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import json
import pytest
from fixtures import *
from fatcat_tools.importers import (
IngestFileResultImporter,
IngestFilesetResultImporter,
IngestWebResultImporter,
JsonLinePusher,
)
@pytest.fixture(scope="function")
def ingest_importer(api):
yield IngestFileResultImporter(api)
@pytest.fixture(scope="function")
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:
JsonLinePusher(ingest_importer, f).run()
def test_ingest_importer(ingest_importer):
last_index = ingest_importer.api.get_changelog(limit=1)[0].index
with open("tests/files/example_ingest.json", "r") as f:
ingest_importer.bezerk_mode = True
counts = JsonLinePusher(ingest_importer, f).run()
assert counts["insert"] == 1
assert counts["exists"] == 0
assert counts["skip"] == 1
# fetch most recent editgroup
change = ingest_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.IngestFileResultImporter" in eg.extra["agent"]
# re-insert; should skip
with open("tests/files/example_ingest.json", "r") as f:
ingest_importer.reset()
ingest_importer.bezerk_mode = False
counts = JsonLinePusher(ingest_importer, f).run()
assert counts["insert"] == 0
assert counts["exists"] == 1
assert counts["skip"] == 1
def test_ingest_importer_xml(ingest_importer):
last_index = ingest_importer.api.get_changelog(limit=1)[0].index
with open("tests/files/example_ingest_xml.json", "r") as f:
ingest_importer.bezerk_mode = True
counts = JsonLinePusher(ingest_importer, f).run()
assert counts["insert"] == 1
assert counts["exists"] == 0
assert counts["skip"] == 0
# fetch most recent editgroup
change = ingest_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.IngestFileResultImporter" in eg.extra["agent"]
# re-import should skip
with open("tests/files/example_ingest_xml.json", "r") as f:
ingest_importer.reset()
ingest_importer.bezerk_mode = False
counts = JsonLinePusher(ingest_importer, f).run()
assert counts["insert"] == 0
assert counts["exists"] == 1
assert counts["skip"] == 0
def test_ingest_importer_web(ingest_web_importer):
last_index = ingest_web_importer.api.get_changelog(limit=1)[0].index
with open("tests/files/example_ingest_html.json", "r") as f:
ingest_web_importer.bezerk_mode = True
counts = JsonLinePusher(ingest_web_importer, f).run()
assert counts["insert"] == 1
assert counts["exists"] == 0
assert counts["skip"] == 0
# fetch most recent editgroup
change = ingest_web_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.IngestWebResultImporter" in eg.extra["agent"]
# re-import should skip
with open("tests/files/example_ingest_html.json", "r") as f:
ingest_web_importer.reset()
ingest_web_importer.bezerk_mode = False
counts = JsonLinePusher(ingest_web_importer, f).run()
assert counts["insert"] == 0
assert counts["exists"] == 1
assert counts["skip"] == 0
def test_ingest_importer_stage(ingest_importer, api):
"""
Tests that ingest importer correctly handles release stage matching
"""
test_table = [
dict(request_stage=None, release_stage=None, status="insert"),
dict(request_stage="published", release_stage=None, status="insert"),
dict(request_stage=None, release_stage="draft", status="insert"),
dict(request_stage="published", release_stage="published", status="insert"),
dict(request_stage="draft", release_stage="published", status="skip-release-stage"),
dict(request_stage="published", release_stage="draft", status="skip-release-stage"),
]
ingest_importer.bezerk_mode = True
with open("tests/files/example_ingest.json", "r") as f:
raw = json.loads(f.readline())
for row in test_table:
# print(row)
# set dummy record stage
eg = quick_eg(api)
r1 = api.lookup_release(doi="10.123/abc")
r1.release_stage = row["release_stage"]
api.update_release(eg.editgroup_id, r1.ident, r1)
api.accept_editgroup(eg.editgroup_id)
# set ingest request stage
raw["request"]["release_stage"] = row["request_stage"]
ingest_importer.reset()
ingest_importer.push_record(raw)
counts = ingest_importer.finish()
assert counts["total"] == 1
assert counts[row["status"]] == 1
def test_ingest_dict_parse(ingest_importer):
with open("tests/files/example_ingest.json", "r") as f:
raw = json.loads(f.readline())
f = ingest_importer.parse_record(raw)
assert f.sha1 == "00242a192acc258bdfdb151943419437f440c313"
assert f.md5 == "f4de91152c7ab9fdc2a128f962faebff"
assert f.mimetype == "application/pdf"
assert f.size == 255629
assert len(f.urls) == 2
for u in f.urls:
if u.rel == "web":
assert u.url.startswith("http://journals.plos.org")
if u.rel == "webarchive":
assert u.url.startswith("https://web.archive.org/")
assert len(f.release_ids) == 1
def test_ingest_dict_parse_old(ingest_importer):
with open("tests/files/example_ingest.old.json", "r") as f:
raw = json.loads(f.readline())
# ancient ingest requests had no type; skip them
f = ingest_importer.parse_record(raw)
assert f is None
raw["request"]["ingest_type"] = "pdf"
f = ingest_importer.parse_record(raw)
assert f.sha1 == "00242a192acc258bdfdb151943419437f440c313"
assert f.md5 == "f4de91152c7ab9fdc2a128f962faebff"
assert f.mimetype == "application/pdf"
assert f.size == 255629
assert len(f.urls) == 2
for u in f.urls:
if u.rel == "web":
assert u.url.startswith("http://journals.plos.org")
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
|
