Merge pull request #140 from kbase/dev-service

Load manifest, wdl, and input.json files to NERSC

cdmtaskservice/jobflows/nersc_jaws.py

@@ -133,7 +133,14 @@ async def download_complete(self, job: models.AdminJobDetails):
         await self._coman.run_coroutine(self._download_complete(job))
 
     async def _download_complete(self, job: models.AdminJobDetails):
-        jaws_job_id = await self._nman.run_JAWS(job)
-        # TODO JAWS record job ID in DB
         logr = logging.getLogger(__name__)
-        logr.info(f"JAWS job id: {jaws_job_id}")
+        try:
+            # TODO PERF configure file download concurrency
+            jaws_job_id = await self._nman.run_JAWS(job)
+            # TODO JAWS record job ID in DB
+            logr.info(f"JAWS job id: {jaws_job_id}")
+        except Exception as e:
+            # TODO LOGGING figure out how logging it going to work etc.
+            logr.exception(f"Error starting JAWS job for job {job.id}")
+            # TODO IMPORTANT ERRORHANDLING update job state to ERROR w/ message and don't raise
+            raise e

cdmtaskservice/nersc/manager.py

@@ -384,22 +384,48 @@ def _base_manifest(self, op: str, concurrency: int, insecure_ssl: bool):
             "sec-per-GB": _SEC_PER_GB,
         }
 
-    async def run_JAWS(self, job: models.Job) -> str:
+    async def run_JAWS(self, job: models.Job, file_download_concurrency: int = 10) -> str:
         """
         Run a JAWS job at NERSC and return the job ID.
+        
+        job - the job to process
+        file_download_concurrency - the number of files at one time to download to NERSC.
         """
+        _check_int(file_download_concurrency, "file_download_concurrency")
         if not _not_falsy(job, "job").job_input.inputs_are_S3File():
             raise ValueError("Job files must be S3File objects")
         manifest_files = generate_manifest_files(job)
         manifest_file_paths = self._get_manifest_file_paths(job.id, len(manifest_files))
         fmap = {m: self._localize_s3_path(job.id, m.file) for m in job.job_input.input_files}
         wdljson = wdl.generate_wdl(job, fmap, manifest_file_paths)
-        # TODO REMOVE these lines
-        logr = logging.getLogger(__name__)
-        for m in manifest_files:
-            logr.info("***")
-            logr.info(m)
-        logr.info(f"*** wdl:\n{wdljson.wdl}\njson:\n{json.dumps(wdljson.input_json, indent=4)}")
+        uploads = {fp: f for fp, f in zip(manifest_file_paths, manifest_files)}
+        pre = self._dtn_scratch / _CTS_SCRATCH_ROOT_DIR / job.id
+        wdlpath = pre / "input.wdl"
+        jsonpath = pre / "input.json"
+        uploads[wdlpath] = wdljson.wdl
+        uploads[jsonpath] = json.dumps(wdljson.input_json, indent=4)
+        cli = self._client_provider()
+        dt = await cli.compute(_DT_TARGET)
+        semaphore = asyncio.Semaphore(file_download_concurrency)
+        async def sem_coro(coro):
+            async with semaphore:
+                return await coro
+        coros = []
+        try:
+            async with asyncio.TaskGroup() as tg:
+                for path, file in uploads.items():
+                    coros.append(self._upload_file_to_nersc(
+                        dt, path, bio=io.BytesIO(file.encode())
+                    ))
+                    tg.create_task(sem_coro(coros[-1]))
+        except ExceptionGroup as eg:
+            e = eg.exceptions[0]  # just pick one, essentially at random
+            raise e from eg
+        finally:
+            # otherwise you can get coroutine never awaited warnings if a failure occurs
+            for c in coros:
+                c.close()
+        # TODO NEXT run jaws job
         return "fake_job_id"
 
     def _get_manifest_file_paths(self, job_id: str, count: int) -> list[Path]: