X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f1943e92b2c83d2884eeaa2829f1b4a07d23b9ee..25107815e9da9483bb7e6055379420113bfc3640:/sdk/cwl/arvados_cwl/executor.py

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index c1f2b54744..eeb44dbd7f 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -59,6 +59,7 @@ class RuntimeStatusLoggingHandler(logging.Handler):
     def __init__(self, runtime_status_update_func):
         super(RuntimeStatusLoggingHandler, self).__init__()
         self.runtime_status_update = runtime_status_update_func
+        self.updatingRuntimeStatus = False
 
     def emit(self, record):
         kind = None
@@ -66,22 +67,27 @@ class RuntimeStatusLoggingHandler(logging.Handler):
             kind = 'error'
         elif record.levelno >= logging.WARNING:
             kind = 'warning'
-        if kind is not None:
-            log_msg = record.getMessage()
-            if '\n' in log_msg:
-                # If the logged message is multi-line, use its first line as status
-                # and the rest as detail.
-                status, detail = log_msg.split('\n', 1)
-                self.runtime_status_update(
-                    kind,
-                    "%s: %s" % (record.name, status),
-                    detail
-                )
-            else:
-                self.runtime_status_update(
-                    kind,
-                    "%s: %s" % (record.name, record.getMessage())
-                )
+        if kind is not None and self.updatingRuntimeStatus is not True:
+            self.updatingRuntimeStatus = True
+            try:
+                log_msg = record.getMessage()
+                if '\n' in log_msg:
+                    # If the logged message is multi-line, use its first line as status
+                    # and the rest as detail.
+                    status, detail = log_msg.split('\n', 1)
+                    self.runtime_status_update(
+                        kind,
+                        "%s: %s" % (record.name, status),
+                        detail
+                    )
+                else:
+                    self.runtime_status_update(
+                        kind,
+                        "%s: %s" % (record.name, record.getMessage())
+                    )
+            finally:
+                self.updatingRuntimeStatus = False
+
 
 class ArvCwlExecutor(object):
     """Execute a CWL tool or workflow, submit work (using either jobs or
@@ -436,17 +442,16 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
                                               num_retries=self.num_retries)
 
         for k,v in generatemapper.items():
-            if k.startswith("_:"):
-                if v.type == "Directory":
+            if v.type == "Directory" and v.resolved.startswith("_:"):
                     continue
-                if v.type == "CreateFile":
-                    with final.open(v.target, "wb") as f:
-                        f.write(v.resolved.encode("utf-8"))
+            if v.type == "CreateFile" and (k.startswith("_:") or v.resolved.startswith("_:")):
+                with final.open(v.target, "wb") as f:
+                    f.write(v.resolved.encode("utf-8"))
                     continue
 
-            if not k.startswith("keep:"):
+            if not v.resolved.startswith("keep:"):
                 raise Exception("Output source is not in keep or a literal")
-            sp = k.split("/")
+            sp = v.resolved.split("/")
             srccollection = sp[0][5:]
             try:
                 reader = self.collection_cache.get(srccollection)
@@ -456,7 +461,8 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
                 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
                 raise
             except IOError as e:
-                logger.warning("While preparing output collection: %s", e)
+                logger.error("While preparing output collection: %s", e)
+                raise
 
         def rewrite(fileobj):
             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
@@ -469,7 +475,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
 
         with final.open("cwl.output.json", "w") as f:
             res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
-            f.write(res)           
+            f.write(res)
 
         final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)