automate ADX api upload

config/log_msgs_config.py

@@ -141,8 +141,11 @@
         ),
         "writing_cmds": "Writing dx run commands to %s",
         "running_cmds": "Running dx run commands using dx run bash script",
+        "running_decision_cmds": "Running decision support commands using bash script",
         "dx_run_err": "Error when setting off dx run command. Command: %s. Stdout: %s. Stderr: %s",
+        "decision_run_err": "Error when setting off decision support command. Command: %s. Stdout: %s. Stderr: %s",
         "dx_run_success": "Dx run commands issued successfully for run %s",
+        "decision_run_success": "Decision support cmd is run successfully for run %s",    
         "uploading_rf": (
             "Uploading rest of run folder to DNAnexus using upload_runfolder, ignoring: %s. Stdout stored in logfile: %s"
         ),

setoff_workflows/setoff_workflows.py

@@ -310,6 +310,8 @@ def __init__(self, rf_obj: RunfolderObject, loggers: dict):
         self.write_dx_run_cmds()
         self.pre_pipeline_upload()
         self.run_dx_run_commands()
+        if self.rf_samples_obj.pipeline == "archerdx":
+            self.run_decision_support_commands()
         self.pipeline_emails = PipelineEmails(
             self.rf_obj,
             self.rf_samples_obj,
@@ -776,6 +778,31 @@ def upload_rest_of_runfolder(self) -> None:
             )
             sys.exit(1)
 
+    def run_decision_support_commands(self) -> None:
+        """
+        Execute the decision_support bash script
+            :return None:
+        """
+        decision_support_run_cmd = f"bash {self.rf_obj.decision_support_upload_script}"
+
+        self.loggers["sw"].info(
+            self.loggers["sw"].log_msgs["running_decision_cmds"],
+        )
+        out, err, returncode = execute_subprocess_command(
+            decision_support_run_cmd, self.loggers["sw"], "exit_on_fail"
+        )
+        if returncode != 0:
+            self.loggers["sw"].error(
+                self.loggers["sw"].log_msgs["decision_run_err"],
+                decision_support_run_cmd,
+                out,
+                err,
+            )
+        else:
+            self.loggers["sw"].info(
+                self.loggers["sw"].log_msgs["decision_run_success"],
+                self.rf_obj.runfolder_name,
+            )    
     def run_dx_run_commands(self) -> None:
         """
         Execute the dx run bash script
@@ -883,6 +910,19 @@ def __init__(self, rf_obj: object, rf_samples: object, logger: logging.Logger):
             self.sql_queries.append(
                 sample_cmds_obj.return_oncology_query()
             )  # Get SQL queries
+        # Return the decision support command 
+        ADX_runfolder = f"run_folder_name={self.rf_obj.runfolder_name}"
+        ADX_jobID = "job_name=$(cat /media/data3/share/${run_folder_name}/RunParameters.xml | grep -oP '(?<=ExperimentName>).*?(?=</ExperimentName)')"
+        docker = "docker run \
+                    -v /media/data3/share/${run_folder_name}/Data/Intensities/BaseCalls:/data \
+                    -v /usr/local/src/mokaguys:/auth_file \
+                    seglh/archer_api_upload:v1.0.0  /data \
+                    auth_file/.archer_authentication_mokaguys.txt \
+                    ${job_name} 2 | tee -a /usr/local/src/mokaguys/automate_demultiplexing_logfiles/archer_api_upload_logfiles/${run_folder_name}_archer_api_logfile.txt"
+
+        docker_api_cmd = [ADX_runfolder, ADX_jobID, docker]
+        for api_cmd in docker_api_cmd:
+            self.decision_support_upload_cmds.append(api_cmd)
 
         # Return downstream app commands
         self.workflow_cmds.extend(