Crunch script doesn't fail in file/directory literals that don't have a 'location...

[arvados.git] / sdk / cwl / arvados_cwl / arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 4c4db171f50bdfb4d80bee9b1f2dc473b326068c..657d5927d0328025eb948f6e8ee62ba215486769 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -1,22 +1,26 @@
 import logging
 import json
 import os
+import urllib
 
 import ruamel.yaml as yaml
 
 from cwltool.errors import WorkflowException
 from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFiles, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
 from cwltool.utils import aslist
 
 import arvados.collection
 
 from .arvdocker import arv_docker_get_image
 from . import done
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location
 from .fsaccess import CollectionFetcher
+from .pathmapper import NoFollowPathMapper, trim_listing
+from .perf import Perf
 
 logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
 class ArvadosContainer(object):
     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
@@ -44,39 +48,83 @@ class ArvadosContainer(object):
         mounts = {
             self.outdir: {
                 "kind": "tmp"
+            },
+            self.tmpdir: {
+                "kind": "tmp"
             }
         }
         scheduling_parameters = {}
 
-        dirs = set()
-        for f in self.pathmapper.files():
-            _, p, tp = self.pathmapper.mapper(f)
-            if tp == "Directory" and '/' not in p[6:]:
-                mounts[p] = {
-                    "kind": "collection",
-                    "portable_data_hash": p[6:]
-                }
-                dirs.add(p[6:])
-        for f in self.pathmapper.files():
-            _, p, tp = self.pathmapper.mapper(f)
-            if p[6:].split("/")[0] not in dirs:
-                mounts[p] = {
-                    "kind": "collection",
-                    "portable_data_hash": p[6:]
-                }
-
-        if self.generatefiles["listing"]:
-            raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
+        rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files]
+        rf.sort(key=lambda k: k.resolved)
+        prevdir = None
+        for resolved, target, tp, stg in rf:
+            if not stg:
+                continue
+            if prevdir and target.startswith(prevdir):
+                continue
+            if tp == "Directory":
+                targetdir = target
+            else:
+                targetdir = os.path.dirname(target)
+            sp = resolved.split("/", 1)
+            pdh = sp[0][5:]   # remove "keep:"
+            mounts[targetdir] = {
+                "kind": "collection",
+                "portable_data_hash": pdh
+            }
+            if len(sp) == 2:
+                if tp == "Directory":
+                    path = sp[1]
+                else:
+                    path = os.path.dirname(sp[1])
+                if path and path != "/":
+                    mounts[targetdir]["path"] = path
+            prevdir = targetdir + "/"
+
+        with Perf(metrics, "generatefiles %s" % self.name):
+            if self.generatefiles["listing"]:
+                vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
+                                                    keep_client=self.arvrunner.keep_client,
+                                                    num_retries=self.arvrunner.num_retries)
+                generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
+                                                    separateDirs=False)
+
+                with Perf(metrics, "createfiles %s" % self.name):
+                    for f, p in generatemapper.items():
+                        if not p.target:
+                            pass
+                        elif p.type in ("File", "Directory"):
+                            source, path = self.arvrunner.fs_access.get_collection(p.resolved)
+                            vwd.copy(path, p.target, source_collection=source)
+                        elif p.type == "CreateFile":
+                            with vwd.open(p.target, "w") as n:
+                                n.write(p.resolved.encode("utf-8"))
+
+                with Perf(metrics, "generatefiles.save_new %s" % self.name):
+                    vwd.save_new()
+
+                for f, p in generatemapper.items():
+                    if not p.target:
+                        continue
+                    mountpoint = "%s/%s" % (self.outdir, p.target)
+                    mounts[mountpoint] = {"kind": "collection",
+                                          "portable_data_hash": vwd.portable_data_hash(),
+                                          "path": p.target}
 
         container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
         if self.environment:
             container_request["environment"].update(self.environment)
 
         if self.stdin:
-            raise UnsupportedRequirement("Stdin redirection currently not suppported")
+            sp = self.stdin[6:].split("/", 1)
+            mounts["stdin"] = {"kind": "collection",
+                                "portable_data_hash": sp[0],
+                                "path": sp[1]}
 
         if self.stderr:
-            raise UnsupportedRequirement("Stderr redirection currently not suppported")
+            mounts["stderr"] = {"kind": "file",
+                                "path": "%s/%s" % (self.outdir, self.stderr)}
 
         if self.stdout:
             mounts["stdout"] = {"kind": "file",
@@ -103,7 +151,7 @@ class ArvadosContainer(object):
         runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
         if runtime_req:
             if "keep_cache" in runtime_req:
-                runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
+                runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
 
         partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
         if partition_req:
@@ -192,6 +240,8 @@ class RunnerContainer(Runner):
         """
 
         adjustDirObjs(self.job_order, trim_listing)
+        adjustFileObjs(self.job_order, trim_anonymous_location)
+        adjustDirObjs(self.job_order, trim_anonymous_location)
 
         container_req = {
             "owner_uuid": self.arvrunner.project_uuid,