fix named process pooling and renaming issues (#1904)

bihealth · Mar 13, 2024 · c7d2995 · c7d2995
1 parent 5b9c817
commit c7d2995
Show file tree

Hide file tree

Showing 9 changed files with 374 additions and 160 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -48,6 +48,7 @@ Changed
     - Refactor ``IrodsDataRequestModifyMixin`` timeline helpers (#1913)
     - Rename ``get_igv_omit_override()`` to ``get_igv_omit_list()`` (#1924)
     - Rename ``check_igv_file_name()`` to ``check_igv_file_path()`` (#1923)
+    - Named process pooling and renaming in sheet editor (#1904)
 - **Taskflowbackend**
     - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
     - Set zone status on uncaught errors in ``run_flow()`` (#1458)

diff --git a/...tests/edit/i_small_assay_insert_pool.json → ...t/i_small_assay_insert_pool_material.json b/...tests/edit/i_small_assay_insert_pool.json → ...t/i_small_assay_insert_pool_material.json
diff --git a/samplesheets/tests/edit/i_small_assay_insert_pool_process.json b/samplesheets/tests/edit/i_small_assay_insert_pool_process.json
@@ -0,0 +1,124 @@
+{
+  "study": "11111111-1111-1111-1111-111111111111",
+  "assay": "22222222-2222-2222-2222-222222222222",
+  "nodes": [
+    {
+      "cells": [
+        {
+          "uuid": "11111111-1111-1111-5555-000000000000",
+          "obj_cls": "GenericMaterial",
+          "value": "0818-N1"
+        }
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "library preparation",
+          "uuid_ref": "22222222-2222-2222-bbbb-000000000000",
+          "header_name": "Protocol",
+          "header_type": "protocol",
+          "header_field": "col10",
+          "obj_cls": "Process"
+        }
+      ],
+      "headers": [
+        "Protocol REF"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "0818-N1-DNA1",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col11",
+          "obj_cls": "GenericMaterial",
+          "item_type": "MATERIAL"
+        }
+      ],
+      "headers": [
+        "Library Name"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": "22222222-2222-2222-2222-000000000003",
+          "value": "nucleic acid sequencing",
+          "obj_cls": "Process"
+        }
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "0818-N1-DNA1-WES1-R1.fastq.qz",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col14",
+          "obj_cls": "GenericMaterial",
+          "item_type": "DATA"
+        }
+      ],
+      "headers": [
+        "Raw Data File"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "0818-N1-DNA1-WES1-R2.fastq.qz",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col15",
+          "obj_cls": "GenericMaterial",
+          "item_type": "DATA"
+        }
+      ],
+      "headers": [
+        "Raw Data File"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "somatic variant calling-2",
+          "unit": "",
+          "header_name": "Data Transformation Name",
+          "header_type": "process_name",
+          "header_field": "col16",
+          "obj_cls": "Process"
+        }
+      ],
+      "headers": [
+        "Data Transformation Name"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "new-somatic.vcf.gz",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col17",
+          "obj_cls": "GenericMaterial",
+          "item_type": "DATA"
+        }
+      ],
+      "headers": [
+        "Derived Data File"
+      ]
+    }
+  ]
+}