Modify how HCA cache is cleared (#431)

* Modify how HCA cache is cleared

- Changed refresh_swagger to clear_cache
- Fixed typo in clear_cache documentation
- Adding clear-hca-cache to CLI to clear the cache of all SwaggerClients subclasses.
- Updated tests and tutorials.

hca/__init__.py

@@ -2,3 +2,10 @@
 
 from .config import HCAConfig, get_config, logger
 from . import dss, upload, query
+
+
+def clear_hca_cache(args):
+    """Clear the cached HCA API definitions. This can help resolve errors communicating with the API."""
+    from hca.util import SwaggerClient
+    for swagger_client in SwaggerClient.__subclasses__():
+        swagger_client().clear_cache()

hca/cli.py

@@ -29,6 +29,7 @@
 from .upload import cli as upload_cli
 from .query import cli as query_cli
 from .util.compat import USING_PYTHON2
+from . import clear_hca_cache
 from . import logger, get_config
 
 
@@ -94,6 +95,7 @@ def get_parser(help_menu=False):
     parser.add_argument("--log-level", default=get_config().get("log_level"),
                         help=str([logging.getLevelName(i) for i in range(10, 60, 10)]),
                         choices={logging.getLevelName(i) for i in range(10, 60, 10)})
+    parser.add_parser_func(clear_hca_cache, help=clear_hca_cache.__doc__)
 
     def help(args):
         parser.print_help()

hca/util/__init__.py

@@ -249,7 +249,7 @@ def __init__(self, config=None, swagger_url=None, **session_kwargs):
         else:
             self.__class__.__doc__ = _md2rst(self.swagger_spec["info"]["description"])
         self.methods = {}
-        self.commands = [self.login, self.logout, self.refresh_swagger]
+        self.commands = [self.login, self.logout]
         self.http_paths = collections.defaultdict(dict)
         if "openapi" in self.swagger_spec:
             server = self.swagger_spec["servers"][0]
@@ -314,9 +314,9 @@ def _get_swagger_filename(self, swagger_url):
         swagger_filename = os.path.join(self.config.user_config_dir, swagger_filename)
         return swagger_filename
 
-    def refresh_swagger(self):
+    def clear_cache(self):
         """
-        Manually refresh the swagger document. This can help resolve errors communicate with the API.
+        Clear the cached API definitions for a component. This can help resolve errors communicating with the API.
         """
         try:
             os.remove(self._get_swagger_filename(self.swagger_url))

test/integration/dss/test_dss_api.py

@@ -368,14 +368,14 @@ def test_get_bundle_iteration_pagination(self, limit=128):
                 if ix > limit:
                     break
 
-    def test_refresh_swagger(self):
-        """Testing refresh_swagger by comparing the creation date of the old swagger with the refreshed swagger that
+    def test_clear_cache(self):
+        """Testing clear_cache by comparing the creation date of the old swagger with the refreshed swagger that
         replaces it"""
         client = hca.dss.DSSClient()
         swagger_filename = client._get_swagger_filename(client.swagger_url)
         self.assertTrue(os.path.isfile(swagger_filename), "Pass if file exists initially")
         old_swagger = datetime.datetime.fromtimestamp(os.path.getmtime(swagger_filename))
-        client.refresh_swagger()
+        client.clear_cache()
         new_swagger = datetime.datetime.fromtimestamp(os.path.getmtime(swagger_filename))
         self.assertGreater(new_swagger, old_swagger)
 

test/tutorial/scripts/api/refresh_swagger_api.py → test/tutorial/scripts/api/clear_cache_api.py

@@ -2,4 +2,4 @@
 
 dss = DSSClient()
 
-dss.refresh_swagger()
+dss.clear_cache()

test/tutorial/scripts/tutorial/get_file_tutorial.py

@@ -12,7 +12,7 @@
 dss.login(access_token=access_token)
 
 # Refreshes Swagger document. Can help resolve errors communicate with the API.
-dss.refresh_swagger()
+dss.clear_cache()
 
 # JSON query and returns matching bundle identifiers.
 for results in dss.post_search.iterate(replica="aws", es_query={}):