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-rw-r--r--python/fatcat_tools/importers/common.py11
-rw-r--r--python/fatcat_tools/importers/ingest.py32
-rw-r--r--python/tests/files/example_fileset_ingest_result.json20
-rw-r--r--python/tests/import_ingest.py63
4 files changed, 110 insertions, 16 deletions
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 @@
+{"archiveorg_item_name":"zenodo.org-1028059","cdx":{"datetime":"20200211074218","mimetype":"text/html","sha1b32":"N754JJAQWWTHMZMMNECQFOPCSTDWNP7I","sha1hex":"6ffbc4a410b5a676658c690502b9e294c766bfe8","status_code":200,"surt":"org,zenodo)/record/1028059","url":"https://zenodo.org/record/1028059","warc_csize":9720,"warc_offset":79299,"warc_path":"DATACITE-DOI-CRAWL-2020-01-20200211071817172-07303-07367-wbgrp-svc280/DATACITE-DOI-CRAWL-2020-01-20200211074221315-07339-3211~wbgrp-svc280.us.archive.org~8443.warc.gz"},"file_count":3,"file_meta":{"md5hex":"c318f2e8cc85a432e52fbeda2209f5b8","mimetype":"text/html","sha1hex":"6ffbc4a410b5a676658c690502b9e294c766bfe8","sha256hex":"60e27cff98b7b51edae1b3b90cc94930de0309166974bc2b8ee7870c8c2a2e89","size_bytes":40140},"hit":true,"hops":["https://doi.org/10.5281/zenodo.1028059","https://zenodo.org/record/1028059"],"html_biblio":{"container_name":"Zenodo","contrib_names":["Javer, Avelino","Currie, Michael","Hokanson, Jim","Lee, Chee Wai","Li, Kezhi","Yemini, Eviatar","Grundy, Laura J","Li, Chris","Ch'ng, Quee-Lim","Schafer, William R","Kerr, Rex","Brown, André EX"],"doi":"10.123/abc","release_date":"2017-10-20","title":"N2 Schafer Lab N2 (Bristol, UK) | 2010-03-25T10:53:27+00:00"},"ingest_strategy":"archiveorg-fileset","manifest":[{"md5":"caf4d9fc2c6ebd0d9251ac84e0b6b006","mimetype":"application/x-hdf","path":"N2 on food R_2010_03_25__10_53_27___4___1_features.hdf5","platform_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","sha1":"c0669e84e7b9052cc0f342e8ce7d31d59956326a","sha256":"d218694facb90e96a65f008e1205c1514bae54bdb4e1c2296c1c8dcc31dece9d","size":16799750,"status":"success"},{"md5":"961f88355395408ac9464cc1b33dab4a","mimetype":"application/x-hdf","path":"N2 on food R_2010_03_25__10_53_27___4___1.hdf5","platform_url":"https://zenodo.org/api/files/563203f6-6de5-46d9-b305-ba42604f2508/N2%20on%20food%20R_2010_03_25__10_53_27___4___1.hdf5","sha1":"088976277004081586186e81874dc28acc7ef5e7","sha256":"1e4e0025615eac7ebdd779a7d788234386b5d9e72717b2cb782ecf3f49639845","size":218752636,"status":"success"},{"md5":"f0ede89416863c9571eb9081d7dbc2ce","mimetype":"application/zip","path":"N2 on food R_2010_03_25__10_53_27___4___1.wcon.zip","platform_url":"https://zenodo.org/api/files/563203f6-6de5-46d9-b305-ba42604f2508/N2%20on%20food%20R_2010_03_25__10_53_27___4___1.wcon.zip","sha1":"efe9b640003725cb7e5dfd778ec50f242ada4651","sha256":"aedd1d5fd4a8857fa8dda294ec95a2ff473060402aadb4f068fe26b258ad5d71","size":15161284,"status":"success"}],"platform_base_url":null,"platform_domain":"zenodo.org","platform_id":"1028059","platform_name":"zenodo","request":{"base_url":"https://doi.org/10.5281/zenodo.1028059","ext_ids":{"doi":"10.5281/zenodo.1028059"},"fatcat":{"release_ident":"aaaaaaaaaaaaarceaaaaaaaaam","work_ident":"5ouiftuywfdzxagyow5e7o4tkm"},"ingest_request_source":"fatcat-ingest","ingest_type":"dataset","link_source":"doi","link_source_id":"10.5281/zenodo.1028059","release_stage":"published"},"status":"success","terminal":{"terminal_dt":"20200211074218","terminal_sha1hex":"6ffbc4a410b5a676658c690502b9e294c766bfe8","terminal_status_code":200,"terminal_url":"https://zenodo.org/record/1028059"},"total_size":250713670}
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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