Merge branch 'bnewbold-xml-html-ingest' into 'master'

HTML webcapture ingest (and XML file ingest)

See merge request webgroup/fatcat!88

4 files changed, 69 insertions, 3 deletions

diff --git a/python/tests/files/example_ingest.json b/python/tests/files/example_ingest.json
index cea67fa7..a9791587 100644
--- a/python/tests/files/example_ingest.json
+++ b/python/tests/files/example_ingest.json
@@ -1,2 +1,2 @@
-{"file_meta": {"sha1hex": "00242a192acc258bdfdb151943419437f440c313", "md5hex": "f4de91152c7ab9fdc2a128f962faebff", "sha256hex": "ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362", "size_bytes": 255629, "mimetype": "application/pdf"}, "request": {"ingest_request_source": "fatcat-changelog", "link_source": "doi", "link_source_id":"10.123/abc","ext_ids": {"doi": "10.123/abc"}}, "terminal": {"terminal_url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable", "terminal_dt": "20170227164644", "terminal_sha1hex": "00242a192acc258bdfdb151943419437f440c313"}, "cdx": { "datetime": "20170227164644", "url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable" }, "grobid": {"status_code": 200 }, "hit": true, "status": "success"}
+{"file_meta": {"sha1hex": "00242a192acc258bdfdb151943419437f440c313", "md5hex": "f4de91152c7ab9fdc2a128f962faebff", "sha256hex": "ffc1005680cb620eec4c913437dfabbf311b535cfe16cbaeb2faec1f92afc362", "size_bytes": 255629, "mimetype": "application/pdf"}, "request": {"ingest_type": "pdf", "ingest_request_source": "fatcat-changelog", "link_source": "doi", "link_source_id":"10.123/abc","ext_ids": {"doi": "10.123/abc"}}, "terminal": {"terminal_url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable", "terminal_dt": "20170227164644", "terminal_sha1hex": "00242a192acc258bdfdb151943419437f440c313"}, "cdx": { "datetime": "20170227164644", "url": "http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.0020124&type=printable" }, "grobid": {"status_code": 200 }, "hit": true, "status": "success"}
 {"request":{"ingest_type":"pdf","ingest_request_source":"fatcat-changelog","base_url":"https://doi.org/10.3917/popav.748.0017","release_stage":"published","fatcat":{"release_ident":"weeqjkvsx5abze2bhithyrx6wu","work_ident":"ujatsk25yrdw5gofubw7nogzgq"},"ext_ids":{"doi":"10.3917/popav.748.0017"},"link_source":"doi","link_source_id":"10.3917/popav.748.0017"},"hit":false,"hops":["https://doi.org/10.3917/popav.748.0017"],"status":"wayback-error","error_message":"replay fetch didn't return X-Archive-Src in headers"}
diff --git a/python/tests/files/example_ingest_html.json b/python/tests/files/example_ingest_html.json
new file mode 100644
index 00000000..6c646814
--- /dev/null
+++ b/python/tests/files/example_ingest_html.json
@@ -0,0 +1 @@
+{"cdx": {"datetime": "20200708025309", "mimetype": "text/html", "sha1b32": "THJFFZJR2VYN2FAR7X7LHFGRU2X5IC2U", "sha1hex": "99d252e531d570dd1411fdfeb394d1a6afd40b54", "status_code": 200, "surt": "py,una,iics,scielo)/scielo.php?lng=en&nrm=iso&pid=s1683-98032015000200002&script=sci_arttext&tlng=es", "url": "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es", "warc_csize": 13123, "warc_offset": 77579308, "warc_path": "SCIELO-CRAWL-2020-07-20200707211940442-00279-00347-wbgrp-svc206/SCIELO-CRAWL-2020-07-20200708024511243-00332-13069~wbgrp-svc206.us.archive.org~8443.warc.gz"}, "file_meta": {"md5hex": "515a61845a2f898438e3986e4506da8f", "mimetype": "text/html", "sha1hex": "99d252e531d570dd1411fdfeb394d1a6afd40b54", "sha256hex": "c4559d548476a325891461b71c796beee717e820d6a00cb8411176ce83a0f23f", "size_bytes": 47442}, "hit": true, "hops": ["http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es"], "html_biblio": {"container_issn": "1683-9803", "container_name": "Pediatr\u00eda (Asunci\u00f3n)", "contrib_names": ["Ruiz Valiente, Syntia Carolina", "Ruiz Ca\u00f1ete, Manuel", "Cohene Velazquez, Bartola"], "doi": "10.18004/ped.2015.agosto.102-107", "first_page": "102", "html_fulltext_url": "http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=es", "issue": "2", "last_page": "107", "pdf_fulltext_url": "http://scielo.iics.una.py/pdf/ped/v42n2/v42n2a02.pdf", "publisher": "Sociedad Paraguaya de Pediatr\u00eda", "release_date": "2015-08-06", "title": "Prevalence of malnutrition and eating habits in children under 5 years of age in indigenous communities in Azote'y and Yby Yau, 2011", "volume": "42", "xml_fulltext_url": "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en"}, "html_body": {"agent": "trafilatura/0.5.1", "status": "success", "word_count": 3500}, "html_resources": [{"mimetype": "image/gif", "resource_type": "image", "sha1hex": "4991aa771874daf8cba79be38d18d534f946b5d6", "sha256hex": "5e76fad755b873a439dd5e775684696c547008d45cc901606132e9a1ed970757", "size": 220, "status_code": 200, "surt": "py,una,iics,scielo)/img/en/alpha.gif", "timestamp": "2020-10-31T14:07:30", "url": "http://scielo.iics.una.py/img/en/alpha.gif"}, {"mimetype": "text/plain", "resource_type": "script", "sha1hex": "fd28e342fa1b40b84cc17dc66d22df3bf260170b", "sha256hex": "9cf2e81dd65d5a64200970bbd1cd9497b46b2af232e2fbfb79fef95b070f23d1", "size": 3653, "status_code": 200, "surt": "py,una,iics,scielo)/applications/scielo-org/js/toolbox.js", "timestamp": "2020-10-31T20:14:35", "url": "http://scielo.iics.una.py/applications/scielo-org/js/toolbox.js"}, {"mimetype": "image/gif", 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diff --git a/python/tests/files/example_ingest_xml.json b/python/tests/files/example_ingest_xml.json
new file mode 100644
index 00000000..2f525998
--- /dev/null
+++ b/python/tests/files/example_ingest_xml.json
@@ -0,0 +1 @@
+{"cdx": {"datetime": "20200710091403", "mimetype": "text/xml", "sha1b32": "PWMQ2L4RHPJ3NVWC66GIJC36L5FXPOM6", "sha1hex": "7d990d2f913bd3b6d6c2f78c848b7e5f4b77b99e", "status_code": 200, "surt": "py,una,iics,scielo)/scieloorg/php/articlexml.php?lang=en&pid=s1683-98032015000200002", "url": "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en", "warc_csize": 12108, "warc_offset": 94730348, "warc_path": "SCIELO-CRAWL-2020-07-20200710082036515-00773-00843-wbgrp-svc206/SCIELO-CRAWL-2020-07-20200710085423121-00779-13069~wbgrp-svc206.us.archive.org~8443.warc.gz"}, "file_meta": {"md5hex": "cda133a706ce02a07fae8bd8d2694a2a", "mimetype": "application/jats+xml", "sha1hex": "7d990d2f913bd3b6d6c2f78c848b7e5f4b77b99e", "sha256hex": "be982ca211e4debb3f93f36d9f9dc1c80f99a8809eb4c41569b2b9503c27e751", "size_bytes": 49242}, "hit": true, "hops": ["http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en"], "request": {"link_source": "doi", "ingest_request_source": "fatcat-changelog","base_url": "http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso&tlng=en", "ext_ids": {"doi": "10.123/abc"}, "fatcat": {"release_ident": null}, "ingest_type": "xml"}, "status": "success", "terminal": {"terminal_dt": "20200710091403", "terminal_sha1hex": "7d990d2f913bd3b6d6c2f78c848b7e5f4b77b99e", "terminal_status_code": 200, "terminal_url": "http://scielo.iics.una.py/scieloOrg/php/articleXML.php?pid=S1683-98032015000200002&lang=en"}, "xml_meta": {"status": "success"}}
diff --git a/python/tests/import_ingest.py b/python/tests/import_ingest.py
index 4a46232a..92539f1a 100644
--- a/python/tests/import_ingest.py
+++ b/python/tests/import_ingest.py
@@ -2,7 +2,7 @@
 import json
 import pytest
 
-from fatcat_tools.importers import IngestFileResultImporter, JsonLinePusher
+from fatcat_tools.importers import IngestFileResultImporter, IngestWebResultImporter, JsonLinePusher
 from fixtures import *
 
 
@@ -10,6 +10,10 @@ from fixtures import *
 def ingest_importer(api):
     yield IngestFileResultImporter(api)
 
+@pytest.fixture(scope="function")
+def ingest_web_importer(api):
+    yield IngestWebResultImporter(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:
@@ -41,6 +45,60 @@ def test_ingest_importer(ingest_importer):
     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()
+    print(counts)
+    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()
+    print(counts)
+    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
@@ -57,7 +115,7 @@ def test_ingest_importer_stage(ingest_importer, api):
     with open('tests/files/example_ingest.json', 'r') as f:
         raw = json.loads(f.readline())
     for row in test_table:
-        print(row)
+        #print(row)
 
         # set dummy record stage
         eg = quick_eg(api)
@@ -94,6 +152,12 @@ def test_ingest_dict_parse(ingest_importer):
 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 == None
+        raw['request']['ingest_type'] = 'pdf'
+
         f = ingest_importer.parse_record(raw)
         assert f.sha1 == "00242a192acc258bdfdb151943419437f440c313"
         assert f.md5 == "f4de91152c7ab9fdc2a128f962faebff"