14725: Don't give a cluster_id when updating container request record

* When transferring files from http to keep, explicitly open in binary
  mode

* Bump arvados-python-client dependency for python3 support

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

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index e921b26dfe78279c1ee22fb6a19c5e93569ed542..af7c02a8f30010bfe85e51a6928e63a5a617d37e 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -499,6 +499,9 @@ class RunnerContainer(Runner):
             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 
         if runtimeContext.submit_request_uuid:
+            if "cluster_id" in extra_submit_params:
+                # Doesn't make sense for "update" and actually fails
+                del extra_submit_params["cluster_id"]
             response = self.arvrunner.api.container_requests().update(
                 uuid=runtimeContext.submit_request_uuid,
                 body=job_spec,

diff --git a/sdk/cwl/arvados_cwl/http.py b/sdk/cwl/arvados_cwl/http.py
index ccc2e793b067f4e0853da275947a08d3630723a3..47a304372c58a27ecde8d8c13bb55d6435f9cf79 100644 (file)
--- a/sdk/cwl/arvados_cwl/http.py
+++ b/sdk/cwl/arvados_cwl/http.py
@@ -132,7 +132,7 @@ def http_to_keep(api, project_uuid, url, utcnow=datetime.datetime.utcnow):
     count = 0
     start = time.time()
     checkpoint = start
-    with c.open(name, "w") as f:
+    with c.open(name, "wb") as f:
         for chunk in req.iter_content(chunk_size=1024):
             count += len(chunk)
             f.write(chunk)

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 711796374849c115296e089e31a44729330f45fb..22c49a01bf4ed31592db013ac5f2cb49c4e789cd 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -37,7 +37,7 @@ setup(name='arvados-cwl-runner',
           'schema-salad==3.0.20181129082112',
           'typing >= 3.6.4',
           'ruamel.yaml >=0.15.54, <=0.15.77',
-          'arvados-python-client>=1.2.1.20181130020805',
+          'arvados-python-client>=1.3.0.20190205182514',
           'setuptools',
           'ciso8601 >=1.0.6, <2.0.0',
           'subprocess32>=3.5.1',