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authorBryan Newbold <bnewbold@robocracy.org>2018-06-20 17:54:54 -0700
committerBryan Newbold <bnewbold@robocracy.org>2018-06-20 17:54:54 -0700
commit43e74c2e81c64d6d4f4e644cc5a6f75945ff660d (patch)
tree769cae1607f3b8b9fff43fce99028bda571c2145 /python
parent381fe70c56b1a936d4eef676ee8ba546f6a3cf30 (diff)
downloadfatcat-43e74c2e81c64d6d4f4e644cc5a6f75945ff660d.tar.gz
fatcat-43e74c2e81c64d6d4f4e644cc5a6f75945ff660d.zip
more progress on crossref+orcid importers
Diffstat (limited to 'python')
-rwxr-xr-xpython/client.py28
-rw-r--r--python/fatcat/crossref_importer.py85
-rw-r--r--python/fatcat/importer_common.py44
-rw-r--r--python/tests/crossref.py8
-rw-r--r--python/tests/files/ISSN-to-ISSN-L.snip.txt10
-rw-r--r--python/tests/files/crossref-works.2018-01-21.badsample.json3
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. Lett." }, { "key" : "10.1002/1097-0231(20001230)14:24<2357::AID-RCM168>3.0.CO;2-2-BIB2", "author" : "Chenevert", "first-page" : "782", "year" : "1982", "journal-title" : "Synthesis", "DOI" : "10.1055/s-1982-29945", "doi-asserted-by" : "crossref" }, { "key" : "10.1002/1097-0231(20001230)14:24<2357::AID-RCM168>3.0.CO;2-2-BIB3", "author" : "Porter", "first-page" : "296", "year" : "1985", "unstructured" : "Mass Spectrometry of Heterocyclic Compounds (2nd edn). John Wiley & Sons: New York, 1985; 296.", "volume-title" : "Mass Spectrometry of Heterocyclic Compounds" }, { "key" : "10.1002/1097-0231(20001230)14:24<2357::AID-RCM168>3.0.CO;2-2-BIB4", "author" : "Ková??ik", "volume" : "34", "first-page" : "1322", "year" : "1999", "journal-title" : "J. 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" ] }
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