13627: Improve error reporting.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 2dd5497355f6891268f8767170b72c7b578493d1..a7e698b6dc346c1a6041763ccf8cc7a14d97d687 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -147,7 +147,7 @@ class ArvCwlRunner(object):
         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
             return ArvadosWorkflow(self, toolpath_object, loadingContext)
         else:
-            return cwltool.workflow.defaultMakeTool(toolpath_object, loadingContext)
+            return cwltool.workflow.default_make_tool(toolpath_object, loadingContext)
 
     def output_callback(self, out, processStatus):
         with self.workflow_eval_lock:
@@ -157,7 +157,7 @@ class ArvCwlRunner(object):
                     self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
                                                          body={"state": "Complete"}).execute(num_retries=self.num_retries)
             else:
-                logger.warn("Overall process status is %s", processStatus)
+                logger.error("Overall process status is %s", processStatus)
                 if self.pipeline:
                     self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
                                                          body={"state": "Failed"}).execute(num_retries=self.num_retries)

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index cb362187b969d40559eb13d0924333d76b063b0b..8e98e9604225f57b308a095a23e03dd7b2382d22 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -309,7 +309,7 @@ class ArvadosContainer(JobBase):
                                                            api_client=self.arvrunner.api,
                                                            keep_client=self.arvrunner.keep_client,
                                                            num_retries=self.arvrunner.num_retries)
-                done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
+                done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 
             if record["output_uuid"]:
                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 0ab065d7874149296382c94a2e593bc88ab5fb1c..e3bce68e6abdeb56fb03144c1496fe8103c55714 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -252,7 +252,7 @@ class ArvadosJob(JobBase):
                                 dirs[g.group(1)] = g.group(2)
 
                     if processStatus == "permanentFail":
-                        done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
+                        done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 
                     with Perf(metrics, "output collection %s" % self.name):
                         outputs = done.done(self, record, dirs["tmpdir"],

diff --git a/sdk/cwl/arvados_cwl/done.py b/sdk/cwl/arvados_cwl/done.py
index e9254c013845292b68b03be4fc867c0d0db41558..25efade2ab21900dd49dc16978fc9daac536efed 100644 (file)
--- a/sdk/cwl/arvados_cwl/done.py
+++ b/sdk/cwl/arvados_cwl/done.py
@@ -55,10 +55,10 @@ def done_outputs(self, record, tmpdir, outdir, keepdir):
 crunchstat_re = re.compile(r"^\d{4}-\d\d-\d\d_\d\d:\d\d:\d\d [a-z0-9]{5}-8i9sb-[a-z0-9]{15} \d+ \d+ stderr crunchstat:")
 timestamp_re = re.compile(r"^(\d{4}-\d\d-\d\dT\d\d:\d\d:\d\d\.\d+Z) (.*)")
 
-def logtail(logcollection, logger, header, maxlen=25):
+def logtail(logcollection, logfunc, header, maxlen=25):
     if len(logcollection) == 0:
-        logger.info(header)
-        logger.info("  ** log is empty **")
+        logfunc(header)
+        logfunc("  ** log is empty **")
         return
 
     containersapi = ("crunch-run.txt" in logcollection)
@@ -95,5 +95,5 @@ def logtail(logcollection, logger, header, maxlen=25):
         loglines = mergelogs.values()[0]
 
     logtxt = "\n  ".join(l.strip() for l in loglines)
-    logger.info(header)
-    logger.info("\n  %s", logtxt)
+    logfunc(header)
+    logfunc("\n  %s", logtxt)

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index a1c8c1bfb5891c72126c9f28f9d63cc5e972eeb0..12a847503b836d20e9a523ce28b2efb900023b10 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -414,7 +414,7 @@ class Runner(object):
                                                            api_client=self.arvrunner.api,
                                                            keep_client=self.arvrunner.keep_client,
                                                            num_retries=self.arvrunner.num_retries)
-                done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self), maxlen=40)
+                done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 
             self.final_output = record["output"]
             outc = arvados.collection.CollectionReader(self.final_output,

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index c288603753373cc60165ef101f966a4ac15f0736..45464a9ea7928be42614973f0301931091a85d03 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -33,7 +33,7 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20180614214548',
+          'cwltool==1.0.20180615135742',
           'schema-salad==2.7.20180501211602',
           'typing >= 3.5.3',
           'ruamel.yaml >=0.13.11, <0.15',