toil 5.12.0__py3-none-any.whl → 6.1.0__py3-none-any.whl

toil/worker.py

@@ -11,7 +11,6 @@
 # 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 argparse
 import base64
 import copy
 import json
@@ -29,6 +28,8 @@ import traceback
 from contextlib import contextmanager
 from typing import Any, Callable, Iterator, List, Optional
 
+from configargparse import ArgParser
+
 from toil import logProcessContext
 from toil.common import Config, Toil, safeUnpickleFromStream
 from toil.cwl.utils import (CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION,
@@ -49,7 +50,7 @@ logger = logging.getLogger(__name__)
 class StatsDict(MagicExpando):
     """Subclass of MagicExpando for type-checking purposes."""
 
-    jobs: List[str]
+    jobs: List[MagicExpando]
 
 
 def nextChainable(predecessor: JobDescription, jobStore: AbstractJobStore, config: Config) -> Optional[JobDescription]:
@@ -222,7 +223,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     #Setup the temporary directories.
     ##########################################
     # Dir to put all this worker's temp files in.
-    assert config.workflowID is not None
+    if config.workflowID is None:
+        raise RuntimeError("The worker workflow ID was never set.")
     toilWorkflowDir = Toil.getLocalWorkflowDir(config.workflowID, config.workDir)
     # Dir to put lock files in, ideally not on NFS.
     toil_coordination_dir = Toil.get_local_workflow_coordination_dir(config.workflowID, config.workDir, config.coordination_dir)
@@ -250,8 +252,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
     if redirectOutputToLogFile:
         # Announce that we are redirecting logging, and where it will now go.
-        # This is important if we are trying to manually trace a faulty worker invocation.
-        logger.info("Redirecting logging to %s", tempWorkerLogPath)
+        # This is only important if we are trying to manually trace a faulty worker invocation.
+        logger.debug("Redirecting logging to %s", tempWorkerLogPath)
         sys.stdout.flush()
         sys.stderr.flush()
 
@@ -285,13 +287,14 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
     jobAttemptFailed = False
     failure_exit_code = 1
+    first_job_cores = None
     statsDict = StatsDict()  # type: ignore[no-untyped-call]
     statsDict.jobs = []
-    statsDict.workers.logsToMaster = []
+    statsDict.workers.logs_to_leader = []
+    statsDict.workers.logging_user_streams = []
 
     def blockFn() -> bool:
         return True
-    listOfJobs = [jobName]
     job = None
     try:
 
@@ -311,7 +314,6 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         ##########################################
 
         jobDesc = jobStore.load_job(jobStoreID)
-        listOfJobs[0] = str(jobDesc)
         logger.debug("Parsed job description")
 
         ##########################################
@@ -345,7 +347,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             if next(jobDesc.successorsAndServiceHosts(), None) is not None:
                 logger.debug("Checkpoint has failed; restoring")
                 # Reduce the try count
-                assert jobDesc.remainingTryCount >= 0
+                if jobDesc.remainingTryCount < 0:
+                    raise RuntimeError("The try count of the job cannot be negative.")
                 jobDesc.remainingTryCount = max(0, jobDesc.remainingTryCount - 1)
                 jobDesc.restartCheckpoint(jobStore)
             # Otherwise, the job and successors are done, and we can cleanup stuff we couldn't clean
@@ -360,6 +363,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         ##########################################
 
         if config.stats:
+            # Remember the cores from the first job, which is how many we have reserved for us.
+            statsDict.workers.requested_cores = jobDesc.cores
             startClock = get_total_cpu_time()
 
         startTime = time.time()
@@ -371,7 +376,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             logger.info("Working on job %s", jobDesc)
 
             if jobDesc.command is not None:
-                assert jobDesc.command.startswith("_toil ")
+                if not jobDesc.command.startswith("_toil "):
+                    raise RuntimeError("Job command must start with '_toil' before being converted to an executable command.")
                 logger.debug("Got a command to run: %s" % jobDesc.command)
                 # Load the job. It will use the same JobDescription we have been using.
                 job = Job.loadJob(jobStore, jobDesc)
@@ -402,8 +408,13 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                             # versions of Cactus.
                             job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
 
+                            # When the executor for the job finishes it will
+                            # kick off a commit with the command link to the
+                            # job body cut.
+
                 # Accumulate messages from this job & any subsequent chained jobs
-                statsDict.workers.logsToMaster += fileStore.loggingMessages
+                statsDict.workers.logs_to_leader += fileStore.logging_messages
+                statsDict.workers.logging_user_streams += fileStore.logging_user_streams
 
                 logger.info("Completed body for %s", jobDesc)
 
@@ -426,7 +437,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
                 logger.info("Not chaining from job %s", jobDesc)
 
-                # TODO: Somehow the commit happens even if we don't start it here.
+                # No need to commit because the _executor context manager did it.
 
                 break
 
@@ -434,33 +445,25 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
             ##########################################
             # We have a single successor job that is not a checkpoint job. We
-            # reassign the ID of the current JobDescription to the successor.
-            # We can then delete the successor JobDescription (under its old
-            # ID) in the jobStore, as it is wholly incorporated into the
-            # current one.
+            # reassign the ID of the current JobDescription to the successor,
+            # and take responsibility for both jobs' associated files in the
+            # combined job.
             ##########################################
 
             # Make sure nothing has gone wrong and we can really chain
-            assert jobDesc.memory >= successor.memory
-            assert jobDesc.cores >= successor.cores
+            if jobDesc.memory < successor.memory:
+                raise RuntimeError("Cannot chain jobs. A job's memory cannot be less than it's successor.")
+            if jobDesc.cores < successor.cores:
+                raise RuntimeError("Cannot chain jobs. A job's cores cannot be less than it's successor.")
 
             # Save the successor's original ID, so we can clean it (and its
             # body) up after we finish executing it.
             successorID = successor.jobStoreID
 
-            # add the successor to the list of jobs run
-            listOfJobs.append(str(successor))
-
             # Now we need to become that successor, under the original ID.
             successor.replace(jobDesc)
             jobDesc = successor
 
-            # Problem: successor's job body is a file that will be cleaned up
-            # when we delete the successor job by ID. We can't just move it. So
-            # we need to roll up the deletion of the successor job by ID with
-            # the deletion of the job ID we're currently working on.
-            jobDesc.jobsToDelete.append(successorID)
-
             # Clone the now-current JobDescription (which used to be the successor).
             # TODO: Why??? Can we not?
             jobDesc = copy.deepcopy(jobDesc)
@@ -476,15 +479,6 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             # This will update the job once the previous job is done updating
             fileStore.startCommit(jobState=True)
 
-            # Clone the current job description again, so that further updates
-            # to it (such as new successors being added when it runs) occur
-            # after the commit process we just kicked off, and aren't committed
-            # early or partially.
-            jobDesc = copy.deepcopy(jobDesc)
-            # Bump its version since saving will do that too and we don't want duplicate versions.
-            jobDesc.pre_update_hook()
-
-
             logger.debug("Starting the next job")
 
         ##########################################
@@ -495,6 +489,16 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             statsDict.workers.time = str(time.time() - startTime)
             statsDict.workers.clock = str(totalCPUTime - startClock)
             statsDict.workers.memory = str(totalMemoryUsage)
+            # Say the worker used the max disk we saw from any job
+            max_bytes = 0
+            for job_stats in statsDict.jobs:
+                if "disk" in job_stats:
+                    max_bytes = max(max_bytes, int(job_stats.disk))
+            statsDict.workers.disk = str(max_bytes)
+            # Count the jobs executed.
+            # TODO: toil stats could compute this but its parser is too general to hook into simply.
+            statsDict.workers.jobs_run  = len(statsDict.jobs)
+
 
         # log the worker log path here so that if the file is truncated the path can still be found
         if redirectOutputToLogFile:
@@ -505,13 +509,16 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     ##########################################
     #Trapping where worker goes wrong
     ##########################################
-    except Exception as e: #Case that something goes wrong in worker
+    except BaseException as e: #Case that something goes wrong in worker, or we are asked to stop
         traceback.print_exc()
         logger.error("Exiting the worker because of a failed job on host %s", socket.gethostname())
         if isinstance(e, CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION):
             # We need to inform the leader that this is a CWL workflow problem
             # and it needs to inform its caller.
             failure_exit_code = CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE
+        elif isinstance(e, SystemExit) and isinstance(e.code, int) and e.code != 0:
+            # We're meant to be exiting with a particular code.
+            failure_exit_code = e.code
         AbstractFileStore._terminateEvent.set()
     finally:
         # Get rid of our deferred function manager now so we can't mistake it
@@ -587,7 +594,6 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         jobDesc.logJobStoreFileID = logJobStoreFileID = jobStore.getEmptyFileStoreID(
             jobDesc.jobStoreID, cleanup=True
         )
-        jobDesc.chainedJobs = listOfJobs
         with jobStore.update_file_stream(logJobStoreFileID) as w:
             with open(tempWorkerLogPath, 'rb') as f:
                 if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit !=0:
@@ -611,10 +617,13 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             # Make sure lines are Unicode so they can be JSON serialized as part of the dict.
             # We may have damaged the Unicode text by cutting it at an arbitrary byte so we drop bad characters.
             logMessages = [line.decode('utf-8', 'skip') for line in logFile.read().splitlines()]
-        statsDict.logs.names = listOfJobs
+        statsDict.logs.names = [names.stats_name for names in jobDesc.get_chain()]
         statsDict.logs.messages = logMessages
 
-    if (debugging or config.stats or statsDict.workers.logsToMaster) and not jobAttemptFailed:  # We have stats/logging to report back
+    if debugging or config.stats or statsDict.workers.logs_to_leader or statsDict.workers.logging_user_streams:
+        # We have stats/logging to report back.
+        # We report even if the job attempt failed.
+        # TODO: Will that upset analysis of the stats?
         jobStore.write_logs(json.dumps(statsDict, ensure_ascii=True))
 
     # Remove the temp dir
@@ -637,17 +646,17 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
     # This must happen after the log file is done with, else there is no place to put the log
     if (not jobAttemptFailed) and jobDesc.is_subtree_done():
-        # We can now safely get rid of the JobDescription, and all jobs it chained up
-        for otherID in jobDesc.jobsToDelete:
-            jobStore.delete_job(otherID)
-        jobStore.delete_job(str(jobDesc.jobStoreID))
+        for merged_in in jobDesc.get_chain():
+            # We can now safely get rid of the JobDescription, and all jobs it chained up
+            jobStore.delete_job(merged_in.job_store_id)
+        
 
     if jobAttemptFailed:
         return failure_exit_code
     else:
         return 0
 
-def parse_args(args: List[str]) -> argparse.Namespace:
+def parse_args(args: List[str]) -> Any:
     """
     Parse command-line arguments to the worker.
     """
@@ -656,7 +665,7 @@ def parse_args(args: List[str]) -> argparse.Namespace:
     args = args[1:]
 
     # Make the parser
-    parser = argparse.ArgumentParser()
+    parser = ArgParser()
 
     # Now add all the options to it
 

toil-6.1.0.dist-info/METADATA

@@ -0,0 +1,124 @@
+Metadata-Version: 2.1
+Name: toil
+Version: 6.1.0
+Summary: Pipeline management software for clusters.
+Home-page: https://github.com/DataBiosphere/toil
+Author: Benedict Paten and the Toil community
+Author-email: toil-community@googlegroups.com
+License: Apache License v2.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: System :: Distributed Computing
+Classifier: Topic :: Utilities
+Requires-Python: >=3.8
+License-File: LICENSE
+Requires-Dist: dill <0.4,>=0.3.2
+Requires-Dist: requests <3,>=2
+Requires-Dist: docker <8,>=6.1.0
+Requires-Dist: urllib3 <3,>=1.26.0
+Requires-Dist: python-dateutil
+Requires-Dist: psutil <6,>=3.0.1
+Requires-Dist: PyPubSub <5,>=4.0.3
+Requires-Dist: addict <2.5,>=2.2.1
+Requires-Dist: pytz >=2012
+Requires-Dist: enlighten <2,>=1.5.2
+Requires-Dist: configargparse <2,>=1.7
+Requires-Dist: ruamel.yaml >=0.15
+Requires-Dist: pyyaml <7,>=6
+Requires-Dist: typing-extensions <5,>=4.6.2
+Provides-Extra: all
+Requires-Dist: boto <3,>=2.48.0 ; extra == 'all'
+Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] <2,>=1.28.3.post2 ; extra == 'all'
+Requires-Dist: mypy-boto3-iam <2,>=1.28.3.post2 ; extra == 'all'
+Requires-Dist: moto <5,>=4.1.11 ; extra == 'all'
+Requires-Dist: cwltool ==3.1.20240112164112 ; extra == 'all'
+Requires-Dist: schema-salad <9,>=8.4.20230128170514 ; extra == 'all'
+Requires-Dist: galaxy-tool-util <23 ; extra == 'all'
+Requires-Dist: galaxy-util <23 ; extra == 'all'
+Requires-Dist: ruamel.yaml <=0.19,>=0.15 ; extra == 'all'
+Requires-Dist: ruamel.yaml.clib >=0.2.6 ; extra == 'all'
+Requires-Dist: networkx !=2.8.1,<4 ; extra == 'all'
+Requires-Dist: CacheControl[filecache] ; extra == 'all'
+Requires-Dist: pynacl <2,>=1.4.0 ; extra == 'all'
+Requires-Dist: apache-libcloud <3,>=2.2.1 ; extra == 'all'
+Requires-Dist: google-cloud-storage <=2.8.0,>=2 ; extra == 'all'
+Requires-Dist: google-auth <3,>=2.18.1 ; extra == 'all'
+Requires-Dist: kubernetes <22,>=12.0.1 ; extra == 'all'
+Requires-Dist: kubernetes-stubs ==v22.6.0post1 ; extra == 'all'
+Requires-Dist: types-urllib3 ; extra == 'all'
+Requires-Dist: types-PyYAML ; extra == 'all'
+Requires-Dist: idna >=2 ; extra == 'all'
+Requires-Dist: miniwdl ==1.11.1 ; extra == 'all'
+Requires-Dist: wdlparse ==0.1.0 ; extra == 'all'
+Requires-Dist: connexion[swagger-ui] <3,>=2.10.0 ; extra == 'all'
+Requires-Dist: flask <3,>=2.0 ; extra == 'all'
+Requires-Dist: werkzeug <3,>=2.0 ; extra == 'all'
+Requires-Dist: flask-cors ==4.0.0 ; extra == 'all'
+Requires-Dist: gunicorn ==21.2.0 ; extra == 'all'
+Requires-Dist: celery <6,>=5.1.0 ; extra == 'all'
+Requires-Dist: wes-service <5,>=4.0.0 ; extra == 'all'
+Requires-Dist: ruamel.yaml <0.19,>=0.15 ; extra == 'all'
+Requires-Dist: pymesos <0.4,>=0.3.15 ; (python_version < "3.11") and extra == 'all'
+Requires-Dist: graphlib-backport ==1.0 ; (python_version < "3.9") and extra == 'all'
+Provides-Extra: aws
+Requires-Dist: boto <3,>=2.48.0 ; extra == 'aws'
+Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] <2,>=1.28.3.post2 ; extra == 'aws'
+Requires-Dist: mypy-boto3-iam <2,>=1.28.3.post2 ; extra == 'aws'
+Requires-Dist: moto <5,>=4.1.11 ; extra == 'aws'
+Provides-Extra: cwl
+Requires-Dist: cwltool ==3.1.20240112164112 ; extra == 'cwl'
+Requires-Dist: schema-salad <9,>=8.4.20230128170514 ; extra == 'cwl'
+Requires-Dist: galaxy-tool-util <23 ; extra == 'cwl'
+Requires-Dist: galaxy-util <23 ; extra == 'cwl'
+Requires-Dist: ruamel.yaml <=0.19,>=0.15 ; extra == 'cwl'
+Requires-Dist: ruamel.yaml.clib >=0.2.6 ; extra == 'cwl'
+Requires-Dist: networkx !=2.8.1,<4 ; extra == 'cwl'
+Requires-Dist: CacheControl[filecache] ; extra == 'cwl'
+Provides-Extra: encryption
+Requires-Dist: pynacl <2,>=1.4.0 ; extra == 'encryption'
+Provides-Extra: google
+Requires-Dist: apache-libcloud <3,>=2.2.1 ; extra == 'google'
+Requires-Dist: google-cloud-storage <=2.8.0,>=2 ; extra == 'google'
+Requires-Dist: google-auth <3,>=2.18.1 ; extra == 'google'
+Provides-Extra: htcondor
+Requires-Dist: htcondor <11,>=10.2.0.post1 ; (sys_platform!="darwin") and extra == 'htcondor'
+Provides-Extra: kubernetes
+Requires-Dist: kubernetes <22,>=12.0.1 ; extra == 'kubernetes'
+Requires-Dist: kubernetes-stubs ==v22.6.0post1 ; extra == 'kubernetes'
+Requires-Dist: types-urllib3 ; extra == 'kubernetes'
+Requires-Dist: types-PyYAML ; extra == 'kubernetes'
+Requires-Dist: idna >=2 ; extra == 'kubernetes'
+Provides-Extra: mesos
+Requires-Dist: pymesos <0.4,>=0.3.15 ; (python_version < "3.11") and extra == 'mesos'
+Provides-Extra: server
+Requires-Dist: connexion[swagger-ui] <3,>=2.10.0 ; extra == 'server'
+Requires-Dist: flask <3,>=2.0 ; extra == 'server'
+Requires-Dist: werkzeug <3,>=2.0 ; extra == 'server'
+Requires-Dist: flask-cors ==4.0.0 ; extra == 'server'
+Requires-Dist: gunicorn ==21.2.0 ; extra == 'server'
+Requires-Dist: celery <6,>=5.1.0 ; extra == 'server'
+Requires-Dist: wes-service <5,>=4.0.0 ; extra == 'server'
+Requires-Dist: ruamel.yaml <0.19,>=0.15 ; extra == 'server'
+Provides-Extra: wdl
+Requires-Dist: miniwdl ==1.11.1 ; extra == 'wdl'
+Requires-Dist: wdlparse ==0.1.0 ; extra == 'wdl'
+Requires-Dist: graphlib-backport ==1.0 ; (python_version < "3.9") and extra == 'wdl'
+

toil-6.1.0.dist-info/RECORD

@@ -0,0 +1,241 @@
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{toil-5.12.0.dist-info → toil-6.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.0)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any