12526: Fix tests

[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 e82fd9feef1f3d88c4068e7d0d6cbfee6232c3f2..ee0a73de1456b15cd7347e740bacbd26f8c68998 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -23,6 +23,7 @@ import cwltool.main
 import cwltool.workflow
 import cwltool.process
 from schema_salad.sourceline import SourceLine
+import schema_salad.validate as validate
 
 import arvados
 import arvados.config
@@ -42,7 +43,7 @@ from ._version import __version__
 from cwltool.pack import pack
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
-from cwltool.draft2tool import compute_checksums
+from cwltool.command_line_tool import compute_checksums
 from arvados.api import OrderedJsonModel
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -224,13 +225,16 @@ class ArvCwlRunner(object):
 
     def check_features(self, obj):
         if isinstance(obj, dict):
-            if obj.get("writable"):
-                raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported")
+            if obj.get("writable") and self.work_api != "containers":
+                raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported with --api=jobs")
             if obj.get("class") == "DockerRequirement":
                 if obj.get("dockerOutputDirectory"):
-                    # TODO: can be supported by containers API, but not jobs API.
-                    raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
-                        "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
+                    if self.work_api != "containers":
+                        raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
+                            "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.")
+                    if not obj.get("dockerOutputDirectory").startswith('/'):
+                        raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError(
+                            "Option 'dockerOutputDirectory' must be an absolute path.")
             for v in obj.itervalues():
                 self.check_features(v)
         elif isinstance(obj, list):
@@ -279,7 +283,7 @@ class ArvCwlRunner(object):
 
         def rewrite(fileobj):
             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
-            for k in ("basename", "listing", "contents", "nameext", "nameroot", "dirname"):
+            for k in ("listing", "contents", "nameext", "nameroot", "dirname"):
                 if k in fileobj:
                     del fileobj[k]
 
@@ -402,6 +406,7 @@ class ArvCwlRunner(object):
                         "success")
 
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
+        self.eval_timeout = kwargs.get("eval_timeout")
 
         kwargs["make_fs_access"] = make_fs_access
         kwargs["enable_reuse"] = kwargs.get("enable_reuse")
@@ -410,11 +415,15 @@ class ArvCwlRunner(object):
         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
 
         if self.work_api == "containers":
+            if self.ignore_docker_for_reuse:
+                raise Exception("--ignore-docker-for-reuse not supported with containers API.")
             kwargs["outdir"] = "/var/spool/cwl"
             kwargs["docker_outdir"] = "/var/spool/cwl"
             kwargs["tmpdir"] = "/tmp"
             kwargs["docker_tmpdir"] = "/tmp"
         elif self.work_api == "jobs":
+            if kwargs["priority"] != 500:
+                raise Exception("--priority not implemented for jobs API.")
             kwargs["outdir"] = "$(task.outdir)"
             kwargs["docker_outdir"] = "$(task.outdir)"
             kwargs["tmpdir"] = "$(task.tmpdir)"
@@ -437,7 +446,8 @@ class ArvCwlRunner(object):
                                                 on_error=kwargs.get("on_error"),
                                                 submit_runner_image=kwargs.get("submit_runner_image"),
                                                 intermediate_output_ttl=kwargs.get("intermediate_output_ttl"),
-                                                merged_map=merged_map)
+                                                merged_map=merged_map,
+                                                priority=kwargs.get("priority"))
             elif self.work_api == "jobs":
                 runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"),
                                       self.output_name,
@@ -657,6 +667,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
                         default=0)
 
+    parser.add_argument("--priority", type=int,
+                        help="Workflow priority (range 1000 - 1, higher has precedence over lower, containers api only)",
+                        default=500)
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--trash-intermediate", action="store_true",
                         default=False, dest="trash_intermediate",
@@ -671,8 +685,8 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     return parser
 
 def add_arv_hints():
-    cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
-    cwltool.draft2tool.ACCEPTLIST_RE = cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE
+    cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
+    cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
     use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
     res.close()