s3 region should have a single config param (#1386)

* s3 region should have a single config param

The s3 region can also now be automatically determined to further
reduce errors.

This patch also fixes a bug with order of handling the config params.
The tiledb config needs to be fixed before attempting to load
(need to handle_adaptor before handle_single_dataset)

server/common/app_config.py

@@ -6,6 +6,8 @@ import sys
 from urllib.parse import urlparse
 import yaml
 import copy
+import boto3
+import botocore
 
 from server.common.default_config import get_default_config
 from server.common.errors import ConfigurationError, DatasetAccessError, OntologyLoadFailure
@@ -188,13 +190,13 @@ class AppConfig(object):
 
         self.handle_server(context)
         self.handle_data_locator(context)
+        self.handle_adaptor(context)  # may depend on data_locator
         self.handle_presentation(context)
-        self.handle_single_dataset(context)
-        self.handle_multi_dataset(context)
+        self.handle_single_dataset(context)  # may depend on adaptor
+        self.handle_multi_dataset(context)  # may depend on adaptor
         self.handle_user_annotations(context)
         self.handle_embeddings(context)
         self.handle_diffexp(context)
-        self.handle_adaptor(context)
         self.handle_limits(context)
 
         self.is_completed = True
@@ -255,7 +257,22 @@ class AppConfig(object):
         self.server__flask_secret_key = environ.get("CXG_SECRET_KEY", self.server__flask_secret_key)
 
     def handle_data_locator(self, context):
-        self.__check_attr("data_locator__s3__region_name", (type(None), str))
+        self.__check_attr("data_locator__s3__region_name", (type(None), bool, str))
+        if self.data_locator__s3__region_name is True:
+            path = self.single_dataset__datapath or self.multi_dataset__dataroot
+            if path and path.startswith("s3:"):
+                bucket = urlparse(path).netloc
+                client = boto3.client("s3")
+                try:
+                    res = client.head_bucket(Bucket=bucket)
+                except botocore.exceptions.ClientError:
+                    raise ConfigurationError(f"Unable to determine region from {path}")
+
+                region = res.get("ResponseMetadata", {}).get("HTTPHeaders", {}).get("x-amz-bucket-region")
+                if region:
+                    self.data_locator__s3__region_name = region
+                else:
+                    raise ConfigurationError(f"Unable to determine region from {path}")
 
     def handle_presentation(self, context):
         self.__check_attr("presentation__max_categories", int)
@@ -281,7 +298,7 @@ class AppConfig(object):
             self.matrix_data_cache_manager = MatrixDataCacheManager(max_cached=1, timelimit_s=None)
 
         # preload this data set
-        matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath)
+        matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self)
         try:
             matrix_data_loader.pre_load_validation()
         except DatasetAccessError as e:
@@ -404,7 +421,7 @@ class AppConfig(object):
 
         if self.single_dataset__datapath:
             if self.embeddings__enable_reembedding:
-                matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath)
+                matrix_data_loader = MatrixDataLoader(self.single_dataset__datapath, app_config=self)
                 if matrix_data_loader.matrix_data_type() != MatrixDataType.H5AD:
                     raise ConfigurationError("'enable-reembedding is only supported with H5AD files.")
                 if self.adaptor__anndata_adaptor__backed:
@@ -425,6 +442,11 @@ class AppConfig(object):
     def handle_adaptor(self, context):
         # cxg
         self.__check_attr("adaptor__cxg_adaptor__tiledb_ctx", dict)
+        regionkey = "vfs.s3.region"
+        if regionkey not in self.adaptor__cxg_adaptor__tiledb_ctx:
+            if type(self.data_locator__s3__region_name) == str:
+                self.adaptor__cxg_adaptor__tiledb_ctx[regionkey] = self.data_locator__s3__region_name
+
         from server.data_cxg.cxg_adaptor import CxgAdaptor
 
         CxgAdaptor.set_tiledb_context(self.adaptor__cxg_adaptor__tiledb_ctx)

server/common/default_config.py

@@ -68,14 +68,20 @@ diffexp:
 
 data_locator:
   s3:
-    region_name: us-east-1
+    # s3 region name.
+    #   if true, then the s3 location is automatically determined from the datapath or dataroot.
+    #   if false/null, then do not set.
+    #   if a string, then use that value (e.g. us-east-1).
+    region_name: true
 
 adaptor:
   cxg_adaptor:
+    # The key/values under tiledb_ctx will be used to initialize the tiledb Context.
+    # If 'vfs.s3.region' is not set, then it will automatically use the setting from
+    # data_locator / s3 / region_name.
     tiledb_ctx:
       sm.tile_cache_size:  8589934592
       sm.num_reader_threads:  32
-      vfs.s3.region: us-east-1
 
   anndata_adaptor:
       backed: false

server/requirements.txt

@@ -1,4 +1,5 @@
 anndata>=0.6.20
+boto3>=1.12.18
 click>=6.7
 fastobo>=0.6.1
 Flask>=1.0.2