Merge branch 'bnewbold-crude-auth'

Fixed a conflict in:
  python/fatcat_export.py

12 files changed, 191 insertions, 16 deletions

diff --git a/python/tests/cli.sh b/python/tests/cli.sh
new file mode 100755
index 00000000..eba6d3a7
--- /dev/null
+++ b/python/tests/cli.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+set -eu -o pipefail
+set -x
+
+# This is a helper script to at least partially exersize the fatcat_*.py
+# scripts. It expects to be run from the top-level directory, inside a 'pipenv
+# shell' or 'pipenv run' invocation.
+
+./fatcat_export.py changelog --start 1 --end 10 - > /dev/null
+
+# no easy way to run this without harvest a whole day (at the moment)
+./fatcat_harvest.py crossref -h
+
+./fatcat_import.py crossref tests/files/crossref-works.2018-01-21.badsample.json tests/files/ISSN-to-ISSN-L.snip.txt
+./fatcat_import.py orcid tests/files/0000-0001-8254-7103.json
+./fatcat_import.py issn tests/files/journal_extra_metadata.snip.csv
+./fatcat_import.py matched tests/files/matched_sample.json
+./fatcat_import.py matched tests/files/example_matched.json
+./fatcat_import.py grobid-metadata tests/files/example_grobid_metadata_lines.tsv
+
+./fatcat_webface.py -h
+./fatcat_worker.py -h
+
+set +x
+echo "Done running CLI examples (SUCCESS)"
diff --git a/python/tests/codegen_tests/test_auth_oidc.py b/python/tests/codegen_tests/test_auth_oidc.py
new file mode 100644
index 00000000..f799da55
--- /dev/null
+++ b/python/tests/codegen_tests/test_auth_oidc.py
@@ -0,0 +1,40 @@
+# coding: utf-8
+
+"""
+    fatcat
+
+    A scalable, versioned, API-oriented catalog of bibliographic entities and file metadata  # noqa: E501
+
+    OpenAPI spec version: 0.1.0
+    
+    Generated by: https://github.com/swagger-api/swagger-codegen.git
+"""
+
+
+from __future__ import absolute_import
+
+import unittest
+
+import fatcat_client
+from fatcat_client.models.auth_oidc import AuthOidc  # noqa: E501
+from fatcat_client.rest import ApiException
+
+
+class TestAuthOidc(unittest.TestCase):
+    """AuthOidc unit test stubs"""
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def testAuthOidc(self):
+        """Test AuthOidc"""
+        # FIXME: construct object with mandatory attributes with example values
+        # model = fatcat_client.models.auth_oidc.AuthOidc()  # noqa: E501
+        pass
+
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/python/tests/codegen_tests/test_auth_oidc_result.py b/python/tests/codegen_tests/test_auth_oidc_result.py
new file mode 100644
index 00000000..d99ef446
--- /dev/null
+++ b/python/tests/codegen_tests/test_auth_oidc_result.py
@@ -0,0 +1,40 @@
+# coding: utf-8
+
+"""
+    fatcat
+
+    A scalable, versioned, API-oriented catalog of bibliographic entities and file metadata  # noqa: E501
+
+    OpenAPI spec version: 0.1.0
+    
+    Generated by: https://github.com/swagger-api/swagger-codegen.git
+"""
+
+
+from __future__ import absolute_import
+
+import unittest
+
+import fatcat_client
+from fatcat_client.models.auth_oidc_result import AuthOidcResult  # noqa: E501
+from fatcat_client.rest import ApiException
+
+
+class TestAuthOidcResult(unittest.TestCase):
+    """AuthOidcResult unit test stubs"""
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def testAuthOidcResult(self):
+        """Test AuthOidcResult"""
+        # FIXME: construct object with mandatory attributes with example values
+        # model = fatcat_client.models.auth_oidc_result.AuthOidcResult()  # noqa: E501
+        pass
+
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/python/tests/codegen_tests/test_default_api.py b/python/tests/codegen_tests/test_default_api.py
index ebc66cda..9a632824 100644
--- a/python/tests/codegen_tests/test_default_api.py
+++ b/python/tests/codegen_tests/test_default_api.py
@@ -35,6 +35,18 @@ class TestDefaultApi(unittest.TestCase):
         """
         pass
 
+    def test_auth_check(self):
+        """Test case for auth_check
+
+        """
+        pass
+
+    def test_auth_oidc(self):
+        """Test case for auth_oidc
+
+        """
+        pass
+
     def test_create_container(self):
         """Test case for create_container
 
@@ -515,6 +527,12 @@ class TestDefaultApi(unittest.TestCase):
         """
         pass
 
+    def test_update_editor(self):
+        """Test case for update_editor
+
+        """
+        pass
+
     def test_update_file(self):
         """Test case for update_file
 
diff --git a/python/tests/fixtures.py b/python/tests/fixtures.py
index 567e9132..6a880c48 100644
--- a/python/tests/fixtures.py
+++ b/python/tests/fixtures.py
@@ -4,12 +4,14 @@ import time
 import json
 import signal
 import pytest
+from dotenv import load_dotenv
 import fatcat_web
 import fatcat_client
 
 
 @pytest.fixture
 def full_app():
+    load_dotenv(dotenv_path="./env.example")
     fatcat_web.app.testing = True
     fatcat_web.app.debug = False
     return fatcat_web.app
@@ -20,8 +22,11 @@ def app(full_app):
 
 @pytest.fixture
 def api():
+    load_dotenv(dotenv_path="./env.example")
     conf = fatcat_client.Configuration()
     conf.host = "http://localhost:9411/v0"
+    conf.api_key["Authorization"] = os.getenv("FATCAT_API_AUTH_TOKEN")
+    conf.api_key_prefix["Authorization"] = "Bearer"
     api_client = fatcat_client.DefaultApi(fatcat_client.ApiClient(conf))
     return api_client
 
diff --git a/python/tests/import_crossref.py b/python/tests/import_crossref.py
index 1fb4a70f..e2ca6122 100644
--- a/python/tests/import_crossref.py
+++ b/python/tests/import_crossref.py
@@ -2,17 +2,18 @@
 import json
 import pytest
 from fatcat_tools.importers import CrossrefImporter
+from fixtures import api
 
 
 @pytest.fixture(scope="function")
-def crossref_importer():
+def crossref_importer(api):
     with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
-        yield CrossrefImporter("http://localhost:9411/v0", issn_file, 'tests/files/example_map.sqlite3', check_existing=False)
+        yield CrossrefImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', check_existing=False)
 
 @pytest.fixture(scope="function")
-def crossref_importer_existing():
+def crossref_importer_existing(api):
     with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
-        yield CrossrefImporter("http://localhost:9411/v0", issn_file, 'tests/files/example_map.sqlite3', check_existing=True)
+        yield CrossrefImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', check_existing=True)
 
 def test_crossref_importer_batch(crossref_importer):
     with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f:
@@ -21,6 +22,13 @@ def test_crossref_importer_batch(crossref_importer):
 def test_crossref_importer(crossref_importer):
     with open('tests/files/crossref-works.2018-01-21.badsample.json', 'r') as f:
         crossref_importer.process_source(f)
+    # fetch most recent editgroup
+    changes = crossref_importer.api.get_changelog(limit=1)
+    eg = changes[0].editgroup
+    assert eg.description
+    assert "crossref" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.CrossrefImporter" in eg.extra['agent']
 
 def test_crossref_mappings(crossref_importer):
     assert crossref_importer.map_release_type('journal-article') == "article-journal"
diff --git a/python/tests/import_grobid_metadata.py b/python/tests/import_grobid_metadata.py
index 459b247b..97ebcaef 100644
--- a/python/tests/import_grobid_metadata.py
+++ b/python/tests/import_grobid_metadata.py
@@ -4,6 +4,7 @@ import json
 import base64
 import pytest
 from fatcat_tools.importers import GrobidMetadataImporter
+from fixtures import api
 
 """
 WARNING: these tests are currently very fragile because they have database
@@ -11,8 +12,8 @@ side-effects. Should probably be disabled or re-written.
 """
 
 @pytest.fixture(scope="function")
-def grobid_metadata_importer():
-    yield GrobidMetadataImporter("http://localhost:9411/v0")
+def grobid_metadata_importer(api):
+    yield GrobidMetadataImporter(api)
 
 # TODO: use API to check that entities actually created...
 #def test_grobid_metadata_importer_batch(grobid_metadata_importer):
@@ -54,3 +55,11 @@ def test_file_metadata_parse(grobid_metadata_importer):
 def test_grobid_metadata_importer(grobid_metadata_importer):
     with open('tests/files/example_grobid_metadata_lines.tsv', 'r') as f:
         grobid_metadata_importer.process_source(f)
+
+    # fetch most recent editgroup
+    changes = grobid_metadata_importer.api.get_changelog(limit=1)
+    eg = changes[0].editgroup
+    assert eg.description
+    assert "grobid" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.GrobidMetadataImporter" in eg.extra['agent']
diff --git a/python/tests/import_issn.py b/python/tests/import_issn.py
index 98a9f4a7..6b5978d9 100644
--- a/python/tests/import_issn.py
+++ b/python/tests/import_issn.py
@@ -1,11 +1,12 @@
 
 import pytest
 from fatcat_tools.importers import IssnImporter
+from fixtures import api
 
 
 @pytest.fixture(scope="function")
-def issn_importer():
-    yield IssnImporter("http://localhost:9411/v0")
+def issn_importer(api):
+    yield IssnImporter(api)
 
 # TODO: use API to check that entities actually created...
 def test_issn_importer_batch(issn_importer):
@@ -15,3 +16,11 @@ def test_issn_importer_batch(issn_importer):
 def test_issn_importer(issn_importer):
     with open('tests/files/journal_extra_metadata.snip.csv', 'r') as f:
         issn_importer.process_csv_source(f)
+
+    # fetch most recent editgroup
+    changes = issn_importer.api.get_changelog(limit=1)
+    eg = changes[0].editgroup
+    assert eg.description
+    assert "container" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.IssnImporter" in eg.extra['agent']
diff --git a/python/tests/import_matched.py b/python/tests/import_matched.py
index 46a9ef85..080674ac 100644
--- a/python/tests/import_matched.py
+++ b/python/tests/import_matched.py
@@ -2,11 +2,12 @@
 import json
 import pytest
 from fatcat_tools.importers import MatchedImporter
+from fixtures import api
 
 
 @pytest.fixture(scope="function")
-def matched_importer():
-    yield MatchedImporter("http://localhost:9411/v0")
+def matched_importer(api):
+    yield MatchedImporter(api)
 
 # TODO: use API to check that entities actually created...
 def test_matched_importer_batch(matched_importer):
@@ -17,6 +18,14 @@ def test_matched_importer(matched_importer):
     with open('tests/files/example_matched.json', 'r') as f:
         matched_importer.process_source(f)
 
+    # fetch most recent editgroup
+    changes = matched_importer.api.get_changelog(limit=1)
+    eg = changes[0].editgroup
+    assert eg.description
+    assert "file-to-release" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.MatchedImporter" in eg.extra['agent']
+
 def test_matched_dict_parse(matched_importer):
     with open('tests/files/example_matched.json', 'r') as f:
         raw = json.loads(f.readline())
diff --git a/python/tests/import_orcid.py b/python/tests/import_orcid.py
index 18199888..717a1328 100644
--- a/python/tests/import_orcid.py
+++ b/python/tests/import_orcid.py
@@ -2,11 +2,12 @@
 import json
 import pytest
 from fatcat_tools.importers import OrcidImporter
+from fixtures import api
 
 
 @pytest.fixture(scope="function")
-def orcid_importer():
-    yield OrcidImporter("http://localhost:9411/v0")
+def orcid_importer(api):
+    yield OrcidImporter(api)
 
 # TODO: use API to check that entities actually created...
 def test_orcid_importer_batch(orcid_importer):
@@ -21,6 +22,14 @@ def test_orcid_importer(orcid_importer):
     with open('tests/files/0000-0001-8254-7103.json', 'r') as f:
         orcid_importer.process_source(f)
 
+    # fetch most recent editgroup
+    changes = orcid_importer.api.get_changelog(limit=1)
+    eg = changes[0].editgroup
+    assert eg.description
+    assert "orcid" in eg.description.lower()
+    assert eg.extra['git_rev']
+    assert "fatcat_tools.OrcidImporter" in eg.extra['agent']
+
 def test_orcid_importer_x(orcid_importer):
     with open('tests/files/0000-0003-3953-765X.json', 'r') as f:
         orcid_importer.process_source(f)
diff --git a/python/tests/importer.py b/python/tests/importer.py
index f228a9b2..34efa5d8 100644
--- a/python/tests/importer.py
+++ b/python/tests/importer.py
@@ -2,11 +2,12 @@
 
 import pytest
 from fatcat_tools.importers import FatcatImporter
+from fixtures import api
 
 
-def test_issnl_mapping_lookup():
+def test_issnl_mapping_lookup(api):
     with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
-        fi = FatcatImporter("http://localhost:9411/v0", issn_file)
+        fi = FatcatImporter(api, issn_map_file=issn_file)
 
     assert fi.issn2issnl('0000-0027') == '0002-0027'
     assert fi.issn2issnl('0002-0027') == '0002-0027'
@@ -14,10 +15,10 @@ def test_issnl_mapping_lookup():
 
     assert fi.lookup_issnl('9999-9999') == None
 
-def test_identifiers():
+def test_identifiers(api):
 
     with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file:
-        fi = FatcatImporter("http://localhost:9411/v0", issn_file)
+        fi = FatcatImporter(api, issn_map_file=issn_file)
 
     assert fi.is_issnl("1234-5678") == True
     assert fi.is_issnl("1234-5678.") == False
diff --git a/python/tests/transform_tests.py b/python/tests/transform_tests.py
index a42db244..e9d23250 100644
--- a/python/tests/transform_tests.py
+++ b/python/tests/transform_tests.py
@@ -3,6 +3,7 @@ import json
 import pytest
 from fatcat_tools import *
 from fatcat_client import *
+from fixtures import api
 
 from import_crossref import crossref_importer