improve datacite field mapping and import

Current version succeeded to import a random sample of 100000 records
(0.5%) from datacite.

The --debug (write JSON to stdout) and --insert-log-file (log batch
before committing to db) flags are temporary added to help debugging.

Add few unit tests.

Some edge cases:

a) Existing keys without value requires a slightly awkward:

```
titles = attributes.get('titles', []) or []
```

b) There can be 0, 1, or more (first one wins) titles.

c) Date handling is probably not ideal. Datacite has a potentiall fine
grained list of dates.

The test case (tests/files/datacite_sample.jsonl) refers to
https://ssl.fao.org/glis/doi/10.18730/8DYM9, which has date (main
descriptor) 1986. The datacite record contains: 2017 (publicationYear,
probably the year of record creation with reference system), 1978-06-03
(collected, e.g. experimental sample), 1986 ("Accepted"). The online
version of the resource knows even one more date (2019-06-05 10:14:43 by
WIEWS update).

3 files changed, 92 insertions, 17 deletions

diff --git a/python/tests/files/datacite_1k_records.jsonl.gz b/python/tests/files/datacite_1k_records.jsonl.gz
new file mode 100644
index 00000000..28ea6e37
--- /dev/null
+++ b/python/tests/files/datacite_1k_records.jsonl.gz
diff --git a/python/tests/files/datacite_sample.jsonl b/python/tests/files/datacite_sample.jsonl
new file mode 100644
index 00000000..dba3e267
--- /dev/null
+++ b/python/tests/files/datacite_sample.jsonl
@@ -0,0 +1 @@
+{"id":"10.18730/8dym9","type":"dois","attributes":{"doi":"10.18730/8dym9","identifiers":[{"identifier":"https://doi.org/10.18730/8dym9","identifierType":"DOI"},{"identifier":"ICDW 20791","identifierType":"Other"}],"creators":[{"name":"GLIS Of The ITPGRFA","affiliation":[]}],"titles":[{"title":"Triticum turgidum L. subsp. durum (Desf.) Husn. 97090"}],"publisher":"International Centre for Agricultural Research in Dry Areas","container":{},"publicationYear":2017,"subjects":[{"subject":"Plant Genetic Resource for Food and Agriculture"}],"contributors":[{"name":"International Centre For Agricultural Research In Dry Areas","affiliation":[]}],"dates":[{"date":"1986","dateType":"Accepted"},{"date":"1978-06-03","dateType":"Collected"},{"date":"2017","dateType":"Issued"}],"language":"en","types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"CreativeWork","resourceType":"PGRFA Material","resourceTypeGeneral":"PhysicalObject"},"relatedIdentifiers":[{"schemeUri":"http://www.fao.org/plant-treaty/areas-of-work/global-information-system/descriptors","schemeType":"XML","relationType":"HasMetadata","relatedIdentifier":"https://ssl.fao.org/glisapi/v1/pgrfas?doi=10.18730/8DYM9","relatedIdentifierType":"URL","relatedMetadataScheme":"GLIS Descriptors"},{"schemeUri":"http://rs.tdwg.org/dwc/terms/guides/text/index.htm","schemeType":"DwC-A","relationType":"HasMetadata","relatedIdentifier":"https://ssl.fao.org/glisapi/v1/pgrfas?_format=dwc&doi=10.18730/8DYM9","relatedIdentifierType":"URL","relatedMetadataScheme":"Darwin Core Archive"}],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[{"description":"Plant Genetic Resource.<br>Taxonomy: Triticum turgidum L. subsp. durum (Desf.) Husn.<br>Common name(s): Wheat<br>Conserved by: International Centre for Agricultural Research in Dry Areas (ICARDA), Lebanon<br>Local sample unique identifier: 97090<br>Method of creation: Acquisition<br>Date: 1986<br>Biological status: Traditional cultivar/landrace<br>Other identifiers: ICDW 20791<br>MLS status: Included<br>Historical: No","descriptionType":"Abstract"}],"geoLocations":[{"geoLocationPlace":"Collecting site","geoLocationPoint":{"pointLatitude":"35.5","pointLongitude":"23.7333"}}],"fundingReferences":[],"url":"https://ssl.fao.org/glis/doi/10.18730/8DYM9","contentUrl":null,"metadataVersion":3,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"created":"2017-11-11T12:26:01.000Z","registered":"2017-11-11T12:26:02.000Z","published":"2017","updated":"2019-08-02T16:34:56.000Z"},"relationships":{"client":{"data":{"id":"fao.itpgrfa","type":"clients"}}}}
diff --git a/python/tests/import_datacite.py b/python/tests/import_datacite.py
index 0bbaba2e..9c542fc6 100644
--- a/python/tests/import_datacite.py
+++ b/python/tests/import_datacite.py
@@ -1,25 +1,99 @@
 """
 Test datacite importer.
+"""
 
-Datacite is a aggregator, hence inputs are quite varied.
+import datetime
+import pytest
+import gzip
+from fatcat_tools.importers import DataciteImporter, JsonLinePusher
+from fixtures import api
+import json
 
-Here is small sample of ID types taken from a sample:
 
-    497344 "DOI"
-     65013 "URL"
-     22210 "CCDC"
-     17853 "GBIF"
-     17635 "Other"
-     11474 "uri"
-      9170 "Publisher ID"
-      7775 "URN"
-      6196 "DUCHAS"
-      5624 "Handle"
-      5056 "publisherId"
+@pytest.fixture(scope="function")
+def datacite_importer(api):
+    with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
+        yield DataciteImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3',
+                               bezerk_mode=True)
 
-A nice tool, not yet existing tool (maybe named indigo) would do the following:
+@pytest.fixture(scope="function")
+def datacite_importer_existing(api):
+    with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
+        yield DataciteImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3',
+                               bezerk_mode=False)
 
-    $ shuf -n 100000 datacite.ndjson | indigo -t md > data.md
 
-TODO(martin): Write tests.
-"""
+@pytest.mark.skip(reason="larger datacite import slows tests down")
+def test_datacite_importer_huge(datacite_importer):
+    last_index = datacite_importer.api.get_changelog(limit=1)[0].index
+    with gzip.open('tests/files/datacite_1k_records.jsonl.gz', 'rt') as f:
+        datacite_importer.bezerk_mode = True
+        counts = JsonLinePusher(datacite_importer, f).run()
+    assert counts['insert'] == 998
+    change = datacite_importer.api.get_changelog_entry(index=last_index+1)
+    release = datacite_importer.api.get_release(change.editgroup.edits.releases[0].ident)
+    assert len(release.contribs) == 3
+
+
+def test_datacite_importer(datacite_importer):
+    last_index = datacite_importer.api.get_changelog(limit=1)[0].index
+    with open('tests/files/datacite_sample.jsonl', 'r') as f:
+        datacite_importer.bezerk_mode = True
+        counts = JsonLinePusher(datacite_importer, f).run()
+    assert counts['insert'] == 1
+    assert counts['exists'] == 0
+    assert counts['skip'] == 0
+
+    # fetch most recent editgroup
+    change = datacite_importer.api.get_changelog_entry(index=last_index+1)
+    eg = change.editgroup
+    assert eg.description
+    assert "datacite" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.DataciteImporter" in eg.extra['agent']
+
+    last_index = datacite_importer.api.get_changelog(limit=1)[0].index
+    with open('tests/files/datacite_sample.jsonl', 'r') as f:
+        datacite_importer.bezerk_mode = False
+        datacite_importer.reset()
+        counts = JsonLinePusher(datacite_importer, f).run()
+    assert counts['insert'] == 0
+    assert counts['exists'] == 1
+    assert counts['skip'] == 0
+    assert last_index == datacite_importer.api.get_changelog(limit=1)[0].index
+
+def test_datacite_dict_parse(datacite_importer):
+    with open('tests/files/datacite_sample.jsonl', 'r') as f:
+        raw = json.load(f)
+        r = datacite_importer.parse_record(raw)
+        # ensure the API server is ok with format
+        JsonLinePusher(datacite_importer, [json.dumps(raw)]).run()
+
+        print(r.extra)
+        assert r.title == "Triticum turgidum L. subsp. durum (Desf.) Husn. 97090"
+        assert r.publisher == "International Centre for Agricultural Research in Dry Areas"
+        assert r.release_type == "article"
+        assert r.release_stage == "published"
+        assert r.license_slug == None
+        assert r.original_title == "Triticum turgidum L. subsp. durum (Desf.) Husn. 97090"
+        assert r.ext_ids.doi == "10.18730/8dym9"
+        assert r.ext_ids.isbn13 == None
+        assert r.language == "enc"
+        assert r.subtitle == None
+        assert r.release_date == None
+        assert r.release_year == 1986
+        assert 'subtitle' not in r.extra
+        assert 'subtitle' not in r.extra['datacite']
+        assert 'funder' not in r.extra
+        assert 'funder' not in r.extra['datacite']
+        # matched by ISSN, so shouldn't be in there
+        #assert extra['container_name'] == "International Journal of Quantum Chemistry"
+        assert r.extra['datacite']['url'] == 'https://ssl.fao.org/glis/doi/10.18730/8DYM9'
+        assert r.extra['datacite']['subjects'] == [{'subject': 'Plant Genetic Resource for Food and Agriculture'}]
+        assert len(r.abstracts) == 1
+        assert len(r.abstracts[0].content) == 421
+        assert len(r.contribs) == 1
+        assert r.contribs[0].raw_name == "GLIS Of The ITPGRFA"
+        assert r.contribs[0].given_name == None
+        assert r.contribs[0].surname == None
+        assert len(r.refs) == 0