Invoking Volume Tracking messages through Traction ServiceΒΆ
There are multiple ways the volume tracking message can be triggered.
In this instance, we will use traction-service without using the UI of Traction.
How the users trigger this would be using Traction UI, and it is documented elsewhere.
We will use Rails' REPL console to trigger a message into the warehouse.
Read this before running through this section
This section assumes that you have already went through the setting up process that was explained in a section before.
You will not need a running traction-service instance but you will need a running tol-lab-share instance.
First, we need to enter into the Rails console. This can be done by the following command in traction-service directory.
This will give an interactive Rails console where you can invoke Rails syntax.
Next, we will trigger the volume tracking process. This involves a series of Ruby expressions.
Tip
You can paste (using Cmd+V ) the code fragment displayed above in the Rails console and press Enter to publish volume tracking messages.
This should produce the results as the console outputs and screenshots attached below. Note that given below is a tabbed group of outputs, and you can switch between tabs to see the output of each component (e.g., Rails Console Output, Tol Lab Share Output, Volume Tracking Queue and MLWH Warehouse Queue).
[1] pry(main)> library = Pacbio::Library.first
pool = Pacbio::Pool.first
aliquot = Aliquot.new(uuid:SecureRandom.uuid, volume:10,concentration:2.5,template_prep_kit_box_barcode: "AB123456",source:library,used_by:pool, aliquot_type:'derived',created_at:Time.now, insert_size: 100)
[1] pry(main)> library = Pacbio::Library.first
pool = Pacbio::Pool.firstiquot,Pipelines.pacbio,'volume_tracking')
aliquot = Aliquot.new(uuid:SecureRandom.uuid, volume:10,concentration:2.5,template_prep_kit_box_barcode: "AB123456",source:library,used_by:pool, aliquot_type:'derived',created_at:Time.now, insert_size: 100)
Emq::Publisher.publish(aliquot,Pipelines.pacbio,'volume_tracking')
Pacbio::Library Load (0.6ms) SELECT `pacbio_libraries`.* FROM `pacbio_libraries` ORDER BY `pacbio_libraries`.`id` ASC LIMIT 1
Pacbio::Pool Load (0.4ms) SELECT `pacbio_pools`.* FROM `pacbio_pools` ORDER BY `pacbio_pools`.`id` ASC LIMIT 1
DEPRECATION WARNING: Defining enums with keyword arguments is deprecated and will be removed
in Rails 8.0. Positional arguments should be used instead:
enum :state, {:created=>0, :used=>1}
(called from <class:Aliquot> at /Users/dp27/Documents/Projects/traction-service/app/models/aliquot.rb:10)
DEPRECATION WARNING: Defining enums with keyword arguments is deprecated and will be removed
in Rails 8.0. Positional arguments should be used instead:
enum :aliquot_type, {:primary=>0, :derived=>1}
(called from <class:Aliquot> at /Users/dp27/Documents/Projects/traction-service/app/models/aliquot.rb:11)
Tube Load (0.5ms) SELECT `tubes`.* FROM `tubes` WHERE `tubes`.`id` = 1 LIMIT 1
Pacbio::Request Load (0.9ms) SELECT `pacbio_requests`.* FROM `pacbio_requests` WHERE `pacbio_requests`.`id` = 1 LIMIT 1
DEPRECATION WARNING: Defining enums with keyword arguments is deprecated and will be removed
in Rails 8.0. Positional arguments should be used instead:
enum :retention_instruction, {:destroy_after_2_years=>0, :return_to_customer_after_2_years=>1, :long_term_storage=>2}
(called from <class:Sample> at /Users/dp27/Documents/Projects/traction-service/app/models/sample.rb:9)
Sample Load (1.5ms) SELECT `samples`.* FROM `samples` INNER JOIN `requests` ON `samples`.`id` = `requests`.`sample_id` WHERE `requests`.`requestable_id` = 1 AND `requests`.`requestable_type` = 'Pacbio::Request' LIMIT 1
Using cached schema for create-aliquot-in-mlwh v1
Published volume tracking message to EMQ
=> true
2024-08-18 11:35:00,290 rabbit_messages :271 INFO Received message # 1 with body: b'\xc3\x01.\xa3Vl\x13\x82\x81\x9dHf8449d34-93d8-4dd1-89e3-17f8ee9b6ef8\xe4\xe3\xef\xd0\xacd\x10TractionH6538ddbe-25e2-46e7-887e-bfc4227fa607\x02\x04\x10TRAC-2-1BsangerId-TOLTESTING-PLATE-1-1-0-1\x06\x00\x00\x00 A\x02\x00\x00 @\x02\xc8\x01\xa6\xe3\xef\xd0\xacd'
2024-08-18 11:35:00,309 rabbit_messages :45 INFO Decoded binary message body:
[{'messageUuid': UUID('f8449d34-93d8-4dd1-89e3-17f8ee9b6ef8'), 'messageCreateDateUtc': datetime.datetime(2024, 8, 18, 10, 35, 0, 210000, tzinfo=datetime.timezone.utc), 'limsId': 'Traction', 'aliquotUuid': UUID('6538ddbe-25e2-46e7-887e-bfc4227fa607'), 'aliquotType': 'derived', 'sourceType': 'library', 'sourceBarcode': 'TRAC-2-1', 'sampleName': 'sangerId-TOLTESTING-PLATE-1-1-0-1', 'usedByType': 'none', 'usedByBarcode': '', 'volume': 10.0, 'concentration': 2.5, 'insertSize': 100, 'recordedAt': datetime.datetime(2024, 8, 18, 10, 35, 0, 179000, tzinfo=datetime.timezone.utc)}]
2024-08-18 11:35:00,310 tol_lab_share.processors.create_aliquot_processor:47 INFO Message received: <lab_share_lib.processing.rabbit_message.RabbitMessage object at 0x100b6f250>
2024-08-18 11:35:00,310 tol_lab_share.messages.mlwh.create_aliquot_message:115 INFO Sending json to the warehouse queue: {"lims": "Traction", "aliquot": {"id_lims": "Traction", "aliquot_uuid": "6538ddbe-25e2-46e7-887e-bfc4227fa607", "aliquot_type": "derived", "source_type": "library", "source_barcode": "TRAC-2-1", "sample_name": "sangerId-TOLTESTING-PLATE-1-1-0-1", "used_by_type": "none", "used_by_barcode": "", "volume": 10.0, "concentration": 2.5, "insert_size": 100, "last_updated": "2024-08-18T10:35:00Z", "recorded_at": "2024-08-18T10:35:00Z", "created_at": "2024-08-18T10:35:00Z"}}
2024-08-18 11:35:00,310 lab_share_lib.rabbit.basic_publisher :73 INFO Publishing message to exchange 'psd.tol-lab-share', routing key 'development.saved.aliquot', schema subject 'None', schema version 'None'.
2024-08-18 11:35:00,310 rabbit_messages :77 INFO Published message body: {"lims": "Traction", "aliquot": {"id_lims": "Traction", "aliquot_uuid": "6538ddbe-25e2-46e7-887e-bfc4227fa607", "aliquot_type": "derived", "source_type": "library", "source_barcode": "TRAC-2-1", "sample_name": "sangerId-TOLTESTING-PLATE-1-1-0-1", "used_by_type": "none", "used_by_barcode": "", "volume": 10.0, "concentration": 2.5, "insert_size": 100, "last_updated": "2024-08-18T10:35:00Z", "recorded_at": "2024-08-18T10:35:00Z", "created_at": "2024-08-18T10:35:00Z"}}
2024-08-18 11:35:00,322 lab_share_lib.rabbit.basic_publisher :117 INFO The message was published to RabbitMQ successfully.
2024-08-18 11:35:00,323 tol_lab_share.processors.create_aliquot_processor:63 INFO Message processing completed.
2024-08-18 11:35:00,323 lab_share_lib.rabbit.async_consumer :281 INFO Acknowledging message # 1
Why does the warehouse queue have one message remaining?
We have not configured a unified_warehouse instance to consume the message coming into the warehouse queue (i.e. psd.mlwh.multi-lims-warehouse-consumer).
If we had, this message would have been consumed and persisted in the database.