Merge pull request #450 from ssjunnebo/release_ONT

Release ONT DDS project

VERSIONLOG.md

@@ -1,6 +1,11 @@
 # TACA Version Log
 
+## 20241210.3
+
+Add support for releasing DDS projects
+
 ## 20241210.2
+
 Add support for uploading ONT data to DDS
 
 ## 20241210.1

taca/__init__.py

@@ -1,3 +1,3 @@
 """Main TACA module"""
 
-__version__ = "1.4.0"
+__version__ = "1.5.0"

taca/delivery/cli.py

@@ -113,13 +113,24 @@ def upload(
 ### Release data ###
 @delivery.command()
 @click.option(
-    "-d",
-    "--dds_id",
+    "--dds_project",
     type=str,
     required=True,
-    help="DDS PID generated by the upload command",
+    help="DDS PID to release, generated by the upload command",
+)
+@click.option(
+    "--dds_deadline",
+    default=45,
+    type=click.IntRange(1, 90),
+    help="Deadline for DDS project in days [min 1; max 90; default 45]",
+)
+@click.option(
+    "--no_dds_mail",
+    is_flag=True,
+    default=False,
+    help="Do not send DDS e-mail notifications regarding project updates",
 )
 @click.argument("project")
-def release(project, dds_id):
-    """Release a DDS project."""
-    deliver.release_dds_project(project, dds_id)
+def release(project, dds_project, dds_deadline, no_dds_mail):
+    """Release a DDS project to user."""
+    deliver.release_dds_project(project, dds_project, dds_deadline, no_dds_mail)

taca/delivery/deliver.py

@@ -4,7 +4,11 @@
 import os
 import sys
 
-from taca.delivery.delivery_classes import get_staging_object, get_upload_object
+from taca.delivery.delivery_classes import (
+    get_release_object,
+    get_staging_object,
+    get_upload_object,
+)
 from taca.utils.config import CONFIG
 
 logger = logging.getLogger(__name__)
@@ -72,8 +76,10 @@ def upload_to_dds(
         )
 
 
-def release_dds_project(project, dds_id):
+def release_dds_project(project, dds_project, dds_deadline, no_dds_mail):
     """Release DDS project to user"""
-    # Release DDS project
-    # Update statusdb with status "delivered"
+    # Future todo: Add query to confirm release
+    release_object = get_release_object(project, dds_project, dds_deadline, no_dds_mail)
+    release_object.release_project()
+    # Future todo: Update statusdb with status "delivered"
     pass

taca/delivery/delivery_classes.py

@@ -47,6 +47,10 @@ def get_upload_object(
     )
 
 
+def get_release_object(project, dds_project, dds_deadline=45, no_dds_mail=False):
+    return ReleaseNanopore(project, dds_project, dds_deadline, no_dds_mail)
+
+
 class Stage:
     """Defines a generic staging object."""
 
@@ -389,3 +393,70 @@ class UploadElement(Upload):
 
     def __init__(self, project, stage_dir):
         super().__init__(project, stage_dir)
+
+
+class Release:
+    """Defines a generic release object."""
+
+    def __init__(self, project, dds_project, dds_deadline, no_dds_mail):
+        self.project_id = project
+        self.dds_project = dds_project
+        self.dds_deadline = dds_deadline
+        self.no_dds_mail = no_dds_mail
+
+    def release_project(self):
+        """Release DDS project to user."""
+        try:
+            cmd = [
+                "dds",
+                "--no-prompt",
+                "project",
+                "status",
+                "release",
+                "--project",
+                self.dds_project,
+                "--deadline",
+                str(self.dds_deadline),
+            ]
+            if self.no_dds_mail:
+                cmd.append("--no-mail")
+            process_handle = subprocess.run(cmd)
+            process_handle.check_returncode()
+            logger.info(
+                f"Project {self.project_id} succefully delivered. Delivery project {self.dds_project} was released to the user."
+            )
+        except subprocess.CalledProcessError as e:
+            logger.error(
+                f"Could not release project {self.project_id}, an error occurred."
+            )
+            raise e
+
+
+class ReleaseNanopore(Release):
+    """Defines an object for releasing Nanopore data."""
+
+    def __init__(self, project, dds_project, dds_deadline, no_dds_mail):
+        super().__init__(project, dds_project, dds_deadline, no_dds_mail)
+
+    def update_statusdb(self):
+        pass
+
+
+class ReleaseIllumina(Release):
+    """Defines an object for releasing Illumina data."""
+
+    def __init__(self, project, dds_project, dds_deadline, no_dds_mail):
+        super().__init__(project, dds_project, dds_deadline, no_dds_mail)
+
+    def update_statusdb(self):
+        pass
+
+
+class ReleaseElement(Release):
+    """Defines an object for releasing Element data."""
+
+    def __init__(self, project, dds_project, dds_deadline, no_dds_mail):
+        super().__init__(project, dds_project, dds_deadline, no_dds_mail)
+
+    def update_statusdb(self):
+        pass