From f50c43c3eec9a736a8d095c62e50fbc66626c175 Mon Sep 17 00:00:00 2001 From: Fabrice Brito Date: Mon, 25 Nov 2024 15:20:59 +0100 Subject: [PATCH] fixes --- tests/tests_water_bodies.py | 9 +++++---- zoo_argowf_runner/cwl2argo.py | 4 ++++ zoo_argowf_runner/runner.py | 4 +--- 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/tests/tests_water_bodies.py b/tests/tests_water_bodies.py index 302a37e..3993bc5 100644 --- a/tests/tests_water_bodies.py +++ b/tests/tests_water_bodies.py @@ -27,17 +27,18 @@ def _(self, message): os.environ["ARGO_WF_ENDPOINT"] = "http://localhost:2746" os.environ["ARGO_WF_TOKEN"] = ( - "" + "eyJhbGciOiJSUzI1NiIsImtpZCI6ImZSUUYycDZNbnI4MTZLeXVFUnpyZk9FcUJGTHdQQzI4SURGdHhQc0pzRXMifQ.eyJpc3MiOiJrdWJlcm5ldGVzL3NlcnZpY2VhY2NvdW50Iiwia3ViZXJuZXRlcy5pby9zZXJ2aWNlYWNjb3VudC9uYW1lc3BhY2UiOiJuczEiLCJrdWJlcm5ldGVzLmlvL3NlcnZpY2VhY2NvdW50L3NlY3JldC5uYW1lIjoiYXJnby5zZXJ2aWNlLWFjY291bnQtdG9rZW4iLCJrdWJlcm5ldGVzLmlvL3NlcnZpY2VhY2NvdW50L3NlcnZpY2UtYWNjb3VudC5uYW1lIjoiYXJnbyIsImt1YmVybmV0ZXMuaW8vc2VydmljZWFjY291bnQvc2VydmljZS1hY2NvdW50LnVpZCI6IjExZjI1NDUxLWE4OGEtNDFkZC1hNGIxLTJlNTM3ZGUyOGU3NiIsInN1YiI6InN5c3RlbTpzZXJ2aWNlYWNjb3VudDpuczE6YXJnbyJ9.dUVo3WCJgoVN5NVh3VVeKw7uF6hE6moCj8Mu5W7ioJ4M_lG_bJ4BZ7XRaJVrQMF--vMQAiNDr-_GSC0R7ItKmRqhafkONy61MeEDz_6u-j0ay4fj8qofgBatnF7lWcVVvNklVZxZ4IGb62SJepAvzerxsz5HhSG8icn9U0cUsyg4Vw_wsHntic-yFY4Eyp6kYSEXO5G2v_0KXLKcpLB41YLfMQaE8cu0ghmE5mFmKkKOf0oDHhLlch-j_K0IpGvXKcjZGlwjiukD1dCL3E6BSHYMutuz4n27Bg62nf3rZBErUkJB2GRjN-tKIoYMrEuwyEbv7TSuCeqHGyfWn3Tu0A" ) os.environ["ARGO_WF_SYNCHRONIZATION_CM"] = "semaphore-water-bodies" + os.environ["DEFAULT_VOLUME_SIZE"] = "12Gi" cls.zoo = zoo conf = {} - conf["lenv"] = {"message": ""} - conf["lenv"] = {"Identifier": "water-bodies", "usid": "1234"} + conf["lenv"] = {"message": "", "Identifier": "water-bodies", "usid": "1234"} conf["tmpPath"] = "/tmp" - conf["main"] = {"tmpUrl": "http://localhost/logs/", "namespace": "ns1"} + conf["main"] = {"tmpUrl": "http://localhost/logs/"} + conf["auth_env"] = {"user": "ns1"} cls.conf = conf inputs = { diff --git a/zoo_argowf_runner/cwl2argo.py b/zoo_argowf_runner/cwl2argo.py index 6fdc562..61702e1 100644 --- a/zoo_argowf_runner/cwl2argo.py +++ b/zoo_argowf_runner/cwl2argo.py @@ -126,6 +126,10 @@ def cwl_to_argo( "name": "stac-catalog", "expression": "steps['argo-cwl'].outputs.parameters['stac-catalog']", }, + { + "name": "feature-collection", + "expression": "steps['argo-cwl'].outputs.parameters['feature-collection']", + }, ], outputs_artifacts=[ { diff --git a/zoo_argowf_runner/runner.py b/zoo_argowf_runner/runner.py index 1751aff..ec02108 100644 --- a/zoo_argowf_runner/runner.py +++ b/zoo_argowf_runner/runner.py @@ -153,9 +153,7 @@ def execute(self): self.update_status(progress=15, message="upload required files") self.execution = Execution( - namespace=self.zoo_conf.conf["main"][ - "namespace" - ], # TODO check this with Gerald + namespace=self.zoo_conf.conf["auth_env"]["user"], workflow=self.cwl, entrypoint=self.get_workflow_id(), workflow_name=self.get_workflow_uid(),