10812: Use packed workflows for all run modes.

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index b7173e8d9aa9c047a91796b9cb8f30ce4f9e2a3f..02eca644d30eee769d38cfe083ae513f4b5f49e8 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -17,18 +17,21 @@ import pkg_resources  # part of setuptools
 from cwltool.errors import WorkflowException
 import cwltool.main
 import cwltool.workflow
 from cwltool.errors import WorkflowException
 import cwltool.main
 import cwltool.workflow

+import cwltool.process

 import schema_salad
 import schema_salad

+from schema_salad.sourceline import SourceLine

 
 import arvados
 import arvados.config
 
 import arvados
 import arvados.config

+from arvados.keep import KeepClient

 from arvados.errors import ApiError
 
 from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
 from arvados.errors import ApiError
 
 from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate

-from. runner import Runner, upload_instance
+from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps

 from .arvtool import ArvadosCommandTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .arvtool import ArvadosCommandTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow

-from .fsaccess import CollectionFsAccess
+from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver

 from .perf import Perf
 from .pathmapper import FinalOutputPathMapper
 from ._version import __version__
 from .perf import Perf
 from .pathmapper import FinalOutputPathMapper
 from ._version import __version__


@@ -43,6 +46,9 @@ logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 logger.setLevel(logging.INFO)
 
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 logger.setLevel(logging.INFO)
 

+arvados.log_handler.setFormatter(logging.Formatter(
+        '%(asctime)s %(name)s %(levelname)s: %(message)s',
+        '%Y-%m-%d %H:%M:%S'))

 
 class ArvCwlRunner(object):
     """Execute a CWL tool or workflow, submit work (using either jobs or
 
 class ArvCwlRunner(object):
     """Execute a CWL tool or workflow, submit work (using either jobs or


@@ -50,7 +56,7 @@ class ArvCwlRunner(object):
 
     """
 
 
     """
 

-    def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None):
+    def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None, num_retries=4):

         self.api = api_client
         self.processes = {}
         self.lock = threading.Lock()
         self.api = api_client
         self.processes = {}
         self.lock = threading.Lock()


@@ -58,7 +64,7 @@ class ArvCwlRunner(object):
         self.final_output = None
         self.final_status = None
         self.uploaded = {}
         self.final_output = None
         self.final_status = None
         self.uploaded = {}

-        self.num_retries = 4
+        self.num_retries = num_retries

         self.uuid = None
         self.stop_polling = threading.Event()
         self.poll_api = None
         self.uuid = None
         self.stop_polling = threading.Event()
         self.poll_api = None


@@ -93,6 +99,9 @@ class ArvCwlRunner(object):
 
     def arv_make_tool(self, toolpath_object, **kwargs):
         kwargs["work_api"] = self.work_api
 
     def arv_make_tool(self, toolpath_object, **kwargs):
         kwargs["work_api"] = self.work_api

+        kwargs["fetcher_constructor"] = partial(CollectionFetcher,
+                                                api_client=self.api,
+                                                keep_client=self.keep_client)

         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
             return ArvadosCommandTool(self, toolpath_object, **kwargs)
         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
             return ArvadosCommandTool(self, toolpath_object, **kwargs)
         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":


@@ -121,7 +130,7 @@ class ArvCwlRunner(object):
                     uuid = event["object_uuid"]
                     with self.lock:
                         j = self.processes[uuid]
                     uuid = event["object_uuid"]
                     with self.lock:
                         j = self.processes[uuid]

-                        logger.info("Job %s (%s) is Running", j.name, uuid)
+                        logger.info("%s %s is Running", self.label(j), uuid)

                         j.running = True
                         j.update_pipeline_component(event["properties"]["new_attributes"])
                 elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
                         j.running = True
                         j.update_pipeline_component(event["properties"]["new_attributes"])
                 elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):


@@ -129,14 +138,16 @@ class ArvCwlRunner(object):
                     try:
                         self.cond.acquire()
                         j = self.processes[uuid]
                     try:
                         self.cond.acquire()
                         j = self.processes[uuid]

-                        txt = self.work_api[0].upper() + self.work_api[1:-1]
-                        logger.info("%s %s (%s) is %s", txt, j.name, uuid, event["properties"]["new_attributes"]["state"])
+                        logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])

                         with Perf(metrics, "done %s" % j.name):
                             j.done(event["properties"]["new_attributes"])
                         self.cond.notify()
                     finally:
                         self.cond.release()
 
                         with Perf(metrics, "done %s" % j.name):
                             j.done(event["properties"]["new_attributes"])
                         self.cond.notify()
                     finally:
                         self.cond.release()
 

+    def label(self, obj):
+        return "[%s %s]" % (self.work_api[0:-1], obj.name)
+

     def poll_states(self):
         """Poll status of jobs or containers listed in the processes dict.
 
     def poll_states(self):
         """Poll status of jobs or containers listed in the processes dict.
 


@@ -166,7 +177,7 @@ class ArvCwlRunner(object):
 
                 for p in proc_states["items"]:
                     self.on_message({
 
                 for p in proc_states["items"]:
                     self.on_message({

-                        "object_uuid": p["uuid"],
+                       "object_uuid": p["uuid"],

                         "event_type": "update",
                         "properties": {
                             "new_attributes": p
                         "event_type": "update",
                         "properties": {
                             "new_attributes": p


@@ -187,15 +198,25 @@ class ArvCwlRunner(object):
     def add_uploaded(self, src, pair):
         self.uploaded[src] = pair
 
     def add_uploaded(self, src, pair):
         self.uploaded[src] = pair
 

-    def check_writable(self, obj):
+    def check_features(self, obj):

         if isinstance(obj, dict):
         if isinstance(obj, dict):

+            if obj.get("class") == "InitialWorkDirRequirement":
+                if self.work_api == "containers":
+                    raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")

             if obj.get("writable"):
             if obj.get("writable"):

-                raise UnsupportedRequirement("InitialWorkDir feature 'writable: true' not supported")
+                raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported")
+            if obj.get("class") == "CommandLineTool":
+                if self.work_api == "containers":
+                    if obj.get("stdin"):
+                        raise SourceLine(obj, "stdin", UnsupportedRequirement).makeError("Stdin redirection currently not suppported with --api=containers")
+                    if obj.get("stderr"):
+                        raise SourceLine(obj, "stderr", UnsupportedRequirement).makeError("Stderr redirection currently not suppported with --api=containers")

             for v in obj.itervalues():
             for v in obj.itervalues():

-                self.check_writable(v)
-        if isinstance(obj, list):
-            for v in obj:
-                self.check_writable(v)
+                self.check_features(v)
+        elif isinstance(obj, list):
+            for i,v in enumerate(obj):
+                with SourceLine(obj, i, UnsupportedRequirement):
+                    self.check_features(v)

 
     def make_output_collection(self, name, tagsString, outputObj):
         outputObj = copy.deepcopy(outputObj)
 
     def make_output_collection(self, name, tagsString, outputObj):
         outputObj = copy.deepcopy(outputObj)


@@ -304,7 +325,7 @@ class ArvCwlRunner(object):
     def arv_executor(self, tool, job_order, **kwargs):
         self.debug = kwargs.get("debug")
 
     def arv_executor(self, tool, job_order, **kwargs):
         self.debug = kwargs.get("debug")
 

-        tool.visit(self.check_writable)
+        tool.visit(self.check_features)

 
         self.project_uuid = kwargs.get("project_uuid")
         self.pipeline = None
 
         self.project_uuid = kwargs.get("project_uuid")
         self.pipeline = None


@@ -313,21 +334,44 @@ class ArvCwlRunner(object):
                                                                  keep_client=self.keep_client)
         self.fs_access = make_fs_access(kwargs["basedir"])
 
                                                                  keep_client=self.keep_client)
         self.fs_access = make_fs_access(kwargs["basedir"])
 

+        if not kwargs.get("name"):
+            kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+
+        # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
+        # Also uploads docker images.
+        upload_workflow_deps(self, tool)
+
+        # Reload tool object which may have been updated by
+        # upload_workflow_deps
+        tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
+                                  makeTool=self.arv_make_tool,
+                                  loader=tool.doc_loader,
+                                  avsc_names=tool.doc_schema,
+                                  metadata=tool.metadata)
+
+        # Upload local file references in the job order.
+        job_order = upload_job_order(self, "%s input" % kwargs["name"],
+                                     tool, job_order)
+

         existing_uuid = kwargs.get("update_workflow")
         if existing_uuid or kwargs.get("create_workflow"):
         existing_uuid = kwargs.get("update_workflow")
         if existing_uuid or kwargs.get("create_workflow"):

+            # Create a pipeline template or workflow record and exit.

             if self.work_api == "jobs":
                 tmpl = RunnerTemplate(self, tool, job_order,
                                       kwargs.get("enable_reuse"),
                                       uuid=existing_uuid,
             if self.work_api == "jobs":
                 tmpl = RunnerTemplate(self, tool, job_order,
                                       kwargs.get("enable_reuse"),
                                       uuid=existing_uuid,

-                                      submit_runner_ram=kwargs.get("submit_runner_ram"))
+                                      submit_runner_ram=kwargs.get("submit_runner_ram"),
+                                      name=kwargs["name"])

                 tmpl.save()
                 # cwltool.main will write our return value to stdout.
                 tmpl.save()
                 # cwltool.main will write our return value to stdout.

-                return tmpl.uuid
-            else:
-                return upload_workflow(self, tool, job_order,
-                                       self.project_uuid,
-                                       uuid=existing_uuid,
-                                       submit_runner_ram=kwargs.get("submit_runner_ram"))
+                return (tmpl.uuid, "success")
+            elif self.work_api == "containers":
+                return (upload_workflow(self, tool, job_order,
+                                        self.project_uuid,
+                                        uuid=existing_uuid,
+                                        submit_runner_ram=kwargs.get("submit_runner_ram"),
+                                        name=kwargs["name"]),
+                        "success")

 
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 
 
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 


@@ -335,7 +379,6 @@ class ArvCwlRunner(object):
         kwargs["enable_reuse"] = kwargs.get("enable_reuse")
         kwargs["use_container"] = True
         kwargs["tmpdir_prefix"] = "tmp"
         kwargs["enable_reuse"] = kwargs.get("enable_reuse")
         kwargs["use_container"] = True
         kwargs["tmpdir_prefix"] = "tmp"

-        kwargs["on_error"] = "continue"

         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
 
         if self.work_api == "containers":
         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
 
         if self.work_api == "containers":


@@ -348,25 +391,39 @@ class ArvCwlRunner(object):
             kwargs["docker_outdir"] = "$(task.outdir)"
             kwargs["tmpdir"] = "$(task.tmpdir)"
 
             kwargs["docker_outdir"] = "$(task.outdir)"
             kwargs["tmpdir"] = "$(task.tmpdir)"
 

-        upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
-

         runnerjob = None
         if kwargs.get("submit"):
         runnerjob = None
         if kwargs.get("submit"):

+            # Submit a runner job to run the workflow for us.

             if self.work_api == "containers":
                 if tool.tool["class"] == "CommandLineTool":
             if self.work_api == "containers":
                 if tool.tool["class"] == "CommandLineTool":

+                    kwargs["runnerjob"] = tool.tool["id"]
+                    upload_dependencies(self,
+                                        kwargs["name"],
+                                        tool.doc_loader,
+                                        tool.tool,
+                                        tool.tool["id"],
+                                        False)

                     runnerjob = tool.job(job_order,
                                          self.output_callback,
                                          **kwargs).next()
                 else:
                     runnerjob = tool.job(job_order,
                                          self.output_callback,
                                          **kwargs).next()
                 else:

-                    runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name,
-                                                self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"),
-                                                name=kwargs.get("name"))
-            else:
-                runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name,
-                                      self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"),
-                                      name=kwargs.get("name"))
-
-        if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
+                    runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"),
+                                                self.output_name,
+                                                self.output_tags,
+                                                submit_runner_ram=kwargs.get("submit_runner_ram"),
+                                                name=kwargs.get("name"),
+                                                on_error=kwargs.get("on_error"),
+                                                submit_runner_image=kwargs.get("submit_runner_image"))
+            elif self.work_api == "jobs":
+                runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"),
+                                      self.output_name,
+                                      self.output_tags,
+                                      submit_runner_ram=kwargs.get("submit_runner_ram"),
+                                      name=kwargs.get("name"),
+                                      on_error=kwargs.get("on_error"),
+                                      submit_runner_image=kwargs.get("submit_runner_image"))
+
+        if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and self.work_api == "jobs":

             # Create pipeline for local run
             self.pipeline = self.api.pipeline_instances().create(
                 body={
             # Create pipeline for local run
             self.pipeline = self.api.pipeline_instances().create(
                 body={


@@ -378,7 +435,7 @@ class ArvCwlRunner(object):
 
         if runnerjob and not kwargs.get("wait"):
             runnerjob.run(wait=kwargs.get("wait"))
 
         if runnerjob and not kwargs.get("wait"):
             runnerjob.run(wait=kwargs.get("wait"))

-            return runnerjob.uuid
+            return (runnerjob.uuid, "success")

 
         self.poll_api = arvados.api('v1')
         self.polling_thread = threading.Thread(target=self.poll_states)
 
         self.poll_api = arvados.api('v1')
         self.polling_thread = threading.Thread(target=self.poll_states)


@@ -456,14 +513,11 @@ class ArvCwlRunner(object):
             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
             self.set_crunch_output()
 
             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
             self.set_crunch_output()
 

-        if self.final_status != "success":
-            raise WorkflowException("Workflow failed.")
-

         if kwargs.get("compute_checksum"):
             adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 
         if kwargs.get("compute_checksum"):
             adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 

-        return self.final_output
+        return (self.final_output, self.final_status)

 
 
 def versionstring():
 
 
 def versionstring():


@@ -532,6 +586,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
                         default=True, dest="wait")
 
     exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
                         default=True, dest="wait")
 

+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
+                        default=True, dest="log_timestamps")
+    exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
+                        default=True, dest="log_timestamps")
+

     parser.add_argument("--api", type=str,
                         default=None, dest="work_api",
                         help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.")
     parser.add_argument("--api", type=str,
                         default=None, dest="work_api",
                         help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.")


@@ -544,10 +604,18 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
                         default=1024)
 
                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
                         default=1024)
 

+    parser.add_argument("--submit-runner-image", type=str,
+                        help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
+                        default=None)
+

     parser.add_argument("--name", type=str,
                         help="Name to use for workflow execution instance.",
                         default=None)
 
     parser.add_argument("--name", type=str,
                         help="Name to use for workflow execution instance.",
                         default=None)
 

+    parser.add_argument("--on-error", type=str,
+                        help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
+                        "Default is 'continue'.", default="continue", choices=("stop", "continue"))
+

     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 
     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 


@@ -596,7 +664,11 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
     try:
         if api_client is None:
             api_client=arvados.api('v1', model=OrderedJsonModel())
     try:
         if api_client is None:
             api_client=arvados.api('v1', model=OrderedJsonModel())

-        runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name, output_tags=arvargs.output_tags)
+        if keep_client is None:
+            keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
+        runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client,
+                              num_retries=4, output_name=arvargs.output_name,
+                              output_tags=arvargs.output_tags)

     except Exception as e:
         logger.error(e)
         return 1
     except Exception as e:
         logger.error(e)
         return 1


@@ -612,9 +684,17 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
         metrics.setLevel(logging.DEBUG)
         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 
         metrics.setLevel(logging.DEBUG)
         logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
 

+    if arvargs.log_timestamps:
+        arvados.log_handler.setFormatter(logging.Formatter(
+            '%(asctime)s %(name)s %(levelname)s: %(message)s',
+            '%Y-%m-%d %H:%M:%S'))
+    else:
+        arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
+

     arvargs.conformance_test = None
     arvargs.use_container = True
     arvargs.relax_path_checks = True
     arvargs.conformance_test = None
     arvargs.use_container = True
     arvargs.relax_path_checks = True

+    arvargs.validate = None

 
     return cwltool.main.main(args=arvargs,
                              stdout=stdout,
 
     return cwltool.main.main(args=arvargs,
                              stdout=stdout,


@@ -623,4 +703,11 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
                              makeTool=runner.arv_make_tool,
                              versionfunc=versionstring,
                              job_order_object=job_order_object,
                              makeTool=runner.arv_make_tool,
                              versionfunc=versionstring,
                              job_order_object=job_order_object,

-                             make_fs_access=partial(CollectionFsAccess, api_client=api_client))
+                             make_fs_access=partial(CollectionFsAccess,
+                                                    api_client=api_client,
+                                                    keep_client=keep_client),
+                             fetcher_constructor=partial(CollectionFetcher,
+                                                         api_client=api_client,
+                                                         keep_client=keep_client),
+                             resolver=partial(collectionResolver, api_client),
+                             logger_handler=arvados.log_handler)