[arvados] updated: 2.1.0-2888-g3cfe5fc65

[git repository hosting]

Summary of changes:
 sdk/cwl/arvados_cwl/arvcontainer.py | 2 ++
 sdk/cwl/arvados_cwl/executor.py     | 7 +++++++
 2 files changed, 9 insertions(+)

       via  3cfe5fc65c2883cef65087e016b8f6210d23cc8e (commit)
       via  8032cee83c73d333a6b20c400e86f0d17b8da273 (commit)
      from  bb1e867b5ed774d99b2291348f8a6bfa8c57325e (commit)

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commit 3cfe5fc65c2883cef65087e016b8f6210d23cc8e
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Sep 8 18:42:19 2022 -0400

    19464: Misspelled items
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 35d4622c6..34d50c1b6 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -574,7 +574,7 @@ The 'jobs' API is no longer supported.
 
     def set_container_request_properties(self, container, properties):
         resp = self.api.container_requests().list(filters=[["container_uuid", "=", container["uuid"]]], select=["uuid", "properties"]).execute(num_retries=self.num_retries)
-        for cr in resp["item"]:
+        for cr in resp["items"]:
             cr["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in properties.items()})
             self.api.container_requests().update(uuid=cr["uuid"], body={"container_request": {"properties": cr["properties"]}}).execute(num_retries=self.num_retries)
 

commit 8032cee83c73d333a6b20c400e86f0d17b8da273
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Sep 8 18:37:20 2022 -0400

    19464: Record git info as properties
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index c763cb7ef..e9b58bc83 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -524,6 +524,8 @@ class RunnerContainer(Runner):
             if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
                 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 
+        container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
+
         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
         if properties_req:
             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index f32c18941..35d4622c6 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -572,6 +572,12 @@ The 'jobs' API is no longer supported.
 
         return gitproperties
 
+    def set_container_request_properties(self, container, properties):
+        resp = self.api.container_requests().list(filters=[["container_uuid", "=", container["uuid"]]], select=["uuid", "properties"]).execute(num_retries=self.num_retries)
+        for cr in resp["item"]:
+            cr["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in properties.items()})
+            self.api.container_requests().update(uuid=cr["uuid"], body={"container_request": {"properties": cr["properties"]}}).execute(num_retries=self.num_retries)
+
     def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
         self.debug = runtimeContext.debug
 
@@ -776,6 +782,7 @@ The 'jobs' API is no longer supported.
         current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
         if current_container:
             logger.info("Running inside container %s", current_container.get("uuid"))
+            self.set_container_request_properties(current_container, git_info)
 
         self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout)
         self.polling_thread = threading.Thread(target=self.poll_states)

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