more work swapping ssh and scp commands for when run in local mode

coordinator/ProcessorEnvironment.py

@@ -40,11 +40,12 @@ def process_in_job_env2_0(jobPath,status,config,component):
 
     # TODO: perform ssh file transfer in python instead of subprocess
     server_name: str = config['ServerName']
-    machine_seperator: str = ":"
-    if not server_name:
-        machine_seperator = ""
+    if server_name == "":
+        cmd_scp: list = ["scp", f"{file_path}/{file_name}.tar.gz", jobPath]
+    else:
+        cmd_scp: list = ["scp", "-i", config['ServerKey'], "-o", "StrictHostKeyChecking=no",
+                         f"{config['ServerName']}:{file_path}/{file_name}.tar.gz", jobPath]
 
-    cmd_scp: list = ["scp","-i",config['ServerKey'],"-o","StrictHostKeyChecking=no",f"{config['ServerName']}{machine_seperator}{file_path}/{file_name}.tar.gz", jobPath]
     description_short = 'env2 scp'
     description_long = 'Copying file from remote server to job directory'
     # lawrence comment in/out

coordinator/ProcessorServer.py

@@ -42,7 +42,7 @@ def process_pre_job_server_download(input_args: dict):
         timenow = datetime.datetime.now(tz=datetime.timezone.utc).time()
 
         server_name: str = config['ServerName']
-        full_file_path = f"{file_path} / {file_name}.tar.gz"
+        full_file_path = f"{file_path}/{file_name}.tar.gz"
         if server_name == "":
             cmd_check_file = [f"test -f {full_file_path} && tar -tzf {full_file_path} > /dev/null"]
             run_in_shell: bool = True
@@ -57,7 +57,7 @@ def process_pre_job_server_download(input_args: dict):
         status = subprocess_and_log(cmd_check_file, description_short, description_long, check = False,
                                     shell = run_in_shell)
 
-        if status.returncode == 1:
+        if status.returncode > 0:
 
             # a time check in UTC. If it's late, raise warning, if very late, raise error
 
@@ -122,15 +122,26 @@ def upload(config,FilesToSend,component):
 
     logger.debug("Making path directory on remote server if it doesn't already exist")
 
-    ssh_cmd = ["ssh","-i",config['ServerKey'],"-o","StrictHostKeyChecking=no",config['ServerName'], f"mkdir -p {OutputServerPath}"]
+    server_key = config['ServerKey']
+    if server_key == "":
+        ssh_cmd = ["ssh", f"mkdir -p {OutputServerPath}"]
+        run_in_shell: bool = True
+    else:
+        ssh_cmd = ["ssh", "-i", server_key, "-o", "StrictHostKeyChecking=no", config['ServerName'],
+                   f"mkdir -p {OutputServerPath}"]
+        run_in_shell: bool = False
 
     description_short = 'upload ssh'
     description_long = 'make remote directory'
-    subprocess_and_log(ssh_cmd, description_short, description_long)
+    subprocess_and_log(ssh_cmd, description_short, description_long, shell=run_in_shell)
 
     logger.debug('Sending file(s) to remote server')
 
-    scp_cmd = ["scp","-ri",config['ServerKey'],"-o","StrictHostKeyChecking=no",*FilesToSend, f"{config['ServerName']}:{OutputServerPath}"]
+    if server_key == "":
+        scp_cmd = ["scp", *FilesToSend, {OutputServerPath}]
+    else:
+        scp_cmd = ["scp", "-ri", server_key, "-o", "StrictHostKeyChecking=no", *FilesToSend,
+                   f"{config['ServerName']}:{OutputServerPath}"]
 
     description_short = 'upload scp'
     description_long = 'scp files to remote directory'

tests/test_data/test_deployment/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json

@@ -148,7 +148,7 @@
     },
     "Epidemiology" : {
         "DiseaseNames" : ["StemRust"],
-        "CalculationSpanDays" : ["20220501",5],
+        "CalculationSpanDays" : [0,1],
         "TimeStep_hours": "3",
         "ProcessPreJob" : "process_pre_job_epi",
         "ProcessInJob" : "process_in_job_epi",
@@ -220,7 +220,7 @@
         "ProcessPreJob" : "query_past_successes",
         "ProcessInJob" : "process_in_job_advisory",
         "ProcessEWSPlotting" : "do_nothing",
-        "seasonStartString" : "20220501",
+        "seasonStartString" : "20210901",
         "Environment" : {
             "SuccessFileTemplate" : "${WorkspacePath}ENVIRONMENT_2.0_${StartString}/STATUS_SUCCESS",
             "DataPathTemplate" : "${WorkspacePath}/ENVIRONMENT_2.0_${dateString}/plotting/${SubRegionNameLower}/input_csvs/",
@@ -270,7 +270,7 @@
             }
         },
         "Surveys" : {
-            "variety_names_tidy_fn" : "/media/scratch/lb584_scratch/projects/ews_local_prod/regions/EastAfrica/resources/advisory_builder/configs/config_EastAfrica_variety_names_tidy.json",
+            "variety_names_tidy_fn" : "../test_data/test_deployment/regions/EastAfrica/resources/advisory_builder/configs/config_EastAfrica_variety_names_tidy.json",
             "CountryColumnName" : "surveyor_infromation-country",
             "EastAfrica" : {
                 "ShapeFilenameAdmin0" : "../test_data/test_deployment/regions/EastAfrica/resources/advisory_builder/assets/EthKen_admin0.shp",