diff options
Diffstat (limited to 'python')
| -rwxr-xr-x | python/fatcat_import.py | 21 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/__init__.py | 1 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/common.py | 4 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/fileset_generic.py | 83 | ||||
| -rw-r--r-- | python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json | 1 | ||||
| -rw-r--r-- | python/tests/import_fileset_generic.py | 59 |
6 files changed, 169 insertions, 0 deletions
diff --git a/python/fatcat_import.py b/python/fatcat_import.py index b82e81c7..6f331aaa 100755 --- a/python/fatcat_import.py +++ b/python/fatcat_import.py @@ -325,6 +325,14 @@ def run_file_meta(args): ) JsonLinePusher(fmi, args.json_file).run() +def run_fileset(args): + fmi = FilesetImporter( + args.api, + edit_batch_size=100, + skip_release_fileset_check=args.skip_release_fileset_check, + ) + JsonLinePusher(fmi, args.json_file).run() + def main(): parser = argparse.ArgumentParser( formatter_class=argparse.ArgumentDefaultsHelpFormatter) @@ -750,6 +758,19 @@ def main(): help="File with jsonlines from file_meta schema to import from", default=sys.stdin, type=argparse.FileType('r')) + sub_fileset = subparsers.add_parser('fileset', + help="generic fileset importer") + sub_fileset.set_defaults( + func=run_fileset, + auth_var="FATCAT_API_AUTH_TOKEN", + ) + sub_fileset.add_argument('json_file', + help="File with jsonlines of fileset entities to import", + default=sys.stdin, type=argparse.FileType('r')) + sub_fileset.add_argument('--skip-release-fileset-check', + action='store_true', + help="create without checking if releases already have related filesets") + args = parser.parse_args() if not args.__dict__.get("func"): print("tell me what to do!") diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py index 9cb18506..5da669e1 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -33,3 +33,4 @@ from .file_meta import FileMetaImporter from .doaj_article import DoajArticleImporter from .dblp_release import DblpReleaseImporter from .dblp_container import DblpContainerImporter +from .fileset_generic import FilesetImporter diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index e936477c..680b4f9c 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -447,6 +447,10 @@ class EntityImporter: existing.urls = [u for u in existing.urls if u.url not in redundant_urls] return existing + @staticmethod + def generic_fileset_cleanups(existing): + return existing + def match_existing_release_fuzzy(self, release: ReleaseEntity) -> Optional[Tuple[str, str, ReleaseEntity]]: """ This helper function uses fuzzycat (and elasticsearch) to look for diff --git a/python/fatcat_tools/importers/fileset_generic.py b/python/fatcat_tools/importers/fileset_generic.py new file mode 100644 index 00000000..f0ad5460 --- /dev/null +++ b/python/fatcat_tools/importers/fileset_generic.py @@ -0,0 +1,83 @@ + +import fatcat_openapi_client + +from fatcat_tools import entity_from_dict +from .common import EntityImporter + + +class FilesetImporter(EntityImporter): + """ + General purpose importer for fileset entities. Simply fileset schema JSON + and inserts. + + By default requires release_ids to be non-empty, and will check each + release_id to see if a fileset is already associated; if so, skips the + import. This behavior may change in the future, and can be disabled. + + Currently only creates (insert), no updates. + """ + + def __init__(self, api, **kwargs): + + eg_desc = kwargs.pop('editgroup_description', None) or "Generic Fileset entity import" + eg_extra = kwargs.pop('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.FilesetImporter') + kwargs['do_updates'] = bool(kwargs.get("do_updates", False)) + self.skip_release_fileset_check = bool(kwargs.get("skip_release_fileset_check", False)) + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs) + + # bezerk mode doesn't make sense for this importer + assert self.bezerk_mode == False + + def want(self, row): + if not row.get('release_ids'): + self.counts['skip-no-release-ids'] += 1 + return False + if not row.get('urls'): + self.counts['skip-no-urls'] += 1 + return False + if not row.get('manifest'): + self.counts['skip-no-files'] += 1 + return False + + for f in row.get('manifest'): + for k in ('sha1', 'md5'): + if not f.get(k): + self.counts['skip-missing-file-field'] += 1 + return False + return True + + def parse_record(self, row): + + fse = entity_from_dict( + row, + fatcat_openapi_client.FilesetEntity, + api_client=self.api.api_client, + ) + fse = self.generic_fileset_cleanups(fse) + return fse + + def try_update(self, fse): + + if not self.skip_release_fileset_check: + for release_id in fse.release_ids: + # don't catch 404, that would be an error + release = self.api.get_release(release_id, expand='filesets', hide='abstracts,refs') + assert release.state == 'active' + if release.filesets: + self.counts['exists'] += 1 + self.counts['exists-via-release-filesets'] += 1 + return False + + # do the insert + return True + + def insert_batch(self, batch): + self.api.create_fileset_auto_batch(fatcat_openapi_client.FilesetAutoBatch( + editgroup=fatcat_openapi_client.Editgroup( + description=self.editgroup_description, + extra=self.editgroup_extra), + entity_list=batch)) diff --git a/python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json b/python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json new file mode 100644 index 00000000..6ba9d573 --- /dev/null +++ b/python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json @@ -0,0 +1 @@ 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diff --git a/python/tests/import_fileset_generic.py b/python/tests/import_fileset_generic.py new file mode 100644 index 00000000..44310304 --- /dev/null +++ b/python/tests/import_fileset_generic.py @@ -0,0 +1,59 @@ + +import json +import pytest + +from fatcat_tools.importers import FilesetImporter, JsonLinePusher +from fixtures import * + + +@pytest.fixture(scope="function") +def fileset_importer(api): + yield FilesetImporter(api) + +# TODO: use API to check that entities actually created... +def test_fileset_importer_basic(fileset_importer): + with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f: + JsonLinePusher(fileset_importer, f).run() + +def test_fileset_importer(fileset_importer): + last_index = fileset_importer.api.get_changelog(limit=1)[0].index + with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f: + fileset_importer.bezerk_mode = True + counts = JsonLinePusher(fileset_importer, f).run() + assert counts['insert'] == 1 + assert counts['exists'] == 0 + assert counts['skip'] == 0 + + # fetch most recent editgroup + change = fileset_importer.api.get_changelog_entry(index=last_index+1) + eg = change.editgroup + assert eg.description + assert "generic fileset" in eg.description.lower() + assert eg.extra['git_rev'] + assert "fatcat_tools.FilesetImporter" in eg.extra['agent'] + + # re-insert; should skip + with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f: + fileset_importer.reset() + fileset_importer.bezerk_mode = False + counts = JsonLinePusher(fileset_importer, f).run() + assert counts['insert'] == 0 + assert counts['exists'] == 1 + assert counts['skip'] == 0 + +def test_fileset_dict_parse(fileset_importer): + with open('tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json', 'r') as f: + raw = json.loads(f.readline()) + fs = fileset_importer.parse_record(raw) + + assert fs.manifest[0].sha1 == "cc9bd558ca79b30b2966714da7ef4129537fde0c" + assert fs.manifest[0].md5 == "742c40404c9a4dbbd77c0985201c639f" + assert fs.manifest[0].sha256 == "3a7c07ad17ce3638d5a1dd21f995a496e430b952eef00270ad741d506984370f" + assert fs.manifest[0].size == 640500 + assert fs.manifest[0].path == "070111_LatA_100nM.txt" + assert fs.manifest[0].extra['mimetype'] == "text/plain" + assert len(fs.urls) == 3 + for u in fs.urls: + if u.rel == "repo": + assert u.url == "https://merritt.cdlib.org/d/ark%3A%2Fb5068%2Fd1rp49/1/" + assert len(fs.release_ids) == 1 |