Merge branch 'martin-kafka-bs4-import' into 'master'

pubmed and arxiv harvest preparations

See merge request webgroup/fatcat!28

3 files changed, 80 insertions, 0 deletions

diff --git a/python/tests/files/pubmedsample_2019.xml.gz b/python/tests/files/pubmedsample_2019.xml.gz
new file mode 100644
index 00000000..bafad833
--- /dev/null
+++ b/python/tests/files/pubmedsample_2019.xml.gz
diff --git a/python/tests/files/pubmedsample_no_pmid_2019.xml.gz b/python/tests/files/pubmedsample_no_pmid_2019.xml.gz
new file mode 100644
index 00000000..8785a06d
--- /dev/null
+++ b/python/tests/files/pubmedsample_no_pmid_2019.xml.gz
diff --git a/python/tests/harvest_pubmed.py b/python/tests/harvest_pubmed.py
new file mode 100644
index 00000000..f8db46b6
--- /dev/null
+++ b/python/tests/harvest_pubmed.py
@@ -0,0 +1,80 @@
+"""
+Test pubmed FTP harvest.
+"""
+
+import datetime
+import json
+import os
+
+import pytest
+
+from fatcat_tools.harvest import *
+from fatcat_tools.harvest.pubmed import generate_date_file_map
+
+
+def test_pubmed_harvest_date(mocker):
+
+    # mock out the harvest state object so it doesn't try to actually connect
+    # to Kafka
+    mocker.patch('fatcat_tools.harvest.harvest_common.HarvestState.initialize_from_kafka')
+
+    # Mocking a file fetched from FTP, should contain some 'PubmedArticle' elements.
+    # $ zcat tests/files/pubmedsample_2019.xml.gz | grep -c '<PubmedArticle>'
+    # 176
+    file_to_retrieve = os.path.join(os.path.dirname(__file__), 'files/pubmedsample_2019.xml.gz')
+    ftpretr = mocker.patch('fatcat_tools.harvest.pubmed.ftpretr')
+    ftpretr.return_value = file_to_retrieve
+
+    test_date = '2020-02-20'
+
+    # We'll need one entry in the date_file_map.
+    generate_date_file_map = mocker.patch('fatcat_tools.harvest.pubmed.generate_date_file_map')
+    generate_date_file_map.return_value = {test_date: set(['dummy'])}
+
+    # For cleanup.
+    os.remove = mocker.Mock()
+
+    harvester = PubmedFTPWorker(
+        kafka_hosts="dummy",
+        produce_topic="dummy-produce-topic",
+        state_topic="dummy-state-topic",
+    )
+
+    harvester.producer = mocker.Mock()
+    harvester.date_file_map = generate_date_file_map()
+    # Since we mock out the FTP fetch, the concrete date does not matter here.
+    harvester.fetch_date(datetime.datetime.strptime(test_date, '%Y-%m-%d'))
+
+    # check that we published the expected number of DOI objects were published
+    # to the (mock) kafka topic
+    assert harvester.producer.produce.call_count == 176
+    assert harvester.producer.flush.call_count == 1
+    assert os.remove.call_count == 2
+
+def test_pubmed_harvest_date_no_pmid(mocker):
+    # mock out the harvest state object so it doesn't try to actually connect
+    # to Kafka
+    mocker.patch('fatcat_tools.harvest.harvest_common.HarvestState.initialize_from_kafka')
+
+    file_to_retrieve = os.path.join(os.path.dirname(__file__), 'files/pubmedsample_no_pmid_2019.xml.gz')
+    ftpretr = mocker.patch('fatcat_tools.harvest.pubmed.ftpretr')
+    ftpretr.return_value = file_to_retrieve
+
+    test_date = '2020-02-20'
+
+    # We'll need one entry in the date_file_map.
+    generate_date_file_map = mocker.patch('fatcat_tools.harvest.pubmed.generate_date_file_map')
+    generate_date_file_map.return_value = {test_date: set(['dummy'])}
+
+    harvester = PubmedFTPWorker(
+        kafka_hosts="dummy",
+        produce_topic="dummy-produce-topic",
+        state_topic="dummy-state-topic",
+    )
+
+    harvester.producer = mocker.Mock()
+
+    # The file has not PMID, not importable.
+    with pytest.raises(ValueError):
+        harvester.fetch_date(datetime.datetime.strptime(test_date, '%Y-%m-%d'))
+