Merge branch '10401-limit-dir-expansion' closes #10401

[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 36fe6efbb28ca7be90044e4e2ebd6368a73237ee..7c24310bdb7dcd79369c4a548495b936fe280957 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -11,6 +11,7 @@ import threading
 import hashlib
 import copy
 import json
+import re
 from functools import partial
 import pkg_resources  # part of setuptools
 
@@ -37,8 +38,8 @@ from .pathmapper import NoFollowPathMapper
 from ._version import __version__
 
 from cwltool.pack import pack
-from cwltool.process import shortname, UnsupportedRequirement, getListing
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
 from cwltool.draft2tool import compute_checksums
 from arvados.api import OrderedJsonModel
 
@@ -202,12 +203,6 @@ class ArvCwlRunner(object):
         if isinstance(obj, dict):
             if obj.get("writable"):
                 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")
             if obj.get("class") == "DockerRequirement":
                 if obj.get("dockerOutputDirectory"):
                     # TODO: can be supported by containers API, but not jobs API.
@@ -520,7 +515,7 @@ class ArvCwlRunner(object):
             self.set_crunch_output()
 
         if kwargs.get("compute_checksum"):
-            adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
+            adjustDirObjs(self.final_output, partial(get_listing, self.fs_access))
             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 
         return (self.final_output, self.final_status)
@@ -628,16 +623,19 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     return parser
 
 def add_arv_hints():
-    cache = {}
+    cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
-    cache["http://arvados.org/cwl"] = res.read()
+    use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
     res.close()
-    document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
-    _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache)
-    for n in extnames.names:
-        if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
-            cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
-        document_loader.idx["http://arvados.org/cwl#"+n] = {}
+    cwltool.process.supportedProcessRequirements.extend([
+        "http://arvados.org/cwl#RunInSingleContainer",
+        "http://arvados.org/cwl#OutputDirType",
+        "http://arvados.org/cwl#RuntimeConstraints",
+        "http://arvados.org/cwl#PartitionRequirement",
+        "http://arvados.org/cwl#APIRequirement",
+        "http://commonwl.org/cwltool#LoadListingRequirement"
+    ])
+
 
 def main(args, stdout, stderr, api_client=None, keep_client=None):
     parser = arg_parser()
@@ -719,4 +717,5 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
                                                          keep_client=keep_client,
                                                          num_retries=runner.num_retries),
                              resolver=partial(collectionResolver, api_client, num_retries=runner.num_retries),
-                             logger_handler=arvados.log_handler)
+                             logger_handler=arvados.log_handler,
+                             custom_schema_callback=add_arv_hints)