ebi-eva-common-pyutils 0.6.3__py3-none-any.whl → 0.6.5__py3-none-any.whl

ebi_eva_common_pyutils/network_utils.py

@@ -11,7 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
+import time
 
 import requests
 import subprocess
@@ -43,6 +43,13 @@ def forward_remote_port_to_local_port(remote_host: str, remote_port: int, local_
     port_forward_command = 'ssh -N -L{0}:localhost:{1} {2}'.format(local_port, remote_port, remote_host)
     logger.info("Forwarding port to local port using command: " + port_forward_command)
     proc = subprocess.Popen(port_forward_command.split(" "))
+    time.sleep(5)
+    # Ensure that the process is still running
+    poll = proc.poll()
+    if poll is not None:
+        # The process already completed which mean it most likely crashed
+        logger.error(f'Port Forwarding {remote_host}:{remote_port} -> {local_port} failed!')
+        raise subprocess.CalledProcessError(proc.returncode, proc.args)
     return proc.pid
 
 

{ebi_eva_common_pyutils-0.6.3.dist-info → ebi_eva_common_pyutils-0.6.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: ebi-eva-common-pyutils
-Version: 0.6.3
+Name: ebi_eva_common_pyutils
+Version: 0.6.5
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -19,5 +19,5 @@ Requires-Dist: retry
 Provides-Extra: eva-internal
 Requires-Dist: psycopg2-binary ; extra == 'eva-internal'
 Requires-Dist: pymongo ; extra == 'eva-internal'
-Requires-Dist: networkx (<=2.5) ; extra == 'eva-internal'
+Requires-Dist: networkx <=2.5 ; extra == 'eva-internal'
 

{ebi_eva_common_pyutils-0.6.3.dist-info → ebi_eva_common_pyutils-0.6.5.dist-info}/RECORD

@@ -7,7 +7,7 @@ ebi_eva_common_pyutils/ena_utils.py,sha256=S2MmnWQ_9MJjlkaQY_by1-GGbTyi8SKp8XRcp
 ebi_eva_common_pyutils/file_utils.py,sha256=eIlQKSVKkEjMNX7emrDzaQyQdGvQdb64gnfEhb6uYsE,1375
 ebi_eva_common_pyutils/logger.py,sha256=hT20ktN_oGeB_5ofVfd_aGXB6xYOe0Y5b3EVRYCuFb8,5093
 ebi_eva_common_pyutils/ncbi_utils.py,sha256=sh9E_oDhDtliihJ0-FZuDd7paeidW5GfqRr5vBTo2k4,4859
-ebi_eva_common_pyutils/network_utils.py,sha256=_Qf5oNONA4pUzvxfdk25G-dKuWe44aC_Hewvdp-VZyU,2285
+ebi_eva_common_pyutils/network_utils.py,sha256=iJjs5PPzT1V4CceZnCHOTs711AmpwlDo59wb1XHdTak,2648
 ebi_eva_common_pyutils/assembly/__init__.py,sha256=KSWPwBY5nZj00odxWFntk8Sqg_rw273xH8S5D6Jo-T4,67
 ebi_eva_common_pyutils/assembly/assembly.py,sha256=IEmleROX4ZchPyhINKCuMmET_Ih1Jg4ok-opAKY6Z9A,3142
 ebi_eva_common_pyutils/contig_alias/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -19,7 +19,7 @@ ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
 ebi_eva_common_pyutils/taxonomy/taxonomy.py,sha256=p3XV4g3y0hEjyeZ4PwgN7Q3Et9G515ctQkSIo1kdDbU,2259
 ebi_eva_common_pyutils/variation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_common_pyutils/variation/contig_utils.py,sha256=kMNEW_P2yPnd8Xx1tep19hy5ee7ojxz6ZOO1grTQsRQ,5230
-ebi_eva_common_pyutils-0.6.3.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.6.5.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
 ebi_eva_internal_pyutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_internal_pyutils/archive_directory.py,sha256=IxVEfh_gaCiT652k0Q_-58fonRusy1yzXu7BCO8yVLo,4989
 ebi_eva_internal_pyutils/config_utils.py,sha256=EGRC5rsmU_ug7OY9-t1UW1XZXRsauSyZB9xPcBux8ts,7909
@@ -28,11 +28,11 @@ ebi_eva_internal_pyutils/mongo_utils.py,sha256=YxKHtb5ygDiGLOtEiiAMFCP2ow6FL9Kq0
 ebi_eva_internal_pyutils/pg_utils.py,sha256=FUQVwiX_7F2-4sSzoaCVX2me0zAqR8nGIj6NW5d304A,4398
 ebi_eva_internal_pyutils/spring_properties.py,sha256=WjPozWtXbAZGNqlgvY6GHps2KFB1rY9OaTs46obW3pM,15265
 ebi_eva_internal_pyutils/mongodb/__init__.py,sha256=0oyTlkYZCV7udlPl09Zl-sDyE3c97QZMMTEFIa6uYIw,76
-ebi_eva_internal_pyutils/mongodb/mongo_database.py,sha256=im0HgBgG_9E1nq7fQcNl3Ogc8oka6DI97SgsfeboRm0,9676
+ebi_eva_internal_pyutils/mongodb/mongo_database.py,sha256=kesaJaaxYFeF_uYZBgL8tbufGKUXll7bXb4WlOS9vKM,9596
 ebi_eva_internal_pyutils/nextflow/__init__.py,sha256=OOiJS8jZOz98q0t77NNog7aI_fFrVxi4kGmiSskuAqM,122
 ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py,sha256=ew623hhK8jmFLQjJwLZbgBmW9RTiJBEULVqHfIUv_dc,10114
-ebi_eva_common_pyutils-0.6.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.6.3.dist-info/METADATA,sha256=mS6_0RNspk_TgcAfQp1WGuYbntDmf6XDwqmzp32U8do,824
-ebi_eva_common_pyutils-0.6.3.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-ebi_eva_common_pyutils-0.6.3.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.6.3.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.6.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.6.5.dist-info/METADATA,sha256=RLaCUwFMStLAYr29_xwuX0jvNEGTPNmVfEY389lvgNw,822
+ebi_eva_common_pyutils-0.6.5.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+ebi_eva_common_pyutils-0.6.5.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.6.5.dist-info/RECORD,,

{ebi_eva_common_pyutils-0.6.3.dist-info → ebi_eva_common_pyutils-0.6.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

ebi_eva_internal_pyutils/mongodb/mongo_database.py

@@ -111,9 +111,7 @@ class MongoDatabase(AppLogger):
             shard_collection_command = f'sh.shardCollection(' \
                                        f'"{self.db_name}.{collection_name}", ' \
                                        f'{shard_key_repr}, {str(shard_key_uniqueness_flag).lower()})'
-            sharding_command = f"mongo --host {self.uri}  " \
-                               f"--eval " \
-                               f"'{shard_collection_command}' "
+            sharding_command = f"mongosh --eval '{shard_collection_command}' {self.uri} "
             sharding_command += self._get_optional_secrets_file_stdin()
             run_command_with_output(f"Sharding collection {collection_name} in the database {self.uri_with_db_name} "
                                     f"with key {shard_key_repr}...", sharding_command,