Unit testing for workspace uploader

test/src/loaders/workspace_uploader/workspace_uploader_test.py

@@ -1,5 +1,209 @@
+import os
+import pytest
+import shutil
+import uuid
+from multiprocessing import Queue
+
+from pathlib import Path
+from unittest.mock import Mock
+
+from src.loaders.common import loader_helper
 from src.loaders.workspace_uploader import workspace_uploader
 
 
-def test_noop():
-    assert True
+@pytest.fixture(scope="function")
+def setup_and_teardown():
+    print('starting workspace uploader tests')
+    tmp_dir = 'result_{}'.format(uuid.uuid4().hex)
+    os.makedirs(tmp_dir)
+
+    # set up sourcedata and collectionssource dirs and soft link them
+    sourcedata_dir = Path(tmp_dir) / "sourcedata" / "NCBI" / "NONE"
+    collection_source_dir = Path(tmp_dir) / "collectionssource"
+    sourcedata_dir.mkdir(parents=True)
+    collection_source_dir.mkdir()
+
+    workspace_id = 12345
+    upload_env_key = "CI"
+    upas = ["12345_58_1", "12345_58_2"]
+    assembly_dir_names = ["GCF_000979855.1", "GCF_000979175.1"]
+    assembly_names = ["GCF_000979855.1_gtlEnvA5udCFS_genomic.fna.gz",
+                      "GCF_000979175.1_gtlEnvA5udCFS_genomic.fna.gz"]
+
+    assembly_dirs, target_files = list(), list()
+    for assembly_dir_name, assembly_name in zip(assembly_dir_names, assembly_names):
+        target_dir_path = sourcedata_dir.joinpath(assembly_dir_name)
+        target_dir_path.mkdir()
+        target_file_path = target_dir_path.joinpath(assembly_name)
+        target_file_path.touch()
+        new_dir_path = collection_source_dir.joinpath(assembly_dir_name)
+        os.symlink(target_dir_path.resolve(), new_dir_path.resolve(), target_is_directory=True)
+        assembly_dirs.append(str(new_dir_path))
+        target_files.append(str(target_file_path))
+
+    yield tmp_dir, assembly_dirs, assembly_names, upas, workspace_id, upload_env_key, target_files
+
+    shutil.rmtree(tmp_dir, ignore_errors=True)
+
+
+def test_get_yaml_file_path(setup_and_teardown):
+    _, assembly_dirs, _, _, _, _, _ = setup_and_teardown
+    yaml_path = workspace_uploader._get_yaml_file_path(assembly_dirs[0])
+
+    assert os.path.exists(yaml_path)
+
+
+def test_get_source_file(setup_and_teardown):
+    _, assembly_dirs, assembly_names, _, _, _, target_files = setup_and_teardown
+    assembly_dir, assembly_name = assembly_dirs[0], assembly_names[0]
+
+    file_path = workspace_uploader._get_source_file(assembly_dir, assembly_name)
+    expected_target_file_path = os.path.abspath(target_files[0])
+
+    assert expected_target_file_path == file_path
+
+
+def test_read_upload_status_yaml_file(setup_and_teardown):
+    _, assembly_dirs, assembly_names, _, workspace_id, upload_env_key, _ = setup_and_teardown
+    assembly_dir = assembly_dirs[0]
+    assembly_name = assembly_names[0]
+
+    data, uploaded = workspace_uploader._read_upload_status_yaml_file(
+        upload_env_key, workspace_id, assembly_dir, assembly_name
+    )
+
+    expected_data = {upload_env_key: {workspace_id: dict()}}
+
+    assert not uploaded
+    assert expected_data == data
+
+
+def test_update_upload_status_yaml_file(setup_and_teardown):
+    _, assembly_dirs, assembly_names, upas, workspace_id, upload_env_key, _ = setup_and_teardown
+    upa = upas[0]
+    assembly_dir = assembly_dirs[0]
+    assembly_name = assembly_names[0]
+
+    workspace_uploader._update_upload_status_yaml_file(
+        upload_env_key, workspace_id, upa, assembly_dir, assembly_name
+    )
+    data, uploaded = workspace_uploader._read_upload_status_yaml_file(
+        upload_env_key, workspace_id, assembly_dir, assembly_name
+    )
+
+    expected_data = {
+        upload_env_key: {workspace_id: {"file_name": assembly_name, "upa": upa}}
+    }
+
+    assert uploaded
+    assert expected_data == data
+
+
+def test_fetch_assemblies_to_upload(setup_and_teardown):
+    tmp_dir, assembly_dirs, assembly_names, _, workspace_id, upload_env_key, _ = setup_and_teardown
+    collection_source_dir = Path(tmp_dir) / "collectionssource"
+    upload_file_ext = ["genomic.fna.gz"]
+
+    count, wait_to_upload_assemblies = workspace_uploader._fetch_assemblies_to_upload(
+        upload_env_key, workspace_id, collection_source_dir, upload_file_ext
+    )
+
+    expected_count = len(assembly_names)
+    expected_wait_to_upload_assemblies = {
+        assembly_name: assembly_dir
+        for assembly_name, assembly_dir in zip(assembly_names, assembly_dirs)
+    }
+
+    assert expected_count == count
+    assert expected_wait_to_upload_assemblies == wait_to_upload_assemblies
+
+
+def test_prepare_skd_job_dir_to_upload(setup_and_teardown):
+    tmp_dir, assembly_dirs, assembly_names, _, _, _, _ = setup_and_teardown
+    wait_to_upload_assemblies = {
+        assembly_name: assembly_dir
+        for assembly_name, assembly_dir in zip(assembly_names, assembly_dirs)
+    }
+
+    conf = Mock()
+    username = "kbase"
+    job_dir = loader_helper.make_job_dir(tmp_dir, username)
+    conf.job_data_dir = loader_helper.make_job_data_dir(job_dir)
+    data_dir = workspace_uploader._prepare_skd_job_dir_to_upload(conf, wait_to_upload_assemblies)
+
+    assert sorted(os.listdir(data_dir)) == sorted(assembly_names)
+
+
+def test_post_process(setup_and_teardown):
+    tmp_dir, assembly_dirs, assembly_names, upas, workspace_id, upload_env_key, _ = setup_and_teardown
+    upload_dir = Path(tmp_dir) / "upload_dir"
+    upload_dir.mkdir()
+    output_dir = Path(tmp_dir) / "output_dir"
+    output_dir.mkdir()
+
+    upa = upas[0]
+    host_assembly_dir = assembly_dirs[0]
+    assembly_name = assembly_names[0]
+
+    workspace_uploader._post_process(
+        upload_env_key,
+        workspace_id,
+        host_assembly_dir,
+        assembly_name,
+        upload_dir,
+        output_dir,
+        upa,
+    )
+
+    data, uploaded = workspace_uploader._read_upload_status_yaml_file(
+        upload_env_key, workspace_id, host_assembly_dir, assembly_name
+    )
+    expected_data = {
+        upload_env_key: {workspace_id: {"file_name": assembly_name, "upa": upa}}
+    }
+
+    assert uploaded
+    assert expected_data == data
+    assert os.readlink(os.path.join(upload_dir, upa)) == os.path.join(output_dir, upa)
+
+
+def test_upload_assembly_to_workspace(setup_and_teardown):
+    _, _, assembly_names, upas, workspace_id, _, _  = setup_and_teardown
+    upa = upas[0]
+    assembly_name = assembly_names[0]
+    file_path = "/path/to/file/in/AssembilyUtil"
+
+    conf = Mock()
+    conf.asu.save_assembly_from_fasta2.return_value = {"upa": upa}
+    upa_res = workspace_uploader._upload_assembly_to_workspace(
+        conf, workspace_id, file_path, assembly_name
+    )
+
+    expected_upa = upa.replace("/", "_")
+    assert expected_upa == upa_res
+    assert conf.asu.save_assembly_from_fasta2.call_count == 1
+
+
+def test_assembly_files_in_parallel(setup_and_teardown):
+    tmp_dir, assembly_dirs, assembly_names, upas, workspace_id, upload_env_key, _ = setup_and_teardown
+    upload_dir = Path(tmp_dir) / "upload_dir"
+    upload_dir.mkdir()
+
+    wait_to_upload_assemblies = {
+        assembly_name: assembly_dir
+        for assembly_name, assembly_dir in zip(assembly_names, assembly_dirs)
+    }
+
+    conf = Mock()
+    conf.workers = 5
+    conf.input_queue = Queue()
+    conf.output_queue = Queue()
+    for assembly_name, upa in zip(assembly_names, upas):
+        conf.output_queue.put((assembly_name, upa))
+
+    failed_names = workspace_uploader._upload_assembly_files_in_parallel(
+        conf, upload_env_key, workspace_id, upload_dir, wait_to_upload_assemblies
+    )
+
+    assert conf.output_queue.empty()
+    assert failed_names == []