20257: Mark functions and classes internal not intended for use

[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 21b629f37ab9b50812415ecdad4a766345b28f32..fe27b91ab2165754dd94f7a85878328db6126b4d 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -36,6 +36,7 @@ from arvados.api import OrderedJsonModel
 from .perf import Perf
 from ._version import __version__
 from .executor import ArvCwlExecutor
+from .fsaccess import workflow_uuid_pattern
 
 # These aren't used directly in this file but
 # other code expects to import them from here
@@ -199,6 +200,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         action="store_false", default=True,
                         help=argparse.SUPPRESS)
 
+    parser.add_argument("--disable-git", dest="git_info",
+                        action="store_false", default=True,
+                        help=argparse.SUPPRESS)
+
     parser.add_argument("--disable-color", dest="enable_color",
                         action="store_false", default=True,
                         help=argparse.SUPPRESS)
@@ -207,12 +212,25 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         action="store_true", default=False,
                         help=argparse.SUPPRESS)
 
+    parser.add_argument("--fast-parser", dest="fast_parser",
+                        action="store_true", default=False,
+                        help=argparse.SUPPRESS)
+
     parser.add_argument("--thread-count", type=int,
                         default=0, help="Number of threads to use for job submit and output collection.")
 
     parser.add_argument("--http-timeout", type=int,
                         default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
 
+    parser.add_argument("--defer-downloads", action="store_true", default=False,
+                        help="When submitting a workflow, defer downloading HTTP URLs to workflow launch instead of downloading to Keep before submit.")
+
+    parser.add_argument("--varying-url-params", type=str, default="",
+                        help="A comma separated list of URL query parameters that should be ignored when storing HTTP URLs in Keep.")
+
+    parser.add_argument("--prefer-cached-downloads", action="store_true", default=False,
+                        help="If a HTTP URL is found in Keep, skip upstream URL freshness check (will not notice if the upstream has changed, but also not error if upstream is unavailable).")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-preemptible", dest="enable_preemptible", default=None, action="store_true", help="Use preemptible instances. Control individual steps with arv:UsePreemptible hint.")
     exgroup.add_argument("--disable-preemptible", dest="enable_preemptible", default=None, action="store_false", help="Don't use preemptible instances.")
@@ -265,6 +283,9 @@ def add_arv_hints():
         "http://arvados.org/cwl#ProcessProperties",
         "http://commonwl.org/cwltool#CUDARequirement",
         "http://arvados.org/cwl#UsePreemptible",
+        "http://arvados.org/cwl#OutputCollectionProperties",
+        "http://arvados.org/cwl#KeepCacheTypeRequirement",
+        "http://arvados.org/cwl#OutOfMemoryRetry",
     ])
 
 def exit_signal_handler(sigcode, frame):
@@ -313,12 +334,15 @@ def main(args=sys.argv[1:],
         if api_client is None:
             api_client = arvados.safeapi.ThreadSafeApiCache(
                 api_params={"model": OrderedJsonModel(), "timeout": arvargs.http_timeout},
-                keep_params={"num_retries": 4})
+                keep_params={"num_retries": 4},
+                version='v1',
+            )
             keep_client = api_client.keep
             # Make an API object now so errors are reported early.
             api_client.users().current().execute()
         if keep_client is None:
-            keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
+            block_cache = arvados.keep.KeepBlockCache(disk_cache=True)
+            keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4, block_cache=block_cache)
         executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4, stdout=stdout)
     except WorkflowException as e:
         logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
@@ -329,6 +353,12 @@ def main(args=sys.argv[1:],
 
     # Note that unless in debug mode, some stack traces related to user
     # workflow errors may be suppressed.
+
+    # Set the logging on most modules INFO (instead of default which is WARNING)
+    logger.setLevel(logging.INFO)
+    logging.getLogger('arvados').setLevel(logging.INFO)
+    logging.getLogger('arvados.keep').setLevel(logging.WARNING)
+
     if arvargs.debug:
         logger.setLevel(logging.DEBUG)
         logging.getLogger('arvados').setLevel(logging.DEBUG)
@@ -358,6 +388,11 @@ def main(args=sys.argv[1:],
         # unit tests.
         stdout = None
 
+    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:
+            executor.fast_submit = True
+
     return cwltool.main.main(args=arvargs,
                              stdout=stdout,
                              stderr=stderr,