diff options
| -rwxr-xr-x | python/client.py | 28 | ||||
| -rw-r--r-- | python/fatcat/crossref_importer.py | 85 | ||||
| -rw-r--r-- | python/fatcat/importer_common.py | 44 | ||||
| -rw-r--r-- | python/tests/crossref.py | 8 | ||||
| -rw-r--r-- | python/tests/files/ISSN-to-ISSN-L.snip.txt | 10 | ||||
| -rw-r--r-- | python/tests/files/crossref-works.2018-01-21.badsample.json | 3 |
6 files changed, 126 insertions, 52 deletions
diff --git a/python/client.py b/python/client.py index 9631318a..9a2ed50d 100755 --- a/python/client.py +++ b/python/client.py @@ -7,13 +7,19 @@ from fatcat.orcid_importer import FatcatOrcidImporter def run_import_crossref(args): fcc = FatcatCrossrefClient(args.host_url) - fcc.import_crossref_file(args.json_file) - # create_containers=args.create_containers + fcc.import_crossref_file( + args.json_file, + issn_map_file=args.issn_map_file, + create_containers=(not args.no_create_containers)) def run_import_orcid(args): foi = FatcatOrcidImporter(args.host_url) foi.process_batch(args.json_file, size=args.batch_size) +def run_import_manifest(args): + fmi = FatcatManifestImporter(args.host_url) + fmi.process_db(args.db_path, size=args.batch_size) + def health(args): rfac = RawFatcatApiClient(args.host_url) print(rfac.health()) @@ -32,10 +38,11 @@ def main(): sub_import_crossref.set_defaults(func=run_import_crossref) sub_import_crossref.add_argument('json_file', help="crossref JSON file to import from") - # TODO: - #sub_import_crossref.add_argument('--create-containers', - # action='store_true', - # help="if true, create containers based on ISSN") + sub_import_crossref.add_argument('issn_map_file', + help="ISSN to ISSN-L mapping file") + sub_import_crossref.add_argument('--no-create-containers', + action='store_true', + help="skip creation of new container entities based on ISSN") sub_import_orcid = subparsers.add_parser('import-orcid') sub_import_orcid.set_defaults(func=run_import_orcid) @@ -46,6 +53,15 @@ def main(): help="size of batch to send", default=50, type=int) + sub_import_manifest = subparsers.add_parser('import-orcid') + sub_import_manifest.set_defaults(func=run_import_orcid) + sub_import_manifest.add_argument('db_path', + help="sqlite3 database to import from", + type=argparse.FileType('r')) + sub_import_orcid.add_argument('--batch-size', + help="size of batch to send", + default=50, type=int) + sub_health = subparsers.add_parser('health') sub_health.set_defaults(func=health) diff --git a/python/fatcat/crossref_importer.py b/python/fatcat/crossref_importer.py index 4c68230d..a7166bc3 100644 --- a/python/fatcat/crossref_importer.py +++ b/python/fatcat/crossref_importer.py @@ -8,7 +8,9 @@ from fatcat.importer_common import FatcatImporter class FatcatCrossrefImporter(FatcatImporter): - # TODO: overload __init__ to handle create_containers + def __init__(self, host_url, issn_map_file, create_containers=True): + super().__init__(host_url, issn_map_file) + self.create_containers = create_containers def parse_crossref_dict(self, obj): """ @@ -19,50 +21,49 @@ class FatcatCrossrefImporter(FatcatImporter): # contribs contribs = [] for i, am in enumerate(obj['author']): + creator_id = None + if 'ORCID' in am.keys(): + creator_id = self.lookup_orcid(am['ORCID'].split('/')[-1]) contribs.append(fatcat_client.ReleaseContrib( - creator_id=None, # TODO: orcid lookup - index=i, + creator_id=creator_id, + index=i+1, # Sorry humans :( raw="{} {}".format(am['given'], am['family']), role="author")) # container - # TODO: ISSN vs. ISSN-L issn = obj.get('ISSN', [None])[0] - container_id = self.lookup_issnl(issn) + issnl = self.issn2issnl(issn) + container_id = None + if issnl: + container_id = self.lookup_issnl(issnl) + publisher = obj['publisher'] - ## TODO: create containers in-line like this? - #container = dict( - # issn=issn, - # name=obj['container-title'][0], - # container=container_id, - # #sortname=obj['short-container-title'][0]) - # publisher=obj['publisher']) - #if container_id is None and self.create_containers and issn != None: - # rv = self.post('/v0/container', data=dict( - # issn=container['issn'], - # publisher=container['publisher'])) - # assert rv.status_code == 201 - # container_id = rv.json()['id'] - # print("created container: {}".format(issn)) - # container['id'] = container_id - # self._issn_map[issn] = container_id + ce = None + if container_id is None and self.create_containers and issnl != None: + ce = fatcat_client.ContainerEntity( + issnl=issnl, + publisher=publisher, + name=obj['container-title'][0]) + print("created container: {}".format(issnl)) # references refs = [] for i, rm in enumerate(obj.get('reference', [])): + try: + year = int(rm.get('year')) + except: + year = None refs.append(fatcat_client.ReleaseRef( - index=i, + index=i+1, target_release_id=None, # TODO: DOI lookup: rm.get("DOI", None), - # TODO: all these - key=None, - year=None, - container_title=None, - title=None, - locator=None, - # TODO: how to generate a proper stub here from k/v objdata? - # TODO: just dump JSON here if we didn't get a match? - raw="| ".join(rm.values()))) + # unreliable for crossref: key=rm['key'].split('|')[-1], + year=year, + container_title=rm.get('volume-title'), + title=rm.get('title'), + locator=rm.get('first-page'), + # TODO: just dump JSON somewhere here? + raw=rm.get('unstructured'))) # work we = fatcat_client.WorkEntity( @@ -73,34 +74,38 @@ class FatcatCrossrefImporter(FatcatImporter): extra = dict(crossref={ 'links': obj.get('link', []), 'subject': obj.get('subject'), - 'crossref-type': obj['type'], + 'type': obj['type'], + 'license': obj.get('license', [dict(URL=None)])[0]['URL'] or None, 'alternative-id': obj.get('alternative-id', [])}) re = fatcat_client.ReleaseEntity( - work_id='null', # XXX: + work_id='tbd', # gets set later, I promise! title=obj['title'][0], contribs=contribs, refs=refs, container_id=container_id, release_type=obj['type'], - doi=obj['DOI'], + doi=obj['DOI'].lower(), release_date=obj['created']['date-time'], - #license=obj.get('license', [dict(URL=None)])[0]['URL'] or None, issue=obj.get('issue'), volume=obj.get('volume'), pages=obj.get('page'), extra=extra) - return (we, re) + return (we, re, ce) def create_row(self, row, editgroup_id=None): if row is None: - continue + return obj = json.loads(row) - both = self.parse_crossref_dict(obj) - if both is not None: - (we, re) = both + entities = self.parse_crossref_dict(obj) + if entities is not None: + (we, re, ce) = entities we.editgroup_id = editgroup_id re.editgroup_id = editgroup_id + if ce is not None: + ce.editgroup_id = editgroup_id + container = self.api.create_container(ce) + re.container_id = container.ident created = self.api.create_work(we) re.work_id = created.ident self.api.create_release(re) diff --git a/python/fatcat/importer_common.py b/python/fatcat/importer_common.py index 98bfb26e..c24565b4 100644 --- a/python/fatcat/importer_common.py +++ b/python/fatcat/importer_common.py @@ -13,11 +13,15 @@ def grouper(iterable, n, fillvalue=None): class FatcatImporter: - def __init__(self, host_url): + def __init__(self, host_url, issn_map_file=None): conf = fatcat_client.Configuration() conf.host = host_url self.api = fatcat_client.DefaultApi(fatcat_client.ApiClient(conf)) - self._issnl_map = dict() + self._issnl_id_map = dict() + self._orcid_id_map = dict() + self._issn_issnl_map = None + if issn_map_file: + self.read_issn_map_file(issn_map_file) def process_source(self, source, group_size=100): """Creates and auto-accepts editgropu every group_size rows""" @@ -40,8 +44,8 @@ class FatcatImporter: def lookup_issnl(self, issnl): """Caches calls to the ISSN-L lookup API endpoint in a local dict""" assert len(issnl) == 9 and issnl[4] == '-' - if issnl in self._issnl_map: - return self._issnl_map[issn] + if issnl in self._issnl_id_map: + return self._issnl_id_map[issn] container_id = None try: rv = self.api.lookup_container(issnl=issnl) @@ -49,5 +53,35 @@ class FatcatImporter: except ApiException as ae: # If anything other than a 404 (not found), something is wrong assert ae.status == 404 - self._issnl_map[issnl] = container_id # might be None + self._issnl_id_map[issnl] = container_id # might be None return container_id + + def lookup_orcid(self, orcid): + """Caches calls to the Orcid lookup API endpoint in a local dict""" + assert len(orcid) == 19 and orcid[4] == '-' + if orcid in self._orcid_id_map: + return self._orcid_id_map[orcid] + creator_id = None + try: + rv = self.api.lookup_creator(orcid=orcid) + creator_id = rv.ident + except ApiException as ae: + # If anything other than a 404 (not found), something is wrong + assert ae.status == 404 + self._orcid_id_map[orcid] = creator_id # might be None + return creator_id + + def read_issn_map_file(self, issn_map_file): + self._issn_issnl_map = dict() + for line in issn_map_file: + if line.startswith("ISSN") or len(line) == 0: + continue + (issn, issnl) = line.split()[0:2] + self._issn_issnl_map[issn] = issnl + # double mapping makes lookups easy + self._issn_issnl_map[issnl] = issnl + + def issn2issnl(self, issn): + if issn is None: + return None + self._issn_issnl_map.get(issn) diff --git a/python/tests/crossref.py b/python/tests/crossref.py index e72f7d02..402195d7 100644 --- a/python/tests/crossref.py +++ b/python/tests/crossref.py @@ -5,7 +5,8 @@ from fatcat.crossref_importer import FatcatCrossrefImporter @pytest.fixture(scope="function") def crossref_importer(): - yield FatcatCrossrefImporter("http://localhost:9411/v0") + with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file: + yield FatcatCrossrefImporter("http://localhost:9411/v0", issn_file) def test_crossref_importer_batch(crossref_importer): with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f: @@ -14,3 +15,8 @@ def test_crossref_importer_batch(crossref_importer): def test_crossref_importer(crossref_importer): with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f: crossref_importer.process_source(f) + +def test_crossref_importer_create(crossref_importer): + crossref_importer.create_containers = True + with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f: + crossref_importer.process_source(f) diff --git a/python/tests/files/ISSN-to-ISSN-L.snip.txt b/python/tests/files/ISSN-to-ISSN-L.snip.txt new file mode 100644 index 00000000..965a49d6 --- /dev/null +++ b/python/tests/files/ISSN-to-ISSN-L.snip.txt @@ -0,0 +1,10 @@ +ISSN ISSN-L +0000-0019 0000-0019 +0000-0027 0000-0027 +0000-0043 0000-0043 +0000-0051 0000-0051 +0000-006X 0000-006X +0000-0078 0000-0078 +0000-0094 0000-0094 +0000-0108 0000-0108 +0000-0140 0000-0140 diff --git a/python/tests/files/crossref-works.2018-01-21.badsample.json b/python/tests/files/crossref-works.2018-01-21.badsample.json index 143adf3e..84271489 100644 --- a/python/tests/files/crossref-works.2018-01-21.badsample.json +++ b/python/tests/files/crossref-works.2018-01-21.badsample.json @@ -8,3 +8,6 @@ { "_id" : { "$oid" : "5a55165c88a035a45bd7e535" }, "indexed" : { "date-parts" : [ [ 2017, 10, 23 ] ], "date-time" : "2017-10-23T14:27:04Z", "timestamp" : { "$numberLong" : "1508768824539" } }, "reference-count" : 6, "publisher" : "Wiley-Blackwell", "issue" : "24", "license" : [ { "URL" : "http://doi.wiley.com/10.1002/tdm_license_1.1", "start" : { "date-parts" : [ [ 2015, 9, 1 ] ], "date-time" : "2015-09-01T00:00:00Z", "timestamp" : { "$numberLong" : "1441065600000" } }, "delay-in-days" : 5722, "content-version" : "tdm" } ], "content-domain" : { "domain" : [], "crossmark-restriction" : false }, "short-container-title" : [ "Rapid Commun. Mass Spectrom." ], "published-print" : { "date-parts" : [ [ 2000, 12, 30 ] ] }, "DOI" : "10.1002/1097-0231(20001230)14:24<2357::aid-rcm168>3.0.co;2-2", "type" : "journal-article", "created" : { "date-parts" : [ [ 2002, 9, 11 ] ], "date-time" : "2002-09-11T00:24:57Z", "timestamp" : { "$numberLong" : "1031703897000" } }, "page" : "2357-2361", "source" : "Crossref", "is-referenced-by-count" : 2, "title" : [ "Electron impact fragmentation mechanisms of some cyclic esters with helical structures" ], "prefix" : "10.1002", "volume" : "14", "author" : [ { "given" : "Jiangtao", "family" : "He", "affiliation" : [] }, { "given" : "Aihua", "family" : "Nie", "affiliation" : [] }, { "given" : "Meiyu", "family" : "He", "affiliation" : [] }, { "given" : "Xiaoran", "family" : "He", "affiliation" : [] }, { "given" : "Zhenpei", "family" : "Yu", "affiliation" : [] }, { "given" : "Xiulin", "family" : "Ye", "affiliation" : [] }, { "given" : "Qiyi", "family" : "Xing", "affiliation" : [] } ], "member" : "311", "published-online" : { "date-parts" : [ [ 2000 ] ] }, "reference" : [ { "key" : "10.1002/1097-0231(20001230)14:24<2357::AID-RCM168>3.0.CO;2-2-BIB1", "author" : "Nie", "volume" : "8", "first-page" : "141", "year" : "1997", "journal-title" : "Chinese Chem. 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Mass Spectrom.", "DOI" : "10.1002/(SICI)1096-9888(199912)34:12<1322::AID-JMS888>3.0.CO;2-#", "doi-asserted-by" : "crossref" }, { "key" : "10.1002/1097-0231(20001230)14:24<2357::AID-RCM168>3.0.CO;2-2-BIB5", "author" : "Mclafferty", "year" : "1993", "unstructured" : "Interpretation of Mass Spectra (4th edn). University Science Books: Sansalito, CA, 1993.", "volume-title" : "Interpretation of Mass Spectra" }, { "key" : "10.1002/1097-0231(20001230)14:24<2357::AID-RCM168>3.0.CO;2-2-BIB6", "author" : "Williams", "year" : "1996", "unstructured" : "Spectroscopic Methods in Organic Chemistry (5th edn). McGraw-Hill: London, 1996.", "volume-title" : "Spectroscopic Methods in Organic Chemistry" } ], "container-title" : [ "Rapid Communications in Mass Spectrometry" ], "link" : [ { "URL" : "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2F1097-0231(20001230)14:24%3C2357::AID-RCM168%3E3.0.CO;2-2", "content-type" : "unspecified", "content-version" : "vor", "intended-application" : "text-mining" } ], "deposited" : { "date-parts" : [ [ 2017, 7, 31 ] ], "date-time" : "2017-07-31T21:16:20Z", "timestamp" : { "$numberLong" : "1501535780000" } }, "score" : 1, "issued" : { "date-parts" : [ [ 2000 ] ] }, "references-count" : 6, "URL" : "http://dx.doi.org/10.1002/1097-0231(20001230)14:24<2357::aid-rcm168>3.0.co;2-2", "relation" : { "cites" : [] }, "ISSN" : [ "0951-4198", "1097-0231" ], "issn-type" : [ { "value" : "0951-4198", "type" : "print" }, { "value" : "1097-0231", "type" : "electronic" } ], "subject" : [ "Organic Chemistry", "Analytical Chemistry", "Spectroscopy" ] } { "_id" : { "$oid" : "5a55196988a035a45bda0cb1" }, "indexed" : { "date-parts" : [ [ 2017, 10, 23 ] ], "date-time" : "2017-10-23T14:41:48Z", "timestamp" : { "$numberLong" : "1508769708308" } }, "reference-count" : 44, "publisher" : "Elsevier BV", "issue" : "1", "license" : [ { "URL" : "http://www.elsevier.com/tdm/userlicense/1.0/", "start" : { "date-parts" : [ [ 1998, 11, 1 ] ], "date-time" : "1998-11-01T00:00:00Z", "timestamp" : { "$numberLong" : "909878400000" } }, "delay-in-days" : 0, "content-version" : "tdm" } ], "content-domain" : { "domain" : [], "crossmark-restriction" : false }, "short-container-title" : [ "Toxicology and Applied Pharmacology" ], "published-print" : { "date-parts" : [ [ 1998, 11 ] ] }, "DOI" : "10.1006/taap.1998.8543", "type" : "journal-article", "created" : { "date-parts" : [ [ 2002, 9, 18 ] ], "date-time" : "2002-09-18T22:01:25Z", "timestamp" : { "$numberLong" : "1032386485000" } }, "page" : "102-108", "source" : "Crossref", "is-referenced-by-count" : 44, "title" : [ "Role of CYP1A2 in the Hepatotoxicity of Acetaminophen: Investigations UsingCyp1a2Null Mice" ], "prefix" : "10.1006", "volume" : "153", "author" : [ { "given" : "Robert P.", "family" : "Tonge", "affiliation" : [] }, { "given" : "Edward J.", "family" : "Kelly", "affiliation" : [] }, { "given" : "Sam A.", "family" : "Bruschi", "affiliation" : [] }, { "given" : "Tom", "family" : "Kalhorn", "affiliation" : [] }, { "given" : "David L.", "family" : "Eaton", "affiliation" : [] }, { "given" : "Daniel W.", "family" : "Nebert", "affiliation" : [] }, { "given" : "Sidney D.", "family" : "Nelson", "affiliation" : [] } ], "member" : "78", "container-title" : [ "Toxicology and Applied Pharmacology" ], "link" : [ { "URL" : "http://api.elsevier.com/content/article/PII:S0041008X9898543X?httpAccept=text/xml", "content-type" : "text/xml", "content-version" : "vor", "intended-application" : "text-mining" }, { "URL" : "http://api.elsevier.com/content/article/PII:S0041008X9898543X?httpAccept=text/plain", "content-type" : "text/plain", "content-version" : "vor", "intended-application" : "text-mining" } ], "deposited" : { "date-parts" : [ [ 2017, 6, 14 ] ], "date-time" : "2017-06-14T16:51:33Z", "timestamp" : { "$numberLong" : "1497459093000" } }, "score" : 1, "issued" : { "date-parts" : [ [ 1998, 11 ] ] }, "references-count" : 44, "alternative-id" : [ "S0041008X9898543X" ], "URL" : "http://dx.doi.org/10.1006/taap.1998.8543", "ISSN" : [ "0041-008X" ], "issn-type" : [ { "value" : "0041-008X", "type" : "print" } ], "subject" : [ "Toxicology", "Pharmacology" ] } { "_id" : { "$oid" : "5a55170088a035a45bd8490d" }, "indexed" : { "date-parts" : [ [ 2017, 10, 23 ] ], "date-time" : "2017-10-23T14:30:12Z", "timestamp" : { "$numberLong" : "1508769012416" } }, "reference-count" : 37, "publisher" : "Wiley-Blackwell", "issue" : "2", "license" : [ { "URL" : "http://doi.wiley.com/10.1002/tdm_license_1.1", "start" : { "date-parts" : [ [ 2015, 9, 1 ] ], "date-time" : "2015-09-01T00:00:00Z", "timestamp" : { "$numberLong" : "1441065600000" } }, "delay-in-days" : 5356, "content-version" : "tdm" } ], "content-domain" : { "domain" : [], "crossmark-restriction" : false }, "short-container-title" : [ "Am. 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