Add command line test

pysqa/cmd.py

@@ -3,14 +3,16 @@
 import json
 import getopt
 from pysqa.queueadapter import QueueAdapter
+from pysqa.utils.execute import execute_command
 
 
-def command_line(argv):
+def command_line(argv, execute_command=execute_command):
     """
     Parse the command line arguments.
 
     Args:
         argv: Command line arguments
+        execute_command: function to comunicate with shell process
 
     """
     directory = "~/.queues"
@@ -94,7 +96,7 @@ def command_line(argv):
                 print("cmd.py help ... coming soon.")
                 sys.exit()
         if mode_submit or mode_delete or mode_reservation or mode_status:
-            qa = QueueAdapter(directory=directory)
+            qa = QueueAdapter(directory=directory, execute_command=execute_command)
             if mode_submit:
                 print(
                     qa.submit_job(

pysqa/ext/modular.py

@@ -3,11 +3,14 @@
 
 import pandas
 from pysqa.utils.basic import BasisQueueAdapter
+from pysqa.utils.execute import execute_command
 
 
 class ModularQueueAdapter(BasisQueueAdapter):
-    def __init__(self, config, directory="~/.queues"):
-        super(ModularQueueAdapter, self).__init__(config=config, directory=directory)
+    def __init__(self, config, directory="~/.queues", execute_command=execute_command):
+        super(ModularQueueAdapter, self).__init__(
+            config=config, directory=directory, execute_command=execute_command
+        )
         self._queue_to_cluster_dict = {
             k: v["cluster"] for k, v in self._config["queues"].items()
         }

pysqa/ext/remote.py

@@ -8,11 +8,14 @@
 import warnings
 from tqdm import tqdm
 from pysqa.utils.basic import BasisQueueAdapter
+from pysqa.utils.execute import execute_command
 
 
 class RemoteQueueAdapter(BasisQueueAdapter):
-    def __init__(self, config, directory="~/.queues"):
-        super(RemoteQueueAdapter, self).__init__(config=config, directory=directory)
+    def __init__(self, config, directory="~/.queues", execute_command=execute_command):
+        super(RemoteQueueAdapter, self).__init__(
+            config=config, directory=directory, execute_command=execute_command
+        )
         self._ssh_host = config["ssh_host"]
         self._ssh_username = config["ssh_username"]
         self._ssh_known_hosts = os.path.abspath(

pysqa/queueadapter.py

@@ -6,6 +6,7 @@
 from pysqa.ext.modular import ModularQueueAdapter
 from pysqa.ext.remote import RemoteQueueAdapter
 from pysqa.utils.config import read_config
+from pysqa.utils.execute import execute_command
 
 __author__ = "Jan Janssen"
 __copyright__ = "Copyright 2019, Jan Janssen"
@@ -44,14 +45,16 @@ class QueueAdapter(object):
             Queues available for auto completion QueueAdapter().queues.<queue name> returns the queue name.
     """
 
-    def __init__(self, directory="~/.queues"):
+    def __init__(self, directory="~/.queues", execute_command=execute_command):
         queue_yaml = os.path.join(directory, "queue.yaml")
         clusters_yaml = os.path.join(directory, "clusters.yaml")
         self._adapter = None
         if os.path.exists(queue_yaml):
             self._queue_dict = {
                 "default": set_queue_adapter(
-                    config=read_config(file_name=queue_yaml), directory=directory
+                    config=read_config(file_name=queue_yaml),
+                    directory=directory,
+                    execute_command=execute_command,
                 )
             }
             primary_queue = "default"
@@ -61,6 +64,7 @@ def __init__(self, directory="~/.queues"):
                 k: set_queue_adapter(
                     config=read_config(file_name=os.path.join(directory, v)),
                     directory=directory,
+                    execute_command=execute_command,
                 )
                 for k, v in config["cluster"].items()
             }
@@ -296,7 +300,7 @@ def check_queue_parameters(
         )
 
 
-def set_queue_adapter(config, directory):
+def set_queue_adapter(config, directory, execute_command=execute_command):
     """
     Initialize the queue adapter
 
@@ -305,10 +309,16 @@ def set_queue_adapter(config, directory):
         directory (str): directory which contains the queue configurations
     """
     if config["queue_type"] in ["SGE", "TORQUE", "SLURM", "LSF", "MOAB"]:
-        return BasisQueueAdapter(config=config, directory=directory)
+        return BasisQueueAdapter(
+            config=config, directory=directory, execute_command=execute_command
+        )
     elif config["queue_type"] in ["GENT"]:
-        return ModularQueueAdapter(config=config, directory=directory)
+        return ModularQueueAdapter(
+            config=config, directory=directory, execute_command=execute_command
+        )
     elif config["queue_type"] in ["REMOTE"]:
-        return RemoteQueueAdapter(config=config, directory=directory)
+        return RemoteQueueAdapter(
+            config=config, directory=directory, execute_command=execute_command
+        )
     else:
         raise ValueError

tests/test_cmd.py

@@ -0,0 +1,57 @@
+import os
+import unittest
+from pysqa.cmd import command_line
+
+
+class TestCMD(unittest.TestCase):
+    def test_help(self):
+        with self.assertRaises(SystemExit):
+            command_line(["--help"])
+
+    def test_wrong_option(self):
+        with self.assertRaises(SystemExit):
+            command_line(["--error"])
+
+    def test_submit(self):
+        def execute_command(
+            commands,
+            working_directory=None,
+            split_output=True,
+            shell=False,
+            error_filename="pysqa.err",
+        ):
+            return "1\n"
+
+        test_dir = os.path.abspath(os.path.dirname(__file__))
+        with self.assertRaises(SystemExit):
+            command_line(
+                [
+                    "--config_directory", os.path.join(test_dir, "config", "slurm"),
+                    "--submit",
+                    "--queue", "slurm",
+                    "--job_name", "test",
+                    "--working_directory", ".",
+                    "--cores", "2",
+                    "--memory", "1GB",
+                    "--run_time", "10",
+                    "--command", "echo hello"
+                ],
+                execute_command=execute_command
+            )
+        with open("run_queue.sh") as f:
+            output = f.readlines()
+        content = [
+            '#!/bin/bash\n',
+            '#SBATCH --output=time.out\n',
+            '#SBATCH --job-name=test\n',
+            '#SBATCH --chdir=.\n',
+            '#SBATCH --get-user-env=L\n',
+            '#SBATCH --partition=slurm\n',
+            '#SBATCH --time=4320\n',
+            '#SBATCH --mem=1GBG\n',
+            '#SBATCH --cpus-per-task=10\n',
+            '\n',
+            'echo hello'
+        ]
+        self.assertEqual(output, content)
+        os.remove("run_queue.sh")