allow additional controls for terminal output

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: Allows controlling how commandline interface terminal output is handled.
 
 Release 0.7.0 (Dec 18, 2012)
 ============================

doc/users/config_file.rst

@@ -114,6 +114,14 @@ Execution
     version information is available. Please notify developers or submit a
     patch.
 
+*commandline_output (CommandLine interfaces only)*
+    Controls how terminal output from a command line is handled. There are 4
+    possible options. (default: 'stream' for current compatibility)
+    `stream`: line by line streaming to terminal
+    `allatonce`: streams after command has terminated
+    `file`: writes output to stdout.nipype and stderr.nipype
+    `none`: suppresses all output
+
 Example
 ~~~~~~~
 

nipype/interfaces/base.py

@@ -1038,42 +1038,76 @@ def run_command(runtime, timeout=0.01):
                              shell=True,
                              cwd=runtime.cwd,
                              env=runtime.environ)
-    streams = [
-        Stream('stdout', proc.stdout),
-        Stream('stderr', proc.stderr)
-        ]
+    result = {}
+    if config.get('execution', 'commandline_output').lower() == 'stream':
+        streams = [
+            Stream('stdout', proc.stdout),
+            Stream('stderr', proc.stderr)
+            ]
 
-    def _process(drain=0):
-        try:
-            res = select.select(streams, [], [], timeout)
-        except select.error, e:
-            iflogger.info(str(e))
-            if e[0] == errno.EINTR:
-                return
+        def _process(drain=0):
+            try:
+                res = select.select(streams, [], [], timeout)
+            except select.error, e:
+                iflogger.info(str(e))
+                if e[0] == errno.EINTR:
+                    return
+                else:
+                    raise
             else:
-                raise
-        else:
-            for stream in res[0]:
-                stream.read(drain)
-
-    while proc.returncode is None:
-        proc.poll()
-        _process()
-    runtime.returncode = proc.returncode
-    _process(drain=1)
+                for stream in res[0]:
+                    stream.read(drain)
+
+        while proc.returncode is None:
+            proc.poll()
+            _process()
+        runtime.returncode = proc.returncode
+        _process(drain=1)
+
+        # collect results, merge and return
+        temp = []
+        for stream in streams:
+            rows = stream._rows
+            temp += rows
+            result[stream._name] = [r[2] for r in rows]
+        temp.sort()
+        result['merged'] = [r[1] for r in temp]
+    elif config.get('execution', 'commandline_output').lower() == 'allatonce':
+        stdout, stderr = proc.communicate()
+        result['stdout'] = stdout.split('\n')
+        result['stderr'] = stderr.split('\n')
+        result['merged'] = ''
+    elif config.get('execution', 'commandline_output').lower() == 'file':
+        errfile = os.path.join(runtime.cwd, 'stderr.nipype')
+        outfile = os.path.join(runtime.cwd, 'stdout.nipype')
+        stderr =  open(errfile, 'wt')
+        stdout =  open(outfile, 'wt')
+        proc = subprocess.Popen(runtime.cmdline,
+                            stdout=stdout,
+                            stderr=stderr,
+                            shell=True,
+                            cwd=runtime.cwd,
+                            env=runtime.environ)
+        ret_code = proc.wait()
+        stderr.flush()
+        stdout.flush()
+        result['stdout'] = [line.strip() for line in open(outfile).readlines()]
+        result['stderr'] = [line.strip() for line in open(errfile).readlines()]
+        result['merged'] = ''
+    elif config.get('execution', 'commandline_output').lower() == 'none':
+        proc.communicate()
+        result['stdout'] = []
+        result['stderr'] = []
+        result['merged'] = ''
+    else:
+        raise ValueError(("Unknown input for config['execution']"
+                          "['commandline_output']. Should be one of 'stream', "
+                          "'allatonce', 'file', or 'none'"))
 
-    # collect results, merge and return
-    result = {}
-    temp = []
-    for stream in streams:
-        rows = stream._rows
-        temp += rows
-        result[stream._name] = [r[2] for r in rows]
-    temp.sort()
-    result['merged'] = [r[1] for r in temp]
     runtime.stderr = '\n'.join(result['stderr'])
     runtime.stdout = '\n'.join(result['stdout'])
     runtime.merged = result['merged']
+    runtime.returncode = proc.returncode
     return runtime
 
 

nipype/interfaces/tests/test_base.py

@@ -461,3 +461,36 @@ def test_Commandline_environ():
     ci3.inputs.environ = {'DISPLAY' : ':2'}
     res = ci3.run()
     yield assert_equal, res.runtime.environ['DISPLAY'], ':2'
+
+
+def test_CommandLine_output():
+    from nipype import config
+    config.set_default_config()
+    config.set('execution', 'commandline_output', 'foo')
+    ci = nib.CommandLine(command='ls -l')
+    yield assert_raises, ValueError, ci.run
+
+    tmp_infile = setup_file()
+    tmpd, name = os.path.split(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+    yield assert_true, os.path.exists(tmp_infile)
+    config.set('execution', 'commandline_output', 'allatonce')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_equal, res.runtime.merged, ''
+    yield assert_true, name in res.runtime.stdout
+    config.set('execution', 'commandline_output', 'file')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_true, 'stdout.nipype' in res.runtime.stdout
+    config.set('execution', 'commandline_output', 'none')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_equal, res.runtime.stdout, ''
+    config.set('execution', 'commandline_output', 'stream')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_true, 'stdout.nipype' in res.runtime.stdout
+    os.chdir(pwd)
+    teardown_file(tmpd)

nipype/pipeline/utils.py

@@ -670,7 +670,8 @@ def clean_working_directory(outputs, cwd, inputs, needed_outputs, config,
         input_files.extend(walk_outputs(inputdict))
         needed_files += [path for path, type in input_files if type == 'f']
     for extra in ['_0x*.json', 'provenance.xml', 'pyscript*.m',
-                  'command.txt', 'result*.pklz', '_inputs.pklz', '_node.pklz']:
+                  'command.txt', 'result*.pklz', '_inputs.pklz', '_node.pklz',
+                  'stderr.nipype', 'stdout.nipype']:
         needed_files.extend(glob(os.path.join(cwd, extra)))
     if files2keep:
         needed_files.extend(filename_to_list(files2keep))

nipype/utils/config.py

@@ -46,6 +46,7 @@
 stop_on_first_rerun = false
 use_relative_paths = false
 stop_on_unknown_version = false
+commandline_output = stream
 
 [check]
 interval = 1209600