From: Peter Amstutz <pamstutz@veritasgenetics.com>
Date: Mon, 11 Feb 2019 15:09:24 +0000 (-0500)
Subject: 14725: Don't give a cluster_id when updating container request record
X-Git-Tag: 1.4.0~156^2~1
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/171b9ac5962c21dead1d04f4c53460a81b9b9993

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 e921b26dfe..af7c02a8f3 100644
--- 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 ccc2e793b0..47a304372c 100644
--- 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 7117963748..22c49a01bf 100644
--- 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',