diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/.gitignore | 2 | ||||
| -rwxr-xr-x | python/fatcat_import.py | 95 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/__init__.py | 3 | ||||
| -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/fatcat_tools/importers/ingest.py | 248 | ||||
| -rw-r--r-- | python/fatcat_tools/transforms/ingest.py | 16 | ||||
| -rw-r--r-- | python/tests/files/fileset_ltjp7k2nrbes3or5h4na5qgxlu.json | 1 | ||||
| -rw-r--r-- | python/tests/import_fileset_generic.py | 59 |
9 files changed, 507 insertions, 4 deletions
diff --git a/python/.gitignore b/python/.gitignore index e11492e6..b3d22ecf 100644 --- a/python/.gitignore +++ b/python/.gitignore @@ -6,6 +6,8 @@ dist/ *.egg-info *.json.gz fatcat-*.tar.gz +old/ +TODO* !example.env !.coveragerc diff --git a/python/fatcat_import.py b/python/fatcat_import.py index b82e81c7..41a51ad4 100755 --- a/python/fatcat_import.py +++ b/python/fatcat_import.py @@ -164,6 +164,27 @@ def run_ingest_web(args): else: JsonLinePusher(iwri, args.json_file).run() +def run_ingest_fileset(args): + ifri = IngestFilesetResultImporter(args.api, + editgroup_description=args.editgroup_description_override, + skip_source_allowlist=args.skip_source_allowlist, + do_updates=args.do_updates, + default_link_rel=args.default_link_rel, + edit_batch_size=args.batch_size) + if args.kafka_mode: + KafkaJsonPusher( + ifri, + args.kafka_hosts, + args.kafka_env, + "ingest-fileset-results", + "fatcat-{}-ingest-fileset-result".format(args.kafka_env), + kafka_namespace="sandcrawler", + consume_batch_size=args.batch_size, + force_flush=True, + ).run() + else: + JsonLinePusher(ifri, args.json_file).run() + def run_savepapernow_file(args): ifri = SavePaperNowFileImporter(args.api, editgroup_description=args.editgroup_description_override, @@ -200,6 +221,24 @@ def run_savepapernow_web(args): else: JsonLinePusher(ifri, args.json_file).run() +def run_savepapernow_fileset(args): + ifri = SavePaperNowFilesetImporter(args.api, + editgroup_description=args.editgroup_description_override, + edit_batch_size=args.batch_size) + if args.kafka_mode: + KafkaJsonPusher( + ifri, + args.kafka_hosts, + args.kafka_env, + "ingest-file-results", + "fatcat-{}-savepapernow-fileset-result".format(args.kafka_env), + kafka_namespace="sandcrawler", + consume_batch_size=args.batch_size, + force_flush=True, + ).run() + else: + JsonLinePusher(ifri, args.json_file).run() + def run_grobid_metadata(args): fmi = GrobidMetadataImporter(args.api, edit_batch_size=args.batch_size, @@ -325,6 +364,14 @@ 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) @@ -561,6 +608,28 @@ def main(): default="web", help="default URL rel for matches (eg, 'publisher', 'web')") + sub_ingest_fileset = subparsers.add_parser('ingest-fileset-results', + help="add/update fileset entities linked to releases based on sandcrawler ingest results") + sub_ingest_fileset.set_defaults( + func=run_ingest_fileset, + auth_var="FATCAT_AUTH_WORKER_CRAWL", + ) + sub_ingest_fileset.add_argument('json_file', + help="ingest_fileset JSON file to import from", + default=sys.stdin, type=argparse.FileType('r')) + sub_ingest_fileset.add_argument('--skip-source-allowlist', + action='store_true', + help="don't filter import based on request source allowlist") + sub_ingest_fileset.add_argument('--kafka-mode', + action='store_true', + help="consume from kafka topic (not stdin)") + sub_ingest_fileset.add_argument('--do-updates', + action='store_true', + help="update pre-existing fileset entities if new match (instead of skipping)") + sub_ingest_fileset.add_argument('--default-link-rel', + default="fileset", + help="default URL rel for matches (eg, 'publisher', 'web')") + sub_savepapernow_file = subparsers.add_parser('savepapernow-file-results', help="add file entities crawled due to async Save Paper Now request") sub_savepapernow_file.set_defaults( @@ -587,6 +656,19 @@ def main(): action='store_true', help="consume from kafka topic (not stdin)") + sub_savepapernow_fileset = subparsers.add_parser('savepapernow-fileset-results', + help="add fileset entities crawled due to async Save Paper Now request") + sub_savepapernow_fileset.set_defaults( + func=run_savepapernow_fileset, + auth_var="FATCAT_AUTH_WORKER_SAVEPAPERNOW", + ) + sub_savepapernow_fileset.add_argument('json_file', + help="ingest-file JSON file to import from", + default=sys.stdin, type=argparse.FileType('r')) + sub_savepapernow_fileset.add_argument('--kafka-mode', + action='store_true', + help="consume from kafka topic (not stdin)") + sub_grobid_metadata = subparsers.add_parser('grobid-metadata', help="create release and file entities based on GROBID PDF metadata extraction") sub_grobid_metadata.set_defaults( @@ -750,6 +832,19 @@ 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..a2224081 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -27,9 +27,10 @@ from .orcid import OrcidImporter from .arabesque import ArabesqueMatchImporter, ARABESQUE_MATCH_WHERE_CLAUSE from .wayback_static import auto_wayback_static from .cdl_dash_dat import auto_cdl_dash_dat -from .ingest import IngestFileResultImporter, SavePaperNowFileImporter, IngestWebResultImporter, SavePaperNowWebImporter +from .ingest import IngestFileResultImporter, SavePaperNowFileImporter, IngestWebResultImporter, SavePaperNowWebImporter, IngestFilesetResultImporter, SavePaperNowFilesetImporter from .shadow import ShadowLibraryImporter 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/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index bc759219..288c4cff 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -64,6 +64,9 @@ class IngestFileResultImporter(EntityImporter): "application/jats+xml", "application/tei+xml", "text/xml"): self.counts['skip-mimetype'] += 1 return False + elif row['request'].get('ingest_type') in ['component', 'src', 'dataset-file']: + # we rely on sandcrawler for these checks + pass else: self.counts['skip-ingest-type'] += 1 return False @@ -336,7 +339,7 @@ class SavePaperNowFileImporter(IngestFileResultImporter): eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled after a public 'Save Paper Now' request" eg_extra = kwargs.pop('editgroup_extra', dict()) - eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileSavePaperNow') + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.SavePaperNowFileImporter') kwargs['submit_mode'] = submit_mode kwargs['require_grobid'] = False kwargs['do_updates'] = False @@ -533,7 +536,7 @@ class SavePaperNowWebImporter(IngestWebResultImporter): eg_desc = kwargs.pop('editgroup_description', None) or "Webcaptures crawled after a public 'Save Paper Now' request" eg_extra = kwargs.pop('editgroup_extra', dict()) - eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestWebSavePaperNow') + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.SavePaperNowWebImporter') kwargs['submit_mode'] = submit_mode kwargs['do_updates'] = False super().__init__(api, @@ -573,3 +576,244 @@ class SavePaperNowWebImporter(IngestWebResultImporter): return False return True + + +class IngestFilesetResultImporter(IngestFileResultImporter): + """ + Variant of IngestFileResultImporter for processing, eg, dataset ingest + results into fileset objects. + """ + + def __init__(self, api, **kwargs): + + eg_desc = kwargs.pop('editgroup_description', None) or "Filesets crawled from web using sandcrawler ingest tool" + eg_extra = kwargs.pop('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFilesetResultImporter') + kwargs['do_updates'] = False + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs) + self.max_file_count = 300 + + def want_fileset(self, row): + + if not row.get('manifest') or len(row.get('manifest')) == 0: + self.counts['skip-empty-manifest'] += 1 + return False + + if len(row.get('manifest')) == 1: + self.counts['skip-single-file'] += 1 + return False + + if len(row.get('manifest')) > self.max_file_count: + self.counts['skip-too-many-files'] += 1 + return False + + return True + + def want(self, row): + + if not self.want_ingest(row): + return False + + # fileset-specific filters + if row['request'].get('ingest_type') not in ['dataset',]: + self.counts['skip-ingest-type'] += 1 + return False + + if not self.want_fileset(row): + return False + + return True + + def parse_fileset_urls(self, row): + if not row.get('strategy'): + return [] + strategy = row['strategy'] + urls = [] + if strategy == 'archiveorg-fileset' and row.get('archiveorg_item_name'): + urls.append(fatcat_openapi_client.FilesetUrl( + url=f"https://archive.org/download/{row['archiveorg_item_name']}/", + rel="archive-base", + )) + if row['strategy'].startswith('web-') and row.get('platform_base_url'): + urls.append(fatcat_openapi_client.FilesetUrl( + url=f"https://web.archive.org/web/{row['web_base_url_dt']}/{row['web_base_url']}", + rel="webarchive-base", + )) + # TODO: repository-base + # TODO: web-base + + if row['strategy'] == 'archiveorg-fileset-bundle' and row.get('archiveorg_item_name'): + # TODO: bundle path + urls.append(fatcat_openapi_client.FilesetUrl( + url=f"https://archive.org/download/{row['archiveorg_item_name']}/{bundle_path}", + rel="archive-bundle", + )) + + if row['strategy'] == 'web-fileset-bundle' and row.get('platform_bundle_url'): + urls.append(fatcat_openapi_client.FilesetUrl( + url=f"https://web.archive.org/web/{row['web_bundle_url_dt']}/{row['web_bundle_url']}", + rel="webarchive-bundle", + )) + + # add any additional / platform URLs here + if row.get('platform_bundle_url'): + urls.append(fatcat_openapi_client.FilesetUrl( + url=row['platform_bundle_url'], + rel="repository-bundle", + )) + if row.get('platform_base_url'): + urls.append(fatcat_openapi_client.FilesetUrl( + url=row['platform_bundle_url'], + rel="repository-base", + )) + return urls + + def parse_record(self, row): + + request = row['request'] + + # double check that want() filtered request correctly + if request.get('ingest_type') not in ["dataset",]: + self.counts['skip-ingest-type'] += 1 + return None + + # identify release by fatcat ident, or extid lookup + release_ident = self.parse_ingest_release_ident(row) + + if not release_ident: + self.counts['skip-release-not-found'] += 1 + return None + + entity_extra = dict() + edit_extra = self.parse_edit_extra(row) + edit_extra['ingest_strategy'] = row['ingest_strategy'] + if row.get('platform'): + edit_extra['platform'] = row['platform'] + if row.get('platform_id'): + edit_extra['platform_id'] = row['platform_id'] + + entity_urls = self.parse_fileset_urls(row) + if not entity_urls: + self.counts['skip-no-access-url'] += 1 + return None + + assert row['file_count'] == len(row['manifest']) + if row['file_count'] > self.max_file_count: + self.counts['skip-too-many-manifest-files'] += 1 + return None + + manifest = [] + for ingest_file in row['manifest']: + fsf = fatcat_openapi_client.FilesetFile( + path=ingest_file['path'], + size=ingest_file['size'], + md5=ingest_file['md5'], + sha1=ingest_file['sha1'], + sha256=ingest_file.get('sha256'), + extra=dict( + mimetype=ingest_file['mimetype'], + ), + ) + if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size): + self.counts['skip-partial-file-info'] += 1 + return None + if ingest_file.get('platform_url'): + # XXX: should we include this? + fsf.extra['original_url'] = ingest_file['platform_url'] + if ingest_file.get('terminal_url') and ingest_file.get('terminal_dt'): + fsf.extra['wayback_url'] = f"https://web.archive.org/web/{ingest_file['terminal_dt']}/{ingest_file['terminal_url']}" + manifest.append(fsf) + + fe = fatcat_openapi_client.FilesetEntity( + manifest=manifest, + urls=entity_urls, + release_ids=[release_ident], + ) + + if entity_extra: + fe.extra = entity_extra + if edit_extra: + fe.edit_extra = edit_extra + return fe + + def try_update(self, wc): + + # check for existing edits-in-progress with same URL + for other in self._entity_queue: + # XXX: how to duplicate check? + if other.original_url == wc.original_url: + self.counts['skip-in-queue'] += 1 + return False + + # lookup sha1, or create new entity (TODO: API doesn't support this yet) + #existing = None + + # NOTE: in lieu of existing checks (by lookup), only allow one fileset per release + release = self.api.get_release(wc.release_ids[0], expand="filesets") + if release.filesets: + # XXX: how to duplicate check filesets? + # check if this is an existing match, or just a similar hit + for other in release.filesets: + if wc.original_url == other.original_url: + # TODO: compare very similar timestamps of same time (different formats) + self.counts['exists'] += 1 + return False + self.counts['skip-release-has-fileset'] += 1 + return False + + return True + + def insert_batch(self, batch): + if self.submit_mode: + eg = self.api.create_editgroup(fatcat_openapi_client.Editgroup( + description=self.editgroup_description, + extra=self.editgroup_extra)) + for fe in batch: + self.api.create_fileset(eg.editgroup_id, fe) + self.api.update_editgroup(eg.editgroup_id, eg, submit=True) + else: + 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)) + + +class SavePaperNowFilesetImporter(IngestFilesetResultImporter): + """ + Like SavePaperNowFileImporter, but for fileset/dataset ingest. + """ + + def __init__(self, api, submit_mode=True, **kwargs): + + eg_desc = kwargs.pop('editgroup_description', None) or "Fileset crawled after a public 'Save Paper Now' request" + eg_extra = kwargs.pop('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.SavePaperNowFilesetImporter') + kwargs['submit_mode'] = submit_mode + kwargs['do_updates'] = False + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs) + + def want(self, row): + + source = row['request'].get('ingest_request_source') + if not source: + self.counts['skip-ingest_request_source'] += 1 + return False + if not source.startswith('savepapernow'): + self.counts['skip-not-savepapernow'] += 1 + return False + + if row.get('hit') != True: + self.counts['skip-hit'] += 1 + return False + + if not self.want_fileset(row): + return False + + return True diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py index 42927b2a..9101a4ec 100644 --- a/python/fatcat_tools/transforms/ingest.py +++ b/python/fatcat_tools/transforms/ingest.py @@ -32,8 +32,22 @@ def release_ingest_request(release, ingest_request_source='fatcat', ingest_type= if (not ingest_type) and release.container_id: ingest_type = INGEST_TYPE_CONTAINER_MAP.get(release.container_id) + if not ingest_type: - ingest_type = 'pdf' + if release.release_type == 'stub': + return None + elif release.release_type in ['component', 'graphic']: + ingest_type = 'component' + elif release.release_type == 'dataset': + ingest_type = 'dataset' + elif release.release_type == 'software': + ingest_type = 'software' + elif release.release_type == 'post-weblog': + ingest_type = 'html' + elif release.release_type in ['article-journal', 'article', 'chapter', 'paper-conference', 'book', 'report', 'thesis']: + ingest_type = 'pdf' + else: + ingest_type = 'pdf' # generate a URL where we expect to find fulltext url = None 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 @@ +{"extra":{"cdl_dash":{"version":1}},"ident":"ltjp7k2nrbes3or5h4na5qgxlu","manifest":[{"extra":{"mimetype":"text/plain"},"md5":"742c40404c9a4dbbd77c0985201c639f","path":"070111_LatA_100nM.txt","sha1":"cc9bd558ca79b30b2966714da7ef4129537fde0c","sha256":"3a7c07ad17ce3638d5a1dd21f995a496e430b952eef00270ad741d506984370f","size":640500},{"extra":{"mimetype":"text/plain"},"md5":"e45d39263eda5e7763002cf61f708ce4","path":"060111_Ctrl_DMSO.txt","sha1":"3c90a1d86e7a2b11ce4994afe950031dfb99ddf2","sha256":"c1d5a888bce2a12478b2aca1113c0db923fb3a9978858497889b81902165927c","size":1499484},{"extra":{"mimetype":"text/plain"},"md5":"548523f7b4c5170cc220a091bf480e32","path":"052311_CytoB.txt","sha1":"4862246b5f48ac8f446ff65fdffe0a5af5520dc9","sha256":"4203b83eab45d7adbe8f738527bef9ddbc1730ceeeff05dfa4193a442064049c","size":121910},{"extra":{"mimetype":"text/plain"},"md5":"b387e141c84292ec637eb4333287dd1e","path":"062812_CytoB4_8uL.txt","sha1":"ecd5dce5e1214401d6cf09c8df6565818610d75b","sha256":"fa40b428a57cf4a95f68286988c742cfc1e919130d42e5090de3fb6963c3eafb","size":215477},{"extra":{"mimetype":"text/plain"},"md5":"e143909e79f1a7ee70ac411c6e61ef8c","path":"021611_H929.txt","sha1":"135096114b2d993e6729c81a2e2df0909dc999bc","sha256":"b0d409b90c9f9c4e1d9c84b712cd955e37544cb5749e9e3f398b90ee86a760b6","size":173751},{"extra":{"mimetype":"text/plain"},"md5":"7a73dd72af5c59612bb2d3a5450aedee","path":"062912_LatA200nM.txt","sha1":"7211121b8f8fc7ba76c55c35cc5d7e64c554914e","sha256":"ef2ed92a5a5c21816d713b2bdbcc2a406a39d2ea8f8dde961f4a976dc116d1f8","size":578291},{"extra":{"mimetype":"text/plain"},"md5":"f3eeac4f72e71b6e58dff8c39d92220b","path":"022212_DMSO.txt","sha1":"ede26cbc8d9ebc881277f81c962c212c09b1680f","sha256":"3b5b613ae6c0a06b0c013e3f439a3fd709677c30758516661fcf8134880a7199","size":1748533},{"extra":{"mimetype":"text/plain"},"md5":"b9feaaed607da9054b8aa7ec949a821d","path":"062012_LatA50nM.txt","sha1":"45ed08cf4734c44146dd900785a7a9ba8bcf72d9","sha256":"39522709b157d1e479cd102e53221a367488c9f8535c4ce85aabbf8dc457b70b","size":1320060},{"extra":{"mimetype":"text/plain"},"md5":"a3c3cf340773ac2d16e946a7c10cfddb","path":"070612_DMSO.txt","sha1":"4296e1cd6ef8e32aa7224eac8377f47ca7d645c1","sha256":"700966fc77dddf7438863ed118d64ed31ffe57b239781bb8b9594e9136d2c91f","size":1565988},{"extra":{"mimetype":"text/plain"},"md5":"fdc8c5c7dced7b38752d5dd44a51e8e8","path":"030712_Ctrl.txt","sha1":"98e1c3f6af26ad4cf0d1ab6b43ac1b4aa779cef9","sha256":"7b0c8bcfaf0df17f206c977aaf7950b26d99480579a56bc53f447b3d7a630e7b","size":1326229},{"extra":{"mimetype":"text/plain"},"md5":"408220ddeef9a5741354ee544bf0b348","path":"022012_Taxol.txt","sha1":"3bb86d180ebf2b7179b38d90094cbc7bea7406f7","sha256":"d10e473da5557296df0954bf198678661e64b3656f3920e93127ad1d31684713","size":1635260},{"extra":{"mimetype":"text/plain"},"md5":"80a782103b95a22beb76cbb1f577aa68","path":"021912_DMSO.txt","sha1":"a79f45942044684a768e8bfda0c8e5f4c659882e","sha256":"23ba99985e98e2d87eda793e4e0c637716844c91051f217b0964cd8b7cc7345a","size":1082779},{"extra":{"mimetype":"text/plain"},"md5":"1c1f27ff119969d809dbeef3d47656af","path":"021812_LatA.txt","sha1":"f070f9265add073d052af20021b96ed8ef1ab57b","sha256":"cda3a1ff0d94a61577a267205797a8e4f5432b0cc586b91f2fd251b7019b16b3","size":1229189},{"extra":{"mimetype":"text/plain"},"md5":"1d7dfd73ae5fe71d2548746181de5758","path":"061611_CytoB.txt","sha1":"9e277c91d99f064566b3df67c2453d2c3d85b77e","sha256":"b4740947b9330f5f234eb597f25e917c801ad75106f0361a4bf4c795543636d6","size":548117},{"extra":{"mimetype":"text/plain"},"md5":"04702e0535a62adebd50ccab4ef9b9d3","path":"040312_Ctrl.txt","sha1":"e9becc2ef210540bdd17ed9c42c25193721b69b2","sha256":"2fafb8eb7c61fc1832eb333b733f60d78cb5fdf39af3e3259fe38563029beb76","size":2027114},{"extra":{"mimetype":"text/plain"},"md5":"f5c291b532a534030046b722f68a362b","path":"072712_CH12.txt","sha1":"c90d5ab0f53f288d953ef84ee3433a8eb6a4578a","sha256":"6dd01fcef271facefa8a6db85dd67f0abfc21b59c7a53dc10c0358680b602752","size":625260},{"extra":{"mimetype":"text/plain"},"md5":"5709144abf8d960bd3d0bdbee87d6fb5","path":"030812_Noco.txt","sha1":"3577e12cc4b9432f95492ca6bb2a822e899a17b0","sha256":"8a421a72194eb815410e33b255dcb6763c46edaa19b8b39685cf1ae3b6a29eca","size":50747},{"extra":{"mimetype":"text/plain"},"md5":"e306220f25c5ad0863733a050de546c9","path":"071612_CH12.txt","sha1":"0fac76b0e579540a475f8ad44e14544cf9dd7e05","sha256":"3b2d040ae222f28774d78ef16c033fc5102a8707d385d0b35d6ff537d1763b5c","size":962172},{"extra":{"mimetype":"text/plain"},"md5":"5b72da6e75f1423bdee3c88cf6ae6233","path":"021712_LatA.txt","sha1":"5a6dd2e329716ccdbb7aeb29ef90b6d25111120c","sha256":"00e161b4a6197563fa58a670c6495378705a2b0aace260159a6a63c6ff4a9548","size":1440446},{"extra":{"mimetype":"text/plain"},"md5":"36ce1748c811d4ecc19c67c08533abcb","path":"062411_Bleb_half.txt","sha1":"0e6292cc9f3110063fdc6273986e2e5aa81bad89","sha256":"d02b01ede98936f9d321660089a3538aeb7db55109c6e1930ee8f8839d2aed14","size":836110},{"extra":{"mimetype":"text/plai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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 |