check_timeout

class GSAHandler

src/constants.ts

@@ -20,6 +20,7 @@ export class Constants {
     MANIFEST_SUFFIX: '.json',
     QUILT_METADATA: 'quilt_metadata.json',
     FASTQ_SENTINEL: 'out/bqsr_report/NA12878.hg38.recal_data.csv',
+    TIMEOUT: 15*60,
   };
 
   public static GET(key: string): any {

src/omics-quilt.ts

@@ -204,7 +204,7 @@ export class OmicsQuiltStack extends Stack {
     return new NodejsFunction(this, name, {
       runtime: Runtime.NODEJS_18_X,
       role: this.lambdaRole,
-      timeout: Duration.seconds(60),
+      timeout: Duration.seconds(this.cc.get('TIMEOUT')),
       retryAttempts: 1,
       environment: this.makeLambdaEnv(env),
     });
@@ -216,7 +216,7 @@ export class OmicsQuiltStack extends Stack {
       index: PYTHON_INDEX,
       runtime: Runtime.PYTHON_3_11,
       role: this.lambdaRole,
-      timeout: Duration.seconds(900),
+      timeout: Duration.seconds(this.cc.get('TIMEOUT')),
       retryAttempts: 1,
       environment: this.makeLambdaEnv(env),
       bundling: {
@@ -237,6 +237,7 @@ export class OmicsQuiltStack extends Stack {
       SENTINEL_FILE: this.packager_sentinel,
       QUILT_METADATA: this.cc.get('QUILT_METADATA'),
       WORKFLOW_ID: this.cc.get('READY2RUN_WORKFLOW_ID'),
+      TIMEOUT: this.cc.get('TIMEOUT'),
       ...env,
     };
     return final_env;

src/packager/packager/__init__.py

@@ -1,5 +1,5 @@
 from .types import KEYED, PseudoContext  # noqa: F401
 from .constants import Constants  # noqa: F401
 from .index import handler  # noqa: F401
-from .handler import Handler  # noqa: F401
+from .gsa_handler import GSAHandler  # noqa: F401
 from .ssm_parameter_store import SSMParameterStore  # noqa: F401

src/packager/packager/constants.py

@@ -2,6 +2,7 @@
 import yaml
 import os
 
+from datetime import datetime
 from dotenv import load_dotenv
 from tempfile import TemporaryDirectory
 from typing import Any, Generator
@@ -115,6 +116,7 @@ def __init__(self, context: KEYED = {}) -> None:
         self.app = self.get("APP_NAME")
         self.account = self.get("CDK_DEFAULT_ACCOUNT", "AWS_ACCOUNT_ID")
         self.region = self.get("CDK_DEFAULT_REGION", "AWS_DEFAULT_REGION")
+        self.ssm = SSMParameterStore(self.app, self.region)
 
     def to_dict(self) -> KEYED:
         return {
@@ -159,5 +161,17 @@ def get_bucket_name(self, type: str) -> str:
     def get_ecr_registry(self) -> str:
         return f"{self.account}.dkr.ecr.{self.region}.amazonaws.com"
 
-    def get_parameter_name(self, name: str) -> str:
-        return f"/vivos/{self.app}/{name}"
+    def timeout(self) -> int:
+        return int(self.get("TIMEOUT"))
+
+    def check_time(self, key: str) -> bool:
+        now = round(datetime.now().timestamp())
+        if key in self.ssm:
+            prior = int(self.ssm[key])
+            delta = now - prior
+            timeout = self.timeout()
+            if delta < timeout:
+                print(f"Too soon: {delta} < {timeout}")
+                return False
+        self.ssm[key] = str(now)
+        return True

src/packager/packager/handler.py → src/packager/packager/gsa_handler.py

@@ -17,7 +17,7 @@
 LOG_STREAM = "OmicsQuiltDemo-{:0>4d}{:0>2d}{:0>2d}"
 
 
-class Handler:
+class GSAHandler:
     @staticmethod
     def ReportRoot(report_uri: str) -> Path:
         report_path = Constants.ToPath(report_uri)
@@ -48,34 +48,43 @@ def __init__(self, context: Any):
 
     def handleEvent(self, event: KEYED) -> KEYED:
         opts = self.parseEvent(event)
+        body = {
+            "message": "N/A",
+            "event": event,
+            "opts": opts,
+        }
         print(f"handleEvent.opts: {opts}")
+        ready = self.cc.check_time(opts["key"])
+        if not ready:
+            body["message"] = "Not ready"
+            return {
+                "statusCode": 200,
+                "body": body,
+            }
         if not opts.get("type"):
+            body["message"] = "ERROR: No type"
             return {
                 "statusCode": 400,  # Bad Request
-                "body": "No type",
+                "body": body,
             }
         if opts["type"] != "ObjectCreated:Put":
+            body["message"] = f"ERROR: Bad type: {opts['type']}"
             return {
                 "statusCode": 404,  # Not Found
-                "body": "No action",
+                "body": body,
             }
 
         report_uri = f"s3://{opts['bucket']}/{opts['key']}"
         root = self.ReportRoot(report_uri)
         print(f"handleEvent.root: {root}")
-        meta = opts
         if not opts.get("debug"):
             tables = self.downloadReport(report_uri, root)
             self.summarizeTables(tables, root)
-            meta = self.packageFolder(root, opts)
+            body["opts"] = self.packageFolder(root, opts)
+            body["message"] = f"{report_uri} @ {root}"
         return {
-            "statusCode": 200,
-            "body": {
-                "root": str(root),
-                "report": report_uri,
-                "meta": meta,
-                "event": event,
-            },
+            "statusCode": 201,
+            "body": body,
         }
 
     def parseEvent(self, event: KEYED) -> KEYED:

src/packager/packager/index.py

@@ -1,9 +1,9 @@
 from typing import Any
 
-from .handler import Handler
+from .gsa_handler import GSAHandler
 from .types import KEYED
 
 
 def handler(event: KEYED, context: Any) -> KEYED:
-    handler = Handler(context)
+    handler = GSAHandler(context)
     return handler.handleEvent(event)

src/packager/tests/conftest.py

@@ -4,4 +4,5 @@
     "EVENT": "../../test/events/event-params.json",
     "S3_URI": "s3://data-yaml-spec-tests/quilt_metadata.json",
     "S3_BUCKET": "data-yaml-spec-tests",
+    "TIMEOUT": "1",
 }

src/packager/tests/test_constants.py

@@ -1,6 +1,7 @@
 from packager import Constants
 from .conftest import CTX
 import pytest
+import time
 
 
 @pytest.fixture
@@ -20,3 +21,11 @@ def test_download_object(cc):
         assert filename
         assert filename.exists()
         assert filename.is_file()
+
+
+def test_check_time(cc):
+    key = "timer"
+    assert cc.check_time(key)
+    assert not cc.check_time(key)
+    time.sleep(1.5 * cc.timeout())
+    assert cc.check_time(key)

src/packager/tests/test_handler.py

@@ -3,7 +3,7 @@
 import pytest
 from datetime import datetime
 
-from packager import Handler
+from packager import GSAHandler
 from tempfile import TemporaryDirectory
 
 # from unittest.mock import MagicMock, patch
@@ -13,7 +13,7 @@
 
 @pytest.fixture
 def handler():
-    return Handler({})
+    return GSAHandler({})
 
 
 @pytest.fixture

src/packager/tests/test_index.py

@@ -42,7 +42,7 @@ def test_valid_type(ctx, event):
     result = handler(event, ctx)
     assert result
     print(record)
-    assert result["statusCode"] == 200
+    assert result["statusCode"] == 201
     body = result["body"]
     assert body
     print(body)

src/packager/tests/test_ssm.py

@@ -10,3 +10,10 @@ def store():
 def test_parameter(store):
     store["key"] = "value"
     assert "value" == store["key"]
+
+
+def test_slashes(store):
+    store["key"] = "value"
+    assert "value" == store["key"]
+    store["key/2"] = "value2"
+    assert "value2" == store["key/2"]