Update

academic_observatory_workflows/workflows/tests/test_orcid_telescope.py

@@ -0,0 +1,192 @@
+# Copyright 2023 Curtin University
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+# Author: Keegan Smith
+
+from __future__ import annotations
+
+import copy
+import datetime
+import gzip
+import json
+import os
+import pathlib
+import csv
+import shutil
+import tempfile
+from typing import Dict
+from unittest.mock import patch
+
+import pendulum
+from airflow.models import Connection
+from airflow.utils.state import State
+from google.cloud import storage
+
+from academic_observatory_workflows.config import test_fixtures_folder
+from academic_observatory_workflows.workflows.orcid_telescope import (
+    OrcidBatch,
+    OrcidRelease,
+    OrcidTelescope,
+    create_orcid_batch_manifest,
+    gsutil_download,
+    latest_modified_record_date,
+    orcid_batch_names,
+    gcs_list_blobs,
+    transform_orcid_record,
+)
+from observatory.platform.api import get_dataset_releases
+from observatory.platform.bigquery import bq_table_id, bq_sharded_table_id
+from observatory.platform.files import save_jsonl_gz, load_file
+from observatory.platform.gcs import gcs_blob_name_from_path
+from observatory.platform.observatory_config import Workflow, CloudWorkspace
+from observatory.platform.observatory_environment import (
+    ObservatoryEnvironment,
+    ObservatoryTestCase,
+    aws_bucket_test_env,
+    find_free_port,
+    load_and_parse_json,
+    random_id,
+)
+
+
+class TestOrcidUtils(ObservatoryTestCase):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.dag_id = "orcid"
+        self.aws_key = (os.getenv("AWS_ACCESS_KEY_ID"), os.getenv("AWS_SECRET_ACCESS_KEY"))
+        self.aws_region_name = os.getenv("AWS_DEFAULT_REGION")
+        self.fixtures_folder = test_fixtures_folder("orcid")
+
+    def test_orcid_batch(self):
+        """Test that the orcid batches are correctly constructed"""
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            download_dir = os.path.join(tmp_dir, "download")
+            transform_dir = os.path.join(tmp_dir, "transform")
+            test_batch_str = "12X"
+
+            # Download/transform dirs don't exist
+            with self.assertRaises(AssertionError):
+                OrcidBatch(download_dir, transform_dir, test_batch_str)
+            shutil.makedirs(download_dir)
+            with self.assertRaises(AssertionError):
+                OrcidBatch(download_dir, transform_dir, test_batch_str)
+            shutil.makedirs(transform_dir)
+
+            # Invalid batch string
+            for batch_str in ["0000", "12C", "99", "XXX"]:
+                with self.assertRaises(AssertionError):
+                    OrcidBatch(download_dir, transform_dir, batch_str)
+
+            # Create a batch for testing
+            test_batch = OrcidBatch(download_dir, transform_dir, test_batch_str)
+
+            # Check that expected folders exist
+            self.assertTrue(os.path.isdir(test_batch.download_dir))
+
+            # Check that file names are as expected
+            self.assertEqual(test_batch.download_batch_dir, os.path.join(download_dir, test_batch_str))
+            self.assertEqual(test_batch.download_log_file, os.path.join(download_dir, f"{test_batch_str}_log.txt"))
+            self.assertEqual(test_batch.download_error_file, os.path.join(download_dir, f"{test_batch_str}_error.txt"))
+            self.assertEqual(test_batch.manifest_file, os.path.join(download_dir, f"{test_batch_str}_manifest.csv"))
+            self.assertEqual(
+                test_batch.transform_upsert_file, os.path.join(download_dir, f"{test_batch_str}_upsert.jsonl.gz")
+            )
+            self.assertEqual(
+                test_batch.transform_delete_file, os.path.join(download_dir, f"{test_batch_str}_delete.jsonl.gz")
+            )
+
+            # Make the manifest file
+            shutil.copy(os.path.join(self.fixtures_folder, "manifest.csv"), test_batch.manifest_file)
+
+            # Check that missing, expected and existing records are correctly identified
+            records = [
+                "0000-0001-5000-5000.xml",
+                "0000-0001-5001-3000.xml",
+                "0000-0001-5002-1000.xml",
+                "0000-0001-5007-2000.xml",
+                "0000-0001-5010-1000.xml",
+            ]
+            self.assertEqual(set(test_batch.expected_records), set(records))
+            self.assertEqual(test_batch.existing_records, [])
+            self.assertEqual(set(test_batch.missing_records), set(records))
+            for record in records:
+                shutil.copy(
+                    os.path.join(self.fixtures_folder, record), os.path.join(test_batch.download_batch_dir, record)
+                )
+            self.assertEqual(set(test_batch.expected_records), set(records))
+            self.assertEqual(test_batch.existing_records, set(records))
+            self.assertEqual(test_batch.missing_records, [])
+
+            # Check that the blob uris are correctly generated
+            expected_blob_uris = [
+                "gs://orcid-testing/orcid_summaries/000/0000-0001-5000-5000.xml",
+                "gs://orcid-testing/orcid_summaries/000/0000-0001-5001-3000.xml",
+                "gs://orcid-testing/orcid_summaries/000/0000-0001-5002-1000.xml",
+                "gs://orcid-testing/orcid_summaries/000/0000-0001-5007-2000.xml",
+                "gs://orcid-testing/orcid_summaries/000/0000-0001-5010-1000.xml",
+            ]
+            self.assertEqual(set(test_batch.blob_uris), set(expected_blob_uris))
+
+    def test_create_orcid_batch_manifest(self):
+        """Tests the create_orcid_batch_manifest function"""
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            download_dir = os.path.join(tmp_dir, "download")
+            transform_dir = os.path.join(tmp_dir, "transform")
+            test_batch_str = "12X"
+            # Create a batch for testing
+            test_batch = OrcidBatch(download_dir, transform_dir, test_batch_str)
+
+            # Upload the .xml files to the test bucket
+            client = storage.Client()
+            bucket_id = f"orcid_test_{random_id()}"
+            bucket = client.create_bucket(bucket_id)
+
+            blob1 = storage.Blob(f"{test_batch_str}/0000-0001-5000-1000.xml", bucket)
+            blob1.upload_from_string("Test data 1")
+            # Make now the reference time - blob1 should be ignored
+            reference_time = pendulum.now()
+            blob2 = storage.Blob(f"{test_batch_str}/0000-0001-5000-2000.xml", bucket)
+            blob2.upload_from_string("Test data 2")
+            blob3 = storage.Blob(f"{test_batch_str}/0000-0001-5000-3000.xml", bucket)
+            blob3.upload_from_string("Test data 3")
+            # Put a blob in a different folder - should be ignored
+            blob4 = storage.Blob(f"somewhere_else/{test_batch_str}/0000-0001-5000-4000.xml", bucket)
+            blob4.upload_from_string("Test data 4")
+
+            create_orcid_batch_manifest(orcid_batch=test_batch, reference_time=reference_time, bucket=bucket_id)
+            with open(test_batch.manifest_file, "w", newline="") as csvfile:
+                reader = csv.reader(csvfile)
+                manifest_rows = [row for row in reader]
+            bucket = [row[0] for row in manifest_rows]
+            blobs = [row[1] for row in manifest_rows]
+            orcid = [row[2] for row in manifest_rows]
+            modification_times = [row[3] for row in manifest_rows]
+            self.assertEqual(len(manifest_rows), 2)
+            self.assertEqual(set(blobs), set([blob2.name, blob3.name]))
+            self.assertEqual(set(orcid), set(["0000-0001-5000-2000", "0000-0001-5000-3000"]))
+            self.assertEqual(set(modification_times), set([blob2.updated.isoformat(), blob3.updated.isoformat()]))
+
+
+class TestOrcidTelescope(ObservatoryTestCase):
+    """Tests for the OpenAlex telescope"""
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.dag_id = "orcid"
+        self.project_id = os.getenv("TEST_GCP_PROJECT_ID")
+        self.data_location = os.getenv("TEST_GCP_DATA_LOCATION")
+        self.aws_access_key_id = os.getenv("AWS_ACCESS_KEY_ID")
+        self.aws_secret_access_key = os.getenv("AWS_SECRET_ACCESS_KEY")
+        self.aws_region_name = os.getenv("AWS_DEFAULT_REGION")