diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/fatcat_tools/cleanups/file_release_bugfix.py | 241 | ||||
| -rw-r--r-- | python/fatcat_tools/cleanups/file_short_wayback_ts.py | 344 | ||||
| -rw-r--r-- | python/fatcat_tools/cleanups/release_lowercase_doi.py | 154 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/common.py | 9 | ||||
| -rw-r--r-- | python/fatcat_web/types.py | 2 |
5 files changed, 749 insertions, 1 deletions
diff --git a/python/fatcat_tools/cleanups/file_release_bugfix.py b/python/fatcat_tools/cleanups/file_release_bugfix.py new file mode 100644 index 00000000..dc27f9b5 --- /dev/null +++ b/python/fatcat_tools/cleanups/file_release_bugfix.py @@ -0,0 +1,241 @@ +import argparse +import os +import sys +from typing import Any, Dict + +import fatcat_openapi_client +from fatcat_openapi_client import ApiClient, FileEntity + +from fatcat_tools import authenticated_api, public_api, uuid2fcid +from fatcat_tools.importers.common import EntityImporter, JsonLinePusher +from fatcat_tools.normal import clean_doi + + +class FileReleaseBugfix(EntityImporter): + """ + This is a one-off / one-time cleanup script for file entities which got + imported with incorrect release ident mappings, due to a bug in the file + ingest importer. + + While this calls itself a cleanup, it is based on the import code path. It + is not integrated into the `fatcat_import` or `fatcat_cleanup` controller; + instead it has a __main__ function and is invoked like: + + python -m fatcat_tools.cleans.file_release_bugfix - < blah.json + """ + + def __init__(self, api: ApiClient, **kwargs): + + eg_desc = ( + kwargs.pop("editgroup_description", None) + or "Correct bad file/release import mappings" + ) + eg_extra = kwargs.pop("editgroup_extra", dict()) + eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.FileReleaseBugfix") + super().__init__( + api, + do_updates=True, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs, + ) + self.testing_mode = False + + def want(self, row: Dict[str, Any]) -> bool: + if not ( + row.get("edit_extra") + and row["edit_extra"].get("link_source") + and row["edit_extra"].get("link_source_id") + ): + self.counts["skip-partial"] += 1 + return False + if row["edit_extra"]["link_source"] not in ["unpaywall", "doi"]: + self.counts["skip-link-source"] += 1 + return False + if row["edit_extra"].get("ingest_request_source") not in [ + "unpaywall", + "fatcat-changelog", + ]: + self.counts["skip-ingest-request-source"] += 1 + return False + if not row["edit_extra"]["link_source_id"].startswith("10."): + self.counts["skip-source-id-not-doi"] += 1 + return False + return True + + def parse_record(self, row: Dict[str, Any]) -> FileEntity: + + # bezerk mode doesn't make sense for this importer + assert self.bezerk_mode is False + + file_ident = uuid2fcid(row["file_ident"]) + wrong_release_ident = uuid2fcid(row["wrong_release_ident"]) + edit_extra = row["edit_extra"] + assert edit_extra["link_source"] in ["unpaywall", "doi"] + file_edit_doi = clean_doi(edit_extra["link_source_id"]) + + if not file_edit_doi: + self.counts["skip-bad-doi"] += 1 + return False + + # check that the "wrong" release exists and doesn't have the DOI + wrong_release = None + try: + wrong_release = self.api.get_release(wrong_release_ident) + except fatcat_openapi_client.rest.ApiException as err: + if err.status != 404: + raise err + + if not wrong_release: + self.counts["skip-wrong-release-missing"] += 1 + return None + + if clean_doi(wrong_release.ext_ids.doi) == file_edit_doi: + self.counts["skip-wrong-release-is-ok"] += 1 + return None + + # fetch the "correct" release, if any + fixed_release_ids = [] + correct_release = None + try: + correct_release = self.api.lookup_release(doi=file_edit_doi) + except fatcat_openapi_client.rest.ApiException as err: + if err.status != 404: + raise err + + if correct_release: + fixed_release_ids.append(correct_release.ident) + + fe = FileEntity( + ident=file_ident, + release_ids=fixed_release_ids, + edit_extra=edit_extra, + ) + fe._wrong_release_ident = wrong_release_ident + return fe + + def try_update(self, fe: FileEntity) -> bool: + + wrong_release_ident = fe._wrong_release_ident + assert len(wrong_release_ident) == 26 + + # should always be existing... but in QA it might not be + existing = None + try: + existing = self.api.get_file(fe.ident) + except fatcat_openapi_client.rest.ApiException as err: + if err.status != 404: + raise err + + if not existing: + self.counts["skip-existing-not-found"] += 1 + return False + + if existing.state != "active": + self.counts["skip-existing-entity-state"] += 1 + return False + + if wrong_release_ident not in existing.release_ids: + self.counts["skip-existing-fixed"] += 1 + return False + + # fetch existing history to verify mismatch + history = self.api.get_file_history(existing.ident) + + for entry in history: + if entry.editgroup.editor.is_bot is not True: + self.counts["skip-existing-edit-history-human"] += 1 + return False + + bad_edit = history[-1].edit + if bad_edit.extra != fe.edit_extra: + self.counts["skip-existing-edit-history-extra-mismatch"] += 1 + return False + + bad_editgroup = history[-1].editgroup + if not bad_editgroup.extra: + self.counts["skip-existing-editgroup-missing-extra"] += 1 + return False + + if ( + bad_editgroup.editor_id != "scmbogxw25evtcesfcab5qaboa" + or bad_editgroup.extra.get("agent") != "fatcat_tools.IngestFileResultImporter" + or not bad_editgroup.extra.get("git_rev", "").startswith("v0.3") + or bad_editgroup.created.year != 2020 + ): + self.counts["skip-existing-edit-history-mismatch"] += 1 + return False + + existing.release_ids = [ri for ri in existing.release_ids if ri != wrong_release_ident] + + if len(fe.release_ids) == 1: + if fe.release_ids[0] not in existing.release_ids: + existing.release_ids.append(fe.release_ids[0]) + + existing.edit_extra = fe.edit_extra + + # not doing a check for "in current editgroup", because the source of + # these corrections (entity dump) contains no dupes + + if not self.testing_mode: + self.api.update_file(self.get_editgroup_id(), existing.ident, existing) + self.counts["update"] += 1 + return False + + +def test_file_release_bugfix() -> None: + api = public_api("http://localhost:9411/v0") + frbc = FileReleaseBugfix(api=api) + frbc.testing_mode = True + + assert frbc.want({"this": "asdf"}) is False + + example_line: Dict[str, Any] = { + "file_ident": "00000000-0000-0000-3333-000000000002", + "wrong_release_ident": "00000000-0000-0000-4444-000000000002", + "edit_extra": { + "link_source": "unpaywall", + "link_source_id": "10.1371/journal.pmed.0020124", + "ingest_request_source": "unpaywall", + }, + } + + fe1 = frbc.parse_record(example_line) + print(frbc.counts) + frbc.try_update(fe1) + + # NOTE: this test is pretty incompleted + + +def main() -> None: + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument( + "--host-url", default="http://localhost:9411/v0", help="connect to this host/port" + ) + parser.add_argument("--batch-size", help="size of batch to send", default=50, type=int) + parser.set_defaults( + auth_var="FATCAT_AUTH_WORKER_CLEANUP", + ) + parser.add_argument( + "json_file", + help="File with jsonlines with cleanup context", + default=sys.stdin, + type=argparse.FileType("r"), + ) + + args = parser.parse_args() + api = authenticated_api( + args.host_url, + # token is an optional kwarg (can be empty string, None, etc) + token=os.environ.get(args.auth_var), + ) + + frbc = FileReleaseBugfix( + api, + edit_batch_size=args.batch_size, + ) + JsonLinePusher(frbc, args.json_file).run() + + +if __name__ == "__main__": + main() diff --git a/python/fatcat_tools/cleanups/file_short_wayback_ts.py b/python/fatcat_tools/cleanups/file_short_wayback_ts.py new file mode 100644 index 00000000..bdd49f9b --- /dev/null +++ b/python/fatcat_tools/cleanups/file_short_wayback_ts.py @@ -0,0 +1,344 @@ +import argparse +import copy +import os +import sys +from typing import Any, Dict + +import fatcat_openapi_client +from fatcat_openapi_client import ApiClient, FileEntity + +from fatcat_tools import authenticated_api, entity_from_dict, public_api +from fatcat_tools.importers.common import EntityImporter, JsonLinePusher + + +class FileShortWaybackTimestampCleanup(EntityImporter): + """ + This is a one-off / one-time cleanup script for file entities, fix short + timestamps in wayback URLs. These timestamps are supposed to have 14 digits + (datetime with year, hour, seconds, etc). Some legacy file imports ended up + with only 4 or 12 digits. + + While this calls itself a cleanup, it is based on the import code path. It + is not integrated into the `fatcat_import` or `fatcat_cleanup` controller; + instead it has a __main__ function and is invoked like: + + python -m fatcat_tools.cleans.file_short_wayback_ts - < blah.json + """ + + def __init__(self, api: ApiClient, **kwargs): + + eg_desc = ( + kwargs.pop("editgroup_description", None) + or "Expand trunacted timestamps in wayback URLs" + ) + eg_extra = kwargs.pop("editgroup_extra", dict()) + eg_extra["agent"] = eg_extra.get( + "agent", "fatcat_tools.FileShortWaybackTimestampCleanup" + ) + super().__init__( + api, + do_updates=True, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs, + ) + self.testing_mode = False + + def want(self, row: Dict[str, Any]) -> bool: + if row["status"].startswith("success"): + return True + else: + self.counts["skip-status"] += 1 + return False + + def parse_record(self, row: Dict[str, Any]) -> FileEntity: + + # bezerk mode doesn't make sense for this importer + assert self.bezerk_mode is False + + fe: FileEntity = entity_from_dict(row["file_entity"], FileEntity) + status: str = row["status"] + assert status.startswith("success") + url_expansions: Dict[str, str] = row["full_urls"] + assert len(url_expansions) >= 1 + + # actual cleanup happens here + any_fixed = False + for fe_url in fe.urls: + if "://web.archive.org/web/" not in fe_url.url: + continue + seq = fe_url.url.split("/") + partial_ts = seq[4] + original_url = "/".join(seq[5:]) + if seq[2] != "web.archive.org": + continue + if len(partial_ts) not in [4, 12]: + continue + if fe_url.url in url_expansions: + fix_url = url_expansions[fe_url.url] + # defensive checks + if not ( + f"/web/{partial_ts}" in fix_url + and fe_url.url.endswith(original_url) + and fix_url.endswith(original_url) + ): + print( + f"bad replacement URL: partial_ts={partial_ts} original={original_url} fix_url={fix_url}", + file=sys.stderr, + ) + self.counts["skip-bad-replacement"] += 1 + return None + assert "://" in fix_url + fe_url.url = fix_url + any_fixed = True + + if not any_fixed: + self.counts["skip-no-fixes"] += 1 + return None + + # do any other generic file entity cleanups + # this includes removing duplicates + fe = self.generic_file_cleanups(fe) + + # verify that there are no exact duplicates + final_urls = [u.url for u in fe.urls] + assert len(final_urls) == len(list(set(final_urls))) + + return fe + + def try_update(self, fe: FileEntity) -> bool: + + # should always be existing + try: + existing = self.api.get_file(fe.ident) + except fatcat_openapi_client.rest.ApiException as err: + if err.status != 404: + raise err + + if not existing: + self.counts["skip-existing-not-found"] += 1 + return False + + if existing.state != "active": + self.counts["skip-existing-entity-state"] += 1 + return False + + if existing.sha1 != fe.sha1: + self.counts["skip-existing-mismatch"] += 1 + return False + + assert fe.revision and existing.revision + if existing.revision != fe.revision: + self.counts["skip-revision-changed"] += 1 + return False + + # verify that at least one URL remains + if not fe.urls or len(fe.urls) < 1: + self.counts["skip-no-urls"] += 1 + return False + + # verify that all wayback urls have 14-digit timestamps, and are generally well-formed + for u in fe.urls: + if "://web.archive.org/web/" not in u.url: + continue + if u.rel != "webarchive": + self.counts["skip-bad-wayback-rel"] += 1 + return False + seg = u.url.split("/") + if ( + len(seg) < 6 + or seg[0] != "https:" + or seg[2] != "web.archive.org" + or seg[3] != "web" + ): + self.counts["skip-bad-wayback"] += 1 + return False + if len(seg[4]) != 14 or not seg[4].isdigit(): + self.counts["skip-bad-wayback-timestamp"] += 1 + return False + + if existing == fe or existing.urls == fe.urls: + self.counts["skip-no-change"] += 1 + return False + + # not doing a check for "in current editgroup", because the source of + # these corrections (entity dump) contains no dupes + + if not self.testing_mode: + # note: passing 'fe' instead of 'existing' here, which is not + # usually how it goes! + self.api.update_file(self.get_editgroup_id(), fe.ident, fe) + self.counts["update"] += 1 + return False + + +def test_short_wayback_ts() -> None: + api = public_api("http://localhost:9411/v0") + fswtc = FileShortWaybackTimestampCleanup(api=api) + fswtc.testing_mode = True + + assert fswtc.want({"status": "fail"}) is False + assert fswtc.want({"status": "success-self"}) is True + + example_line: Dict[str, Any] = { + "status": "success-db", + "file_entity": { + # note: doesn't match actual entity + "release_ids": ["waldfsctnbcpdbmasgduhaaaaa"], + "mimetype": "application/pdf", + "urls": [ + { + "url": "https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971", + "rel": "web", + }, + { + "url": "https://web.archive.org/web/201904301022/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971", + "rel": "webarchive", + }, + ], + "sha256": "0b9e09480ed2e1f08f3c6c72f57ce12b52ea265f580f8810e606b49d64234b29", + "sha1": "be714299b9be21b5afdaa7affd7d710c58269433", + "md5": "9edb542be5b3446a1905e61a8a3abebd", + "size": 666242, + "revision": "fe949be8-7bf9-4c17-be28-8e3e90fb85bd", + "ident": "4ghpvs2t2rdtrdum2mkreh62me", + "state": "active", + }, + "full_urls": { + "https://web.archive.org/web/201904301022/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971": "https://web.archive.org/web/20190430102239/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971" + }, + } + example_fe = entity_from_dict(example_line["file_entity"], FileEntity) + + fe1 = copy.copy(example_fe) + fe1.urls[ + 1 + ].url = "https://web.archive.org/web/20190430102239/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971" + assert fswtc.parse_record(example_line) == fe1 + + # update code path; requires a known file ident and API running locally + assert fswtc.counts["update"] == 0 + dummy_fe = api.get_file("aaaaaaaaaaaaamztaaaaaaaaai") + fe1.ident = dummy_fe.ident + + assert fswtc.try_update(fe1) is False + assert fswtc.counts["skip-existing-mismatch"] == 1 + + fe1.sha1 = dummy_fe.sha1 + assert fswtc.try_update(fe1) is False + assert fswtc.counts["skip-revision-changed"] == 1 + + fe1.revision = dummy_fe.revision + assert fswtc.try_update(fe1) is False + print(fswtc.counts) + assert fswtc.counts["update"] == 1 + + # another example, which failed with an assertion in prod due to duplicated URLs + example_line2: Dict[str, Any] = { + "file_entity": { + "release_ids": ["22jt7euq4fafhblzullmnesso4"], + "mimetype": "application/pdf", + "urls": [ + { + "url": "https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf", + "rel": "repository", + }, + { + "url": "https://web.archive.org/web/201811010021/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf", + "rel": "webarchive", + }, + { + "url": "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf", + "rel": "webarchive", + }, + ], + "sha256": "51ec58e7a2325d28d1deb0a4bc6422c0e4ae7b12ffb0b6298981a7b8b7730b19", + "sha1": "ad96a584fc6073b9a23736bc61ae0ec4a5661433", + "md5": "3d509743359649e34a27ae70c5cd3018", + "size": 430665, + "extra": { + "shadows": {"scimag_doi": "10.4259/ibk.59.1_194", "scimag_id": "69089904"} + }, + "revision": "f1fa11ff-d521-45cf-9db1-cb3c8bd3ea48", + "ident": "duymhmxk3fgtzk37yp2pvthtxq", + "state": "active", + }, + "full_urls": { + "https://web.archive.org/web/201811010021/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf": "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf" + }, + "status": "success-self", + } + + fe2 = fswtc.parse_record(example_line2) + assert len(fe2.urls) == 2 + assert fe2.urls[0].rel == "repository" + assert ( + fe2.urls[1].url + == "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf" + ) + + # ensure URL order is stable + example_line3: Dict[str, Any] = { + "file_entity": { + "release_ids": ["5rin7f2cdvc5hjkqqw53z7sr3i"], + "mimetype": "application/pdf", + "urls": [ + {"url": "https://pubs.usgs.gov/bul/1108/report.pdf", "rel": "web"}, + { + "url": "https://web.archive.org/web/201904291643/https://pubs.usgs.gov/bul/1108/report.pdf", + "rel": "webarchive", + }, + ], + "sha256": "714cd48c2577e9b058b8f16b4574765da685f67582cc53898a9d6933e45d6cc0", + "sha1": "4efbdb517c0ff3f58136e4efbbec2bd9315400d3", + "md5": "89b6e6cc4e0259317e26ddf1a9a336a0", + "size": 41265, + "revision": "926fcf73-e644-4446-a24b-4d0940a2cf65", + "ident": "lvnz23nzijaapf5iti45zez6zu", + "state": "active", + }, + "full_urls": { + "https://web.archive.org/web/201904291643/https://pubs.usgs.gov/bul/1108/report.pdf": "https://web.archive.org/web/20190429164342/https://pubs.usgs.gov/bul/1108/report.pdf" + }, + "status": "success-db", + } + + fe3 = fswtc.parse_record(example_line3) + assert len(fe3.urls) == 2 + assert fe3.urls[0].rel == "web" + assert fe3.urls[0].url == "https://pubs.usgs.gov/bul/1108/report.pdf" + assert fe3.urls[1].rel == "webarchive" + + +def main() -> None: + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument( + "--host-url", default="http://localhost:9411/v0", help="connect to this host/port" + ) + parser.add_argument("--batch-size", help="size of batch to send", default=100, type=int) + parser.set_defaults( + auth_var="FATCAT_AUTH_WORKER_CLEANUP", + ) + parser.add_argument( + "json_file", + help="File with jsonlines from file_meta schema to import from", + default=sys.stdin, + type=argparse.FileType("r"), + ) + + args = parser.parse_args() + api = authenticated_api( + args.host_url, + # token is an optional kwarg (can be empty string, None, etc) + token=os.environ.get(args.auth_var), + ) + + fswtc = FileShortWaybackTimestampCleanup( + api, + edit_batch_size=args.batch_size, + ) + JsonLinePusher(fswtc, args.json_file).run() + + +if __name__ == "__main__": + main() diff --git a/python/fatcat_tools/cleanups/release_lowercase_doi.py b/python/fatcat_tools/cleanups/release_lowercase_doi.py new file mode 100644 index 00000000..5e3275db --- /dev/null +++ b/python/fatcat_tools/cleanups/release_lowercase_doi.py @@ -0,0 +1,154 @@ +import argparse +import os +import sys + +from fatcat_openapi_client import ApiClient, ApiException, ReleaseEntity, ReleaseExtIds + +from fatcat_tools import authenticated_api, public_api +from fatcat_tools.importers.common import EntityImporter, LinePusher + + +class ReleaseLowercaseDoiCleanup(EntityImporter): + """ + This is a one-off / one-time cleanup script for release entities, to fix + upper-case DOIs. In fatcat, all DOIs should be normalized to lowercase. + + While this calls itself a cleanup, it is based on the import code path. It + is not integrated into the `fatcat_import` or `fatcat_cleanup` controller; + instead it has a __main__ function and is invoked like: + + python -m fatcat_tools.cleans.release_lowercase_doi - < blah.tsv + + It expects to get a simple text line on stdin, which is a release entity. + The correction is implemented by fetching the current version of the + entity, verifying the issue, and updating if it is still a problem. + + This does not try to do any merging, just corrects the case in a single + update. + """ + + def __init__(self, api: ApiClient, **kwargs): + + eg_desc = ( + kwargs.pop("editgroup_description", None) + or "Normalize release DOIs (extid) to lower-case" + ) + eg_extra = kwargs.pop("editgroup_extra", dict()) + eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.ReleaseLowercaseDoiCleanup") + super().__init__( + api, + do_updates=True, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs, + ) + self.testing_mode = False + + def want(self, row: str) -> bool: + row = row.strip() + if not row: + return False + row = row.split()[0] + if len(row) == 26: + return True + else: + return False + + def parse_record(self, row: str) -> ReleaseEntity: + + # bezerk mode doesn't make sense for this importer + assert self.bezerk_mode is False + + ident = row.strip().split()[0] + assert len(ident) == 26 + + return ReleaseEntity( + ident=ident, + ext_ids=ReleaseExtIds(), + ) + + def try_update(self, re: ReleaseEntity) -> bool: + + # should always be existing, but sometimes not because of prod/QA flip + existing = None + try: + existing = self.api.get_release(re.ident) + except ApiException as err: + if err.status != 404: + raise err + + if not existing: + self.counts["skip-existing-not-found"] += 1 + return False + + if existing.state != "active": + self.counts["skip-existing-entity-state"] += 1 + return False + + if not existing.ext_ids.doi: + self.counts["skip-existing-no-doi"] += 1 + return False + + if existing.ext_ids.doi == existing.ext_ids.doi.lower(): + self.counts["skip-existing-doi-fine"] += 1 + return False + + existing.ext_ids.doi = existing.ext_ids.doi.lower() + + # not doing a check for "in current editgroup", because the source of + # these corrections (entity dump) contains no dupes + + if not self.testing_mode: + self.api.update_release(self.get_editgroup_id(), existing.ident, existing) + self.counts["update"] += 1 + return False + + +def test_lowercase_doi() -> None: + api = public_api("http://localhost:9411/v0") + rldc = ReleaseLowercaseDoiCleanup(api=api) + rldc.testing_mode = True + + assert rldc.want("") is False + assert rldc.want("aaaaaaaaaaaaarceaaaaaaaaai") is True + assert rldc.want("aaaaaaaaaaaaarceaaaaaaaaai\t10.1234/ABCD") is True + rldc.parse_record("aaaaaaaaaaaaarceaaaaaaaaai") + + dummy_re = api.get_release("aaaaaaaaaaaaarceaaaaaaaaai") + assert rldc.try_update(dummy_re) is False + assert rldc.counts["skip-existing-doi-fine"] == 1 + # this isn't a very complete test, doesn't get to update part + + +def main() -> None: + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument( + "--host-url", default="http://localhost:9411/v0", help="connect to this host/port" + ) + parser.add_argument("--batch-size", help="size of batch to send", default=50, type=int) + parser.set_defaults( + auth_var="FATCAT_AUTH_WORKER_CLEANUP", + ) + parser.add_argument( + "idents_file", + help="File with release identifier to try updating", + default=sys.stdin, + type=argparse.FileType("r"), + ) + + args = parser.parse_args() + api = authenticated_api( + args.host_url, + # token is an optional kwarg (can be empty string, None, etc) + token=os.environ.get(args.auth_var), + ) + + rldc = ReleaseLowercaseDoiCleanup( + api, + edit_batch_size=args.batch_size, + ) + LinePusher(rldc, args.idents_file).run() + + +if __name__ == "__main__": + main() diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index fd472d11..2ec6efda 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -436,6 +436,15 @@ class EntityImporter: if u.rel == "social": u.rel = "academicsocial" + # remove exact URL duplicates, while preserving order, and removing + # "later" copies, not "first" copies + # this is sensitive to both url.url and url.rel combined! + dedupe_urls = [] + for url_pair in existing.urls: + if url_pair not in dedupe_urls: + dedupe_urls.append(url_pair) + existing.urls = dedupe_urls + # remove URLs which are near-duplicates redundant_urls = [] all_urls = [u.url for u in existing.urls] diff --git a/python/fatcat_web/types.py b/python/fatcat_web/types.py index f5182d71..f373825f 100644 --- a/python/fatcat_web/types.py +++ b/python/fatcat_web/types.py @@ -1,4 +1,4 @@ -from typing import Any, Tuple, Union +from typing import Tuple, Union from flask import Response as FlaskResponse from werkzeug.wrappers import Response as WerkzeugResponse |