From 9f4ed2f1efc3e1d903fce2874b68aa10ff0fe083 Mon Sep 17 00:00:00 2001
From: julie-sullivan <julie.sullivan@gmail.com>
Date: Tue, 6 Jul 2021 11:57:52 +0100
Subject: [PATCH] add query retry to pycellbase

---
 .../src/main/python/pycellbase/__init__.py    |  2 +-
 .../main/python/pycellbase/cbrestclients.py   |  4 +-
 .../src/main/python/pycellbase/commons.py     | 41 +++++++++++++++++++
 cellbase-client/src/main/python/setup.py      |  2 +-
 4 files changed, 46 insertions(+), 3 deletions(-)

diff --git a/cellbase-client/src/main/python/pycellbase/__init__.py b/cellbase-client/src/main/python/pycellbase/__init__.py
index 3c9329b277..a0f66580ce 100755
--- a/cellbase-client/src/main/python/pycellbase/__init__.py
+++ b/cellbase-client/src/main/python/pycellbase/__init__.py
@@ -1 +1 @@
-__version__ = '4.7.1'
+__version__ = '5.0.0'
diff --git a/cellbase-client/src/main/python/pycellbase/cbrestclients.py b/cellbase-client/src/main/python/pycellbase/cbrestclients.py
index cff658d190..91240a1a7c 100755
--- a/cellbase-client/src/main/python/pycellbase/cbrestclients.py
+++ b/cellbase-client/src/main/python/pycellbase/cbrestclients.py
@@ -1,6 +1,7 @@
 import sys
+import subprocess
 
-from pycellbase.commons import get, deprecated
+from pycellbase.commons import get, deprecated, retry
 
 
 class _ParentRestClient(object):
@@ -11,6 +12,7 @@ def __init__(self, session, configuration, subcategory, category):
         self._subcategory = subcategory
         self._category = category
 
+    @retry(subprocess.TimeoutExpired)
     def _get(self, resource, query_id=None, options=None):
         """Queries the REST service and returns the result"""
         response = get(session=self._session,
diff --git a/cellbase-client/src/main/python/pycellbase/commons.py b/cellbase-client/src/main/python/pycellbase/commons.py
index 6572cc1bfc..730311d673 100644
--- a/cellbase-client/src/main/python/pycellbase/commons.py
+++ b/cellbase-client/src/main/python/pycellbase/commons.py
@@ -1,6 +1,8 @@
+import logging
 import sys
 import time
 import warnings
+from functools import wraps
 import requests
 import threading
 import itertools
@@ -265,3 +267,42 @@ def new_func(*args, **kwargs):
         warnings.simplefilter('default', DeprecationWarning)  # reset filter
         return func(*args, **kwargs)
     return new_func
+
+def retry(exception_type, total_tries=2, wait_period=2, backoff=2):
+    """
+    Definition of a spicy little decorator-wrapper class
+    This will wrap methods (e.g. samtools reads), catching only specific error types, and replaying the command
+    This uses exponential backoff-retrier logical timing, and a set number of retries/adjustable wait period
+    """
+
+    def retry_decorator(f):
+        @wraps(f)
+        def func_with_retries(*args, **kwargs):
+            _tries, _delay = total_tries + 1, wait_period
+            while _tries > 1:
+
+                try:
+                    return f(*args, **kwargs)
+                except exception_type as e:
+                    _tries -= 1
+                    if _tries == 1:
+                        logging.error(
+                            "Attempted command {} times, without success".format(
+                                total_tries
+                            ),
+                            exc_info=True,
+                        )
+                        raise
+
+                    logging.warning(
+                        "Timeout detected, retrying in {} seconds. Args {}, Kwargs {}".format(
+                            _delay, args, kwargs
+                        )
+                    )
+                    time.sleep(_delay)
+                    # for each failure, extend the wait
+                    _delay *= backoff
+
+        return func_with_retries
+
+    return retry_decorator
\ No newline at end of file
diff --git a/cellbase-client/src/main/python/setup.py b/cellbase-client/src/main/python/setup.py
index 8cf3a57023..f35bf2bbb5 100755
--- a/cellbase-client/src/main/python/setup.py
+++ b/cellbase-client/src/main/python/setup.py
@@ -13,7 +13,7 @@
 
 setup_kwargs = {
     'name': 'pycellbase',
-    'version': '4.7.1',
+    'version': '5.0.0',
     'description': 'Python client for CellBase',
     'long_description': long_description,
     'long_description_content_type': 'text/x-rst',