From ea6ccd227e0f62f5f9e7a66ba8bc90b18a2ca097 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Fri, 11 Feb 2022 09:32:02 -0800 Subject: dataset ingest: JSON object fixes --- python/fatcat_tools/importers/ingest.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 4f1cc3c4..62e0e854 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -675,9 +675,9 @@ class IngestFilesetResultImporter(IngestFileResultImporter): return True def parse_fileset_urls(self, row: Dict[str, Any]) -> List[FilesetUrl]: - if not row.get("strategy"): + if not row.get("ingest_strategy"): return [] - strategy = row["strategy"] + strategy = row["ingest_strategy"] urls = [] if strategy == "archiveorg-fileset" and row.get("archiveorg_item_name"): urls.append( @@ -686,7 +686,7 @@ class IngestFilesetResultImporter(IngestFileResultImporter): rel="archive-base", ) ) - if row["strategy"].startswith("web-") and row.get("platform_base_url"): + if 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']}", @@ -696,7 +696,7 @@ class IngestFilesetResultImporter(IngestFileResultImporter): # TODO: repository-base # TODO: web-base - if row["strategy"] == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): + if strategy == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): urls.append( fatcat_openapi_client.FilesetUrl( url=f"https://archive.org/download/{row['archiveorg_item_name']}/{row['archiveorg_bundle_path']}", @@ -704,7 +704,7 @@ class IngestFilesetResultImporter(IngestFileResultImporter): ) ) - if row["strategy"] == "web-fileset-bundle" and row.get("platform_bundle_url"): + if 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']}", -- cgit v1.2.3 From 515b5ecc6e75aae834958d74883426230532f10d Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Wed, 23 Mar 2022 17:55:54 -0700 Subject: ingest fileset fixes, and some test coverage --- python/fatcat_tools/importers/common.py | 11 ++++ python/fatcat_tools/importers/ingest.py | 32 ++++++----- .../tests/files/example_fileset_ingest_result.json | 20 +++++++ python/tests/import_ingest.py | 63 ++++++++++++++++++++-- 4 files changed, 110 insertions(+), 16 deletions(-) create mode 100644 python/tests/files/example_fileset_ingest_result.json (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index cd51a24c..475cb97a 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -916,3 +916,14 @@ def make_kafka_consumer( ) print("Consuming from kafka topic {}, group {}".format(topic_name, group)) return consumer + + +def filesets_very_similar(a: FilesetEntity, b: FilesetEntity) -> bool: + """ + This helper method checks if two Fileset entities are effectively equivalent: same set of files with comparable hashes. + + Uses a set() of SHA1 hashes to test for equivalence. + """ + a_hashes = set([f.sha1 for f in a.manifest]) + b_hashes = set([f.sha1 for f in b.manifest]) + return a == b diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 62e0e854..c8d04d6f 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -11,7 +11,7 @@ from fatcat_openapi_client import ( WebcaptureEntity, ) -from .common import EntityImporter, make_rel_url +from .common import EntityImporter, filesets_very_similar, make_rel_url class IngestFileResultImporter(EntityImporter): @@ -693,9 +693,6 @@ class IngestFilesetResultImporter(IngestFileResultImporter): rel="webarchive-base", ) ) - # TODO: repository-base - # TODO: web-base - if strategy == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): urls.append( fatcat_openapi_client.FilesetUrl( @@ -727,6 +724,15 @@ class IngestFilesetResultImporter(IngestFileResultImporter): rel="repository-base", ) ) + elif row.get("terminal"): + # fallback generic web URL + urls.append( + fatcat_openapi_client.FilesetUrl( + url=row["terminal"]["terminal_url"], + rel="web", + ) + ) + return urls def parse_record(self, row: Dict[str, Any]) -> FilesetEntity: @@ -781,7 +787,7 @@ class IngestFilesetResultImporter(IngestFileResultImporter): self.counts["skip-partial-file-info"] += 1 return None if ingest_file.get("platform_url"): - # XXX: should we include this? + # TODO: 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[ @@ -805,25 +811,25 @@ class IngestFilesetResultImporter(IngestFileResultImporter): # check for existing edits-in-progress with same URL for other in self._entity_queue: - # XXX: how to duplicate check? - if other.original_url == fse.original_url: + if filesets_very_similar(other, fse): self.counts["skip-in-queue"] += 1 + self.counts["skip"] += 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(fse.release_ids[0], expand="filesets") - if release.filesets: - # XXX: how to duplicate check filesets? + if not self.bezerk_mode: + release = self.api.get_release(fse.release_ids[0], expand="filesets") # check if this is an existing match, or just a similar hit - for other in release.filesets: - if fse.original_url == other.original_url: - # TODO: compare very similar timestamps of same time (different formats) + for other in release.filesets or []: + if filesets_very_similar(other, fse): self.counts["exists"] += 1 return False + # for now, being conservative and just skipping if release has any other fileset self.counts["skip-release-has-fileset"] += 1 + self.counts["skip"] += 1 return False return True diff --git a/python/tests/files/example_fileset_ingest_result.json b/python/tests/files/example_fileset_ingest_result.json new file mode 100644 index 00000000..6b460b33 --- /dev/null +++ b/python/tests/files/example_fileset_ingest_result.json @@ -0,0 +1,20 @@ 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diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py index d9e7d294..d86d6d7b 100644 --- a/python/tests/import_ingest.py +++ b/python/tests/import_ingest.py @@ -5,6 +5,7 @@ from fixtures import * from fatcat_tools.importers import ( IngestFileResultImporter, + IngestFilesetResultImporter, IngestWebResultImporter, JsonLinePusher, ) @@ -20,6 +21,11 @@ def ingest_web_importer(api): yield IngestWebResultImporter(api) +@pytest.fixture(scope="function") +def ingest_fileset_importer(api): + yield IngestFilesetResultImporter(api) + + # TODO: use API to check that entities actually created... def test_ingest_importer_basic(ingest_importer): with open("tests/files/example_ingest.json", "r") as f: @@ -58,7 +64,6 @@ def test_ingest_importer_xml(ingest_importer): with open("tests/files/example_ingest_xml.json", "r") as f: ingest_importer.bezerk_mode = True counts = JsonLinePusher(ingest_importer, f).run() - print(counts) assert counts["insert"] == 1 assert counts["exists"] == 0 assert counts["skip"] == 0 @@ -86,7 +91,6 @@ def test_ingest_importer_web(ingest_web_importer): with open("tests/files/example_ingest_html.json", "r") as f: ingest_web_importer.bezerk_mode = True counts = JsonLinePusher(ingest_web_importer, f).run() - print(counts) assert counts["insert"] == 1 assert counts["exists"] == 0 assert counts["skip"] == 0 @@ -139,7 +143,6 @@ def test_ingest_importer_stage(ingest_importer, api): ingest_importer.reset() ingest_importer.push_record(raw) counts = ingest_importer.finish() - print(counts) assert counts["total"] == 1 assert counts[row["status"]] == 1 @@ -182,3 +185,57 @@ def test_ingest_dict_parse_old(ingest_importer): if u.rel == "webarchive": assert u.url.startswith("https://web.archive.org/") assert len(f.release_ids) == 1 + + +def test_ingest_fileset_dict_parse(ingest_fileset_importer): + with open("tests/files/example_fileset_ingest_result.json", "r") as f: + raw = json.loads(f.readline()) + fs = ingest_fileset_importer.parse_record(raw) + assert len(fs.manifest) == 3 + assert fs.manifest[0].sha1 == "c0669e84e7b9052cc0f342e8ce7d31d59956326a" + assert fs.manifest[0].md5 == "caf4d9fc2c6ebd0d9251ac84e0b6b006" + assert fs.manifest[0].extra["mimetype"] == "application/x-hdf" + assert fs.manifest[0].size == 16799750 + assert fs.manifest[0].path == "N2 on food R_2010_03_25__10_53_27___4___1_features.hdf5" + assert ( + fs.manifest[0].extra["original_url"] + == "https://zenodo.org/api/files/563203f6-6de5-46d9-b305-ba42604f2508/N2%20on%20food%20R_2010_03_25__10_53_27___4___1_features.hdf5" + ) + assert len(fs.urls) == 2 + for u in fs.urls: + if u.rel == "web": + assert u.url == "https://zenodo.org/record/1028059" + if u.rel == "archive-base": + assert u.url == "https://archive.org/download/zenodo.org-1028059/" + assert len(fs.release_ids) == 1 + + +def test_ingest_fileset_importer(ingest_fileset_importer): + last_index = ingest_fileset_importer.api.get_changelog(limit=1)[0].index + with open("tests/files/example_fileset_ingest_result.json", "r") as f: + ingest_fileset_importer.bezerk_mode = True + counts = JsonLinePusher(ingest_fileset_importer, f).run() + assert counts["insert"] == 7 + assert counts["exists"] == 0 + assert counts["skip"] == 13 + assert counts["skip-release-not-found"] == 13 + + # fetch most recent editgroup + change = ingest_fileset_importer.api.get_changelog_entry(index=last_index + 1) + eg = change.editgroup + assert eg.description + assert "filesets crawled from web" in eg.description.lower() + assert eg.extra["git_rev"] + assert "fatcat_tools.IngestFilesetResultImporter" in eg.extra["agent"] + + # re-insert; should skip + with open("tests/files/example_fileset_ingest_result.json", "r") as f: + ingest_fileset_importer.reset() + ingest_fileset_importer.bezerk_mode = False + counts = JsonLinePusher(ingest_fileset_importer, f).run() + + assert counts["insert"] == 0 + assert counts["exists"] == 0 + assert counts["skip"] == 20 + assert counts["skip-release-not-found"] == 13 + assert counts["skip-release-has-fileset"] == 7 -- cgit v1.2.3 From 929f6d1020362a8065d1e0c95d2ee67c88f89b33 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Wed, 23 Mar 2022 18:54:42 -0700 Subject: fix typo in fileset comparison helper --- python/fatcat_tools/importers/common.py | 2 +- python/tests/import_ingest.py | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index 475cb97a..2136d1da 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -926,4 +926,4 @@ def filesets_very_similar(a: FilesetEntity, b: FilesetEntity) -> bool: """ a_hashes = set([f.sha1 for f in a.manifest]) b_hashes = set([f.sha1 for f in b.manifest]) - return a == b + return a_hashes == b_hashes diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py index d86d6d7b..44dd5a0b 100644 --- a/python/tests/import_ingest.py +++ b/python/tests/import_ingest.py @@ -235,7 +235,6 @@ def test_ingest_fileset_importer(ingest_fileset_importer): counts = JsonLinePusher(ingest_fileset_importer, f).run() assert counts["insert"] == 0 - assert counts["exists"] == 0 - assert counts["skip"] == 20 + assert counts["exists"] == 7 + assert counts["skip"] == 13 assert counts["skip-release-not-found"] == 13 - assert counts["skip-release-has-fileset"] == 7 -- cgit v1.2.3 From 134cb050988be2c545af89e0a67c4998307bb819 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Wed, 23 Mar 2022 18:55:21 -0700 Subject: single-file variant of fileset importer for dataset attempts --- python/fatcat_import.py | 58 ++++++ python/fatcat_tools/importers/__init__.py | 1 + python/fatcat_tools/importers/ingest.py | 201 +++++++++++++++++++++ .../files/example_fileset_file_ingest_result.json | 20 ++ python/tests/import_ingest.py | 60 ++++++ 5 files changed, 340 insertions(+) create mode 100644 python/tests/files/example_fileset_file_ingest_result.json (limited to 'python/fatcat_tools') diff --git a/python/fatcat_import.py b/python/fatcat_import.py index f502d4ed..2896577e 100755 --- a/python/fatcat_import.py +++ b/python/fatcat_import.py @@ -25,6 +25,7 @@ from fatcat_tools.importers import ( FilesetImporter, GrobidMetadataImporter, IngestFileResultImporter, + IngestFilesetFileResultImporter, IngestFilesetResultImporter, IngestWebResultImporter, JalcImporter, @@ -232,6 +233,30 @@ def run_ingest_fileset(args: argparse.Namespace) -> None: JsonLinePusher(ifri, args.json_file).run() +def run_ingest_fileset_file(args: argparse.Namespace) -> None: + ifri = IngestFilesetFileResultImporter( + 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: argparse.Namespace) -> None: ifri = SavePaperNowFileImporter( args.api, @@ -750,6 +775,39 @@ def main() -> None: help="default URL rel for matches (eg, 'publisher', 'web')", ) + sub_ingest_fileset_file = subparsers.add_parser( + "ingest-fileset-file-results", + help="add/update file entities linked to releases based on sandcrawler dataset/fileset ingest results", + ) + sub_ingest_fileset_file.set_defaults( + func=run_ingest_fileset_file, + auth_var="FATCAT_AUTH_WORKER_CRAWL", + ) + sub_ingest_fileset_file.add_argument( + "json_file", + help="ingest_fileset JSON file to import from", + default=sys.stdin, + type=argparse.FileType("r"), + ) + sub_ingest_fileset_file.add_argument( + "--skip-source-allowlist", + action="store_true", + help="don't filter import based on request source allowlist", + ) + sub_ingest_fileset_file.add_argument( + "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" + ) + sub_ingest_fileset_file.add_argument( + "--do-updates", + action="store_true", + help="update pre-existing fileset entities if new match (instead of skipping)", + ) + sub_ingest_fileset_file.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", diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py index 654be2e9..e13ab552 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -37,6 +37,7 @@ from .fileset_generic import FilesetImporter from .grobid_metadata import GrobidMetadataImporter from .ingest import ( IngestFileResultImporter, + IngestFilesetFileResultImporter, IngestFilesetResultImporter, IngestWebResultImporter, SavePaperNowFileImporter, diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index c8d04d6f..653b4b0a 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -855,6 +855,207 @@ class IngestFilesetResultImporter(IngestFileResultImporter): ) +class IngestFilesetFileResultImporter(IngestFileResultImporter): + """ + Variant of IngestFileResultImporter for processing dataset (Fileset) ingest + results, which resulted in a single file, into File entities. + """ + + def __init__(self, api: ApiClient, **kwargs) -> None: + + eg_desc = ( + kwargs.pop("editgroup_description", None) + or "Single files crawled from web using sandcrawler ingest tool, in dataset mode" + ) + eg_extra = kwargs.pop("editgroup_extra", dict()) + eg_extra["agent"] = eg_extra.get( + "agent", "fatcat_tools.IngestFilesetFileResultImporter" + ) + 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: Dict[str, Any]) -> bool: + + manifest: Optional[List[Any]] = row.get("manifest") + if not manifest or len(manifest) == 0: + self.counts["skip-empty-manifest"] += 1 + return False + + if len(manifest) > 1: + self.counts["skip-multiple-files"] += 1 + return False + + assert len(manifest) == 1 + return True + + def want(self, row: Dict[str, Any]) -> bool: + + if not self.want_ingest(row): + return False + + if row.get("status") != "success-file": + self.counts["skip-status"] += 1 + 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: Dict[str, Any]) -> List[FilesetUrl]: + if not row.get("ingest_strategy"): + return [] + strategy = row["ingest_strategy"] + urls = [] + # XXX + 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 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", + ) + ) + if strategy == "archiveorg-fileset-bundle" and row.get("archiveorg_item_name"): + urls.append( + fatcat_openapi_client.FilesetUrl( + url=f"https://archive.org/download/{row['archiveorg_item_name']}/{row['archiveorg_bundle_path']}", + rel="archive-bundle", + ) + ) + + if 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", + ) + ) + elif row.get("terminal"): + # fallback generic web URL + urls.append( + fatcat_openapi_client.FilesetUrl( + url=row["terminal"]["terminal_url"], + rel="web", + ) + ) + + return urls + + def parse_record(self, row: Dict[str, Any]) -> FileEntity: + + 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[str, Any] = 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"] + + assert row["file_count"] == len(row["manifest"]) == 1 + file_meta = row["manifest"][0] + # print(file_meta) + assert file_meta["status"] == "success" + + # add file-level access URLs + entity_urls = [] + if file_meta.get("platform_url"): + entity_urls.append(FileUrl(rel="web", url=file_meta["platform_url"])) + if file_meta.get("terminal_url") and file_meta.get("terminal_dt"): + entity_urls.append( + FileUrl( + rel="webarchive", + url=f"https://web.archive.org/web/{file_meta['terminal_dt']}/{file_meta['terminal_url']}", + ) + ) + if row["ingest_strategy"] == "archiveorg-file": + entity_urls.append( + FileUrl( + rel="archive", + url=f"https://archive.org/download/{row['archiveorg_item_name']}/{file_meta['path']}", + ) + ) + + if not entity_urls: + self.counts["skip-no-access-url"] += 1 + return None + + entity_extra = dict() + entity_extra["path"] = file_meta["path"] + + # this is to work around a bug in old sandcrawler ingest code + if file_meta["md5"] == file_meta["sha1"]: + self.counts["skip-bad-hashes"] += 1 + return None + + fe = FileEntity( + md5=file_meta["md5"], + sha1=file_meta["sha1"], + sha256=file_meta["sha256"], + size=file_meta["size"], + mimetype=file_meta["mimetype"], + release_ids=[release_ident], + urls=entity_urls, + extra=entity_extra or None, + ) + if not (fe.md5 and fe.sha1 and fe.sha256 and (fe.size is not None) and fe.mimetype): + self.counts["skip-partial-file-info"] += 1 + return None + + if entity_extra: + fe.extra = entity_extra + edit_extra = self.parse_edit_extra(row) + if edit_extra: + fe.edit_extra = edit_extra + return fe + + class SavePaperNowFilesetImporter(IngestFilesetResultImporter): """ Like SavePaperNowFileImporter, but for fileset/dataset ingest. diff --git a/python/tests/files/example_fileset_file_ingest_result.json b/python/tests/files/example_fileset_file_ingest_result.json new file mode 100644 index 00000000..94ae4cc6 --- /dev/null +++ b/python/tests/files/example_fileset_file_ingest_result.json @@ -0,0 +1,20 @@ 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Thyroid surgery has been considered as a risk factor for the management of difficult airway. Method: We review the relevant literature related to the difficult airway and thyroid surgery. Comments: Endothoracic goiter, deformity of the airway, compression of the airway and thyroid cancer do not appear to have an influence on the difficulty for intubation. Classical parameters have a better predictive value: mouth opening less than 35 mm, Mallampati II-IV, short neck, neck movility less than 80 degrees, thyromental distance less than 60 mm, retrognathia, Cormack index III-IV, macroglossia, inability to protude the teeth and body mass index (BMI) greater than 35 Kg/m2. Conclusions: According to the literature, thyroid disease does not increase the risk for a difficult airway (ventilation / intubation). The risk of an unexpected difficult airway (false negative) cannot be eliminated. 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diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py index 44dd5a0b..8f8a34c7 100644 --- a/python/tests/import_ingest.py +++ b/python/tests/import_ingest.py @@ -5,6 +5,7 @@ from fixtures import * from fatcat_tools.importers import ( IngestFileResultImporter, + IngestFilesetFileResultImporter, IngestFilesetResultImporter, IngestWebResultImporter, JsonLinePusher, @@ -26,6 +27,11 @@ def ingest_fileset_importer(api): yield IngestFilesetResultImporter(api) +@pytest.fixture(scope="function") +def ingest_fileset_file_importer(api): + yield IngestFilesetFileResultImporter(api) + + # TODO: use API to check that entities actually created... def test_ingest_importer_basic(ingest_importer): with open("tests/files/example_ingest.json", "r") as f: @@ -238,3 +244,57 @@ def test_ingest_fileset_importer(ingest_fileset_importer): assert counts["exists"] == 7 assert counts["skip"] == 13 assert counts["skip-release-not-found"] == 13 + + +def test_ingest_fileset_file_dict_parse(ingest_fileset_file_importer): + with open("tests/files/example_fileset_file_ingest_result.json", "r") as f: + raw = json.loads(f.readline()) + fe = ingest_fileset_file_importer.parse_record(raw) + assert fe.sha1 == "6fb020064da66bb7a666c17555611cf6820fc9ae" + assert fe.md5 == "dfc41b617564f99a12e6077a6208876f" + assert fe.sha256 == "2febad53ff0f163a18d7cbb913275bf99ed2544730cda191458837e2b0da9d18" + assert fe.mimetype == "image/tiff" + assert fe.size == 410631015 + assert fe.extra["path"] == "NDVI_Diff_1990_2018_T06.tif" + assert len(fe.urls) == 2 + for u in fe.urls: + if u.rel == "repository": + assert u.url == "https://ndownloader.figshare.com/files/14460875" + if u.rel == "archive": + assert ( + u.url + == "https://archive.org/download/springernature.figshare.com-7767695-v1/NDVI_Diff_1990_2018_T06.tif" + ) + assert len(fe.release_ids) == 1 + + +def test_ingest_fileset_file_importer(ingest_fileset_file_importer): + """ + Similar to the above, but specifically tests 'file'/'success-file' import pathway + """ + last_index = ingest_fileset_file_importer.api.get_changelog(limit=1)[0].index + with open("tests/files/example_fileset_file_ingest_result.json", "r") as f: + ingest_fileset_file_importer.bezerk_mode = True + counts = JsonLinePusher(ingest_fileset_file_importer, f).run() + assert counts["insert"] == 16 + assert counts["exists"] == 0 + assert counts["skip"] == 4 + assert counts["skip-bad-hashes"] == 4 + + # fetch most recent editgroup + change = ingest_fileset_file_importer.api.get_changelog_entry(index=last_index + 1) + eg = change.editgroup + assert eg.description + assert "crawled from web" in eg.description.lower() + assert eg.extra["git_rev"] + assert "fatcat_tools.IngestFilesetFileResultImporter" in eg.extra["agent"] + + # re-insert; should skip + with open("tests/files/example_fileset_file_ingest_result.json", "r") as f: + ingest_fileset_file_importer.reset() + ingest_fileset_file_importer.bezerk_mode = False + counts = JsonLinePusher(ingest_fileset_file_importer, f).run() + assert counts["insert"] == 0 + assert counts["exists"] == 16 + assert counts["skip"] == 4 + assert counts["skip-bad-hashes"] == 4 -- cgit v1.2.3 From 9a99dcb74c13acd98cb4022cb01f28138699e180 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Wed, 23 Mar 2022 19:28:41 -0700 Subject: bugfix: logic flow in fileset release checking --- python/fatcat_tools/importers/ingest.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 653b4b0a..47032b26 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -822,15 +822,18 @@ class IngestFilesetResultImporter(IngestFileResultImporter): # NOTE: in lieu of existing checks (by lookup), only allow one fileset per release if not self.bezerk_mode: release = self.api.get_release(fse.release_ids[0], expand="filesets") + # check if this is an existing match, or just a similar hit for other in release.filesets or []: if filesets_very_similar(other, fse): self.counts["exists"] += 1 return False + # for now, being conservative and just skipping if release has any other fileset - self.counts["skip-release-has-fileset"] += 1 - self.counts["skip"] += 1 - return False + if release.filesets: + self.counts["skip-release-has-fileset"] += 1 + self.counts["skip"] += 1 + return False return True -- cgit v1.2.3 From 0649549664b84d7f5c3d0b9c0b03f1a8b4a88491 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Thu, 31 Mar 2022 12:34:42 -0700 Subject: fileset ingest: fix mimetype handling --- python/fatcat_tools/importers/ingest.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 47032b26..ed948606 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -779,11 +779,10 @@ class IngestFilesetResultImporter(IngestFileResultImporter): md5=ingest_file["md5"], sha1=ingest_file["sha1"], sha256=ingest_file.get("sha256"), - extra=dict( - mimetype=ingest_file["mimetype"], - ), + mimetype=ingest_file["mimetype"], + extra=dict(), ) - if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size): + if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size and fe.mimetype): self.counts["skip-partial-file-info"] += 1 return None if ingest_file.get("platform_url"): @@ -793,6 +792,8 @@ class IngestFilesetResultImporter(IngestFileResultImporter): fsf.extra[ "wayback_url" ] = f"https://web.archive.org/web/{ingest_file['terminal_dt']}/{ingest_file['terminal_url']}" + if not fsf.extra: + fsf.extra = None manifest.append(fsf) fe = fatcat_openapi_client.FilesetEntity( -- cgit v1.2.3 From 5d7bce1ebef2885f3d21b87cadcd18c90ea7d21a Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Mon, 4 Apr 2022 18:10:57 -0700 Subject: filesets: typo bugfix, and test 'mimetype' on entity, not extra --- python/fatcat_tools/importers/ingest.py | 2 +- python/tests/import_ingest.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index ed948606..ca06a988 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -782,7 +782,7 @@ class IngestFilesetResultImporter(IngestFileResultImporter): mimetype=ingest_file["mimetype"], extra=dict(), ) - if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size and fe.mimetype): + if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size and fsf.mimetype): self.counts["skip-partial-file-info"] += 1 return None if ingest_file.get("platform_url"): diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py index 8f8a34c7..77d237c8 100644 --- a/python/tests/import_ingest.py +++ b/python/tests/import_ingest.py @@ -200,7 +200,7 @@ def test_ingest_fileset_dict_parse(ingest_fileset_importer): assert len(fs.manifest) == 3 assert fs.manifest[0].sha1 == "c0669e84e7b9052cc0f342e8ce7d31d59956326a" assert fs.manifest[0].md5 == "caf4d9fc2c6ebd0d9251ac84e0b6b006" - assert fs.manifest[0].extra["mimetype"] == "application/x-hdf" + assert fs.manifest[0].mimetype == "application/x-hdf" assert fs.manifest[0].size == 16799750 assert fs.manifest[0].path == "N2 on food R_2010_03_25__10_53_27___4___1_features.hdf5" assert ( -- cgit v1.2.3 From e0e41462d46b443079b370d296a67f9774f21c55 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Mon, 4 Apr 2022 19:10:01 -0700 Subject: fileset ingest: remove a TODO --- python/fatcat_tools/importers/ingest.py | 1 - 1 file changed, 1 deletion(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index ca06a988..471d673b 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -786,7 +786,6 @@ class IngestFilesetResultImporter(IngestFileResultImporter): self.counts["skip-partial-file-info"] += 1 return None if ingest_file.get("platform_url"): - # TODO: 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[ -- cgit v1.2.3 From 70e905bc21835476f6713289ad0f31e4c56cae32 Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Tue, 5 Apr 2022 12:02:33 -0700 Subject: ingest importer: improved extra/edit_extra code flow --- python/fatcat_tools/importers/ingest.py | 33 +++++++++++++-------------------- 1 file changed, 13 insertions(+), 20 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 471d673b..20963918 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -260,6 +260,16 @@ class IngestFileResultImporter(EntityImporter): edit_extra["grobid_status_code"] = row["grobid"]["status_code"] edit_extra["grobid_version"] = row["grobid"].get("grobid_version") + # fileset/platform metadata + if row.get("ingest_strategy"): + edit_extra["ingest_strategy"] = row["ingest_strategy"] + if row.get("platform_domain"): + edit_extra["platform_domain"] = row["platform_domain"] + if row.get("platform_name"): + edit_extra["platform_name"] = row["platform_name"] + if row.get("platform_id"): + edit_extra["platform_id"] = row["platform_id"] + return edit_extra def parse_record(self, row: Dict[str, Any]) -> FileEntity: @@ -518,7 +528,6 @@ class IngestWebResultImporter(IngestFileResultImporter): ) edit_extra = self.parse_edit_extra(row) - if edit_extra: wc.edit_extra = edit_extra return wc @@ -754,12 +763,6 @@ class IngestFilesetResultImporter(IngestFileResultImporter): return None entity_extra: Dict[str, Any] = 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: @@ -799,10 +802,10 @@ class IngestFilesetResultImporter(IngestFileResultImporter): manifest=manifest, urls=entity_urls, release_ids=[release_ident], + extra=entity_extra or None, ) - if entity_extra: - fe.extra = entity_extra + edit_extra = self.parse_edit_extra(row) if edit_extra: fe.edit_extra = edit_extra return fe @@ -993,14 +996,6 @@ class IngestFilesetFileResultImporter(IngestFileResultImporter): self.counts["skip-release-not-found"] += 1 return None - entity_extra: Dict[str, Any] = 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"] - assert row["file_count"] == len(row["manifest"]) == 1 file_meta = row["manifest"][0] # print(file_meta) @@ -1029,7 +1024,7 @@ class IngestFilesetFileResultImporter(IngestFileResultImporter): self.counts["skip-no-access-url"] += 1 return None - entity_extra = dict() + entity_extra: Dict[str, Any] = dict() entity_extra["path"] = file_meta["path"] # this is to work around a bug in old sandcrawler ingest code @@ -1051,8 +1046,6 @@ class IngestFilesetFileResultImporter(IngestFileResultImporter): self.counts["skip-partial-file-info"] += 1 return None - if entity_extra: - fe.extra = entity_extra edit_extra = self.parse_edit_extra(row) if edit_extra: fe.edit_extra = edit_extra -- cgit v1.2.3 From 610e3086b42d50fc65945664bd8ff74579d88e9a Mon Sep 17 00:00:00 2001 From: Bryan Newbold Date: Tue, 5 Apr 2022 12:02:50 -0700 Subject: fileset ingest: handle missing/partial file-level metadata --- python/fatcat_tools/importers/ingest.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'python/fatcat_tools') diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index 20963918..c1fed31f 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -779,10 +779,10 @@ class IngestFilesetResultImporter(IngestFileResultImporter): fsf = fatcat_openapi_client.FilesetFile( path=ingest_file["path"], size=ingest_file["size"], - md5=ingest_file["md5"], - sha1=ingest_file["sha1"], + md5=ingest_file.get("md5"), + sha1=ingest_file.get("sha1"), sha256=ingest_file.get("sha256"), - mimetype=ingest_file["mimetype"], + mimetype=ingest_file.get("mimetype"), extra=dict(), ) if not (fsf.md5 and fsf.sha1 and fsf.path and fsf.size and fsf.mimetype): -- cgit v1.2.3