summaryrefslogtreecommitdiffstats
path: root/python
diff options
context:
space:
mode:
authorBryan Newbold <bnewbold@robocracy.org>2020-12-17 01:55:30 -0800
committerBryan Newbold <bnewbold@robocracy.org>2020-12-17 23:03:08 -0800
commit58ff361eb481bee9d2ef7249f48f94729d2a830d (patch)
tree9cbcbcf1c7eafa958c81d18fcf5b6a5d27f2f42d /python
parentb2f53077bd05a536b5fdb551755a559b653421d3 (diff)
downloadfatcat-58ff361eb481bee9d2ef7249f48f94729d2a830d.tar.gz
fatcat-58ff361eb481bee9d2ef7249f48f94729d2a830d.zip
very simple dblp container importer
Diffstat (limited to 'python')
-rwxr-xr-xpython/fatcat_import.py36
-rw-r--r--python/fatcat_tools/importers/__init__.py1
-rw-r--r--python/fatcat_tools/importers/dblp_container.py144
-rw-r--r--python/tests/files/ISSN-to-ISSN-L.snip.txt1
-rw-r--r--python/tests/files/dblp_container_map.tsv10
-rw-r--r--python/tests/files/example_dblp_containers.json10
-rw-r--r--python/tests/import_dblp.py61
7 files changed, 256 insertions, 7 deletions
diff --git a/python/fatcat_import.py b/python/fatcat_import.py
index 90b53e5c..1dcfec21 100755
--- a/python/fatcat_import.py
+++ b/python/fatcat_import.py
@@ -274,19 +274,29 @@ def run_doaj_article(args):
JsonLinePusher(dai, args.json_file).run()
def run_dblp_release(args):
- dwi = DblpReleaseImporter(args.api,
+ dri = DblpReleaseImporter(args.api,
dblp_container_map_file=args.dblp_container_map_file,
edit_batch_size=args.batch_size,
do_updates=args.do_updates,
dump_json_mode=args.dump_json_mode,
)
Bs4XmlLargeFilePusher(
- dwi,
+ dri,
args.xml_file,
DblpReleaseImporter.ELEMENT_TYPES,
use_lxml=True,
).run()
+def run_dblp_container(args):
+ dci = DblpContainerImporter(args.api,
+ args.issn_map_file,
+ dblp_container_map_file=args.dblp_container_map_file,
+ dblp_container_map_output=args.dblp_container_map_output,
+ edit_batch_size=args.batch_size,
+ do_updates=args.do_updates,
+ )
+ JsonLinePusher(dci, args.json_file).run()
+
def run_file_meta(args):
# do_updates defaults to true for this importer
fmi = FileMetaImporter(args.api,
@@ -675,6 +685,28 @@ def main():
auth_var="FATCAT_AUTH_WORKER_DBLP",
)
+ sub_dblp_container = subparsers.add_parser('dblp-container',
+ help="import dblp container metadata")
+ sub_dblp_container.add_argument('json_file',
+ help="File with DBLP container JSON to import from (see extra/dblp/)",
+ default=sys.stdin, type=argparse.FileType('rb'))
+ sub_dblp_container.add_argument('--dblp-container-map-file',
+ help="file path to dblp pre-existing prefix to container_id TSV file",
+ default=None, type=argparse.FileType('r'))
+ sub_dblp_container.add_argument('--dblp-container-map-output',
+ help="file path to output new dblp container map TSV to",
+ default=None, type=argparse.FileType('w'))
+ sub_dblp_container.add_argument('--issn-map-file',
+ help="ISSN to ISSN-L mapping file",
+ default=None, type=argparse.FileType('r'))
+ sub_dblp_container.add_argument('--do-updates',
+ action='store_true',
+ help="update any pre-existing container entities")
+ sub_dblp_container.set_defaults(
+ func=run_dblp_container,
+ auth_var="FATCAT_AUTH_WORKER_DBLP",
+ )
+
sub_file_meta = subparsers.add_parser('file-meta',
help="simple update-only importer for file metadata")
sub_file_meta.set_defaults(
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index a14e2cec..6a2edeac 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -32,3 +32,4 @@ from .shadow import ShadowLibraryImporter
from .file_meta import FileMetaImporter
from .doaj_article import DoajArticleImporter
from .dblp_release import DblpReleaseImporter
+from .dblp_container import DblpContainerImporter
diff --git a/python/fatcat_tools/importers/dblp_container.py b/python/fatcat_tools/importers/dblp_container.py
new file mode 100644
index 00000000..a9f993a8
--- /dev/null
+++ b/python/fatcat_tools/importers/dblp_container.py
@@ -0,0 +1,144 @@
+
+"""
+Importer for DBLP container-level (journal/conference/series) metadata,
+pre-scraped in to JSON from HTML pages.
+"""
+
+import sys # noqa: F401
+
+import fatcat_openapi_client
+from fatcat_tools.normal import clean_str
+from fatcat_tools.importers.common import EntityImporter
+
+
+class DblpContainerImporter(EntityImporter):
+
+ def __init__(self, api, issn_map_file, dblp_container_map_file, dblp_container_map_output, **kwargs):
+
+ eg_desc = kwargs.get('editgroup_description',
+ "Automated import of container-level metadata scraped from dblp HTML")
+ eg_extra = kwargs.get('editgroup_extra', dict())
+ eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.DblpContainerImporter')
+ super().__init__(api,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs)
+
+ self.dblp_container_map_output = dblp_container_map_output
+ self.read_dblp_container_map_file(dblp_container_map_file)
+ self.read_issn_map_file(issn_map_file)
+ print("\t".join(["dblp_prefix", "container_id"]), file=self.dblp_container_map_output)
+
+ def read_dblp_container_map_file(self, dblp_container_map_file) -> None:
+ self._dblp_container_map = dict()
+ print("Loading existing dblp prefix container map file...", file=sys.stderr)
+ for line in dblp_container_map_file:
+ if line.startswith("dblp_prefix") or len(line) == 0:
+ continue
+ (prefix, container_id) = line.split()[0:2]
+ assert len(container_id) == 26
+ self._dblp_container_map[prefix] = container_id
+ print("\t".join([prefix, container_id]), file=self.dblp_container_map_output)
+ print("Got {} existing dblp container mappings.".format(len(self._dblp_container_map)), file=sys.stderr)
+
+ def lookup_dblp_prefix(self, prefix):
+ if not prefix:
+ return None
+ return self._dblp_container_map.get(prefix)
+
+ def want(self, raw_record):
+ return True
+
+ def parse_record(self, row):
+ """
+ row is a python dict (parsed from JSON).
+
+ returns a ContainerEntity (or None if invalid or couldn't parse)
+ """
+
+ dblp_prefix = row.get('key') or row.get('dblp_prefix')
+ assert dblp_prefix
+ assert row['title']
+
+ container_type = None
+ if dblp_prefix.startswith('conf/'):
+ container_type = "conference-series"
+ elif dblp_prefix.startswith('journals/'):
+ container_type = "journal"
+ elif dblp_prefix.startswith('series/'):
+ container_type = "book-series"
+
+ issnl = None
+ for issn in row.get('issns', []):
+ issnl = self.issn2issnl(issn)
+ if issnl:
+ break
+
+ extra = {
+ 'dblp': {
+ 'prefix': dblp_prefix,
+ },
+ }
+
+ if row.get('homepage_url'):
+ extra['urls'] = [row['homepage_url']]
+
+ if row.get('acronym'):
+ extra['acronym'] = row['acronym']
+
+ ce = fatcat_openapi_client.ContainerEntity(
+ name=clean_str(row['title']),
+ container_type=container_type,
+ issnl=issnl,
+ wikidata_qid=row.get('wikidata_qid'),
+ extra=extra,
+ )
+ return ce
+
+ def try_update(self, ce):
+
+ dblp_prefix = ce.extra['dblp']['prefix']
+ existing = None
+ existing_container_id = self.lookup_dblp_prefix(dblp_prefix)
+ if existing_container_id:
+ existing = self.api.get_container(existing_container_id)
+ if not existing and ce.issnl:
+ # check if existing by ISSN-L
+ try:
+ existing = self.api.lookup_container(issnl=ce.issnl)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+ if not existing and ce.wikidata_qid:
+ try:
+ existing = self.api.lookup_container(wikidata_qid=ce.wikidata_qid)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+
+ # TODO: plan to add a fuzzy match check here
+
+ if not existing:
+ return True
+
+ if existing:
+ self.counts['exists'] += 1
+ print("\t".join([ce.extra['dblp']['prefix'], existing.ident]), file=self.dblp_container_map_output)
+ return False
+
+ # shouldn't get here
+ raise NotImplementedError()
+
+ def insert_batch(self, batch):
+ """
+ Because we want to print a prefix/container_id match for each row, we
+ require a special batch insert method
+ """
+ eg = self.api.create_container_auto_batch(fatcat_openapi_client.ContainerAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
+ description=self.editgroup_description,
+ extra=self.editgroup_extra),
+ entity_list=batch))
+ for c_edit in eg.edits.containers:
+ c = self.api.get_container(c_edit.ident)
+ print("\t".join([c.extra['dblp']['prefix'], c.ident]), file=self.dblp_container_map_output)
diff --git a/python/tests/files/ISSN-to-ISSN-L.snip.txt b/python/tests/files/ISSN-to-ISSN-L.snip.txt
index c97de279..2569c443 100644
--- a/python/tests/files/ISSN-to-ISSN-L.snip.txt
+++ b/python/tests/files/ISSN-to-ISSN-L.snip.txt
@@ -8,3 +8,4 @@ ISSN ISSN-L
0000-0094 0002-0094
0000-0108 0002-0108
0000-0140 0002-0140
+1877-3273 1877-3273
diff --git a/python/tests/files/dblp_container_map.tsv b/python/tests/files/dblp_container_map.tsv
new file mode 100644
index 00000000..5f3dbacd
--- /dev/null
+++ b/python/tests/files/dblp_container_map.tsv
@@ -0,0 +1,10 @@
+dblp_prefix container_id
+series/atlantis 7xuzjpmxqnaq7enf3qc45diflu
+series/apc ktlimnolmvbwbhthlj66zuooea
+series/swb s2qx5lvrdngvrk6y2arrem3qom
+series/sbece 7g52v6peqrek5l7zmstisnpkdm
+series/wssris iszwbitlzfau5k77dpqifz5tf4
+series/lnm r436k67l3fdm5cgs5hqif5e7hi
+conf/focs aaaaaaaaaaaaaeiraaaaaaaaai
+conf/er aaaaaaaaaaaaaeiraaaaaaaaai
+journals/cacm aaaaaaaaaaaaaeiraaaaaaaaai
diff --git a/python/tests/files/example_dblp_containers.json b/python/tests/files/example_dblp_containers.json
new file mode 100644
index 00000000..c5137604
--- /dev/null
+++ b/python/tests/files/example_dblp_containers.json
@@ -0,0 +1,10 @@
+{"homepage_url": "http://link.springer.com/bookseries/10077", "issns": ["1877-3273"], "key": "series/atlantis", "title": "Atlantis Thinking Machines"}
+{"homepage_url": "http://ebooks.iospress.nl/bookseries/advances-in-parallel-computing", "issns": ["0927-5452", "1879-808X"], "key": "series/apc", "title": "Advances in Parallel Computing"}
+{"homepage_url": "http://link.springer.com/bookseries/7056", "issns": ["1559-7474"], "key": "series/swb", "title": "Semantic Web and Beyond: Computing for Human Experience"}
+{"homepage_url": "http://link.springer.com/bookseries/10059", "issns": ["2191-8112"], "key": "series/sbece", "title": "Springer Briefs in Electrical and Computer Engineering"}
+{"homepage_url": "http://www.worldscientific.com/series/wssris", "issns": [], "key": "series/wssris", "title": "World Scientific Series in Robotics and Intelligent Systems"}
+{"acronym": "LNM", "homepage_url": "http://link.springer.com/bookseries/304", "issns": ["0075-8434"], "key": "series/lnm", "title": "Lecture Notes in Mathematics"}
+{"homepage_url": "https://www.usenix.org/lisa", "issns": [], "key": "series/sage", "title": "Short Topics in System Administration"}
+{"homepage_url": "http://link.springer.com/bookseries/4205", "issns": ["2191-6586", "2191-6594"], "key": "series/acvpr", "title": "Advances in Computer Vision and Pattern Recognition"}
+{"acronym": "STAR", "homepage_url": "http://link.springer.com/bookseries/5208", "issns": ["1610-7438", "1610-742X"], "key": "series/star", "title": "Springer Tracts in Advanced Robotics"}
+{"acronym": "FAIA", "homepage_url": "http://ebooks.iospress.nl/bookseries/frontiers-in-artificial-intelligence-and-applications", "issns": ["0922-6389", "1879-8314"], "key": "series/faia", "title": "Frontiers in Artificial Intelligence and Applications"}
diff --git a/python/tests/import_dblp.py b/python/tests/import_dblp.py
index fd40eb06..5041b509 100644
--- a/python/tests/import_dblp.py
+++ b/python/tests/import_dblp.py
@@ -1,8 +1,9 @@
+import io
import pytest
from bs4 import BeautifulSoup
-from fatcat_tools.importers import DblpReleaseImporter, Bs4XmlLargeFilePusher
+from fatcat_tools.importers import DblpReleaseImporter, DblpContainerImporter, Bs4XmlLargeFilePusher, JsonLinePusher
from fixtures import *
@@ -13,15 +14,21 @@ def dblp_importer(api):
@pytest.fixture(scope="function")
def dblp_importer_existing(api):
- with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
- yield DblpReleaseImporter(api, issn_file, bezerk_mode=False, lookup_refs=True)
+ with open('tests/files/dblp_container_map.tsv', 'r') as tsv_file:
+ yield DblpReleaseImporter(api, tsv_file, bezerk_mode=False)
+
+@pytest.fixture(scope="function")
+def dblp_container_importer(api):
+ with open('tests/files/dblp_container_map.tsv', 'r') as tsv_file:
+ with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
+ yield DblpContainerImporter(api, issn_file, tsv_file, io.StringIO(), bezerk_mode=True)
def test_dblp_importer(dblp_importer):
last_index = dblp_importer.api.get_changelog(limit=1)[0].index
with open('tests/files/example_dblp.xml', 'rb') as f:
dblp_importer.bezerk_mode = True
counts = Bs4XmlLargeFilePusher(dblp_importer, f, dblp_importer.ELEMENT_TYPES, use_lxml=True).run()
- print(counts)
+ #print(counts)
assert counts['insert'] == 3
assert counts['exists'] == 0
assert counts['skip'] == 1
@@ -44,12 +51,56 @@ def test_dblp_importer(dblp_importer):
dblp_importer.bezerk_mode = False
dblp_importer.reset()
counts = Bs4XmlLargeFilePusher(dblp_importer, f, dblp_importer.ELEMENT_TYPES, use_lxml=True).run()
- print(counts)
+ #print(counts)
assert counts['insert'] == 0
assert counts['exists'] == 3
assert counts['skip'] == 1
assert last_index == dblp_importer.api.get_changelog(limit=1)[0].index
+def test_dblp_container_importer(dblp_container_importer):
+ last_index = dblp_container_importer.api.get_changelog(limit=1)[0].index
+ output_tsv_map = io.StringIO()
+ with open('tests/files/example_dblp_containers.json', 'r') as f:
+ dblp_container_importer.bezerk_mode = True
+ dblp_container_importer.dblp_container_map_output = output_tsv_map
+ counts = JsonLinePusher(dblp_container_importer, f).run()
+ assert counts['insert'] == 10
+ assert counts['exists'] == 0
+ assert counts['skip'] == 0
+
+ # fetch most recent editgroup
+ change = dblp_container_importer.api.get_changelog_entry(index=last_index+1)
+ eg = change.editgroup
+ assert eg.description
+ assert "dblp" in eg.description.lower()
+ assert eg.extra['git_rev']
+ assert "fatcat_tools.DblpContainerImporter" in eg.extra['agent']
+
+ # check that entity name mangling was fixed on import
+ eg = dblp_container_importer.api.get_editgroup(eg.editgroup_id)
+ container = dblp_container_importer.api.get_container(eg.edits.containers[0].ident)
+ assert container.name == "Atlantis Thinking Machines"
+ assert container.issnl == "1877-3273"
+ assert container.container_type == "book-series"
+ assert container.extra['dblp']['prefix'] == "series/atlantis"
+ assert container.extra['urls'] == ["http://link.springer.com/bookseries/10077"]
+
+ last_index = dblp_container_importer.api.get_changelog(limit=1)[0].index
+ output_tsv_map.seek(0)
+ print(output_tsv_map.read())
+ output_tsv_map.seek(0)
+ with open('tests/files/example_dblp_containers.json', 'r') as f:
+ dblp_container_importer.reset()
+ dblp_container_importer.bezerk_mode = False
+ dblp_container_importer.dblp_container_map_output = io.StringIO()
+ dblp_container_importer.read_dblp_container_map_file(output_tsv_map)
+ counts = JsonLinePusher(dblp_container_importer, f).run()
+ print(counts)
+ assert counts['insert'] == 0
+ assert counts['exists'] == 10
+ assert counts['skip'] == 0
+ assert last_index == dblp_container_importer.api.get_changelog(limit=1)[0].index
+
def test_dblp_xml_parse(dblp_importer):
with open('tests/files/example_dblp_article.xml', 'r') as f:
soup = BeautifulSoup(f, "xml")