump(args, search): ) if not ingest_request: continue + if args.force_recrawl: + ingest_request['force_recrawl'] = True counts['ingest_request'] += 1 if args.dry_run: continue @@ -206,6 +208,9 @@ def main(): parser.add_argument('--allow-non-oa', action='store_true', help="By default, we limit to OA releases. This removes that filter") + parser.add_argument('--force-recrawl', + action='store_true', + help="Tell ingest worker to skip GWB history lookup and do SPNv2 crawl") 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 03c7cbcc..c26446fd 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -28,3 +28,4 @@ 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 .shadow import ShadowLibraryImporter diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index 5f5c46b8..c000ad62 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -194,6 +194,8 @@ DOMAIN_REL_MAP = { "www.scielo.cl": "repository", "www.scielo.org.mx": "repository", "zenodo.org": "repository", + "www.biorxiv.org": "repository", + "www.medrxiv.org": "repository", "citeseerx.ist.psu.edu": "aggregator", "publisher-connector.core.ac.uk": "aggregator", @@ -220,6 +222,13 @@ DOMAIN_REL_MAP = { "www.nature.com": "publisher", "www.pnas.org": "publisher", "www.tandfonline.com": "publisher", + "www.frontiersin.org": "publisher", + "www.degruyter.com": "publisher", + "www.mdpi.com": "publisher", + "www.ahajournals.org": "publisher", + "ehp.niehs.nih.gov": "publisher", + "journals.tsu.ru": "publisher", + "www.cogentoa.com": "publisher", "www.researchgate.net": "academicsocial", "academia.edu": "academicsocial", diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index fdaba176..4772bfaa 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -32,8 +32,11 @@ class IngestFileResultImporter(EntityImporter): 'fatcat-ingest', 'arabesque', 'mag-corpus', + 'mag', 'unpaywall-corpus', + 'unpaywall', 's2-corpus', + 's2', ] if kwargs.get('skip_source_whitelist', False): self.ingest_request_source_whitelist = [] @@ -137,7 +140,12 @@ class IngestFileResultImporter(EntityImporter): if not 'terminal_dt' in terminal: terminal['terminal_dt'] = terminal['dt'] assert len(terminal['terminal_dt']) == 14 - url = make_rel_url(terminal['terminal_url'], self.default_link_rel) + + 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 @@ -158,8 +166,8 @@ class IngestFileResultImporter(EntityImporter): release_ids=[release_ident], urls=urls, ) - if fatcat and fatcat.get('edit_extra'): - fe.edit_extra = fatcat['edit_extra'] + if request.get('edit_extra'): + fe.edit_extra = request['edit_extra'] else: fe.edit_extra = dict() if request.get('ingest_request_source'): diff --git a/python/fatcat_tools/importers/shadow.py b/python/fatcat_tools/importers/shadow.py new file mode 100644 index 00000000..4cd22775 --- /dev/null +++ b/python/fatcat_tools/importers/shadow.py @@ -0,0 +1,195 @@ + +import sys +import json +import sqlite3 +import itertools +import fatcat_openapi_client + +from fatcat_tools.normal import * +from .common import EntityImporter, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS + + +class ShadowLibraryImporter(EntityImporter): + """ + Importer for shadow library files (matched to releases) + + Input format is JSON with keys: + - shadow + - shadow_corpus (string slug) + - shadow_id (string) + - doi + - pmid + - isbn13 + - file_meta + - sha1hex + - sha256hex + - md5hex + - size_bytes + - mimetype + - cdx (may be null) + - url + - datetime + """ + + def __init__(self, api, **kwargs): + + eg_desc = kwargs.pop('editgroup_description', None) or "Import of 'Shadow Library' file/release matches" + eg_extra = kwargs.pop('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ShadowLibraryImporter') + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs) + self.default_link_rel = kwargs.get("default_link_rel", "web") + + def want(self, raw_record): + """ + Only want to import records with complete file-level metadata + """ + fm = raw_record['file_meta'] + if not (fm['mimetype'] and fm['md5hex'] and fm['sha256hex'] and fm['size_bytes']): + self.counts['skip-file-meta-incomplete'] += 1 + return False + if fm['mimetype'] != 'application/pdf': + self.counts['skip-not-pdf'] += 1 + return False + return True + + def parse_record(self, obj): + """ + We do the release lookup in this method. Try DOI, then PMID, last ISBN13. + """ + + shadow_corpus = obj['shadow']['shadow_corpus'] + assert shadow_corpus == shadow_corpus.strip().lower() + doi = clean_doi(obj['shadow'].get('doi')) + pmid = clean_pmid(obj['shadow'].get('pmid')) + isbn13 = clean_isbn13(obj['shadow'].get('isbn13')) + shadow_id = obj['shadow'].get('shadow_id').strip() + assert shadow_id + + extra = { '{}_id'.format(shadow_corpus): shadow_id } + for (ext_type, ext_id) in [('doi', doi), ('pmid', pmid), ('isbn13', isbn13)]: + if not ext_id: + continue + extra['{}_{}'.format(shadow_corpus, ext_type)] = ext_id + + # lookup release via several idents + re = None + for (ext_type, ext_id) in [('doi', doi), ('pmid', pmid), ('isbn13', isbn13)]: + if not ext_id: + continue + try: + re = self.api.lookup_release(**{ext_type: ext_id}) + except fatcat_openapi_client.rest.ApiException as err: + if err.status not in (404, 400): + raise err + re = None + if re: + break + + if not re: + self.counts['skip-release-not-found'] += 1 + return None + + release_ids = [re.ident,] + + # parse single CDX into URLs (if exists) + urls = [] + if obj.get('cdx'): + url = make_rel_url(obj['cdx']['url'], default_link_rel=self.default_link_rel) + if url != None: + urls.append(url) + wayback = "https://web.archive.org/web/{}/{}".format( + obj['cdx']['datetime'], + obj['cdx']['url']) + urls.append(("webarchive", wayback)) + urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls] + + fe = fatcat_openapi_client.FileEntity( + md5=obj['file_meta']['md5hex'], + sha1=obj['file_meta']['sha1hex'], + sha256=obj['file_meta']['sha256hex'], + size=int(obj['file_meta']['size_bytes']), + mimetype=obj['file_meta']['mimetype'] or None, + release_ids=release_ids, + urls=urls, + extra=dict(shadows=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 + + if not existing: + return True + + if not existing.extra: + existing.extra = {} + + if existing.extra.get('shadows') and list(fe.extra['shadows'].keys())[0] in existing.extra['shadows']: + # already imported from this shadow library; skip + self.counts['exists'] += 1 + return False + + # check for edit conflicts + if existing.ident in [e.ident for e in self._edits_inflight]: + self.counts['skip-update-inflight'] += 1 + return False + if fe.sha1 in [e.sha1 for e in self._edits_inflight]: + raise Exception("Inflight insert; shouldn't happen") + + # minimum viable "existing" URL cleanup to fix dupes and broken links: + # remove 'None' wayback URLs, and set archive.org rel 'archive' + existing.urls = [u for u in existing.urls if not ('://web.archive.org/web/None/' in u.url)] + for i in range(len(existing.urls)): + u = existing.urls[i] + if u.rel == 'repository' and '://archive.org/download/' in u.url: + existing.urls[i].rel = 'archive' + if u.rel == 'social': + u.rel = 'academicsocial' + + # merge the existing into this one and update + merged_urls = {} + for u in fe.urls + existing.urls: + merged_urls[u.url] = u + existing.urls = list(merged_urls.values()) + if not existing.extra.get('shadows'): + existing.extra['shadows'] = fe.extra['shadows'] + else: + existing.extra['shadows'].update(fe.extra['shadows']) + + # do these "plus ones" because we really want to do these updates when possible + if len(existing.urls) > SANE_MAX_URLS + 1: + self.counts['skip-update-too-many-url'] += 1 + return None + existing.release_ids = list(set(fe.release_ids + existing.release_ids)) + if len(existing.release_ids) > SANE_MAX_RELEASES + 1: + self.counts['skip-update-too-many-releases'] += 1 + return None + existing.mimetype = existing.mimetype or fe.mimetype + existing.size = existing.size or fe.size + existing.md5 = existing.md5 or fe.md5 + existing.sha1 = existing.sha1 or fe.sha1 + existing.sha256 = existing.sha256 or fe.sha256 + edit = self.api.update_file(self.get_editgroup_id(), existing.ident, existing) + # add sha1 to non-entity edit row, so we can do more aggressive + # group-level de-dupe + edit.sha1 = existing.sha1 + self._edits_inflight.append(edit) + self.counts['update'] += 1 + return False + + def insert_batch(self, batch): + 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)) + diff --git a/python/fatcat_tools/transforms/__init__.py b/python/fatcat_tools/transforms/__init__.py index 6a4b1bba..3f4700ff 100644 --- a/python/fatcat_tools/transforms/__init__.py +++ b/python/fatcat_tools/transforms/__init__.py @@ -1,5 +1,5 @@ from .entities import entity_to_dict, entity_from_json, entity_from_dict -from .elasticsearch import release_to_elasticsearch, container_to_elasticsearch, changelog_to_elasticsearch +from .elasticsearch import release_to_elasticsearch, container_to_elasticsearch, changelog_to_elasticsearch, file_to_elasticsearch from .csl import release_to_csl, citeproc_csl from .ingest import release_ingest_request diff --git a/python/fatcat_tools/transforms/elasticsearch.py b/python/fatcat_tools/transforms/elasticsearch.py index 3a53db4d..87e054ec 100644 --- a/python/fatcat_tools/transforms/elasticsearch.py +++ b/python/fatcat_tools/transforms/elasticsearch.py @@ -1,6 +1,6 @@ - import collections +import tldextract from fatcat_openapi_client import ApiClient @@ -20,6 +20,7 @@ def test_check_kbart(): assert check_kbart(1950, dict(year_spans=[[1900, 1920], [1990, 2000]])) == False assert check_kbart(1950, dict(year_spans=[[1900, 1920], [1930, 2000]])) == True + def release_to_elasticsearch(entity, force_bool=True): """ Converts from an entity model/schema to elasticsearch oriented schema. @@ -50,6 +51,10 @@ def release_to_elasticsearch(entity, force_bool=True): release_stage = release.release_stage, withdrawn_status = release.withdrawn_status, language = release.language, + volume = release.volume, + issue = release.issue, + pages = release.pages, + number = release.number, license = release.license_slug, doi = release.ext_ids.doi, pmid = release.ext_ids.pmid, @@ -72,7 +77,7 @@ def release_to_elasticsearch(entity, force_bool=True): in_dweb = False in_ia = False in_ia_sim = False - in_shadow = False + in_shadows = False release_year = release.release_year if release.release_date: @@ -85,11 +90,15 @@ def release_to_elasticsearch(entity, force_bool=True): t['any_abstract'] = len(release.abstracts or []) > 0 t['ref_count'] = len(release.refs or []) - t['ref_linked_count'] = 0 - if release.refs: - t['ref_linked_count'] = len([1 for ref in release.refs if ref.target_release_id]) + ref_release_ids = [] + for r in (release.refs or []): + if r.target_release_id: + ref_release_ids.append(r.target_release_id) + t['ref_release_ids'] = ref_release_ids + t['ref_linked_count'] = len(ref_release_ids) t['contrib_count'] = len(release.contribs or []) contrib_names = [] + contrib_affiliations = [] creator_ids = [] for c in (release.contribs or []): if c.raw_name: @@ -98,8 +107,14 @@ def release_to_elasticsearch(entity, force_bool=True): contrib_names.append(c.surname) if c.creator_id: creator_ids.append(c.creator_id) + if c.raw_affiliation: + contrib_affiliations.append(c.raw_affiliation) t['contrib_names'] = contrib_names t['creator_ids'] = creator_ids + t['affiliations'] = contrib_affiliations + + # TODO: mapping... probably by lookup? + t['affiliation_rors'] = None container = release.container if container: @@ -134,14 +149,19 @@ def release_to_elasticsearch(entity, force_bool=True): if c_extra.get('road'): if c_extra['road'].get('as_of'): is_oa = True - if c_extra.get('ezb'): - if c_extra['ezb'].get('color') == 'green': - is_oa = True if c_extra.get('szczepanski'): if c_extra['szczepanski'].get('as_of'): is_oa = True - else: + if c_extra.get('country'): + t['country_code'] = c_extra['country'] + t['country_code_upper'] = c_extra['country'].upper() + + # fall back to release-level container metadata if container not linked or + # missing context + if not t.get('publisher'): t['publisher'] = release.publisher + if not t.get('container_name') and release.extra: + t['container_name'] = release.extra.get('container_name') if release.ext_ids.jstor or (release.ext_ids.doi and release.ext_ids.doi.startswith('10.2307/')): in_jstor = True @@ -187,6 +207,8 @@ def release_to_elasticsearch(entity, force_bool=True): # TODO: more/better checks here, particularly strict *not* OA licenses if release.license_slug.startswith("CC-"): is_oa = True + if release.license_slug.startswith("ARXIV-"): + is_oa = True extra = release.extra or dict() if extra: @@ -203,6 +225,47 @@ def release_to_elasticsearch(entity, force_bool=True): if extra['crossref'].get('archive'): # all crossref archives are KBART, I believe in_kbart = True + # backwards compatible subtitle fetching + if not t['subtitle'] and extra.get('subtitle'): + if type(extra['subtitle']) == list: + t['subtitle'] = extra['subtitle'][0] + else: + t['subtitle'] = extra['subtitle'] + + t['first_page'] = None + if release.pages: + first = release.pages.split('-')[0] + first = first.replace('p', '') + if first.isdigit(): + t['first_page'] = first + # TODO: non-numerical first pages + + t['ia_microfilm_url'] = None + if in_ia_sim: + # TODO: determine URL somehow? I think this is in flux. Will probably + # need extra metadata in the container extra field. + # special case as a demo for now. + if release.container_id == "hl5g6d5msjcl7hlbyyvcsbhc2u" \ + and release.release_year in (2011, 2013) \ + and release.issue \ + and release.issue.isdigit() \ + and t['first_page']: + t['ia_microfilm_url'] = "https://archive.org/details/sim_bjog_{}-{:02d}/page/n{}".format( + release.release_year, + int(release.issue) - 1, + t['first_page'], + ) + + t['doi_registrar'] = None + if extra and t['doi']: + for k in ('crossref', 'datacite', 'jalc'): + if k in extra: + t['doi_registrar'] = k + if not 'doi_registrar' in t: + t['doi_registrar'] = 'crossref' + + if t['doi']: + t['doi_prefix'] = t['doi'].split('/')[0] if is_longtail_oa: is_oa = True @@ -215,6 +278,7 @@ def release_to_elasticsearch(entity, force_bool=True): t['in_jstor'] = bool(in_jstor) t['in_web'] = bool(in_web) t['in_dweb'] = bool(in_dweb) + t['in_shadows'] = bool(in_shadows) else: t['is_oa'] = is_oa t['is_longtail_oa'] = is_longtail_oa @@ -223,11 +287,23 @@ def release_to_elasticsearch(entity, force_bool=True): t['in_jstor'] = in_jstor t['in_web'] = in_web t['in_dweb'] = in_dweb + t['in_shadows'] = in_shadows t['in_ia'] = bool(in_ia) t['is_preserved'] = bool(is_preserved or in_ia or in_kbart or in_jstor) + + if in_ia or t.get('pmcid') or t.get('arxiv_id'): + t['preservation'] = 'bright' + elif in_kbart or in_jstor: + t['preservation'] = 'dark' + elif in_shadows: + t['preservation'] = 'shadows_only' + else: + t['preservation'] = 'none' + return t + def container_to_elasticsearch(entity, force_bool=True): """ Converts from an entity model/schema to elasticsearch oriented schema. @@ -257,23 +333,27 @@ def container_to_elasticsearch(entity, force_bool=True): wikidata_qid = entity.wikidata_qid, ) - # TODO: region, discipline - # TODO: single primary language? if not entity.extra: entity.extra = dict() - for key in ('country', 'languages', 'mimetypes', 'first_year', 'last_year'): + for key in ('country', 'languages', 'mimetypes', 'original_name', + 'first_year', 'last_year', 'aliases', 'abbrev', 'region', + 'discipline'): if entity.extra.get(key): t[key] = entity.extra[key] + if 'country' in t: + t['country_code'] = t.pop('country') + + t['issns'] = [] + if entity.issnl: + t['issns'].append(entity.issnl) + for key in ('issnp', 'issne'): + if entity.extra.get(key): + t['issns'].append(entity.extra[key]) + in_doaj = None in_road = None - # TODO: not currently implemented - in_doi = None - # TODO: would be nice to have 'in_doaj_works', or maybe just "any_pid" - #in_doaj_works = None - in_sherpa_romeo = None is_oa = None - # TODO: not actually set/stored anywhere? is_longtail_oa = None any_kbart = None any_jstor = None @@ -286,17 +366,15 @@ def container_to_elasticsearch(entity, force_bool=True): if extra.get('road'): if extra['road'].get('as_of'): in_road = True - if extra.get('ezb'): - if extra['ezb'].get('color') == 'green': - is_oa = True if extra.get('szczepanski'): if extra['szczepanski'].get('as_of'): is_oa = True if extra.get('default_license'): if extra['default_license'].startswith('CC-'): is_oa = True + t['sherpa_romeo_color'] = None if extra.get('sherpa_romeo'): - in_sherpa_romeo = True + t['sherpa_romeo_color'] = extra['sherpa_romeo'].get('color') if extra['sherpa_romeo'].get('color') == 'white': is_oa = False if extra.get('kbart'): @@ -306,54 +384,128 @@ def container_to_elasticsearch(entity, force_bool=True): if extra.get('ia'): if extra['ia'].get('sim'): any_ia_sim = True + if extra['ia'].get('longtail_oa'): + is_longtail_oa = True t['is_superceded'] = bool(extra.get('superceded')) t['in_doaj'] = bool(in_doaj) t['in_road'] = bool(in_road) - t['in_sherpa_romeo'] = bool(in_sherpa_romeo) t['any_kbart'] = bool(any_kbart) - t['is_longtail_oa'] = bool(is_longtail_oa) if force_bool: - t['in_doi'] = bool(in_doi) - t['is_oa'] = bool(in_doaj or in_road or is_longtail_oa or is_oa) + t['is_oa'] = bool(in_doaj or in_road or is_oa) + t['is_longtail_oa'] = bool(is_longtail_oa) t['any_jstor'] = bool(any_jstor) t['any_ia_sim'] = bool(any_ia_sim) else: - t['in_doi'] = in_doi - t['is_oa'] = in_doaj or in_road or is_longtail_oa or is_oa + t['is_oa'] = in_doaj or in_road or is_oa + t['is_longtail_oa'] = is_longtail_oa t['any_jstor'] = any_jstor t['any_ia_sim'] = any_ia_sim return t +def _type_of_edit(edit): + if edit.revision == None and edit.redirect_ident == None: + return 'delete' + elif edit.redirect_ident: + # redirect + return 'update' + elif edit.prev_revision == None and edit.redirect_ident == None and edit.revision: + return 'create' + else: + return 'update' + + def changelog_to_elasticsearch(entity): + """ + Note that this importer requires expanded fill info to work. Calling code + may need to re-fetch editgroup from API to get the 'editor' field. Some of + the old kafka feed content doesn't includes editor in particular. + """ editgroup = entity.editgroup t = dict( index=entity.index, editgroup_id=entity.editgroup_id, - timestamp=entity.timestamp, + timestamp=entity.timestamp.isoformat(), editor_id=editgroup.editor_id, + username=editgroup.editor.username, + is_bot=editgroup.editor.is_bot, + is_admin=editgroup.editor.is_admin, ) extra = editgroup.extra or dict() if extra.get('agent'): t['agent'] = extra['agent'] - t['containers'] = len(editgroup.edits.containers) - t['creators'] = len(editgroup.edits.containers) - t['files'] = len(editgroup.edits.containers) - t['filesets'] = len(editgroup.edits.containers) - t['webcaptures'] = len(editgroup.edits.containers) - t['releases'] = len(editgroup.edits.containers) - t['works'] = len(editgroup.edits.containers) - - # TODO: parse and pull out counts - #created = 0 - #updated = 0 - #deleted = 0 - #t['created'] = created - #t['updated'] = updated - #t['deleted'] = deleted - #t['total'] = created + updated + deleted + containers = [_type_of_edit(e) for e in editgroup.edits.containers] + creators = [_type_of_edit(e) for e in editgroup.edits.creators] + files = [_type_of_edit(e) for e in editgroup.edits.files] + filesets = [_type_of_edit(e) for e in editgroup.edits.filesets] + webcaptures = [_type_of_edit(e) for e in editgroup.edits.webcaptures] + releases = [_type_of_edit(e) for e in editgroup.edits.releases] + works = [_type_of_edit(e) for e in editgroup.edits.works] + + t['containers'] = len(containers) + t['new_containers'] = len([e for e in containers if e == 'create']) + t['creators'] = len(creators) + t['new_creators'] = len([e for e in creators if e == 'create']) + t['files'] = len(files) + t['new_files'] = len([e for e in files if e == 'create']) + t['filesets'] = len(filesets) + t['new_filesets'] = len([e for e in filesets if e == 'create']) + t['webcaptures'] = len(webcaptures) + t['new_webcaptures'] = len([e for e in webcaptures if e == 'create']) + t['releases'] = len(releases) + t['new_releases'] = len([e for e in releases if e == 'create']) + t['works'] = len(works) + t['new_works'] = len([e for e in works if e == 'create']) + + all_edits = containers + creators + files + filesets + webcaptures + releases + works + + t['created'] = len([e for e in all_edits if e == 'create']) + t['updated'] = len([e for e in all_edits if e == 'update']) + t['deleted'] = len([e for e in all_edits if e == 'delete']) + t['total'] = len(all_edits) + return t + + +def file_to_elasticsearch(entity): + """ + Converts from an entity model/schema to elasticsearch oriented schema. + + Returns: dict + Raises exception on error (never returns None) + """ + + if entity.state in ('redirect', 'deleted'): + return dict( + ident = entity.ident, + state = entity.state, + ) + elif entity.state != 'active': + raise ValueError("Unhandled entity state: {}".format(entity.state)) + + # First, the easy ones (direct copy) + t = dict( + ident = entity.ident, + state = entity.state, + revision = entity.revision, + release_ids = entity.release_ids, + release_count = len(entity.release_ids), + mimetype = entity.mimetype, + size_bytes = entity.size, + sha1 = entity.sha1, + sha256 = entity.sha256, + md5 = entity.md5, + ) + + parsed_urls = [tldextract.extract(u.url) for u in entity.urls] + t['hosts'] = list(set(['.'.join([seg for seg in pu if seg]) for pu in parsed_urls])) + t['domains'] = list(set([pu.registered_domain for pu in parsed_urls])) + t['rels'] = list(set([u.rel for u in entity.urls])) + + t['in_ia'] = bool('archive.org' in t['domains']) + t['in_ia_petabox'] = bool('archive.org' in t['hosts']) + return t diff --git a/python/fatcat_tools/workers/changelog.py b/python/fatcat_tools/workers/changelog.py index 7a9a585d..b84d5e70 100644 --- a/python/fatcat_tools/workers/changelog.py +++ b/python/fatcat_tools/workers/changelog.py @@ -105,6 +105,8 @@ class EntityUpdatesWorker(FatcatWorker): self.live_pdf_ingest_doi_prefix_acceptlist = [ # biorxiv and medrxiv "10.1101/", + # researchgate + "10.13140/", ] def want_live_ingest(self, release, ingest_request): @@ -121,6 +123,33 @@ class EntityUpdatesWorker(FatcatWorker): ingest_type = ingest_request.get('ingest_type') doi = ingest_request.get('ext_ids', {}).get('doi') + is_document = release.release_type in ( + 'article-journal', + 'paper-conference', + 'article', + 'report', + 'chapter', + 'manuscript', + 'review', + 'thesis', + 'letter', + 'editorial', + 'abstract', + 'entry', + 'patent', + 'post', + 'review-book', + ) + is_not_pdf = release.release_type in ( + 'dataset', + 'stub', + 'software', + 'figure', + 'graphic', + ) + + # accept list sets a default "crawl it" despite OA metadata for + # known-OA DOI prefixes in_acceptlist = False if doi: for prefix in self.live_pdf_ingest_doi_prefix_acceptlist: @@ -129,9 +158,18 @@ class EntityUpdatesWorker(FatcatWorker): if self.ingest_oa_only and link_source not in ('arxiv', 'pmc'): es = release_to_elasticsearch(release) - if not es['is_oa'] and not in_acceptlist: + # most datacite documents are in IRs and should be crawled + is_datacite_doc = False + if release.extra and ('datacite' in release.extra) and is_document: + is_datacite_doc = True + if not (es['is_oa'] or in_acceptlist or is_datacite_doc): return False + # if ingest_type is pdf but release_type is almost certainly not a PDF, + # skip it. This is mostly a datacite thing. + if ingest_type == "pdf" and is_not_pdf: + return False + if ingest_type == "pdf" and doi: for prefix in self.ingest_pdf_doi_prefix_blocklist: if doi.startswith(prefix): diff --git a/python/fatcat_transform.py b/python/fatcat_transform.py index ccb13871..23a56109 100755 --- a/python/fatcat_transform.py +++ b/python/fatcat_transform.py @@ -1,6 +1,8 @@ #!/usr/bin/env python3 """ +Utility script for doing bulk conversion/tranforms of entity JSON schema to +other formats """ import sys @@ -15,10 +17,11 @@ from citeproc_styles import get_style_filepath import fatcat_openapi_client from fatcat_openapi_client.rest import ApiException -from fatcat_openapi_client import ReleaseEntity, ContainerEntity, ChangelogEntry +from fatcat_openapi_client import ReleaseEntity, ContainerEntity, FileEntity, ChangelogEntry from fatcat_tools import uuid2fcid, entity_from_json, entity_to_dict, \ release_to_elasticsearch, container_to_elasticsearch, \ - changelog_to_elasticsearch, public_api, release_to_csl, citeproc_csl + file_to_elasticsearch, changelog_to_elasticsearch, public_api, \ + release_to_csl, citeproc_csl def run_elasticsearch_releases(args): @@ -27,6 +30,8 @@ def run_elasticsearch_releases(args): if not line: continue entity = entity_from_json(line, ReleaseEntity, api_client=args.api.api_client) + if entity.state != 'active': + continue args.json_output.write( json.dumps(release_to_elasticsearch(entity)) + '\n') @@ -36,9 +41,22 @@ def run_elasticsearch_containers(args): if not line: continue entity = entity_from_json(line, ContainerEntity, api_client=args.api.api_client) + if entity.state != 'active': + continue args.json_output.write( json.dumps(container_to_elasticsearch(entity)) + '\n') +def run_elasticsearch_files(args): + for line in args.json_input: + line = line.strip() + if not line: + continue + entity = entity_from_json(line, FileEntity, api_client=args.api.api_client) + if entity.state != 'active': + continue + args.json_output.write( + json.dumps(file_to_elasticsearch(entity)) + '\n') + def run_elasticsearch_changelogs(args): for line in args.json_input: line = line.strip() @@ -54,6 +72,8 @@ def run_citeproc_releases(args): if not line: continue entity = entity_from_json(line, ReleaseEntity, api_client=args.api.api_client) + if entity.state != 'active': + continue csl_json = release_to_csl(entity) csl_json['id'] = "release:" + (entity.ident or "unknown") out = citeproc_csl(csl_json, args.style, args.html) @@ -87,6 +107,16 @@ def main(): help="where to send output", default=sys.stdout, type=argparse.FileType('w')) + sub_elasticsearch_files = subparsers.add_parser('elasticsearch-files', + help="convert fatcat file JSON schema to elasticsearch file schema") + sub_elasticsearch_files.set_defaults(func=run_elasticsearch_files) + sub_elasticsearch_files.add_argument('json_input', + help="JSON-per-line of file entities", + default=sys.stdin, type=argparse.FileType('r')) + sub_elasticsearch_files.add_argument('json_output', + help="where to send output", + default=sys.stdout, type=argparse.FileType('w')) + sub_elasticsearch_changelogs = subparsers.add_parser('elasticsearch-changelogs', help="convert fatcat changelog JSON schema to elasticsearch changelog schema") sub_elasticsearch_changelogs.set_defaults(func=run_elasticsearch_changelogs) diff --git a/python/fatcat_web/entity_helpers.py b/python/fatcat_web/entity_helpers.py index af0fea83..591dda80 100644 --- a/python/fatcat_web/entity_helpers.py +++ b/python/fatcat_web/entity_helpers.py @@ -53,6 +53,10 @@ def enrich_release_entity(entity): entity._es = release_to_elasticsearch(entity, force_bool=False) if entity.container and entity.container.state == "active": entity.container._es = container_to_elasticsearch(entity.container, force_bool=False) + if entity.files: + # remove shadows-only files with no URLs + entity.files = [f for f in entity.files + if not (f.extra and f.extra.get('shadows') and not f.urls)] if entity.filesets: for fs in entity.filesets: fs._total_size = sum([f.size for f in fs.manifest]) diff --git a/python/fatcat_web/search.py b/python/fatcat_web/search.py index 7c60a6dd..6b2b9cc1 100644 --- a/python/fatcat_web/search.py +++ b/python/fatcat_web/search.py @@ -77,7 +77,7 @@ def do_release_search(q, limit=30, fulltext_only=True, offset=0): "default_operator": "AND", "analyze_wildcard": True, "lenient": True, - "fields": ["title^5", "contrib_names^2", "container_title"], + "fields": ["biblio"], }, }, } @@ -106,7 +106,7 @@ def do_container_search(q, limit=30, offset=0): "default_operator": "AND", "analyze_wildcard": True, "lenient": True, - "fields": ["name^5", "publisher"], + "fields": ["biblio"], }, }, } diff --git a/python/fatcat_web/templates/release_view.html b/python/fatcat_web/templates/release_view.html index 83ecd1c8..961b4759 100644 --- a/python/fatcat_web/templates/release_view.html +++ b/python/fatcat_web/templates/release_view.html @@ -196,8 +196,9 @@ </tbody> </table> {% else %} -<p>There are no known files associated with this release (you could try -<a href="/work/{{ release.work_id }}">other releases for this work?</a>). +<p>There are no accessible files associated with this release. You could check +<a href="/work/{{ release.work_id }}">other releases for this work</a> for an +accessible version. {% endif %} {% endif %} diff --git a/python/tests/files/changelog_3469683.json b/python/tests/files/changelog_3469683.json new file mode 100644 index 00000000..7a847b16 --- /dev/null +++ b/python/tests/files/changelog_3469683.json @@ -0,0 +1 @@ +{"index":3469683,"editgroup_id":"jebmpiqsjja7jozze7hoy3bir4","timestamp":"2020-01-30T05:04:39.738601Z","editgroup":{"editgroup_id":"jebmpiqsjja7jozze7hoy3bir4","editor_id":"scmbogxw25evtcesfcab5qaboa","editor":{"editor_id":"scmbogxw25evtcesfcab5qaboa","username":"crawl-bot","is_admin":true,"is_bot":true,"is_active":true},"changelog_index":3469683,"created":"2020-01-30T05:04:39.738601Z","description":"Files crawled from web using sandcrawler ingest 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+{"shadow":{"shadow_corpus":"scimag","shadow_id":"30603850","sha1hex":"000002c1abd521f18aa23d9e8f464e697e218ab1","doi":"10.1109/spire.1998.712983","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"000002c1abd521f18aa23d9e8f464e697e218ab1","sha256hex":"777e2c472e9d2fec3bbd26bad788562cf1e08e5850315c25cfb6e46d38e7e4af","md5hex":"3a3c92fabaf6cf437bb596d9e9255ff6","size_bytes":113768,"mimetype":"application/pdf"},"cdx":{"url":"http://proteomics.bioprojects.org/pavel/papers/SST_versus_EST_in_gene_recognition..pdf","datetime":"20081121222143","sha1hex":"000002c1abd521f18aa23d9e8f464e697e218ab1","cdx_sha1hex":null,"mimetype":"application/pdf","warc_path":"1227992340180_31-c/1227992509265_9.arc.gz","warc_csize":61212,"warc_offset":62956683,"row_created":"2020-01-07T02:06:33.965383+00:00"}} 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+{"shadow":{"shadow_corpus":"scimag","shadow_id":"74272862","sha1hex":"000003a94022be58305ccc2a018a6359eeb226db","doi":"10.1002/slct.201802783","pmid":null,"isbn13":null},"file_meta":{"sha1hex":"000003a94022be58305ccc2a018a6359eeb226db","sha256hex":"f277eefc7b1466df814a7a892ab8e2e7f08db1faae0bf73b893211e5f5b37193","md5hex":"27534b8494f54ba5de47c16fb2590b04","size_bytes":1372272,"mimetype":"application/pdf"},"cdx":null} diff --git a/python/tests/files/file_bcah4zp5tvdhjl5bqci2c2lgfa.json b/python/tests/files/file_bcah4zp5tvdhjl5bqci2c2lgfa.json new file mode 100644 index 00000000..bed8977d --- /dev/null +++ b/python/tests/files/file_bcah4zp5tvdhjl5bqci2c2lgfa.json @@ -0,0 +1 @@ +{"release_ids":["5tbuas2e4vd6jaowbgzmmhhqxe"],"mimetype":"application/pdf","urls":[{"url":"https://web.archive.org/web/20200130042753/https://www.zhros.ru/jour/article/download/811/542","rel":"webarchive"},{"url":"https://www.zhros.ru/jour/article/download/811/542","rel":"web"}],"sha256":"1665cdb90b73c684233038601c52995acef77bb37aefc6e63ae13e4194d48261","sha1":"3ad4df99ff1354ec0b5a333a59fba9a3a5d9812a","md5":"39159f9c8e98a245f954c9000b0f2810","size":739980,"revision":"dcc7a975-725d-4bc9-8c3f-cd0476cd485e","ident":"bcah4zp5tvdhjl5bqci2c2lgfa","state":"active"}
\ No newline at end of file diff --git a/python/tests/files/release_etodop5banbndg3faecnfm6ozi.json b/python/tests/files/release_etodop5banbndg3faecnfm6ozi.json new file mode 100644 index 00000000..1204c95d --- /dev/null +++ b/python/tests/files/release_etodop5banbndg3faecnfm6ozi.json @@ -0,0 +1 @@ +{"abstracts":[],"refs":[{"index":0,"extra":{"issue":"Suppl 1","volume":"118"},"key":"10.1111/j.1471-0528.2011.03098.x-BIB1|cit1","year":2011,"container_name":"BJOG","title":"Saving Mothers' Lives: reviewing maternal deaths to make motherhood safer-2006-2008. The Eighth Report of the Confidential Enquiries into Maternal Deaths in the United Kingdom"}],"contribs":[{"index":0,"raw_name":"Philip Steer","role":"author","extra":{"seq":"first"}}],"language":"en","publisher":"Wiley","pages":"1404-1404","issue":"11","volume":"118","ext_ids":{"doi":"10.1111/j.1471-0528.2011.03098.x"},"release_year":2011,"release_date":"2011-09-09","release_stage":"published","release_type":"article-journal","container_id":"hl5g6d5msjcl7hlbyyvcsbhc2u","webcaptures":[],"filesets":[],"files":[],"container":{"wikidata_qid":"Q15724571","issnl":"1470-0328","publisher":"Wiley (Blackwell Publishing)","container_type":"journal","name":"BJOG: an International Journal of Obstetrics and Gynaecology","extra":{"abbrev":"BJOG","country":"gb","ia":{"sim":{"year_spans":[[1902,1915],[1921,2015]]}},"issne":"1471-0528","issnp":"1470-0328","kbart":{"clockss":{"year_spans":[[1989,1989],[1993,1993],[2002,2003],[2009,2017]]},"portico":{"year_spans":[[1902,2019]]}},"languages":["en"],"sherpa_romeo":{"color":"yellow"},"urls":["http://www.bjog.org/view/0/index.html"]},"revision":"ec26766c-c1fe-453b-837d-087cc254fe07","ident":"hl5g6d5msjcl7hlbyyvcsbhc2u","state":"active"},"work_id":"wmwe5wwkzfcs7gyjfgdeanksha","title":"Saving Mothers' Lives. Reviewing maternal deaths to make motherhood safer: 2006-2008","state":"active","ident":"etodop5banbndg3faecnfm6ozi","revision":"deb7e050-6df6-42ed-9704-788a0e30facf","extra":{"crossref":{"type":"journal-article"},"subtitle":["Correpondence"]}}
\ No newline at end of file diff --git a/python/tests/import_shadow.py b/python/tests/import_shadow.py new file mode 100644 index 00000000..70a918d2 --- /dev/null +++ b/python/tests/import_shadow.py @@ -0,0 +1,61 @@ + +import json +import pytest +from fatcat_tools.importers import ShadowLibraryImporter, JsonLinePusher +from fixtures import api + + +@pytest.fixture(scope="function") +def shadow_importer(api): + yield ShadowLibraryImporter(api) + +# TODO: use API to check that entities actually created... +def test_shadow_importer_basic(shadow_importer): + with open('tests/files/example_shadow.json', 'r') as f: + JsonLinePusher(shadow_importer, f).run() + +def test_shadow_importer(shadow_importer): + last_index = shadow_importer.api.get_changelog(limit=1)[0].index + with open('tests/files/example_shadow.json', 'r') as f: + shadow_importer.bezerk_mode = True + counts = JsonLinePusher(shadow_importer, f).run() + assert counts['insert'] == 2 + assert counts['exists'] == 0 + assert counts['skip'] == 8 + + # fetch most recent editgroup + change = shadow_importer.api.get_changelog_entry(index=last_index+1) + eg = change.editgroup + assert eg.description + assert "shadow library" in eg.description.lower() + assert eg.extra['git_rev'] + assert "fatcat_tools.ShadowLibraryImporter" in eg.extra['agent'] + + # re-insert; should skip + with open('tests/files/example_shadow.json', 'r') as f: + shadow_importer.reset() + shadow_importer.bezerk_mode = False + counts = JsonLinePusher(shadow_importer, f).run() + assert counts['insert'] == 0 + assert counts['exists'] == 2 + assert counts['skip'] == 8 + +def test_shadow_dict_parse(shadow_importer): + with open('tests/files/example_shadow.json', 'r') as f: + raw = json.loads(f.readline()) + f = shadow_importer.parse_record(raw) + + assert f.sha1 == "0000002922264275f11cca7b1c3fb662070d0dd7" + assert f.md5 == "debd8db178fa08a7a0aaec6e42832a8e" + assert f.sha256 == "b4728210cc0f70d8a8f8c39bd97fcbbab3eaca4309ac4bdfbce5df3b66c82f79" + assert f.mimetype == "application/pdf" + assert f.size == 206121 + assert len(f.urls) == 2 + for u in f.urls: + if u.rel == "publisher": + assert u.url.startswith("https://link.springer.com/content/pdf/10.1007%2Fs11626-008-9119-8.pdf") + if u.rel == "webarchive": + assert u.url.startswith("https://web.archive.org/") + assert "20180729135948" in u.url + assert len(f.release_ids) == 1 + diff --git a/python/tests/transform_tests.py b/python/tests/transform_elasticsearch.py index f254e117..a954fc4d 100644 --- a/python/tests/transform_tests.py +++ b/python/tests/transform_elasticsearch.py @@ -7,6 +7,7 @@ from fixtures import api from import_journal_metadata import journal_metadata_importer from import_crossref import crossref_importer +from import_matched import matched_importer def test_basic_elasticsearch_convert(crossref_importer): with open('tests/files/crossref-works.single.json', 'r') as f: @@ -72,14 +73,67 @@ def test_rich_elasticsearch_convert(): assert es['ref_count'] == 2 assert es['ref_linked_count'] == 1 -def test_elasticsearch_from_json(): - r = entity_from_json(open('./tests/files/math_universe.json', 'r').read(), ReleaseEntity) - release_to_elasticsearch(r) +def test_elasticsearch_release_from_json(): + r = entity_from_json(open('./tests/files/release_etodop5banbndg3faecnfm6ozi.json', 'r').read(), ReleaseEntity) + es = release_to_elasticsearch(r) + + assert es['subtitle'] == "Correpondence" + assert es['ident'] == "etodop5banbndg3faecnfm6ozi" + assert es['container_name'] == "BJOG: an International Journal of Obstetrics and Gynaecology" + assert es['first_page'] == "1404" + assert es['issue'] == "11" + assert es['volume'] == "118" + assert es['number'] == None + assert es['in_ia_sim'] == True + assert es['in_kbart'] == True -def test_elasticsearch_container_convert(journal_metadata_importer): +def test_elasticsearch_container_transform(journal_metadata_importer): with open('tests/files/journal_metadata.sample.json', 'r') as f: raw = json.loads(f.readline()) c = journal_metadata_importer.parse_record(raw) c.state = 'active' es = container_to_elasticsearch(c) assert es['publisher'] == c.publisher + +def test_elasticsearch_file_transform(matched_importer): + f = entity_from_json(open('./tests/files/file_bcah4zp5tvdhjl5bqci2c2lgfa.json', 'r').read(), FileEntity) + + f.state = 'active' + es = file_to_elasticsearch(f) + assert es['sha1'] == f.sha1 + assert es['sha256'] == f.sha256 + assert es['md5'] == f.md5 + assert es['size_bytes'] == f.size + assert es['mimetype'] == f.mimetype + assert es['in_ia'] == True + + assert 'web' in es['rels'] + assert 'www.zhros.ru' in es['hosts'] + assert 'zhros.ru' in es['domains'] + assert 'archive.org' in (es['hosts'] + es['domains']) + assert 'web.archive.org' in (es['hosts'] + es['domains']) + # old regression + assert not '.archive.org' in (es['hosts'] + es['domains']) + +def test_elasticsearch_changelog_transform(matched_importer): + ce = entity_from_json(open('./tests/files/changelog_3469683.json', 'r').read(), ChangelogEntry) + + es = changelog_to_elasticsearch(ce) + assert es['index'] == 3469683 + # len("2020-01-30T05:04:39") => 19 + assert es['timestamp'][:19] == "2020-01-30T05:04:39.738601Z"[:19] + assert es['editor_id'] == "scmbogxw25evtcesfcab5qaboa" + assert es['username'] == "crawl-bot" + assert es['is_bot'] == True + assert es['is_admin'] == True + assert es['agent'] == "fatcat_tools.IngestFileResultImporter" + + assert es['total'] == 50 + assert es['files'] == 50 + assert es['new_files'] == 50 + assert es['created'] == 50 + + assert es['releases'] == 0 + assert es['new_releases'] == 0 + assert es['updated'] == 0 + assert es['deleted'] == 0 |