diff venv/lib/python2.7/site-packages/planemo/io.py @ 0:d67268158946 draft

planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venv/lib/python2.7/site-packages/planemo/io.py	Mon Oct 12 17:43:33 2015 -0400
@@ -0,0 +1,116 @@
+from __future__ import print_function
+import contextlib
+import os
+import shutil
+import sys
+import tempfile
+import time
+
+import click
+from galaxy.tools.deps import commands
+from galaxy.tools.deps.commands import which
+
+
+def communicate(cmds, **kwds):
+    info(cmds)
+    p = commands.shell_process(cmds, **kwds)
+    ret_val = p.communicate()
+    if p.returncode != 0:
+        template = "Problem executing commands {0} - ({1}, {2})"
+        msg = template.format(cmds, ret_val[0], ret_val[1])
+        raise RuntimeError(msg)
+    return ret_val
+
+
+def shell(cmds, **kwds):
+    info(cmds)
+    return commands.shell(cmds, **kwds)
+
+
+def info(message, *args):
+    if args:
+        message = message % args
+    _echo(click.style(message, bold=True, fg='green'))
+
+
+def can_write_to_path(path, **kwds):
+    if not kwds["force"] and os.path.exists(path):
+        error("%s already exists, exiting." % path)
+        return False
+    return True
+
+
+def error(message, *args):
+    if args:
+        message = message % args
+    _echo(click.style(message, bold=True, fg='red'), err=True)
+
+
+def warn(message, *args):
+    if args:
+        message = message % args
+    _echo(click.style(message, fg='red'), err=True)
+
+
+def _echo(message, err=False):
+    if sys.version_info[0] == 2:
+        click.echo(message, err=err)
+    else:
+        print(message)
+
+
+def write_file(path, content):
+    with open(path, "w") as f:
+        f.write(content)
+
+
+def untar_to(url, path, tar_args):
+    if which("wget"):
+        download_cmd = "wget -q --recursive -O - '%s'"
+    else:
+        download_cmd = "curl '%s'"
+    download_cmd = download_cmd % url
+    if tar_args:
+        if not os.path.exists(path):
+            os.makedirs(path)
+
+        untar_cmd = "tar %s" % tar_args
+        shell("%s | %s" % (download_cmd, untar_cmd))
+    else:
+        shell("%s > '%s'" % (download_cmd, path))
+
+
[e-mail]
+def temp_directory(prefix="planemo_tmp_"):
+    temp_dir = tempfile.mkdtemp(prefix=prefix)
+    try:
+        yield temp_dir
+    finally:
+        shutil.rmtree(temp_dir)
+
+
+def kill_pid_file(pid_file):
+    if not os.path.exists(pid_file):
+        return
+
+    pid = int(open(pid_file, "r").read())
+    kill_posix(pid)
+
+
+def kill_posix(pid):
+    def _check_pid():
+        try:
+            os.kill(pid, 0)
+            return True
+        except OSError:
+            return False
+
+    if _check_pid():
+        for sig in [15, 9]:
+            try:
+                os.kill(pid, sig)
+            except OSError:
+                return
+            time.sleep(1)
+            if not _check_pid():
+                return