diff options
| -rw-r--r-- | python/fatcat_tools/importers/ingest.py | 32 | ||||
| -rw-r--r-- | python/tests/files/example_ingest.json | 2 | ||||
| -rw-r--r-- | python/tests/import_ingest.py | 6 |
3 files changed, 36 insertions, 4 deletions
diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 4b1d3702..c88ec86a 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -20,7 +20,7 @@ class IngestFileResultImporter(EntityImporter): assert self.default_link_rel self.require_grobid = require_grobid if self.require_grobid: - print("Requiring GROBID status == 200") + print("Requiring GROBID status == 200 (for PDFs)") else: print("NOT checking GROBID success") self.ingest_request_source_whitelist = [ @@ -74,8 +74,22 @@ class IngestFileResultImporter(EntityImporter): if not row.get('file_meta'): self.counts['skip-file-meta'] += 1 return False - if self.require_grobid and row.get('grobid', {}).get('status_code') != 200: - self.counts['skip-grobid'] += 1 + + # type-specific filters + if row['request'].get('ingest_type') == 'pdf': + if self.require_grobid and row.get('grobid', {}).get('status_code') != 200: + self.counts['skip-grobid'] += 1 + return False + if row['file_meta'].get('mimetype') not in ("application/pdf",): + self.counts['skip-mimetype'] += 1 + return False + elif row['request'].get('ingest_type') == 'xml': + if row['file_meta'].get('mimetype') not in ("application/xml", + "application/jats+xml", "application/tei+xml", "text/xml"): + self.counts['skip-mimetype'] += 1 + return False + else: + self.counts['skip-ingest-type'] += 1 return False return True @@ -85,6 +99,18 @@ class IngestFileResultImporter(EntityImporter): request = row['request'] fatcat = request.get('fatcat') file_meta = row['file_meta'] + + # double check that want() filtered request correctly (eg, old requests) + if request.get('ingest_type') not in ('pdf', 'xml'): + self.counts['skip-ingest-type'] += 1 + return None + assert (request['ingest_type'], file_meta['mimetype']) in [ + ("pdf", "application/pdf"), + ("xml", "application/xml"), + ("xml", "application/jats+xml"), + ("xml", "application/tei+xml"), + ("xml", "text/xml"), + ] # identify release by fatcat ident, or extid lookup, or biblio-glutton match release_ident = None diff --git a/python/tests/files/example_ingest.json b/python/tests/files/example_ingest.json index cea67fa7..a9791587 100644 --- a/python/tests/files/example_ingest.json +++ b/python/tests/files/example_ingest.json @@ -1,2 +1,2 @@ -{"file_meta": {"sha1hex": "00242a192acc258bdfdb151943419437f440c313", "md5hex": "f4de91152c7ab9fdc2a128f962faebff", "sha256hex": "ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362", "size_bytes": 255629, "mimetype": "application/pdf"}, "request": {"ingest_request_source": "fatcat-changelog", "link_source": "doi", "link_source_id":"10.123/abc","ext_ids": {"doi": "10.123/abc"}}, "terminal": {"terminal_url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable", "terminal_dt": "20170227164644", "terminal_sha1hex": "00242a192acc258bdfdb151943419437f440c313"}, "cdx": { "datetime": "20170227164644", "url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable" }, "grobid": {"status_code": 200 }, "hit": true, "status": "success"} +{"file_meta": {"sha1hex": "00242a192acc258bdfdb151943419437f440c313", "md5hex": "f4de91152c7ab9fdc2a128f962faebff", "sha256hex": "ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362", "size_bytes": 255629, "mimetype": "application/pdf"}, "request": {"ingest_type": "pdf", "ingest_request_source": "fatcat-changelog", "link_source": "doi", "link_source_id":"10.123/abc","ext_ids": {"doi": "10.123/abc"}}, "terminal": {"terminal_url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable", "terminal_dt": "20170227164644", "terminal_sha1hex": "00242a192acc258bdfdb151943419437f440c313"}, "cdx": { "datetime": "20170227164644", "url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable" }, "grobid": {"status_code": 200 }, "hit": true, "status": "success"} {"request":{"ingest_type":"pdf","ingest_request_source":"fatcat-changelog","base_url":"https://doi.org/10.3917/popav.748.0017","release_stage":"published","fatcat":{"release_ident":"weeqjkvsx5abze2bhithyrx6wu","work_ident":"ujatsk25yrdw5gofubw7nogzgq"},"ext_ids":{"doi":"10.3917/popav.748.0017"},"link_source":"doi","link_source_id":"10.3917/popav.748.0017"},"hit":false,"hops":["https://doi.org/10.3917/popav.748.0017"],"status":"wayback-error","error_message":"replay fetch didn't return X-Archive-Src in headers"} diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py index 4a46232a..05287af4 100644 --- a/python/tests/import_ingest.py +++ b/python/tests/import_ingest.py @@ -94,6 +94,12 @@ def test_ingest_dict_parse(ingest_importer): def test_ingest_dict_parse_old(ingest_importer): with open('tests/files/example_ingest.old.json', 'r') as f: raw = json.loads(f.readline()) + + # ancient ingest requests had no type; skip them + f = ingest_importer.parse_record(raw) + assert f == None + raw['request']['ingest_type'] = 'pdf' + f = ingest_importer.parse_record(raw) assert f.sha1 == "00242a192acc258bdfdb151943419437f440c313" assert f.md5 == "f4de91152c7ab9fdc2a128f962faebff" |