cpg-utils 5.0.0__tar.gz → 5.0.2__tar.gz

{cpg-utils-5.0.0 → cpg-utils-5.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cpg-utils
-Version: 5.0.0
+Version: 5.0.2
 Summary: Library of convenience functions specific to the CPG
 Home-page: https://github.com/populationgenomics/cpg-utils
 License: MIT

{cpg-utils-5.0.0 → cpg-utils-5.0.2}/cpg_utils/constants.py

@@ -21,7 +21,7 @@ CROMWELL_AUDIENCE = os.getenv('CROMWELL_AUDIENCE', DEFAULT_CROMWELL_AUDIENCE)
 CROMWELL_URL = os.getenv('CROMWELL_URL', DEFAULT_CROMWELL_URL)
 
 
-class AnsiiColors:
+class AnsiColors:
     """
     Lookup table: https://en.wikipedia.org/wiki/ANSI_escape_code#3/4_bit
     """

{cpg-utils-5.0.0 → cpg-utils-5.0.2}/cpg_utils/cromwell_model.py

@@ -7,7 +7,7 @@ import datetime
 
 from tabulate import tabulate
 
-from cpg_utils.constants import AnsiiColors
+from cpg_utils.constants import AnsiColors
 
 
 class ExecutionStatus(Enum):
@@ -41,17 +41,17 @@ class ExecutionStatus(Enum):
     @property
     def _colors(self):
         return {
-            ExecutionStatus.done: AnsiiColors.BRIGHTGREEN,
-            ExecutionStatus.succeeded: AnsiiColors.BRIGHTGREEN,
-            ExecutionStatus.failed: AnsiiColors.BRIGHTRED,
-            ExecutionStatus.retryablefailure: AnsiiColors.BRIGHTBLUE,
+            ExecutionStatus.done: AnsiColors.BRIGHTGREEN,
+            ExecutionStatus.succeeded: AnsiColors.BRIGHTGREEN,
+            ExecutionStatus.failed: AnsiColors.BRIGHTRED,
+            ExecutionStatus.retryablefailure: AnsiColors.BRIGHTBLUE,
         }
 
     def symbol(self):
         return self._symbols.get(self, '?')
 
     def color(self):
-        return self._colors.get(self, AnsiiColors.RESET)
+        return self._colors.get(self, AnsiColors.RESET)
 
     def is_finished(self):
         _finished_states = {
@@ -296,7 +296,7 @@ class CallMetadata:
         color, rcol = '', ''
         if not monochrome:
             color = self.executionStatus.color() if self.executionStatus else ''
-            rcol = AnsiiColors.RESET
+            rcol = AnsiColors.RESET
 
         extras_str = "".join("\n" + indent(e, '  ') for e in extras)
         return f'{color}[{symbol}] {name} ({duration_str}){extras_str}{rcol}'
@@ -329,7 +329,7 @@ def prepare_inner_calls_string(
     color, rcol = '', ''
     if not monochrome:
         color = collapsed_status.color() if collapsed_status else ''
-        rcol = AnsiiColors.RESET
+        rcol = AnsiColors.RESET
     inner_calls = ''
 
     if len(calls) > 1 and not expand_completed:

{cpg-utils-5.0.0 → cpg-utils-5.0.2}/cpg_utils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cpg-utils
-Version: 5.0.0
+Version: 5.0.2
 Summary: Library of convenience functions specific to the CPG
 Home-page: https://github.com/populationgenomics/cpg-utils
 License: MIT

{cpg-utils-5.0.0 → cpg-utils-5.0.2}/setup.py

@@ -5,13 +5,10 @@ from setuptools import find_packages, setup
 with open('README.md') as f:
     long_description = f.read()
 
-with open('requirements.txt') as f:
-    requirements = f.read().splitlines()
-
 setup(
     name='cpg-utils',
     # This tag is automatically updated by bumpversion
-    version='5.0.0',
+    version='5.0.2',
     description='Library of convenience functions specific to the CPG',
     long_description=long_description,
     long_description_content_type='text/markdown',
@@ -21,7 +18,18 @@ setup(
     package_data={
         'cpg_utils': ['py.typed'],
     },
-    install_requires=requirements,
+    install_requires=[
+        'boto3==1.28.56',
+        'botocore==1.31.56',
+        'cloudpathlib[all]',
+        'frozendict',
+        'google-auth>=1.27.0',
+        'google-cloud-secret-manager',
+        'requests',
+        'tabulate',
+        'toml',
+        'deprecated',
+    ],
     keywords='bioinformatics',
     classifiers=[
         'Environment :: Console',

{cpg-utils-5.0.0 → cpg-utils-5.0.2}/test/test_cromwell.py

@@ -3,6 +3,7 @@ import unittest
 from unittest.mock import MagicMock, patch
 
 from cpg_utils.cromwell import run_cromwell_workflow
+from cpg_utils.cromwell_model import WorkflowMetadataModel
 
 
 class TestCromwellWrapper(unittest.TestCase):
@@ -86,3 +87,44 @@ class TestCromwellWrapper(unittest.TestCase):
             wf_options['final_workflow_outputs_dir'],
             'test://default-bucket/output-prefix',
         )
+
+    def test_cromwell_status_format(self):
+        """
+        Check parsing some basic cromwell metadata, and formatting it for display
+        """
+        model = WorkflowMetadataModel.parse(
+            {
+                'id': '<mocked-id>',
+                'submission': '2021-07-09T09:46:00.000Z',
+                'start': '2021-07-09T09:47:00.000Z',
+                'end': '2021-07-09T09:48:00.000Z',
+                'calls': {
+                    'wf.print': [
+                        {
+                            'name': 'print',
+                            'executionStatus': 'succeeded',
+                            'start': '2021-07-09T09:47:00.000Z',
+                            'end': '2021-07-09T09:48:00.000Z',
+                        },
+                    ],
+                },
+            },
+        )
+        resp = model.display(expand_completed=True, monochrome=True)
+
+        status_str = """
+-----------  ------------------------
+Workflow ID  <mocked-id>
+Name
+Status       preparing
+Submitted    2021-07-09T09:46:00.000Z
+Start        2021-07-09T09:47:00.000Z
+End          2021-07-09T09:48:00.000Z
+Duration     1m:0s
+Walltime     2m:0s
+-----------  ------------------------
+Jobs:
+  [#] print (1m:0s)
+"""
+
+        self.assertEqual(status_str.strip(), resp.strip())