Merge pull request #449 from ssjunnebo/deliver_ont

Upload ONT data to DDS

VERSIONLOG.md

@@ -1,5 +1,8 @@
 # TACA Version Log
 
+## 20241210.2
+Add support for uploading ONT data to DDS
+
 ## 20241210.1
 
 Tweaks and bugfixes for ToulligQC.

requirements.txt

@@ -5,4 +5,5 @@ flowcell_parser @ git+https://github.com/SciLifeLab/flowcell_parser
 pandas
 python_crontab
 python_dateutil
+requests
 setuptools

taca/__init__.py

@@ -1,3 +1,3 @@
 """Main TACA module"""
 
-__version__ = "1.3.0"
+__version__ = "1.4.0"

taca/delivery/cli.py

@@ -1,8 +1,13 @@
 """CLI for the delivery subcommand."""  # furure todo: rename to "deliver" when fully implemented and taca-ngi-pipieline is deprecated
 
+import logging
+
 import click
 
 from taca.delivery import deliver
+from taca.utils.config import load_yaml_config
+
+logger = logging.getLogger(__name__)
 
 
 @click.group()
@@ -11,7 +16,7 @@ def delivery():
     pass
 
 
-# Stage data
+### Stage data ###
 @delivery.command()
 @click.option(
     "-f",
@@ -33,22 +38,79 @@ def stage(project, flowcells, samples):
     deliver.stage(project, flowcells=flowcells_to_stage, samples=samples_to_stage)
 
 
-# Upload data
+### Upload data ###
 @delivery.command()
 @click.option(
-    "-s",
     "--stage_dir",
     type=str,
     required=True,
     help="Staged directory to upload",
 )
+@click.option(
+    "--order_portal",
+    default=None,
+    envvar="ORDER_PORTAL",
+    required=True,
+    type=click.File("r"),
+    help="Path to order portal credentials to retrieve project information",
+)
+@click.option(
+    "--statusdb_config",
+    default=None,
+    envvar="STATUS_DB_CONFIG",
+    required=True,
+    type=click.File("r"),
+    help="Path to statusdb config file",
+)
+@click.option(
+    "--pi_email",
+    default=None,
+    type=str,
+    help="PI email, to override PI email stored in order portal",
+)
+@click.option(
+    "--add_user",
+    multiple=True,
+    type=click.STRING,
+    help="Add additional user to DDS project. Multiple users can be given by calling this option multiple times",
+)
+@click.option(
+    "--project_description",
+    default=None,
+    type=click.STRING,
+    help="Override project description in order portal, e.g. if project not in order portal",
+)
+@click.option(
+    "--ignore_orderportal_members",
+    is_flag=True,
+    default=False,
+    help="Do not fetch member information from the order portal",
+)
 @click.argument("project")
-def upload(project, stage_dir):
+def upload(
+    project,
+    stage_dir,
+    statusdb_config=None,
+    order_portal=None,
+    pi_email=None,
+    add_user=None,
+    project_description=None,
+    ignore_orderportal_members=False,
+):
     """Upload a staged project to DDS."""
-    deliver.upload_to_dds(project, stage_dir)
+    load_yaml_config(statusdb_config.name)
+    load_yaml_config(order_portal.name)
+    deliver.upload_to_dds(
+        project,
+        stage_dir,
+        pi_email=pi_email,
+        add_user=list(set(add_user)),
+        project_description=project_description,
+        ignore_orderportal_members=ignore_orderportal_members,
+    )
 
 
-# Release data
+### Release data ###
 @delivery.command()
 @click.option(
     "-d",

taca/delivery/deliver.py

@@ -4,7 +4,7 @@
 import os
 import sys
 
-from taca.delivery.delivery_classes import get_staging_object
+from taca.delivery.delivery_classes import get_staging_object, get_upload_object
 from taca.utils.config import CONFIG
 
 logger = logging.getLogger(__name__)
@@ -42,11 +42,38 @@ def stage(project, flowcells, samples):
     # future todo: update statusdb with status "staged" (project, FC or sample level? Maybe new delivery DB?)
 
 
-def upload_to_dds(project, dds_id):
-    "Upload staged data to DDS"
-    pass
+def upload_to_dds(
+    project,
+    stage_dir,
+    pi_email=None,
+    add_user=None,
+    project_description=None,
+    ignore_orderportal_members=False,
+):
+    """Upload staged data to DDS"""
+    upload_object = get_upload_object(
+        project,
+        stage_dir,
+        pi_email,
+        add_user,
+        project_description,
+        ignore_orderportal_members,
+    )
+    dds_project_id = upload_object.create_dds_project()
+    delivery_status = upload_object.upload_data(dds_project_id)
+    if delivery_status:
+        logger.info(
+            f"Successfully uploaded {stage_dir} to DDS project {dds_project_id}"
+        )
+        # Future todo: Update statusdb with status "uploaded" and DDS project ID
+    else:
+        logger.error(
+            f"Something went wrong when uploading data to {dds_project_id} for project {project}."
+        )
 
 
 def release_dds_project(project, dds_id):
-    "Release DDS project to user"
+    """Release DDS project to user"""
+    # Release DDS project
+    # Update statusdb with status "delivered"
     pass