[R] Fix: ES client causes urllib3 DeprecationWarning (#5592, PR #5909)

Author: dsotirho-ucsc

bin/wheels/runtime/MarkupSafe-2.1.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

@@ -10,10 +10,10 @@ blinker==1.7.0
 boto3==1.28.63
 boto3-stubs==1.28.63
 botocore==1.31.63
-botocore-stubs==1.34.31
+botocore-stubs==1.34.34
 brotli==1.1.0
 cachetools==5.3.2
-certifi==2023.11.17
+certifi==2024.2.2
 cffi==1.16.0
 chalice==1.30.0+12
 charset-normalizer==3.3.2
@@ -26,7 +26,7 @@ cryptography==42.0.2
 deprecated==1.2.13
 docker==6.1.2
 docutils==0.16
-elasticsearch==7.10.1
+elasticsearch==7.17.9
 elasticsearch-dsl==7.4.0
 et-xmlfile==1.1.0
 fastavro==1.8.2
@@ -51,8 +51,8 @@ google-crc32c==1.5.0
 google-resumable-media==2.7.0
 googleapis-common-protos==1.62.0
 greenlet==3.0.3
-grpcio==1.60.0
-grpcio-status==1.60.0
+grpcio==1.60.1
+grpcio-status==1.60.1
 http-message-signatures==0.4.4
 http_sfv==0.9.9
 httplib2==0.22.0
@@ -68,7 +68,7 @@ jsonschema==4.17.3
 jsonschema-spec==0.1.6
 lazy-object-proxy==1.10.0
 locust==2.12.2
-markupsafe==2.1.4
+markupsafe==2.1.5
 mccabe==0.7.0
 more-itertools==9.0.0
 moto==4.1.13
@@ -107,7 +107,7 @@ pyrsistent==0.20.0
 python-dateutil==2.8.2
 python-editor==1.0.4
 python-gitlab==3.13.0
-pytz==2023.4
+pytz==2024.1
 pyyaml==6.0.1
 pyzmq==25.1.2
 readchar==4.0.5

bin/wheels/runtime/MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

@@ -1,6 +1,6 @@
 blessed==1.20.0
 blinker==1.7.0
-botocore-stubs==1.34.31
+botocore-stubs==1.34.34
 brotli==1.1.0
 click==8.1.7
 colorama==0.4.4

bin/wheels/runtime/certifi-2023.11.17-py3-none-any.whl

@@ -1,19 +1,19 @@
 bagit==1.8.1
 bagit-profile==1.3.1
 cachetools==5.3.2
-certifi==2023.11.17
+certifi==2024.2.2
 cffi==1.16.0
 charset-normalizer==3.3.2
 cryptography==42.0.2
 google-cloud-core==2.4.1
 google-crc32c==1.5.0
 google-resumable-media==2.7.0
 googleapis-common-protos==1.62.0
-grpcio==1.60.0
-grpcio-status==1.60.0
+grpcio==1.60.1
+grpcio-status==1.60.1
 http_sfv==0.9.9
 idna==3.6
-markupsafe==2.1.4
+markupsafe==2.1.5
 orderedmultidict==1.0.1
 packaging==23.2
 proto-plus==1.23.0
@@ -23,7 +23,7 @@ pyasn1-modules==0.3.0
 pycparser==2.21
 pyopenssl==24.0.0
 python-dateutil==2.8.2
-pytz==2023.4
+pytz==2024.1
 s3transfer==0.7.0
 setuptools-scm==5.0.2
 six==1.16.0

bin/wheels/runtime/certifi-2024.2.2-py3-none-any.whl

@@ -6,7 +6,7 @@ botocore==1.31.63
 chevron==0.14.0
 deprecated==1.2.13
 elasticsearch-dsl==7.4.0
-elasticsearch==7.10.1
+elasticsearch==7.17.9
 fastavro==1.8.2
 furl==2.1.3
 google-auth[pyopenssl]==2.23.3

bin/wheels/runtime/elasticsearch-7.10.1-py2.py3-none-any.whl

@@ -20,6 +20,9 @@
     RequestsHttpConnection,
     Urllib3HttpConnection,
 )
+from elasticsearch.transport import (
+    Transport,
+)
 
 from azul import (
     config,
@@ -165,7 +168,8 @@ def _create_client(cls, host, port, timeout):
         # error handling, we disable the implicit retries via max_retries=0.
         common_params = dict(hosts=[dict(host=host, port=port)],
                              timeout=timeout,
-                             max_retries=0)
+                             max_retries=0,
+                             transport_class=ProductAgnosticTransport)
         if host.endswith('.amazonaws.com'):
             aws_auth = CachedBotoAWSRequestsAuth(aws_host=host,
                                                  aws_region=aws.region_name,
@@ -178,3 +182,14 @@ def _create_client(cls, host, port, timeout):
         else:
             return Elasticsearch(connection_class=AzulUrllib3HttpConnection,
                                  **common_params)
+
+
+class ProductAgnosticTransport(Transport):
+    """
+    A transport class that disables client-side product verification. This
+    bypasses the check that would otherwise prevent us from using ES v7.15+ with
+    OpenSearch.
+    """
+
+    def _do_verify_elasticsearch(self, headers, timeout):
+        self._verified_elasticsearch = True

bin/wheels/runtime/elasticsearch-7.17.9-py2.py3-none-any.whl

@@ -401,7 +401,7 @@ def flatten(value: JSON, *path) -> Iterable[tuple[tuple[str, ...], AnyJSON]]:
     def delete_indices(self, catalog: CatalogName):
         es_client = ESClientFactory.get()
         for index_name in self.index_names(catalog):
-            if es_client.indices.exists(index_name):
+            if es_client.indices.exists(index=index_name):
                 es_client.indices.delete(index=index_name)
 
     def contribute(self,

bin/wheels/runtime/grpcio-1.60.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

@@ -137,12 +137,12 @@ class RE(str):
 
                 'Call to deprecated function (or staticmethod) patch_source_cache',
 
-                # FIXME: ES client causes urllib3 DeprecationWarning
-                #        https://github.com/DataBiosphere/azul/issues/5592
-                (
-                    'HTTPResponse.getheaders() is deprecated and will be removed in urllib3 v2.1.0.'
-                    ' Instead access HTTPResponse.headers directly.',
-                    'elasticsearch.connection.http_urllib3'
+                # FIXME: DeprecationWarning for ES body parameter
+                #        https://github.com/DataBiosphere/azul/issues/5912
+                #
+                RE(
+                    'The \'body\' parameter is deprecated for the \'.*\' API '
+                    'and will be removed in .*. Instead use .*'
                 ),
             },
             UserWarning: {

bin/wheels/runtime/grpcio-1.60.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

@@ -180,7 +180,7 @@ def _add_docs(self, num_docs):
                     for doc in docs
                 )
             )
-            self.es_client.bulk(body, index=self._index_name, refresh=True)
+            self.es_client.bulk(body=body, index=self._index_name, refresh=True)
 
     @property
     def _index_name(self):