[ARVADOS] created: 1.2.0-429-g580c55d60

[Git user]

        at  580c55d60829f17118f0c8e57d1d72c84a71b62b (commit)


commit 580c55d60829f17118f0c8e57d1d72c84a71b62b
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Nov 26 10:13:39 2018 -0500

    14198: Restore behavior of creating an empty Builder object
    
    Used for do_eval() on set_cluster_target().  Calling _init_job() turns
    out to have some unintended side effects as well as doing redundant
    work.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 525764530..cd319e55b 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: Apache-2.0
 
 from cwltool.command_line_tool import CommandLineTool
+from cwltool.builder import Builder
 from .arvjob import ArvadosJob
 from .arvcontainer import ArvadosContainer
 from .pathmapper import ArvPathMapper
@@ -36,6 +37,31 @@ def set_cluster_target(tool, arvrunner, builder, runtimeContext):
 
     return runtimeContext
 
+def make_builder(joborder, hints, requirements, runtimeContext):
+    return Builder(
+                 job=joborder,
+                 files=[],               # type: List[Dict[Text, Text]]
+                 bindings=[],            # type: List[Dict[Text, Any]]
+                 schemaDefs={},          # type: Dict[Text, Dict[Text, Any]]
+                 names=None,               # type: Names
+                 requirements=requirements,        # type: List[Dict[Text, Any]]
+                 hints=hints,               # type: List[Dict[Text, Any]]
+                 resources={},           # type: Dict[str, int]
+                 mutation_manager=None,    # type: Optional[MutationManager]
+                 formatgraph=None,         # type: Optional[Graph]
+                 make_fs_access=None,      # type: Type[StdFsAccess]
+                 fs_access=None,           # type: StdFsAccess
+                 job_script_provider=runtimeContext.job_script_provider, # type: Optional[Any]
+                 timeout=runtimeContext.eval_timeout,             # type: float
+                 debug=runtimeContext.debug,               # type: bool
+                 js_console=runtimeContext.js_console,          # type: bool
+                 force_docker_pull=runtimeContext.force_docker_pull,   # type: bool
+                 loadListing="",         # type: Text
+                 outdir="",              # type: Text
+                 tmpdir="",              # type: Text
+                 stagedir="",            # type: Text
+                )
+
 class ArvadosCommandTool(CommandLineTool):
     """Wrap cwltool CommandLineTool to override selected methods."""
 
@@ -62,7 +88,7 @@ class ArvadosCommandTool(CommandLineTool):
                                  "$(task.keep)/%s/%s")
 
     def job(self, joborder, output_callback, runtimeContext):
-        builder = self._init_job(joborder, runtimeContext)
+        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
 
         if runtimeContext.work_api == "containers":
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 4cc01a91c..f514476b9 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -14,7 +14,6 @@ from cwltool.load_tool import fetch_document
 from cwltool.process import shortname
 from cwltool.workflow import Workflow, WorkflowException, WorkflowStep
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
-from cwltool.builder import Builder
 from cwltool.context import LoadingContext
 
 import ruamel.yaml as yaml
@@ -22,7 +21,7 @@ import ruamel.yaml as yaml
 from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
                      trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
 from .pathmapper import ArvPathMapper, trim_listing
-from .arvtool import ArvadosCommandTool, set_cluster_target
+from .arvtool import ArvadosCommandTool, set_cluster_target, make_builder
 from .perf import Perf
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -136,7 +135,7 @@ class ArvadosWorkflowStep(WorkflowStep):
         runtimeContext = runtimeContext.copy()
         runtimeContext.toplevel = True  # Preserve behavior for #13365
 
-        builder = self._init_job({shortname(k): v for k,v in joborder.items()}, runtimeContext)
+        builder = make_builder({shortname(k): v for k,v in joborder.items()}, self.hints, self.requirements, runtimeContext)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
         return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)
 

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hooks/post-receive
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