From eae5839deff4a604ffa1d40d5c10372b63d5fdc6 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Wed, 21 Feb 2024 11:43:25 +0000 Subject: [PATCH] Refactoring minor updates --- tests/db/test_mysql.py | 20 +-- tests/file_processing/test_file_processing.py | 121 +++++++++--------- 2 files changed, 72 insertions(+), 69 deletions(-) diff --git a/tests/db/test_mysql.py b/tests/db/test_mysql.py index 8f30fc72..ebc8cd35 100644 --- a/tests/db/test_mysql.py +++ b/tests/db/test_mysql.py @@ -28,16 +28,6 @@ class MockMySQLConnection(MySQLConnectionAbstract): _execute_query = MagicMock() _open_connection = MagicMock() close = MagicMock() - commit = MagicMock() - cursor = MagicMock() - database = MagicMock() - disconnect = MagicMock() - get_rows = MagicMock() - in_transaction = MagicMock() - info_query = MagicMock() - is_connected = MagicMock() - ping = MagicMock() - rollback = MagicMock() cmd_change_user = MagicMock() cmd_debug = MagicMock() cmd_init_db = MagicMock() @@ -55,8 +45,18 @@ class MockMySQLConnection(MySQLConnectionAbstract): cmd_stmt_prepare = MagicMock() cmd_stmt_reset = MagicMock() cmd_stmt_send_long_data = MagicMock() + commit = MagicMock() connection_id = MagicMock() + cursor = MagicMock() + database = MagicMock() + disconnect = MagicMock() get_row = MagicMock() + get_rows = MagicMock() + in_transaction = MagicMock() + info_query = MagicMock() + is_connected = MagicMock() + ping = MagicMock() + rollback = MagicMock() def test_create_mysql_connection_none(config): diff --git a/tests/file_processing/test_file_processing.py b/tests/file_processing/test_file_processing.py index 78b87bf3..56f97853 100644 --- a/tests/file_processing/test_file_processing.py +++ b/tests/file_processing/test_file_processing.py @@ -1549,65 +1549,68 @@ def test_insert_samples_from_docs_into_mlwh( rows = cursor.fetchall() cursor.close() - assert cast(Dict[str, RowItemType], rows[0])[MLWH_MONGODB_ID] == "5f562d9931d9959b92544728" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_ROOT_SAMPLE_ID] == "ABC00000004" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_COG_UK_ID] == "TEST-123ABC" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_RNA_ID] == "TC-rna-00000029_H11" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_PLATE_BARCODE] == "TC-rna-00000029" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_COORDINATE] == "H11" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_RESULT] == "Negative" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_DATE_TESTED] == date_tested_1 - assert cast(Dict[str, RowItemType], rows[0])[MLWH_SOURCE] == "Test Centre" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_LAB_ID] == "TC" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE_VERSION] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE_TIMESTAMP] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CREATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_UPDATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_MUST_SEQUENCE] == 0 - assert cast(Dict[str, RowItemType], rows[0])[MLWH_PREFERENTIALLY_SEQUENCE] == 1 - - assert cast(Dict[str, RowItemType], rows[1])[MLWH_MONGODB_ID] == "5f562d9931d9959b92544729" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_ROOT_SAMPLE_ID] == "ABC00000005" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_COG_UK_ID] == "TEST-123ABD" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_RNA_ID] == "TC-rna-00000029_H12" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_PLATE_BARCODE] == "TC-rna-00000029" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_COORDINATE] == "H12" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_DATE_TESTED] == date_tested_2 - assert cast(Dict[str, RowItemType], rows[1])[MLWH_SOURCE] == "Test Centre" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_LAB_ID] == "TC" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_TARGET] == "ORF1ab" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_CQ] == Decimal("21.28726211") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_TARGET] == "N gene" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_CQ] == Decimal("18.12736661") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_TARGET] == "S gene" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_CQ] == Decimal("22.63616273") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_TARGET] == "MS2" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_CQ] == Decimal("26.25125612") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE] == 1 - assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE_VERSION] == "v2.3" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE_TIMESTAMP] == filtered_positive_timestamp - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CREATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[1])[MLWH_UPDATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[1])[MLWH_MUST_SEQUENCE] == 1 - assert cast(Dict[str, RowItemType], rows[1])[MLWH_PREFERENTIALLY_SEQUENCE] == 0 + first_row = cast(Dict[str, RowItemType], rows[0]) + second_row = cast(Dict[str, RowItemType], rows[1]) + + assert first_row[MLWH_MONGODB_ID] == "5f562d9931d9959b92544728" + assert first_row[MLWH_ROOT_SAMPLE_ID] == "ABC00000004" + assert first_row[MLWH_COG_UK_ID] == "TEST-123ABC" + assert first_row[MLWH_RNA_ID] == "TC-rna-00000029_H11" + assert first_row[MLWH_PLATE_BARCODE] == "TC-rna-00000029" + assert first_row[MLWH_COORDINATE] == "H11" + assert first_row[MLWH_RESULT] == "Negative" + assert first_row[MLWH_DATE_TESTED] == date_tested_1 + assert first_row[MLWH_SOURCE] == "Test Centre" + assert first_row[MLWH_LAB_ID] == "TC" + assert first_row[MLWH_CH1_TARGET] is None + assert first_row[MLWH_CH1_RESULT] is None + assert first_row[MLWH_CH1_CQ] is None + assert first_row[MLWH_CH2_TARGET] is None + assert first_row[MLWH_CH2_RESULT] is None + assert first_row[MLWH_CH2_CQ] is None + assert first_row[MLWH_CH3_TARGET] is None + assert first_row[MLWH_CH3_RESULT] is None + assert first_row[MLWH_CH3_CQ] is None + assert first_row[MLWH_CH4_TARGET] is None + assert first_row[MLWH_CH4_RESULT] is None + assert first_row[MLWH_CH4_CQ] is None + assert first_row[MLWH_FILTERED_POSITIVE] is None + assert first_row[MLWH_FILTERED_POSITIVE_VERSION] is None + assert first_row[MLWH_FILTERED_POSITIVE_TIMESTAMP] is None + assert first_row[MLWH_CREATED_AT] is not None + assert first_row[MLWH_UPDATED_AT] is not None + assert first_row[MLWH_MUST_SEQUENCE] == 0 + assert first_row[MLWH_PREFERENTIALLY_SEQUENCE] == 1 + + assert second_row[MLWH_MONGODB_ID] == "5f562d9931d9959b92544729" + assert second_row[MLWH_ROOT_SAMPLE_ID] == "ABC00000005" + assert second_row[MLWH_COG_UK_ID] == "TEST-123ABD" + assert second_row[MLWH_RNA_ID] == "TC-rna-00000029_H12" + assert second_row[MLWH_PLATE_BARCODE] == "TC-rna-00000029" + assert second_row[MLWH_COORDINATE] == "H12" + assert second_row[MLWH_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_DATE_TESTED] == date_tested_2 + assert second_row[MLWH_SOURCE] == "Test Centre" + assert second_row[MLWH_LAB_ID] == "TC" + assert second_row[MLWH_CH1_TARGET] == "ORF1ab" + assert second_row[MLWH_CH1_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH1_CQ] == Decimal("21.28726211") + assert second_row[MLWH_CH2_TARGET] == "N gene" + assert second_row[MLWH_CH2_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH2_CQ] == Decimal("18.12736661") + assert second_row[MLWH_CH3_TARGET] == "S gene" + assert second_row[MLWH_CH3_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH3_CQ] == Decimal("22.63616273") + assert second_row[MLWH_CH4_TARGET] == "MS2" + assert second_row[MLWH_CH4_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH4_CQ] == Decimal("26.25125612") + assert second_row[MLWH_FILTERED_POSITIVE] == 1 + assert second_row[MLWH_FILTERED_POSITIVE_VERSION] == "v2.3" + assert second_row[MLWH_FILTERED_POSITIVE_TIMESTAMP] == filtered_positive_timestamp + assert second_row[MLWH_CREATED_AT] is not None + assert second_row[MLWH_UPDATED_AT] is not None + assert second_row[MLWH_MUST_SEQUENCE] == 1 + assert second_row[MLWH_PREFERENTIALLY_SEQUENCE] == 0 def test_insert_samples_from_docs_into_mlwh_date_tested_missing(config, mlwh_connection):