diff env/lib/python3.9/site-packages/planemo/galaxy/ephemeris_sleep.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/galaxy/ephemeris_sleep.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+'''Utility to do a blocking sleep until a Galaxy instance is responsive.
+This is useful in docker images, in RUN steps, where one needs to wait
+for a currently starting Galaxy to be alive, before API requests can be
+made successfully.
+The script functions by making repeated requests to
+``http(s)://fqdn/api/version``, an API which requires no authentication
+to access.'''
+
+import sys
+import time
+from argparse import ArgumentParser
+
+import requests
+from galaxy.util import unicodify
+
+try:
+    from .common_parser import get_common_args
+except ImportError:
+    # This won't stay in Planemo long, main no longer functional.
+    get_common_args = None
+
+DEFAULT_SLEEP_WAIT = 1
+
+
+def _parser():
+    '''Constructs the parser object'''
+    parent = get_common_args(login_required=False)
+    parser = ArgumentParser(parents=[parent], usage="usage: python %(prog)s <options>",
+                            description="Script to sleep and wait for Galaxy to be alive.")
+    parser.add_argument("--timeout",
+                        default=0, type=int,
+                        help="Galaxy startup timeout in seconds. The default value of 0 waits forever")
+    return parser
+
+
+def _parse_cli_options():
+    """
+    Parse command line options, returning `parse_args` from `ArgumentParser`.
+    """
+    parser = _parser()
+    return parser.parse_args()
+
+
+class SleepCondition(object):
+
+    def __init__(self):
+        self.sleep = True
+
+    def cancel(self):
+        self.sleep = False
+
+
+def sleep(galaxy_url, verbose=False, timeout=0, sleep_condition=None):
+    if sleep_condition is None:
+        sleep_condition = SleepCondition()
+
+    count = 0
+    while sleep_condition.sleep:
+        try:
+            result = requests.get(galaxy_url + '/api/version')
+            try:
+                result = result.json()
+                if verbose:
+                    sys.stdout.write("Galaxy Version: %s\n" % result['version_major'])
+                    sys.stdout.flush()
+                break
+            except ValueError:
+                if verbose:
+                    sys.stdout.write("[%02d] No valid json returned... %s\n" % (count, result.__str__()))
+                    sys.stdout.flush()
+        except requests.exceptions.ConnectionError as e:
+            if verbose:
+                sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, unicodify(e)[:100]))
+                sys.stdout.flush()
+        count += 1
+
+        # If we cannot talk to galaxy and are over the timeout
+        if timeout != 0 and count > timeout:
+            sys.stderr.write("Failed to contact Galaxy\n")
+            return False
+
+        time.sleep(DEFAULT_SLEEP_WAIT)
+
+    return True
+
+
+def main():
+    """
+    Main function
+    """
+    options = _parse_cli_options()
+
+    galaxy_alive = sleep(galaxy_url=options.galaxy, verbose=options.verbose, timeout=options.timeout)
+    exit_code = 0 if galaxy_alive else 1
+    sys.exit(exit_code)
+
+
+if __name__ == "__main__":
+    main()