Merge pull request #1364 from sanger/y24-096-aliquot-id-renaming-avro-schema

seenanair · web-flow · commit 06faafbdbb36 · 2024-07-23T13:13:34.000+01:00
refactor(message-builder): renamed limsUuid field to aliquotId
diff --git a/app/exchanges/volume_tracking/message_builder.rb b/app/exchanges/volume_tracking/message_builder.rb
@@ -11,7 +11,7 @@ class MessageBuilder < Message::Message
     #    "messageUuid"=>"0a62ee15-bbf6-46f0-ba95-01d42622d076",
     #    "recordedAt"=>Mon, 15 Jul 2024 15:16:54.867713000 UTC +00:00,
     #    "volume"=>1.5, "concentration"=>10.0, "insertSize"=>100, "aliquotType"=>"primary",
-    #    "limsUuid"=>"", "sourceType"=>"library", "sourceBarcode"=>"TRAC-2-35805",
+    #    "aliquotId"=>"", "sourceType"=>"library", "sourceBarcode"=>"TRAC-2-35805",
     #    "sampleName"=>"Sample1", "usedByBarcode"=>"TRAC-2-35806", "usedByType"=>"pool"}}
 
     def publish_data # rubocop:disable Metrics/MethodLength
@@ -20,7 +20,7 @@ def publish_data # rubocop:disable Metrics/MethodLength
 
       aliquot = object
       data = { source_type: '', source_barcode: '', sample_name: '',
-               used_by_type: 'nil', used_by_barcode: '', lims_uuid: aliquot.id.to_s || '' }
+               used_by_type: 'nil', used_by_barcode: '', aliquot_id: aliquot.id.to_s || '' }
 
       case aliquot.source_type
       when 'Pacbio::Library'
diff --git a/config/pipelines/pacbio.yml b/config/pipelines/pacbio.yml
@@ -333,9 +333,9 @@ default: &default
           aliquotType:
             type: :model
             value: aliquot_type
-          limsUuid:
+          aliquotId:
             type: :self
-            value: publish_data&.lims_uuid
+            value: publish_data&.aliquot_id
           sourceType:
             type: :self
             value: publish_data&.source_type
diff --git a/spec/exchanges/volume_tracking/message_builder_spec.rb b/spec/exchanges/volume_tracking/message_builder_spec.rb
@@ -21,7 +21,7 @@
                                                      sample_name: pacbio_library.sample_name,
                                                      used_by_type: 'nil',
                                                      used_by_barcode: '',
-                                                     lims_uuid: aliquot.id.to_s || ''
+                                                     aliquot_id: aliquot.id.to_s || ''
                                                    })
       end
     end
@@ -37,7 +37,7 @@
                                                      sample_name: pacbio_library.sample_name,
                                                      used_by_type: 'pool',
                                                      used_by_barcode: pacbio_pool.tube.barcode,
-                                                     lims_uuid: aliquot.id.to_s || ''
+                                                     aliquot_id: aliquot.id.to_s || ''
                                                    })
       end
     end
@@ -53,7 +53,7 @@
                                                      sample_name: pacbio_library.sample_name,
                                                      used_by_type: 'well',
                                                      used_by_barcode: "#{pacbio_well.plate.sequencing_kit_box_barcode}:#{pacbio_well.plate.plate_number}:#{pacbio_well.position}",
-                                                     lims_uuid: aliquot.id.to_s || ''
+                                                     aliquot_id: aliquot.id.to_s || ''
                                                    })
       end
     end
diff --git a/spec/fixtures/volume_tracking_avro_response.json b/spec/fixtures/volume_tracking_avro_response.json
@@ -2,5 +2,5 @@
   "subject": "create-aliquot-in-mlwh",
   "version": 1,
   "id": 14,
-  "schema": "{\"type\":\"record\",\"name\":\"CreateAliquotInMLWH\",\"namespace\":\"uk.ac.sanger.psd\",\"doc\":\"Create an Aliquot in MLWH coming from Traction.\",\"fields\":[{\"name\":\"messageUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"Unique message ID.\"},{\"name\":\"messageCreateDateUtc\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"Date (UTC) that the message was created.\"},{\"name\":\"limsId\",\"type\":\"string\",\"doc\":\"The LIMS system that the aliquot was created in\"},{\"name\":\"limsUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"The UUID of the aliquot in the LIMS system\"},{\"name\":\"aliquotType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedAliquotType\",\"symbols\":[\"primary\",\"derived\"]},\"doc\":\"The type of the aliquot\"},{\"name\":\"sourceType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedSourceType\",\"symbols\":[\"well\",\"sample\",\"library\",\"pool\"]},\"doc\":\"The type of the source of the aliquot\"},{\"name\":\"sourceBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the source of the aliquot\"},{\"name\":\"sampleName\",\"type\":\"string\",\"doc\":\"The name of the sample that the aliquot was created from\"},{\"name\":\"usedByType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedUsedByType\",\"symbols\":[\"library\",\"pool\",\"run\",\"none\"],\"default\":\"none\"},\"doc\":\"The type of the entity that the aliquot is used by\"},{\"name\":\"usedByBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the entity that the aliquot is used by\"},{\"name\":\"volume\",\"type\":\"float\",\"doc\":\"The volume of the aliquot (uL)\"},{\"name\":\"concentration\",\"type\":[\"null\",\"float\"],\"doc\":\"The concentration of the aliquot (ng/ul)\",\"default\":null},{\"name\":\"insertSize\",\"type\":[\"null\",\"int\"],\"doc\":\"The insert size for the aliquot\",\"default\":null},{\"name\":\"recordedAt\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"The date and time that the aliquot was recorded\"}]}"
+  "schema": "{\"type\":\"record\",\"name\":\"CreateAliquotInMLWH\",\"namespace\":\"uk.ac.sanger.psd\",\"doc\":\"Create an Aliquot in MLWH coming from Traction.\",\"fields\":[{\"name\":\"messageUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"Unique message ID.\"},{\"name\":\"messageCreateDateUtc\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"Date (UTC) that the message was created.\"},{\"name\":\"limsId\",\"type\":\"string\",\"doc\":\"The LIMS system that the aliquot was created in\"},{\"name\":\"aliquotId\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"The UUID of the aliquot in the LIMS system\"},{\"name\":\"aliquotType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedAliquotType\",\"symbols\":[\"primary\",\"derived\"]},\"doc\":\"The type of the aliquot\"},{\"name\":\"sourceType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedSourceType\",\"symbols\":[\"well\",\"sample\",\"library\",\"pool\"]},\"doc\":\"The type of the source of the aliquot\"},{\"name\":\"sourceBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the source of the aliquot\"},{\"name\":\"sampleName\",\"type\":\"string\",\"doc\":\"The name of the sample that the aliquot was created from\"},{\"name\":\"usedByType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedUsedByType\",\"symbols\":[\"library\",\"pool\",\"run\",\"none\"],\"default\":\"none\"},\"doc\":\"The type of the entity that the aliquot is used by\"},{\"name\":\"usedByBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the entity that the aliquot is used by\"},{\"name\":\"volume\",\"type\":\"float\",\"doc\":\"The volume of the aliquot (uL)\"},{\"name\":\"concentration\",\"type\":[\"null\",\"float\"],\"doc\":\"The concentration of the aliquot (ng/ul)\",\"default\":null},{\"name\":\"insertSize\",\"type\":[\"null\",\"int\"],\"doc\":\"The insert size for the aliquot\",\"default\":null},{\"name\":\"recordedAt\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"The date and time that the aliquot was recorded\"}]}"
 }

Original file line number	Diff line number	Diff line change
`@@ -2,5 +2,5 @@`
`2`	`2`	`"subject": "create-aliquot-in-mlwh",`
`3`	`3`	`"version": 1,`
`4`	`4`	`"id": 14,`
`5`		- "schema": "{\"type\":\"record\",\"name\":\"CreateAliquotInMLWH\",\"namespace\":\"uk.ac.sanger.psd\",\"doc\":\"Create an Aliquot in MLWH coming from Traction.\",\"fields\":[{\"name\":\"messageUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"Unique message ID.\"},{\"name\":\"messageCreateDateUtc\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"Date (UTC) that the message was created.\"},{\"name\":\"limsId\",\"type\":\"string\",\"doc\":\"The LIMS system that the aliquot was created in\"},{\"name\":\"limsUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"The UUID of the aliquot in the LIMS system\"},{\"name\":\"aliquotType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedAliquotType\",\"symbols\":[\"primary\",\"derived\"]},\"doc\":\"The type of the aliquot\"},{\"name\":\"sourceType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedSourceType\",\"symbols\":[\"well\",\"sample\",\"library\",\"pool\"]},\"doc\":\"The type of the source of the aliquot\"},{\"name\":\"sourceBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the source of the aliquot\"},{\"name\":\"sampleName\",\"type\":\"string\",\"doc\":\"The name of the sample that the aliquot was created from\"},{\"name\":\"usedByType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedUsedByType\",\"symbols\":[\"library\",\"pool\",\"run\",\"none\"],\"default\":\"none\"},\"doc\":\"The type of the entity that the aliquot is used by\"},{\"name\":\"usedByBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the entity that the aliquot is used by\"},{\"name\":\"volume\",\"type\":\"float\",\"doc\":\"The volume of the aliquot (uL)\"},{\"name\":\"concentration\",\"type\":[\"null\",\"float\"],\"doc\":\"The concentration of the aliquot (ng/ul)\",\"default\":null},{\"name\":\"insertSize\",\"type\":[\"null\",\"int\"],\"doc\":\"The insert size for the aliquot\",\"default\":null},{\"name\":\"recordedAt\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"The date and time that the aliquot was recorded\"}]}"
	`5`	+ "schema": "{\"type\":\"record\",\"name\":\"CreateAliquotInMLWH\",\"namespace\":\"uk.ac.sanger.psd\",\"doc\":\"Create an Aliquot in MLWH coming from Traction.\",\"fields\":[{\"name\":\"messageUuid\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"Unique message ID.\"},{\"name\":\"messageCreateDateUtc\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"Date (UTC) that the message was created.\"},{\"name\":\"limsId\",\"type\":\"string\",\"doc\":\"The LIMS system that the aliquot was created in\"},{\"name\":\"aliquotId\",\"type\":{\"type\":\"string\",\"logicalType\":\"uuid\"},\"doc\":\"The UUID of the aliquot in the LIMS system\"},{\"name\":\"aliquotType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedAliquotType\",\"symbols\":[\"primary\",\"derived\"]},\"doc\":\"The type of the aliquot\"},{\"name\":\"sourceType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedSourceType\",\"symbols\":[\"well\",\"sample\",\"library\",\"pool\"]},\"doc\":\"The type of the source of the aliquot\"},{\"name\":\"sourceBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the source of the aliquot\"},{\"name\":\"sampleName\",\"type\":\"string\",\"doc\":\"The name of the sample that the aliquot was created from\"},{\"name\":\"usedByType\",\"type\":{\"type\":\"enum\",\"name\":\"allowedUsedByType\",\"symbols\":[\"library\",\"pool\",\"run\",\"none\"],\"default\":\"none\"},\"doc\":\"The type of the entity that the aliquot is used by\"},{\"name\":\"usedByBarcode\",\"type\":\"string\",\"doc\":\"The barcode of the entity that the aliquot is used by\"},{\"name\":\"volume\",\"type\":\"float\",\"doc\":\"The volume of the aliquot (uL)\"},{\"name\":\"concentration\",\"type\":[\"null\",\"float\"],\"doc\":\"The concentration of the aliquot (ng/ul)\",\"default\":null},{\"name\":\"insertSize\",\"type\":[\"null\",\"int\"],\"doc\":\"The insert size for the aliquot\",\"default\":null},{\"name\":\"recordedAt\",\"type\":{\"type\":\"long\",\"logicalType\":\"timestamp-millis\"},\"doc\":\"The date and time that the aliquot was recorded\"}]}"
`6`	`6`	`}`