Double quote escape for bash script ENV_VAR part

aiida/common/escaping.py

@@ -12,7 +12,7 @@
 import re
 
 
-def escape_for_bash(str_to_escape):
+def escape_for_bash(str_to_escape, use_double_quotes=False):
     """
     This function takes any string and escapes it in a way that
     bash will interpret it as a single string.
@@ -34,14 +34,23 @@ def escape_for_bash(str_to_escape):
     Finally, note that for python I have to enclose the string '"'"'
     within triple quotes to make it work, getting finally: the complicated
     string found below.
+
+    :param str_to_escape: the string to escape.
+    :param use_double_quotes: boolean, if ``True``, use double quotes instead of single quotes.
+    :return: the escaped string.
     """
     if str_to_escape is None:
         return ''
 
     str_to_escape = str(str_to_escape)
-
-    escaped_quotes = str_to_escape.replace("'", """'"'"'""")
-    return f"'{escaped_quotes}'"
+    if use_double_quotes:
+        escaped_quotes = str_to_escape.replace('"', '''"'"'"''')
+        escaped = f'"{escaped_quotes}"'
+    else:
+        escaped_quotes = str_to_escape.replace("'", """'"'"'""")
+        escaped = f"'{escaped_quotes}'"
+
+    return escaped
 
 
 # Mapping of "SQL" tokens into corresponding regex expressions

aiida/engine/processes/calcjobs/calcjob.py

@@ -244,6 +244,9 @@ def define(cls, spec: CalcJobProcessSpec) -> None:  # type: ignore[override]
             help='If set to true, the submission script will load the system environment variables',)
         spec.input('metadata.options.environment_variables', valid_type=dict, default=lambda: {},
             help='Set a dictionary of custom environment variables for this calculation',)
+        spec.input('metadata.options.environment_variables_double_quotes', valid_type=bool, default=False,
+            help='If set to True, use double quotes instead of single quotes to escape the environment variables '
+                 'specified in ``environment_variables``.',)
         spec.input('metadata.options.priority', valid_type=str, required=False,
             help='Set the priority of the job to be queued')
         spec.input('metadata.options.max_memory_kb', valid_type=int, required=False,
@@ -731,6 +734,7 @@ def presubmit(self, folder: Folder) -> CalcInfo:
         job_tmpl.import_sys_environment = self.node.get_option('import_sys_environment')
 
         job_tmpl.job_environment = self.node.get_option('environment_variables')
+        job_tmpl.environment_variables_double_quotes = self.node.get_option('environment_variables_double_quotes')
 
         queue_name = self.node.get_option('queue_name')
         account = self.node.get_option('account')

aiida/schedulers/datastructures.py

@@ -248,6 +248,9 @@ class JobTemplate(DefaultFieldsAttributeDict):  # pylint: disable=too-many-insta
       * ``rerunnable``: if the job is rerunnable (boolean)
       * ``job_environment``: a dictionary with environment variables to set
         before the execution of the code.
+      * ``environment_variables_double_quotes``: if set to True, use double quotes
+        instead of single quotes to escape the environment variables specified
+        in ``environment_variables``.
       * ``working_directory``: the working directory for this job. During
         submission, the transport will first do a 'chdir' to this directory,
         and then possibly set a scheduler parameter, if this is supported
@@ -328,6 +331,7 @@ class JobTemplate(DefaultFieldsAttributeDict):  # pylint: disable=too-many-insta
         'submit_as_hold',
         'rerunnable',
         'job_environment',
+        'environment_variables_double_quotes',
         'working_directory',
         'email',
         'email_on_started',

aiida/schedulers/scheduler.py

@@ -182,7 +182,7 @@ def _get_submit_script_environment_variables(self, template):  # pylint: disable
         lines = ['# ENVIRONMENT VARIABLES BEGIN ###']
 
         for key, value in template.job_environment.items():
-            lines.append(f'export {key.strip()}={escape_for_bash(value)}')
+            lines.append(f'export {key.strip()}={escape_for_bash(value, template.environment_variables_double_quotes)}')
 
         lines.append('# ENVIRONMENT VARIABLES END ###')
 

tests/common/test_escaping.py

@@ -8,19 +8,24 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Tests for the :mod:`aiida.common.escaping`."""
+import pytest
+
 from aiida.common.escaping import escape_for_bash
 
 
-def test_escape_for_bash():
+@pytest.mark.parametrize(('to_escape, expected_single_quotes, expected_double_quotes'), (
+    (None, '', ''),
+    ('string', "'string'", '"string"'),
+    ('string with space', "'string with space'", '"string with space"'),
+    (
+        """string with ' single and " double quote""", """'string with '"'"' single and " double quote'""",
+        '''"string with ' single and "'"'" double quote"'''
+    ),
+    (1, "'1'", '"1"'),
+    (2.0, "'2.0'", '"2.0"'),
+    ('$PWD', "'$PWD'", '"$PWD"'),
+))
+def test_escape_for_bash(to_escape, expected_single_quotes, expected_double_quotes):
     """Tests various inputs for `aiida.common.escaping.escape_for_bash`."""
-    tests = (
-        [None, ''],
-        ['string', "'string'"],
-        ['string with space', "'string with space'"],
-        ["string with a ' single quote", """'string with a '"'"' single quote'"""],
-        [1, "'1'"],
-        [2.0, "'2.0'"],
-    )
-
-    for string_input, string_escaped in tests:
-        assert escape_for_bash(string_input) == string_escaped
+    assert escape_for_bash(to_escape, use_double_quotes=False) == expected_single_quotes
+    assert escape_for_bash(to_escape, use_double_quotes=True) == expected_double_quotes

tests/schedulers/test_sge.py

@@ -327,6 +327,7 @@ def test_submit_script(self):
         job_tmpl.priority = None
         job_tmpl.max_wallclock_seconds = '3600'  # "23:59:59"
         job_tmpl.job_environment = {'HOME': '/home/users/dorigm7s/', 'WIENROOT': '$HOME:/WIEN2k'}
+        job_tmpl.environment_variables_double_quotes = True
 
         submit_script_text = sge.get_submit_script(job_tmpl)
 
@@ -335,8 +336,8 @@ def test_submit_script(self):
         self.assertTrue('#$ -q FavQ.q' in submit_script_text)
         self.assertTrue('#$ -l h_rt=01:00:00' in submit_script_text)
         self.assertTrue('# ENVIRONMENT VARIABLES BEGIN ###' in submit_script_text)
-        self.assertTrue("export HOME='/home/users/dorigm7s/'" in submit_script_text)
-        self.assertTrue("export WIENROOT='$HOME:/WIEN2k'" in submit_script_text)
+        self.assertTrue('export HOME="/home/users/dorigm7s/"' in submit_script_text)
+        self.assertTrue('export WIENROOT="$HOME:/WIEN2k"' in submit_script_text)
         self.assertFalse('#$ -r yes' in submit_script_text)
 
     def test_submit_script_rerunnable(self):  # pylint: disable=no-self-use