21356: Remove all Python 2/3 compatibility imports

[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 8108934aaeee5dfb3853a6c1395a0d39e36c9146..30d91b4094265d098b1344b2310470e184565794 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -6,15 +6,13 @@
 # Implement cwl-runner interface for submitting and running work on Arvados, using
 # the Crunch containers API.
 
-from future.utils import viewitems
-from builtins import str
-
 import argparse
+import importlib.metadata
+import importlib.resources
 import logging
 import os
 import sys
 import re
-import pkg_resources  # part of setuptools
 
 from schema_salad.sourceline import SourceLine
 import schema_salad.validate as validate
@@ -32,7 +30,6 @@ import arvados.logging
 from arvados.keep import KeepClient
 from arvados.errors import ApiError
 import arvados.commands._util as arv_cmd
-from arvados.api import OrderedJsonModel
 
 from .perf import Perf
 from ._version import __version__
@@ -58,15 +55,12 @@ arvados.log_handler.setFormatter(logging.Formatter(
 
 def versionstring():
     """Print version string of key packages for provenance and debugging."""
-
-    arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
-    arvpkg = pkg_resources.require("arvados-python-client")
-    cwlpkg = pkg_resources.require("cwltool")
-
-    return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
-                                    "arvados-python-client", arvpkg[0].version,
-                                    "cwltool", cwlpkg[0].version)
-
+    return "{} {}, arvados-python-client {}, cwltool {}".format(
+        sys.argv[0],
+        importlib.metadata.version('arvados-cwl-runner'),
+        importlib.metadata.version('arvados-python-client'),
+        importlib.metadata.version('cwltool'),
+    )
 
 def arg_parser():  # type: () -> argparse.ArgumentParser
     parser = argparse.ArgumentParser(
@@ -124,6 +118,8 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--create-workflow", action="store_true", help="Register an Arvados workflow that can be run from Workbench")
     exgroup.add_argument("--update-workflow", metavar="UUID", help="Update an existing Arvados workflow with the given UUID.")
 
+    exgroup.add_argument("--print-keep-deps", action="store_true", help="To assist copying, print a list of Keep collections that this workflow depends on.")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner, wait for completion.",
                         default=True, dest="wait")
@@ -259,6 +255,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=False, dest="trash_intermediate",
                         help="Do not trash intermediate outputs (default).")
 
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--enable-usage-report", dest="enable_usage_report", default=None, action="store_true", help="Create usage_report.html with a summary of each step's resource usage.")
+    exgroup.add_argument("--disable-usage-report", dest="enable_usage_report", default=None, action="store_false", help="Disable usage report.")
+
     parser.add_argument("workflow", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 
@@ -269,10 +269,8 @@ def add_arv_hints():
     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
     supported_versions = ["v1.0", "v1.1", "v1.2"]
     for s in supported_versions:
-        res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-%s.yml' % s)
-        customschema = res.read().decode('utf-8')
+        customschema = importlib.resources.read_text(__name__, f'arv-cwl-schema-{s}.yml', 'utf-8')
         use_custom_schema(s, "http://arvados.org/cwl", customschema)
-        res.close()
     cwltool.process.supportedProcessRequirements.extend([
         "http://arvados.org/cwl#RunInSingleContainer",
         "http://arvados.org/cwl#OutputDirType",
@@ -325,12 +323,14 @@ def main(args=sys.argv[1:],
             return 1
         arvargs.work_api = want_api
 
-    if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
+    workflow_op = arvargs.create_workflow or arvargs.update_workflow or arvargs.print_keep_deps
+
+    if workflow_op and not arvargs.job_order:
         job_order_object = ({}, "")
 
     add_arv_hints()
 
-    for key, val in viewitems(cwltool.argparser.get_default_args()):
+    for key, val in cwltool.argparser.get_default_args().items():
         if not hasattr(arvargs, key):
             setattr(arvargs, key, val)
 
@@ -338,7 +338,6 @@ def main(args=sys.argv[1:],
         if api_client is None:
             api_client = arvados.safeapi.ThreadSafeApiCache(
                 api_params={
-                    'model': OrderedJsonModel(),
                     'num_retries': arvargs.retries,
                     'timeout': arvargs.http_timeout,
                 },
@@ -418,9 +417,11 @@ def main(args=sys.argv[1:],
         # unit tests.
         stdout = None
 
+    executor.loadingContext.default_docker_image = arvargs.submit_runner_image or "arvados/jobs:"+__version__
+
     if arvargs.workflow.startswith("arvwf:") or workflow_uuid_pattern.match(arvargs.workflow) or arvargs.workflow.startswith("keep:"):
         executor.loadingContext.do_validate = False
-        if arvargs.submit:
+        if arvargs.submit and not workflow_op:
             executor.fast_submit = True
 
     return cwltool.main.main(args=arvargs,
@@ -433,4 +434,4 @@ def main(args=sys.argv[1:],
                              custom_schema_callback=add_arv_hints,
                              loadingContext=executor.loadingContext,
                              runtimeContext=executor.toplevel_runtimeContext,
-                             input_required=not (arvargs.create_workflow or arvargs.update_workflow))
+                             input_required=not workflow_op)