import json import pytest from fixtures import * from fatcat_tools.importers import ( IngestFileResultImporter, IngestFilesetFileResultImporter, 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) @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: 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].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"] == 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