ebi-eva-common-pyutils 0.6.2__tar.gz → 0.6.4__tar.gz

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/CHANGELOG.md

@@ -2,6 +2,17 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.4 (2024-03-21)
+---------------------
+
+- Update Mongodb client to use mongosh instead of the legacy mongo.
+
+## 0.6.3 (2024-02-22)
+---------------------
+
+- Variable log level when running a command
+
+
 ## 0.6.2 (2023-10-30)
 ---------------------
 

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.2
+Version: 0.6.4
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,13 +10,5 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-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"
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/command_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 logging
 import subprocess
 
 from ebi_eva_common_pyutils.logger import logging_config as log_cfg
@@ -20,11 +20,12 @@ logger = log_cfg.get_logger(__name__)
 
 
 def run_command_with_output(command_description, command, return_process_output=False,
-                            log_error_stream_to_output=False):
+                            log_error_stream_to_output=False, stdout_log_level=logging.INFO,
+                            stderr_log_level=logging.ERROR):
     process_output = ""
 
-    logger.info("Starting process: " + command_description)
-    logger.info("Running command: " + command)
+    logger.log(stdout_log_level, "Starting process: " + command_description)
+    logger.log(stdout_log_level, "Running command: " + command)
 
     stdout = subprocess.PIPE
     # Some lame utilities like mongodump and mongorestore output non-error messages to error stream
@@ -35,18 +36,18 @@ def run_command_with_output(command_description, command, return_process_output=
                           shell=True) as process:
         for line in iter(process.stdout.readline, ''):
             line = str(line).rstrip()
-            logger.info(line)
+            logger.log(stdout_log_level, line)
             if return_process_output:
                 process_output += line + "\n"
         if not log_error_stream_to_output:
             for line in iter(process.stderr.readline, ''):
                 line = str(line).rstrip()
-                logger.error(line)
+                logger.log(stderr_log_level, line)
     if process.returncode != 0:
         logger.error(command_description + " failed! Refer to the error messages for details.")
         raise subprocess.CalledProcessError(process.returncode, process.args)
     else:
-        logger.info(command_description + " - completed successfully")
+        logger.log(stdout_log_level, command_description + " - completed successfully")
     if return_process_output:
         return process_output
 

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/logger.py

@@ -127,6 +127,9 @@ class AppLogger:
     """
     log_cfg = logging_config
 
+    def log(self, level, msg, *args, **kwargs):
+        self._logger.log(level, msg, *args, **kwargs)
+
     def debug(self, msg, *args):
         self._logger.debug(msg, *args)
 

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.2
+Version: 0.6.4
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,13 +10,5 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-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"
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,7 +4,6 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
-/data/from_the_firehose/eva-common-pyutils/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
@@ -41,5 +40,4 @@ 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
-tests/test_common.py
+ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py

{ebi_eva_common_pyutils-0.6.2 → ebi_eva_common_pyutils-0.6.4}/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-0.6.2 → ebi_eva_common_pyutils-0.6.4}/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='0.6.2',
+    version='0.6.4',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',

ebi_eva_common_pyutils-0.6.2/tests/test_common.py

@@ -1,22 +0,0 @@
-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']])