ebi-eva-common-pyutils 0.6.3__tar.gz → 0.6.5__tar.gz

{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.5}/CHANGELOG.md

@@ -2,6 +2,17 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.5 (2024-04-02)
+---------------------
+
+- Ensure that the port forwarding command is running before returning the process.
+
+
+## 0.6.4 (2024-03-21)
+---------------------
+
+- Update Mongodb client to use mongosh instead of the legacy mongo.
+
 ## 0.6.3 (2024-02-22)
 ---------------------
 

{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.3
+Version: 0.6.5
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,5 +10,13 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Provides-Extra: eva-internal
 License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: lxml
+Requires-Dist: pyyaml
+Requires-Dist: cached-property
+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"

{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.5}/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 → ebi_eva_common_pyutils-0.6.5}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -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
@@ -10,5 +10,13 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Provides-Extra: eva-internal
 License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: lxml
+Requires-Dist: pyyaml
+Requires-Dist: cached-property
+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"

{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.5}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
+/tmp/ebi_eva_common_pyutils-v0.6.5-999yjogj/gitclone/ebi_eva_internal_pyutils/archive_directory.py
 ebi_eva_common_pyutils/__init__.py
 ebi_eva_common_pyutils/assembly_utils.py
 ebi_eva_common_pyutils/command_utils.py
@@ -40,4 +41,5 @@ ebi_eva_internal_pyutils/spring_properties.py
 ebi_eva_internal_pyutils/mongodb/__init__.py
 ebi_eva_internal_pyutils/mongodb/mongo_database.py
 ebi_eva_internal_pyutils/nextflow/__init__.py
-ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py
+ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py
+tests/test_common.py

{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.5}/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,

{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.5}/setup.py

@@ -7,7 +7,7 @@ setup(
     name='ebi_eva_common_pyutils',
     scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_internal_pyutils', 'archive_directory.py')],
     packages=find_packages(),
-    version='0.6.3',
+    version='0.6.5',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',

ebi_eva_common_pyutils-0.6.5/tests/test_common.py

@@ -0,0 +1,22 @@
+import os
+from unittest import TestCase
+
+from ebi_eva_common_pyutils.common_utils import merge_two_dicts, pretty_print
+
+
+class TestCommon(TestCase):
+
+    resources_folder = os.path.join(os.path.dirname(__file__), 'resources')
+
+
+class TestCommonUtils(TestCase):
+
+    def test_merge_two_dicts(self):
+        d1 = {'a': 1, 'b': 2, 'c': 3}
+        d2 = {'d': 4, 'a': 5, 'e': 6}
+        assert merge_two_dicts(d1, d2) == {'a': 5, 'b': 2, 'c': 3, 'd': 4, 'e': 6}
+        assert merge_two_dicts(d2, d1) == {'a': 1, 'b': 2, 'c': 3, 'd': 4, 'e': 6}
+
+    def test_pretty_print(self):
+        pretty_print(['Header 1', 'Long Header 2'],
+                     [['row1 cell 1', 'row1 cell 2'], ['row2 cell 1', 'Super long row2 cell 2']])