Adding additional tests to repo

ansible/roles/backend/tasks/main.yml

@@ -248,8 +248,6 @@
       environment_variables: 
         JOB_QUEUE_NAME: "{{ project }}-{{ deployment_group }}-job-q"
         OUTPUT_BUCKET: "{{ project }}-{{ deployment_group }}-output"
-        FARGATE_CLUSTER: "{{ project }}-{{ deployment_group }}-cluster"
-        FARGATE_SERVICE: "{{ project }}-{{ deployment_group }}-fargate-service"
       tags:
         Deployment: "{{ deployment_group }}"
     tags: 

lambda_services/job_service/job_service.py

@@ -9,10 +9,9 @@
 from .launcher.utils import _LOGGER
 
 OUTPUT_BUCKET = getenv("OUTPUT_BUCKET")
-FARGATE_CLUSTER = getenv("FARGATE_CLUSTER")
-FARGATE_SERVICE = getenv("FARGATE_SERVICE")
 # Could use SQS URL below instead of a queue name; whichever is easier
 SQS_QUEUE_NAME = getenv("JOB_QUEUE_NAME")
+JOB_QUEUE_REGION = getenv("JOB_QUEUE_REGION", "us-west-2")
 JOB_MAX_RUNTIME = int(getenv("JOB_MAX_RUNTIME", 2000))
 
 # Initialize logger
@@ -125,7 +124,7 @@ def build_status_dict(
 def upload_status_file(object_filename: str, initial_status_dict: dict):
     """Upload the initial status object to S3
 
-    :param object_filename str: the name of the file to download
+    :param object_filename str: the S3 object key of the file to download
     :param initial_status_dict dict: a JSON-compatible dictionary containing
                                      initial status info of the job
     """
@@ -235,7 +234,7 @@ def interpret_job_submission(event: dict, context):
             "command_line_args": job_command_line_args,
             "max_run_time": timeout_seconds,
         }
-        sqs_client = resource("sqs")
+        sqs_client = resource("sqs", JOB_QUEUE_REGION)
         queue = sqs_client.get_queue_by_name(QueueName=SQS_QUEUE_NAME)
         _LOGGER.info("%s Sending message to queue: %s", job_tag, sqs_json)
         queue.send_message(MessageBody=dumps(sqs_json))

lambda_services/job_service/launcher/utils.py

@@ -125,9 +125,9 @@ def s3_object_exists(bucket_name: str, object_name: str) -> bool:
         )
         return True
     except ClientError as err:
-        if err.response["Error"]["Message"] == "NoSuchKey":
+        if err.response["Error"]["Code"] == "404":  # "NoSuchKey" error
             return False
-        elif err.response["Error"]["Message"] == "Forbidden":
+        elif err.response["Error"]["Code"] == "403":
             job_tag: str = _extract_job_tag_from_objectname(object_name)
             _LOGGER.warning(
                 "%s Received '%s' (%d) message on object HEAD: %s",

lambda_services/tests/expected_data/template-output.json

@@ -0,0 +1,7 @@
+[
+    {
+        "name": "",
+        "sqs_message": {},
+        "initial_status": {}
+    }
+]

lambda_services/tests/expected_data/test-job_service-output.json

@@ -0,0 +1,93 @@
+[
+  {
+    "name": "apbs-direct",
+    "sqs_message": {
+      "job_id": "sampleId",
+      "job_type": "apbs",
+      "job_date": "2021-05-16",
+      "job_tag": "2021-05-16/sampleId",
+      "bucket_name": "pytest_input_bucket",
+      "input_files": [
+        "2021-05-16/sampleId/1fas.in",
+        "2021-05-16/sampleId/1fas.pqr"
+      ],
+      "command_line_args": "1fas.in",
+      "max_run_time": 7200
+    },
+    "initial_status": {
+      "jobid": "sampleId",
+      "jobtype": "apbs",
+      "apbs": {
+        "status": "pending",
+        "startTime": 1623172892.2588568,
+        "endTime": null,
+        "subtasks": [],
+        "inputFiles": [
+          "2021-05-16/sampleId/1fas.in",
+          "2021-05-16/sampleId/1fas.pqr"
+        ],
+        "outputFiles": []
+      }
+    }
+  },
+  {
+    "name": "apbs-post_pdb2pqr",
+    "sqs_message": {
+      "job_id": "sampleId",
+      "job_type": "apbs",
+      "job_date": "2021-05-16",
+      "job_tag": "2021-05-16/sampleId",
+      "bucket_name": "pytest_input_bucket",
+      "input_files": [
+        "2021-05-16/sampleId/1fas.pqr",
+        "2021-05-16/sampleId/apbsinput.in"
+      ],
+      "command_line_args": "apbsinput.in",
+      "max_run_time": 7200
+    },
+    "initial_status": {
+      "jobid": "sampleId",
+      "jobtype": "apbs",
+      "apbs": {
+        "status": "pending",
+        "startTime": 1623172892.2588568,
+        "endTime": null,
+        "subtasks": [],
+        "inputFiles": [
+          "2021-05-16/sampleId/1fas.pqr",
+          "2021-05-16/sampleId/apbsinput.in"
+        ],
+        "outputFiles": []
+      }
+    }
+  },
+  {
+    "name": "pdb2pqr-v1-basic",
+    "sqs_message": {
+      "job_date": "2021-05-16",
+      "job_id": "sampleId",
+      "job_tag": "2021-05-16/sampleId",
+      "job_type": "pdb2pqr",
+      "bucket_name": "pytest_input_bucket",
+      "input_files": [
+        "https://files.rcsb.org/download/1fas.pdb"
+      ],
+      "command_line_args": "--with-ph=7.0 --ph-calc-method=propka --drop-water --apbs-input --ff=parse --verbose  1fas.pdb sampleId.pqr",
+      "max_run_time": 2700
+    },
+    "initial_status": {
+      "jobid": "sampleId",
+      "jobtype": "pdb2pqr",
+      "pdb2pqr": {
+        "status": "pending",
+        "startTime": 1623261174.8676486,
+        "endTime": null,
+        "subtasks": [],
+        "inputFiles": [
+          "https://files.rcsb.org/download/1fas.pdb"
+        ],
+        "outputFiles": []
+      }
+    }
+  }
+]

lambda_services/tests/input_data/1fas.in

@@ -0,0 +1,27 @@
+read
+    mol pqr 1fas.pqr
+end
+elec 
+    mg-auto
+    dime 129 97 97
+    cglen 63.1108 45.7300 61.4601
+    fglen 57.1240 45.7300 56.1530
+    cgcent mol 1
+    fgcent mol 1
+    mol 1
+    lpbe
+    bcfl sdh
+    pdie 2.0000
+    sdie 78.5400
+    srfm smol
+    chgm spl2
+    sdens 10.00
+    srad 1.40
+    swin 0.30
+    temp 298.15
+    calcenergy total
+    calcforce no
+    write pot dx 1fas.pqr
+end
+print elecEnergy 1 end
+quit