add generate_computed_file management command

api/scpca_portal/management/commands/generate_computed_file.py

@@ -0,0 +1,50 @@
+import logging
+from typing import Dict
+
+from django.core.management.base import BaseCommand
+
+from scpca_portal import loader
+from scpca_portal.models import Project, Sample
+
+logger = logging.getLogger()
+logger.setLevel(logging.INFO)
+logger.addHandler(logging.StreamHandler())
+
+
+class Command(BaseCommand):
+    help = """
+    This command is meant to be called as an entrypoint to AWS Batch Fargate job instance.
+    Individual files are computed according:
+        - To the project or sample id
+        - An appropriate corresponding download config
+
+    When computation is completed, files are uploaded to S3, and the job is marked as completed.
+
+    At which point the instance which generated this computed file will receive a new job
+    from the job queue and begin computing the next file.
+    """
+
+    def add_arguments(self, parser):
+        parser.add_argument("--project-id", type=str)
+        parser.add_argument("--sample-id", type=str)
+        parser.add_argument("--download-config", type=dict)
+
+    def handle(self, *args, **kwargs):
+        self.generate_computed_file(**kwargs)
+
+    def generate_computed_file(
+        self,
+        project_id: str,
+        sample_id: str,
+        download_config: Dict,
+        **kwargs,
+    ) -> None:
+        """Generates a project's computed files according predetermined download configurations"""
+        loader.prep_data_dirs()
+
+        project = Project.objects.filter(scpca_id=project_id).first() if project_id else None
+        sample = Sample.objects.filter(scpca_id=sample_id).first() if sample_id else None
+
+        loader.generate_computed_file(
+            download_config=download_config, project=project, sample=sample
+        )