Deploy Version 0.1.0

Author: Ezequiel-Valencia

compose_api/api/routers/core.py

@@ -107,13 +107,13 @@ async def submit_simulation(background_tasks: BackgroundTasks, uploaded_file: Up
             pb_allow_list=PBAllowList(
                 allow_list=[
                     "pypi::git+https://github.com/biosimulators/bspil-basico.git@initial_work",
-                    "pypi:cobra",
-                    "pypi:tellurium",
-                    "pypi:copasi-basico",
-                    "pypi:smoldyn",
-                    "pypi:numpy",
-                    "pypi:matplotlib",
-                    "pypi:scipy",
+                    "pypi::cobra",
+                    "pypi::tellurium",
+                    "pypi::copasi-basico",
+                    "pypi::smoldyn",
+                    "pypi::numpy",
+                    "pypi::matplotlib",
+                    "pypi::scipy",
                 ]
             ),
         )

compose_api/version.py

@@ -1 +1 @@
-__version__ = "0.0.1"
+__version__ = "0.1.0"

kustomize/config/compose-api-rke/shared.env

@@ -1,14 +1,15 @@
 #SLURM_SUBMIT_HOST=hamantis.cam.uchc.edu
-SLURM_SUBMIT_HOST=haproxy-ssh
+SLURM_SUBMIT_HOST=mantis-sub-7.cam.uchc.edu
 SLURM_SUBMIT_USER=crbmapi
 #SLURM_SUBMIT_KEY_PATH=/run/secrets/slurmsubmitkeyfile/ssh-privatekey
 SLURM_PARTITION=general
 SLURM_NODE_LIST=mantis-039
+SLURM_BUILD_NODE=mantis-007
 SLURM_QOS=general
 SLURM_LOG_BASE_PATH=/home/FCAM/crbmapi/compose_api/prod/htclogs
-
+SLURM_SBATCH_BASE_PATH=/home/FCAM/crbmapi/compose_api/prod/slurm_sbatch
 HPC_IMAGE_BASE_PATH=/home/FCAM/crbmapi/compose_api/prod/images
-HPC_REPO_BASE_PATH=/home/FCAM/crbmapi/compose_api/prod/repos
+HPC_REPO_BASE_PATH=/home/FCAM/crbmapi/compose_api/prod/repo
 HPC_SIM_BASE_PATH=/home/FCAM/crbmapi/compose_api/prod/sims
 HPC_SIM_CONFIG_FILE=publish-uchc-hpc.json
 
@@ -18,3 +19,5 @@ NATS_WORKER_EVENT_SUBJECT=prod.publish
 NATS_EMITTER_URL=nats://compose.cam.uchc.edu:30052
 NATS_EMITTER_MAGIC_WORD=nats-emitter-magic-word
 MARIMO_API_SERVER=http://api:8000
+
+NAMESPACE=prod

kustomize/overlays/compose-api-rke/kustomization.yaml

@@ -5,7 +5,7 @@ namespace: compose-api-rke
 
 images:
   - name: ghcr.io/biosimulations/compose-api
-    newTag: 0.0.1
+    newTag: 0.1.0
   - name: docker.io/library/mongo
     newTag: 8.0.12
 

tests/api/test_client.py

@@ -39,7 +39,7 @@ async def test_sim_run(
         assert isinstance(sim_experiment, SimulationExperiment)
 
         current_status = await get_simulation_status.asyncio(
-            client=in_memory_api_client, simulation_id=sim_experiment.simulation.database_id
+            client=in_memory_api_client, simulation_id=sim_experiment.simulation_id
         )
 
         if not isinstance(current_status, HpcRun) or not isinstance(current_status.status, JobStatus):
@@ -49,15 +49,15 @@ async def test_sim_run(
         while current_status.status != JobStatus.COMPLETED and num_loops < 10:
             await asyncio.sleep(2)
             current_status = await get_simulation_status.asyncio(
-                client=in_memory_api_client, simulation_id=sim_experiment.simulation.database_id
+                client=in_memory_api_client, simulation_id=sim_experiment.simulation_id
             )
             num_loops += 1
 
             if not isinstance(current_status, HpcRun) or not isinstance(current_status.status, JobStatus):
                 raise TypeError()
 
         current_status = await get_simulation_status.asyncio(
-            client=in_memory_api_client, simulation_id=sim_experiment.simulation.database_id
+            client=in_memory_api_client, simulation_id=sim_experiment.simulation_id
         )
 
         if not isinstance(current_status, HpcRun) or not isinstance(current_status.status, JobStatus):