From d4d9b9fb75525873b291028a622aac70c44a5065 Mon Sep 17 00:00:00 2001
From: Sebastian Luna Valero <sebastian.luna.valero@gmail.com>
Date: Mon, 26 Feb 2018 13:24:52 +0000
Subject: [PATCH]  portability tweaks for OS X

---
 CGATCore/IOTools.py              |  4 ++
 CGATCore/Pipeline/Parameters.py  |  3 ++
 tests/test_pipeline_execution.py | 63 ++++++++++++++++++--------------
 3 files changed, 42 insertions(+), 28 deletions(-)

diff --git a/CGATCore/IOTools.py b/CGATCore/IOTools.py
index 7b8c10f..d8947d9 100644
--- a/CGATCore/IOTools.py
+++ b/CGATCore/IOTools.py
@@ -1421,6 +1421,7 @@ def mount_file(fn):
 
 
 def remote_file_exists(filename, hostname=None, expect=False):
+
     ssh = paramiko.SSHClient()
     ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
     try:
@@ -1428,6 +1429,9 @@ def remote_file_exists(filename, hostname=None, expect=False):
     except paramiko.SSHException as ex:
         # disable test on VM, key issues.
         return expect
+    except TimeoutError as ex:
+        # times out on OS X, localhost
+        return expect
 
     stdin, stdout, ssh_stderr = ssh.exec_command("ls -d {}".format(filename))
     out = stdout.read().decode("utf-8")
diff --git a/CGATCore/Pipeline/Parameters.py b/CGATCore/Pipeline/Parameters.py
index 44268d4..602a1b2 100644
--- a/CGATCore/Pipeline/Parameters.py
+++ b/CGATCore/Pipeline/Parameters.py
@@ -10,6 +10,7 @@
 import collections
 import os
 import sys
+import platform
 import configparser
 import getpass
 import logging
@@ -92,6 +93,8 @@ def __call__(self):
     'jobs_limit_db': 10,
     # ruffus job limits for R
     'jobs_limit_R': 1,
+    # operating system we are running on
+    'os': platform.system(),
 }
 
 # After all configuration files have been read, some
diff --git a/tests/test_pipeline_execution.py b/tests/test_pipeline_execution.py
index 3f49396..72cffb9 100644
--- a/tests/test_pipeline_execution.py
+++ b/tests/test_pipeline_execution.py
@@ -142,39 +142,46 @@ def test_job_should_fail_if_too_little_memory_required(self):
 
         outfile = os.path.join(self.work_dir, "out")
 
-        self.assertRaises(
-            OSError,
-            P.run,
-            "python -c 'import numpy; "
-            "a = numpy.array(numpy.arange(0, {memory}), numpy.int8); "
-            "out = open(\"{outfile}\", \"w\"); "
-            "out.write(str(len(a)) + \"\\n\"); "
-            "out.close()'".format(
-                memory=self.test_memory_size,
-                outfile=outfile),
-            to_cluster=self.to_cluster,
-            job_memory="{}G".format(
-                0.5 * self.test_memory_size / 10**9))
+        if P.get_parameters()['os'] == 'Linux':
+            self.assertRaises(
+                OSError,
+                P.run,
+                "python -c 'import numpy; "
+                "a = numpy.array(numpy.arange(0, {memory}), numpy.int8); "
+                "out = open(\"{outfile}\", \"w\"); "
+                "out.write(str(len(a)) + \"\\n\"); "
+                "out.close()'".format(
+                    memory=self.test_memory_size,
+                    outfile=outfile),
+                to_cluster=self.to_cluster,
+                job_memory="{}G".format(
+                    0.5 * self.test_memory_size / 10**9))
+        else:
+            pass
 
     def test_job_should_fail_if_too_little_memory_required_in_second_statement(self):
 
         outfile = os.path.join(self.work_dir, "out")
         infile = "arv=by_id/glon1-4zz18-3cbje7tmr0nitut/study_list.txt"
-        self.assertRaises(
-            OSError,
-            P.run,
-            "hostname > {outfile}; "
-            "python -c 'import numpy; "
-            "a = numpy.array(numpy.arange(0, {memory}), numpy.int8); "
-            "out = open(\"{outfile}\", \"w\"); "
-            "out.write(str(len(a)) + \"\\n\"); "
-            "out.close()'".format(
-                memory=self.test_memory_size,
-                infile=infile,
-                outfile=outfile),
-            to_cluster=self.to_cluster,
-            job_memory="{}G".format(
-                0.5 * self.test_memory_size / 10**9))
+
+        if P.get_parameters()['os'] == 'Linux':
+            self.assertRaises(
+                OSError,
+                P.run,
+                "hostname > {outfile}; "
+                "python -c 'import numpy; "
+                "a = numpy.array(numpy.arange(0, {memory}), numpy.int8); "
+                "out = open(\"{outfile}\", \"w\"); "
+                "out.write(str(len(a)) + \"\\n\"); "
+                "out.close()'".format(
+                    memory=self.test_memory_size,
+                    infile=infile,
+                    outfile=outfile),
+                to_cluster=self.to_cluster,
+                job_memory="{}G".format(
+                    0.5 * self.test_memory_size / 10**9))
+        else:
+            pass
 
     def test_job_should_pass_if_enough_memory_required(self):
         outfile = os.path.join(self.work_dir, "out")