implemented issue BU-ISCIII#224. Crontab sets directly to error when …

…runParameters is not found

wetlab/utils/common.py

@@ -78,6 +78,22 @@ def check_valid_date_format(date):
             return False
 
 
+def get_samba_atribute_data(conn, shared_folder, remote_path, attribute=None):
+    """_summary_
+
+    Args:
+        conn (_type_): _description_
+        shared_folder (_type_): _description_
+        remote_path (_type_): _description_
+        attribute (_type_, optional): _description_. Defaults to None.
+    """
+    attributes = conn.getAttributes(shared_folder, remote_path)
+    if attribute is not None:
+        atr_field = "attributes." + attribute
+        return eval(atr_field)
+    return attributes
+
+
 def get_samba_connection_data():
     """
     Description:

wetlab/utils/crontab_process.py

@@ -1233,14 +1233,13 @@ def store_sample_sheet_if_not_defined_in_run(
     return sample_sheet_on_database
 
 
-def waiting_time_expired(run_process_obj, time_to_check, maximun_time, experiment_name):
+def waiting_time_expired(time_to_check, maximun_time, experiment_name):
     """
     Description:
         The function get the time run was recorded to compare  with the present time.
         If the value is less that the allowed time to wait  will return False.
         True is returned if the time is bigger
     Input:
-        run_process_obj     # run process object
         time_to_check       # reference time to be checked
         maximun_time        # maximm number of days to wait
         experiment_name     # experiment name to be checked

wetlab/utils/crontab_update_run.py

@@ -120,12 +120,39 @@ def search_update_new_runs(request_reason):
                 wetlab.utils.common.logging_errors(error_message, True, False)
                 experiment_name = "Experiment name NOT FOUND"
                 wetlab.utils.common.logging_errors(error_message, True, False)
-                # we don't have experiment name when there is no run_parameters file.
-                # We used the run folder name instead.
-                run_process_obj = wetlab.utils.crontab_process.get_run_process_obj_or_create_if_not_exists(
-                    new_run
+                # check the run folder creation date to allow more time before
+                # setting the run to error
+                f_created_date = wetlab.utils.common.get_samba_atribute_data(
+                    conn,
+                    wetlab.utils.crontab_process.get_samba_shared_folder(),
+                    new_run,
+                    "created_time",
+                )
+                time_to_check = datetime.datetime.utcfromtimestamp(
+                    f_created_date
+                ).date()
+                max_time_for_run_parameters = (
+                    wetlab.models.ConfigSetting.objects.filter(
+                        configuration_name__exact="MAXIMUM_TIME_WAIT_RUN_PARAMETERS"
+                    )
+                    .last()
+                    .get_configuration_value()
                 )
-                wetlab.utils.crontab_process.handling_errors_in_run(new_run, "21")
+                if wetlab.utils.crontab_process.waiting_time_expired(
+                    time_to_check, max_time_for_run_parameters, experiment_name
+                ):
+                    # Maximum time for waiting run parameter in folder has expired
+                    # we don't have experiment name when there is no run_parameters file.
+                    # We used the run folder name instead.
+                    run_process_obj = wetlab.utils.crontab_process.get_run_process_obj_or_create_if_not_exists(
+                        new_run
+                    )
+                    wetlab.utils.crontab_process.handling_errors_in_run(new_run, "21")
+                else:
+                    logger.debug(
+                        "%s : RunParameter not in folder run. Allowing more time",
+                        experiment_name,
+                    )
                 logger.debug("%s : Deleting RunParameter file", experiment_name)
                 logger.debug(
                     "%s : Aborting the process for this run. Continue with the next.",
@@ -500,7 +527,7 @@ def manage_run_in_recorded_state(conn, run_process_objs):
                     run_process_obj.get_run_generated_date_no_format().date()
                 )
                 if not wetlab.utils.crontab_process.waiting_time_expired(
-                    run_process_obj, time_to_check, maximun_time, experiment_name
+                    time_to_check, maximun_time, experiment_name
                 ):
                     logger.debug(
                         "%s : End the process. Waiting more time to get Sample Sheet file",
@@ -660,7 +687,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs):
             )
             time_to_check = run_process_obj.get_run_generated_date_no_format().date()
             if not wetlab.utils.crontab_process.waiting_time_expired(
-                run_process_obj, time_to_check, maximun_time, experiment_name
+                time_to_check, maximun_time, experiment_name
             ):
                 logger.info(
                     "%s : Waiting more time to get Sequencer completion",
@@ -864,7 +891,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs):
                     )
                     continue
                 if not wetlab.utils.crontab_process.waiting_time_expired(
-                    run_process_obj, time_to_check, maximun_time, experiment_name
+                    time_to_check, maximun_time, experiment_name
                 ):
                     logger.debug(
                         "%s : End the process. Waiting more time to get bcf2fastq stats.",