kind = 'error'
elif record.levelno >= logging.WARNING:
kind = 'warning'
+ if kind == 'warning' and record.name == "salad":
+ # Don't send validation warnings to runtime status,
+ # they're noisy and unhelpful.
+ return
if kind is not None and self.updatingRuntimeStatus is not True:
self.updatingRuntimeStatus = True
try:
arvargs.output_tags = None
arvargs.thread_count = 1
arvargs.collection_cache_size = None
+ arvargs.git_info = True
+ arvargs.submit = False
+ arvargs.defer_downloads = False
self.api = api_client
self.processes = {}
self.fs_access = None
self.secret_store = None
self.stdout = stdout
+ self.fast_submit = False
+ self.git_info = arvargs.git_info
if keep_client is not None:
self.keep_client = keep_client
self.toplevel_runtimeContext.make_fs_access = partial(CollectionFsAccess,
collection_cache=self.collection_cache)
+ self.defer_downloads = arvargs.submit and arvargs.defer_downloads
+
validate_cluster_target(self, self.toplevel_runtimeContext)
page = keys[:pageSize]
try:
proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
- except Exception:
- logger.exception("Error checking states on API server: %s")
+ except Exception as e:
+ logger.exception("Error checking states on API server: %s", e)
remain_wait = self.poll_interval
continue
for req in job_reqs:
tool.requirements.append(req)
- def get_git_info(self, tool):
+ @staticmethod
+ def get_git_info(tool):
in_a_git_repo = False
cwd = None
filepath = None
git_commit = subprocess.run(["git", "log", "--format=%H", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
git_date = subprocess.run(["git", "log", "--format=%cD", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
git_committer = subprocess.run(["git", "log", "--format=%cn <%ce>", "-n1", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
- git_branch = subprocess.run(["git", "branch", "--show-current"], cwd=cwd, capture_output=True, text=True).stdout
+ git_branch = subprocess.run(["git", "rev-parse", "--abbrev-ref", "HEAD"], cwd=cwd, capture_output=True, text=True).stdout
git_origin = subprocess.run(["git", "remote", "get-url", "origin"], cwd=cwd, capture_output=True, text=True).stdout
git_status = subprocess.run(["git", "status", "--untracked-files=no", "--porcelain"], cwd=cwd, capture_output=True, text=True).stdout
- git_describe = subprocess.run(["git", "describe", "--always"], cwd=cwd, capture_output=True, text=True).stdout
+ git_describe = subprocess.run(["git", "describe", "--always", "--tags"], cwd=cwd, capture_output=True, text=True).stdout
git_toplevel = subprocess.run(["git", "rev-parse", "--show-toplevel"], cwd=cwd, capture_output=True, text=True).stdout
git_path = filepath[len(git_toplevel):]
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["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)
+
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
- git_info = self.get_git_info(updated_tool)
+ git_info = self.get_git_info(updated_tool) if self.git_info else {}
if git_info:
- logger.info("Git provenance of %s", updated_tool.tool["id"])
+ logger.info("Git provenance")
for g in git_info:
if git_info[g]:
logger.info(" %s: %s", g.split("#", 1)[1], git_info[g])
controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller)
- updated_tool.visit(self.check_features)
+ if not self.fast_submit:
+ updated_tool.visit(self.check_features)
self.pipeline = None
self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
loadingContext = self.loadingContext.copy()
loadingContext.do_validate = False
loadingContext.disable_js_validation = True
- if submitting:
+ if submitting and not self.fast_submit:
loadingContext.do_update = False
# Document may have been auto-updated. Reload the original
# document with updating disabled because we want to
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
- logger.info("Uploading workflow dependencies")
- with Perf(metrics, "upload_workflow_deps"):
- merged_map = upload_workflow_deps(self, tool, runtimeContext)
+ if not self.fast_submit:
+ logger.info("Uploading workflow dependencies")
+ with Perf(metrics, "upload_workflow_deps"):
+ merged_map = upload_workflow_deps(self, tool, runtimeContext)
+ else:
+ merged_map = {}
# Recreate process object (ArvadosWorkflow or
# ArvadosCommandTool) because tool document may have been
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)