X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/92308b1b044dee2970c4409a0da660ccbecce945..1efba8f3b728a3b8aa3c64c5aa09f441318ff2a8:/sdk/cwl/arvados_cwl/__init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7968fb1e2b..9fc00c0017 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -10,11 +10,12 @@ 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
@@ -57,15 +58,12 @@ 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(
@@ -123,6 +121,8 @@ 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")
@@ -268,10 +268,8 @@ 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",
@@ -324,7 +322,9 @@ 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()
@@ -416,9 +416,11 @@ 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,
@@ -431,4 +433,4 @@ 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)