feat: omics launcher (#18)

* INPUT_METADATA

* rename events

* bump memory size

* try parent

* save metadata successfully

src/constants.ts

@@ -18,8 +18,10 @@ export class Constants {
     READY2RUN_WORKFLOW_ID: '9500764',
     MANIFEST_ROOT: 'fastq',
     MANIFEST_SUFFIX: '.json',
+    INPUT_METADATA: 'input_metadata.json',
     QUILT_METADATA: 'quilt_metadata.json',
     FASTQ_SENTINEL: 'out/bqsr_report/NA12878.hg38.recal_data.csv',
+    MEMORY_SIZE: 8192,
     TIMEOUT: '900',
   };
 

src/omics-quilt.fastq.ts

@@ -62,17 +62,23 @@ export async function handler(event: any, context: any) {
   return { message: 'Success' };
 }
 
-async function save_metadata(item: any, cc: Constants) {
-  const sentinel_file = cc.get('QUILT_METADATA)');
-  if (!sentinel_file) {
-    console.info('No QUILT_METADATA, skipping metadata save');
+export async function save_metadata(id: string, item: any, cc: Constants) {
+  const location = cc.get('OUTPUT_S3_LOCATION');
+  if (!location) {
+    console.info('No OUTPUT_S3_LOCATION, skipping metadata save');
     return;
   }
-  console.info(`Writing input to ${sentinel_file}`);
-  await Constants.SaveObjectURI(sentinel_file, item);
+  const metadata_file = cc.get('INPUT_METADATA');
+  if (!metadata_file) {
+    console.info('No INPUT_METADATA, skipping metadata save');
+    return;
+  }
+  const uri = `${location}/${id}/out/${metadata_file}`;
+  console.info(`Writing input to ${uri}`);
+  await Constants.SaveObjectURI(uri, item);
 }
 
-async function run_workflow(
+export async function run_workflow(
   item: Record<string, string>,
   uri: string,
   cc: Constants,
@@ -111,7 +117,8 @@ async function run_workflow(
         run: response,
         workflow: options,
       };
-      await save_metadata(run_metadata, cc);
+      const id = response.id!;
+      await save_metadata(id, run_metadata, cc);
     }
   } catch (e: any) {
     console.error('Error : ' + e.toString());

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(this.cc.timeout()),
+      timeout: Duration.seconds(60),
       retryAttempts: 1,
       environment: this.makeLambdaEnv(env),
     });
@@ -217,6 +217,7 @@ export class OmicsQuiltStack extends Stack {
       runtime: Runtime.PYTHON_3_11,
       role: this.lambdaRole,
       timeout: Duration.seconds(this.cc.timeout()),
+      memorySize: this.cc.get('MEMORY_SIZE'),
       retryAttempts: 1,
       environment: this.makeLambdaEnv(env),
       bundling: {
@@ -235,6 +236,7 @@ export class OmicsQuiltStack extends Stack {
       OMICS_ROLE: this.omicsRole.roleArn,
       OUTPUT_S3_LOCATION: output.join('/'),
       SENTINEL_FILE: this.packager_sentinel,
+      INPUT_METADATA: this.cc.get('INPUT_METADATA'),
       QUILT_METADATA: this.cc.get('QUILT_METADATA'),
       WORKFLOW_ID: this.cc.get('READY2RUN_WORKFLOW_ID'),
       TIMEOUT: this.cc.get('TIMEOUT'),

src/packager/packager/constants.py

@@ -26,6 +26,7 @@ class Constants:
         "TIMESTAMP_FILE": "quilt_timestamp.json",
         "SOURCE_APP": "omics-quilt",
         "QUILT_METADATA": "quilt_metadata.json",
+        "INPUT_METADATA": "input_metadata.json",
         "QUILT_SUMMARIZE": "quilt_summarize.json",
         "FASTQ_SENTINEL": "out/bqsr_report/NA12878.hg38.recal_data.csv",
     }

src/packager/packager/gsa_handler.py

@@ -21,7 +21,7 @@ class GSAHandler:
     @staticmethod
     def ReportRoot(report_uri: str) -> Path:
         report_path = Constants.ToPath(report_uri)
-        return report_path.parent  # WAS: .parent.parent
+        return report_path.parent.parent
 
     @staticmethod
     def ParseURI(file_uri: str) -> KEYED:
@@ -142,6 +142,10 @@ def packageFolder(self, root: Path, opts: KEYED) -> KEYED:
             meta: KEYED = json.loads(text)
         else:
             meta = {}
+        input_file = root / self.cc.get("INPUT_METADATA")
+        if input_file.exists():
+            text = input_file.read_text()
+            meta["input"] = json.loads(text)
         meta["options"] = opts
         meta["context"] = self.context