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authorMartin Czygan <martin.czygan@gmail.com>2021-10-01 16:56:59 +0200
committerMartin Czygan <martin.czygan@gmail.com>2021-10-01 16:56:59 +0200
commitbdc4347acbbdb9f58b7c3abc2578a488de3d0a85 (patch)
tree1b8c4ba4c23edb299fef488c346b7d2565bb9834
parent519c7e77cf3a54b9620adef07fedac9b37a5f9f2 (diff)
downloadfatcat-bdc4347acbbdb9f58b7c3abc2578a488de3d0a85.tar.gz
fatcat-bdc4347acbbdb9f58b7c3abc2578a488de3d0a85.zip
datacite: skip empty abstracts
Do not add abstracts where `clean` results in the empty string - this violates a constraint: `either abstract_sha1 or content is required`
-rw-r--r--python/fatcat_tools/importers/datacite.py5
-rw-r--r--python/tests/files/datacite/datacite_doc_36.json65
-rw-r--r--python/tests/files/datacite/datacite_result_36.json25
-rw-r--r--python/tests/import_datacite.py2
4 files changed, 95 insertions, 2 deletions
diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py
index 703dbc27..eb49596f 100644
--- a/python/fatcat_tools/importers/datacite.py
+++ b/python/fatcat_tools/importers/datacite.py
@@ -549,10 +549,13 @@ class DataciteImporter(EntityImporter):
lang = langdetect.detect(text)
except (langdetect.lang_detect_exception.LangDetectException, TypeError) as err:
print('[{}] language detection failed with {} on {}'.format(doi, err, text), file=sys.stderr)
+ abstract_text = clean(text)
+ if not abstract_text:
+ continue
abstracts.append(
fatcat_openapi_client.ReleaseAbstract(
mimetype="text/plain",
- content=clean(text),
+ content=abstract_text,
lang=lang,
))
diff --git a/python/tests/files/datacite/datacite_doc_36.json b/python/tests/files/datacite/datacite_doc_36.json
new file mode 100644
index 00000000..66aba00c
--- /dev/null
+++ b/python/tests/files/datacite/datacite_doc_36.json
@@ -0,0 +1,65 @@
+{
+ "id": "10.17912/micropub.biology.000143",
+ "type": "dois",
+ "attributes": {
+ "doi": "10.17912/micropub.biology.000143",
+ "identifiers": null,
+ "creators": [
+ {
+ "name": "Paul Katz",
+ "givenName": "",
+ "familyName": "",
+ "affiliation": [],
+ "role": "author"
+ }
+ ],
+ "titles": [
+ {
+ "lang": "da"
+ },
+ {
+ "title": "Sample"
+ }
+ ],
+ "publisher": "microPublication Biology",
+ "publicationYear": 2019,
+ "types": {
+ "resourceTypeGeneral": "DataPaper"
+ },
+ "relatedIdentifiers": [],
+ "sizes": [],
+ "formats": [],
+ "version": null,
+ "rightsList": [],
+ "descriptions": [
+ {
+ "description": " ",
+ "descriptionType": "Abstract"
+ }
+ ],
+ "geoLocations": [],
+ "fundingReferences": [],
+ "url": "https://www.micropublication.org/journals/biology/micropub.biology.000143",
+ "created": "2019-08-19T14:43:08.000Z",
+ "registered": "2019-08-19T14:43:09.000Z",
+ "published": "2019",
+ "updated": "2019-11-09T12:32:02.000Z",
+ "contributors": [
+ {
+ "name": "Paul Katz",
+ "givenName": "",
+ "familyName": "",
+ "affiliation": [],
+ "role": "illustrator"
+ }
+ ]
+ },
+ "relationships": {
+ "client": {
+ "data": {
+ "id": "caltech.micropub",
+ "type": "clients"
+ }
+ }
+ }
+}
diff --git a/python/tests/files/datacite/datacite_result_36.json b/python/tests/files/datacite/datacite_result_36.json
new file mode 100644
index 00000000..8c958848
--- /dev/null
+++ b/python/tests/files/datacite/datacite_result_36.json
@@ -0,0 +1,25 @@
+{
+ "abstracts": [],
+ "contribs": [
+ {
+ "given_name": "",
+ "index": 0,
+ "raw_name": "Paul Katz",
+ "role": "author"
+ }
+ ],
+ "ext_ids": {
+ "doi": "10.17912/micropub.biology.000143"
+ },
+ "extra": {
+ "datacite": {
+ "resourceTypeGeneral": "DataPaper"
+ },
+ "container_name": "microPublication Biology"
+ },
+ "refs": [],
+ "release_stage": "published",
+ "release_year": 2019,
+ "publisher": "microPublication Biology",
+ "title": "Sample"
+}
diff --git a/python/tests/import_datacite.py b/python/tests/import_datacite.py
index 8b6797ef..edbb6617 100644
--- a/python/tests/import_datacite.py
+++ b/python/tests/import_datacite.py
@@ -400,7 +400,7 @@ def test_datacite_conversions(datacite_importer):
for now.
"""
datacite_importer.debug = True
- for i in range(36):
+ for i in range(37):
src = "tests/files/datacite/datacite_doc_{0:02d}.json".format(i)
dst = "tests/files/datacite/datacite_result_{0:02d}.json".format(i)
with open(src, "r") as f: