Apply black formatting settings to repo

Author: RachelDuffin

ad_email/ad_email.py

@@ -5,6 +5,7 @@
 - AdEmail
     Send email to recipient via SMTP
 """
+
 import sys
 import os
 import jinja2
@@ -111,7 +112,9 @@ def send_email(
             self.msg["Subject"] = email_subject
             self.msg["From"] = self.sender
             self.msg["To"] = recipients
-            self.msg.attach(MIMEText(email_message, "html", "utf-8"))  # Add msg to e-mail body
+            self.msg.attach(
+                MIMEText(email_message, "html", "utf-8")
+            )  # Add msg to e-mail body
             self.logger.info(self.logger.log_msgs["sending_email"], self.msg)
             # Configure SMTP server connection for sending email
             with smtplib.SMTP(

ad_email/test_ad_email.py

@@ -3,6 +3,7 @@
 N.B. test_email_sending_success() will only pass when running on the
 workstation where the required auth details are stored
 """
+
 import os
 import pytest
 from ad_email.ad_email import AdEmail
@@ -12,6 +13,7 @@
 
 # TODO finish this test suite as it is currently incomplete
 
+
 @pytest.fixture(scope="function")
 def logger_obj():
     temp_log = os.path.join(test_data_temp, "temp.log")

ad_logger/ad_logger.py

@@ -1,6 +1,7 @@
 """
 Automate demultiplex logging. Classes required for logging
 """
+
 import sys
 import re
 import logging
@@ -38,7 +39,7 @@ def set_root_logger() -> object:
     as the root logger will use these same syslog handler and stream handler
         :return logger: Logging object
     """
-    sensitive_formatter=SensitiveFormatter(get_logging_formatter())
+    sensitive_formatter = SensitiveFormatter(get_logging_formatter())
     logger = logging.getLogger(AdLoggerConfig.REPO_NAME)
     stream_handler = logging.StreamHandler(sys.stdout)
     stream_handler.setFormatter(sensitive_formatter)
@@ -53,7 +54,7 @@ def set_root_logger() -> object:
         handlers=[
             stream_handler,
             syslog_handler,
-        ]
+        ],
     )
     return logger
 

ad_logger/test_ad_logger.py

@@ -1,5 +1,6 @@
 """ ad_logger.py pytest unit tests. The test suite is currently incomplete
 """
+
 import pytest
 from toolbox import toolbox
 from ad_logger import ad_logger
@@ -47,4 +48,3 @@ def test_get_loggers(self, logfiles_config, caplog):
                 f"Test log message. Logger {loggers[logger_name].name}"
             )
             assert loggers[logger_name].name in caplog.text
-

config/ad_config.py

@@ -9,6 +9,7 @@
 - ToolboxConfig
 - URConfig
 """
+
 import os
 import sys
 import datetime
@@ -86,7 +87,9 @@
 # DNAnexus upload agent path
 UPLOAD_AGENT_EXE = f"{DOCUMENT_ROOT}/apps/dnanexus-upload-agent-1.5.17-linux/ua"
 BCL2FASTQ_DOCKER = "seglh/bcl2fastq2:v2.20.0.422_60dbb5a"
-GATK_DOCKER = "broadinstitute/gatk:4.1.8.1"  # TODO this image should have a hash added in future
+GATK_DOCKER = (
+    "broadinstitute/gatk:4.1.8.1"  # TODO this image should have a hash added in future
+)
 
 LANE_METRICS_SUFFIX = ".illumina_lane_metrics"
 DEMUX_NOT_REQUIRED_MSG = "%s run. Does not need demultiplexing locally"
@@ -262,7 +265,10 @@
 
 DX_CMDS = {
     "create_proj": 'PROJECT_ID="$(dx new project --bill-to %s "%s" --brief --auth ${AUTH})"',
-    "find_proj_name": f"{SDK_SOURCE}; dx find projects --name *%s* " "--auth %s | awk '{print $3}'",
+    "find_proj_name": (
+        f"{SDK_SOURCE}; dx find projects --name *%s* "
+        "--auth %s | awk '{print $3}'"
+    ),
     "proj_name_from_id": f"{SDK_SOURCE}; dx describe %s --auth %s --json | jq -r .name",
     "find_proj_id": f"{SDK_SOURCE}; dx describe %s --auth %s --json | jq -r .id",
     "find_execution_id": (
@@ -366,7 +372,7 @@ class DemultiplexConfig(PanelConfig):
         "checksums_do_not_match": "Checksums do not match",  # Failure message written to md5sum file by integrity check scripts
         "samplesheet_success": "Samplesheet check successful with no errors identified: %s",
         "samplesheet_fail": "Processing halted. SampleSheet contains SampleSheet errors: %s ",
-        "upload_flag_umis": "Runfolder contains UMIs. Runfolder will not be uploaded and requires manual upload: %s"
+        "upload_flag_umis": "Runfolder contains UMIs. Runfolder will not be uploaded and requires manual upload: %s",
     }
     TESTING = TESTING
     BCL2FASTQ2_CMD = (
@@ -417,7 +423,7 @@ class SWConfig(PanelConfig):
     RUNFOLDERS = RUNFOLDERS
     PROD_ORGANISATION = "org-viapath_prod"  # Prod org for billing
     if BRANCH == "main":  # Prod branch
-        
+
         BSPS_ID = "BSPS_MD"
         DNANEXUS_USERS = {  # User access level
             # TODO remove InterpretationRequest user once per-user accounts set up
@@ -538,6 +544,7 @@ class ToolboxConfig(PanelConfig):
     """
     Toolbox configuration
     """
+
     if BRANCH == "master":
         DNANEXUS_PROJECT_PREFIX = "002_"  # Denotes production status of run
     else:
@@ -597,11 +604,13 @@ class URConfig:
         "upload_started": "Upload started",  # Statement to write to DNAnexus upload started file
     }
 
-class RunfolderCleanupConfig():
+
+class RunfolderCleanupConfig:
     """
     Runfolder Cleanup configuration
     """
+
     TIMESTAMP = TIMESTAMP
     RUNFOLDER_PATTERN = RUNFOLDER_PATTERN
     RUNFOLDERS = RUNFOLDERS
-    CREDENTIALS = CREDENTIALS
+    CREDENTIALS = CREDENTIALS

config/panel_config.py

@@ -47,6 +47,7 @@
     dry_lab                         True if required to share with dry lab, None if not
     umis                            True if run has UMIs
 """
+
 # TODO in future do we want to swap physical paths for file IDs
 
 TOOLS_PROJECT = "project-ByfFPz00jy1fk6PjpZ95F27J"  # 001_ToolsReferenceData

conftest.py

@@ -2,13 +2,15 @@
 Variables used across test modules, including the setup and teardown fixture
 that is run before and after every test. This is the top-level testing configuration
 """
+
 import os
 import re
 import shutil
 import pytest
 import tarfile
 import logging
 from shutil import copy
+
 # sys.path.append("..")
 from ad_logger import ad_logger
 from toolbox import toolbox
@@ -65,6 +67,7 @@
     },
 ]
 
+
 def patch_toolbox(monkeypatch):
     """
     Apply patches required for toolbox script. These point the paths to the
@@ -103,7 +106,9 @@ def run_before_and_after_session():
     for destination in to_copy_interop_to:
         shutil.copytree(os.path.join(test_data_dir_unzipped, "InterOp"), destination)
 
-    test_data_unzipped = os.path.join(test_data_dir_unzipped, "demultiplex_test_files", "test_runfolders")
+    test_data_unzipped = os.path.join(
+        test_data_dir_unzipped, "demultiplex_test_files", "test_runfolders"
+    )
 
     directories = [
         os.path.join(test_data_unzipped, d)
@@ -114,7 +119,9 @@ def run_before_and_after_session():
 
     for directory in directories:
         if re.match(".*999999_.*", directory):
-            fastqs_dir = os.path.join(test_data_unzipped, directory, "Data", "Intensities", "BaseCalls/")
+            fastqs_dir = os.path.join(
+                test_data_unzipped, directory, "Data", "Intensities", "BaseCalls/"
+            )
             os.makedirs(fastqs_dir, exist_ok=True)
             copy(dummy_fastq, fastqs_dir)
     yield  # Where the testing happens