cpg-utils 5.1.0__tar.gz → 5.2.0__tar.gz

{cpg-utils-5.1.0 → cpg-utils-5.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cpg-utils
-Version: 5.1.0
+Version: 5.2.0
 Summary: Library of convenience functions specific to the CPG
 Home-page: https://github.com/populationgenomics/cpg-utils
 License: MIT

{cpg-utils-5.1.0 → cpg-utils-5.2.0}/cpg_utils/cromwell.py

@@ -483,6 +483,9 @@ def watch_workflow(  # noqa: C901
             and (datetime.now() - start).total_seconds() >= time_limit_seconds
         ):
             # time to die, Mr. Cromwell
+            logger.info(
+                f'This job has exceeded the max permitted runtime ({time_limit_seconds}s), and will be aborted',
+            )
             auth_header = {'Authorization': f'Bearer {_get_cromwell_oauth_token()}'}
             r = requests.post(abort_url, headers=auth_header, timeout=10)
             if not r.ok:
@@ -491,6 +494,9 @@ def watch_workflow(  # noqa: C901
                 )
                 _remaining_exceptions -= 1
                 continue
+            # quit if we successfully aborted
+            logger.info(f'Successfully aborted workflow {workflow_id}')
+            return
 
         if _remaining_exceptions <= 0:
             raise CromwellError('Unreachable')

{cpg-utils-5.1.0 → cpg-utils-5.2.0}/cpg_utils/hail_batch.py

@@ -15,6 +15,7 @@ from deprecated import deprecated
 
 import hail as hl
 import hailtop.batch as hb
+from hail.backend.service_backend import ServiceBackend as InternalServiceBackend
 from hail.utils.java import Env
 from hailtop.config import get_deploy_config
 
@@ -307,6 +308,15 @@ def make_job_name(
     return name
 
 
+_default_override_revision = None
+
+
+class DefaultOverrideServiceBackend(InternalServiceBackend):
+    @property
+    def jar_spec(self) -> dict:
+        return {'type': 'git_revision', 'value': _default_override_revision}
+
+
 def init_batch(**kwargs: Any):
     """
     Initializes the Hail Query Service from within Hail Batch.
@@ -331,6 +341,13 @@ def init_batch(**kwargs: Any):
         ),
     )
 
+    if revision := config_retrieve(['workflow', 'default_jar_spec_revision'], False):
+        global _default_override_revision
+        _default_override_revision = revision
+        backend = Env.backend()
+        if isinstance(backend, InternalServiceBackend):
+            backend.__class__ = DefaultOverrideServiceBackend
+
 
 def copy_common_env(job: hb.batch.job.Job) -> None:
     """Copies common environment variables that we use to run Hail jobs.

{cpg-utils-5.1.0 → cpg-utils-5.2.0}/cpg_utils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cpg-utils
-Version: 5.1.0
+Version: 5.2.0
 Summary: Library of convenience functions specific to the CPG
 Home-page: https://github.com/populationgenomics/cpg-utils
 License: MIT

{cpg-utils-5.1.0 → cpg-utils-5.2.0}/setup.py

@@ -8,7 +8,7 @@ with open('README.md') as f:
 setup(
     name='cpg-utils',
     # This tag is automatically updated by bumpversion
-    version='5.1.0',
+    version='5.2.0',
     description='Library of convenience functions specific to the CPG',
     long_description=long_description,
     long_description_content_type='text/markdown',