Merge pull request #4454 from branfosj/cmd_filename

allow only alphanumeric characters in the output filename

Author: boegel

easybuild/tools/run.py

@@ -42,6 +42,7 @@
 import re
 import signal
 import shutil
+import string
 import subprocess
 import sys
 import tempfile
@@ -187,6 +188,19 @@ def cache_aware_func(cmd, *args, **kwargs):
 run_shell_cmd_cache = run_cmd_cache
 
 
+def fileprefix_from_cmd(cmd, allowed_chars=False):
+    """
+    Simplify the cmd to only the allowed_chars we want in a filename
+
+    :param cmd: the cmd (string)
+    :param allowed_chars: characters allowed in filename (defaults to string.ascii_letters + string.digits + "_-")
+    """
+    if not allowed_chars:
+        allowed_chars = f"{string.ascii_letters}{string.digits}_-"
+
+    return ''.join([c for c in cmd if c in allowed_chars])
+
+
 @run_shell_cmd_cache
 def run_shell_cmd(cmd, fail_on_error=True, split_stderr=False, stdin=None, env=None,
                   hidden=False, in_dry_run=False, verbose_dry_run=False, work_dir=None, use_bash=True,
@@ -238,7 +252,6 @@ def to_cmd_str(cmd):
         work_dir = os.getcwd()
 
     cmd_str = to_cmd_str(cmd)
-    cmd_name = os.path.basename(cmd_str.split(' ')[0])
 
     thread_id = None
     if asynchronous:
@@ -254,6 +267,7 @@ def to_cmd_str(cmd):
     if output_file:
         toptmpdir = os.path.join(tempfile.gettempdir(), 'run-shell-cmd-output')
         os.makedirs(toptmpdir, exist_ok=True)
+        cmd_name = fileprefix_from_cmd(os.path.basename(cmd_str.split(' ')[0]))
         tmpdir = tempfile.mkdtemp(dir=toptmpdir, prefix=f'{cmd_name}-')
         cmd_out_fp = os.path.join(tmpdir, 'out.txt')
         _log.info(f'run_cmd: Output of "{cmd_str}" will be logged to {cmd_out_fp}')

test/framework/run.py

@@ -35,6 +35,7 @@
 import os
 import re
 import signal
+import string
 import stat
 import subprocess
 import sys
@@ -52,7 +53,7 @@
 from easybuild.tools.config import update_build_option
 from easybuild.tools.filetools import adjust_permissions, change_dir, mkdir, read_file, write_file
 from easybuild.tools.run import RunShellCmdResult, RunShellCmdError, check_async_cmd, check_log_for_errors
-from easybuild.tools.run import complete_cmd, get_output_from_process, parse_log_for_error
+from easybuild.tools.run import complete_cmd, fileprefix_from_cmd, get_output_from_process, parse_log_for_error
 from easybuild.tools.run import run_cmd, run_cmd_qa, run_shell_cmd, subprocess_terminate
 from easybuild.tools.config import ERROR, IGNORE, WARN
 
@@ -194,6 +195,26 @@ def test_run_shell_cmd_basic(self):
             self.assertTrue(isinstance(res.output, str))
             self.assertTrue(res.work_dir and isinstance(res.work_dir, str))
 
+    def test_fileprefix_from_cmd(self):
+        """test simplifications from fileprefix_from_cmd."""
+        cmds = {
+            'abd123': 'abd123',
+            'ab"a': 'aba',
+            'a{:$:S@"a': 'aSa',
+            'cmd-with-dash': 'cmd-with-dash',
+            'cmd_with_underscore': 'cmd_with_underscore',
+        }
+        for cmd, expected_simplification in cmds.items():
+            self.assertEqual(fileprefix_from_cmd(cmd), expected_simplification)
+
+        cmds = {
+            'abd123': 'abd',
+            'ab"a': 'aba',
+            '0a{:$:2@"a': 'aa',
+        }
+        for cmd, expected_simplification in cmds.items():
+            self.assertEqual(fileprefix_from_cmd(cmd, allowed_chars=string.ascii_letters), expected_simplification)
+
     def test_run_cmd_log(self):
         """Test logging of executed commands."""
         fd, logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')