From 16a7cdf9a1a31c8c16698598d551d8d1d0ed52f9 Mon Sep 17 00:00:00 2001
From: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com>
Date: Mon, 24 Jul 2023 17:36:47 -0600
Subject: [PATCH] Reorganize templates and list out extended columns to control
 ordering (#322)

* List out extended columns to control ordering
* Build jsonld

---------

Co-authored-by: nf-osi[bot] <nf-osi@sagebionetworks.org>
---
 NF.jsonld                      | 53 ------------------------------
 modules/Template/Template.yaml | 59 +++++++++++++++++-----------------
 2 files changed, 30 insertions(+), 82 deletions(-)

diff --git a/NF.jsonld b/NF.jsonld
index 10b4dd8f..b4361cf1 100644
--- a/NF.jsonld
+++ b/NF.jsonld
@@ -745,59 +745,6 @@
       "@id" : "bts:comments"
     } ],
     "sms:displayName" : "ImagingAssayTemplate"
-  }, {
-    "rdfs:subClassOf" : [ {
-      "@id" : "bts:SequencingDataTemplate"
-    } ],
-    "@id" : "bts:GenomicsAssayTemplateExtended",
-    "schema:isPartOf" : {
-      "@id" : "http://schema.biothings.io/"
-    },
-    "sms:required" : "sms:false",
-    "sms:requiresComponent" : "",
-    "rdfs:label" : "GenomicsAssayTemplateExtended",
-    "rdfs:comment" : "Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties  for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points.\n",
-    "@type" : "rdfs:Class",
-    "sms:requiresDependency" : [ {
-      "@id" : "bts:Component"
-    }, {
-      "@id" : "bts:Filename"
-    }, {
-      "@id" : "bts:resourceType"
-    }, {
-      "@id" : "bts:progressReportNumber"
-    }, {
-      "@id" : "bts:dataType"
-    }, {
-      "@id" : "bts:assay"
-    }, {
-      "@id" : "bts:platform"
-    }, {
-      "@id" : "bts:individualID"
-    }, {
-      "@id" : "bts:parentSpecimenID"
-    }, {
-      "@id" : "bts:isXenograft"
-    }, {
-      "@id" : "bts:transplantationType"
-    }, {
-      "@id" : "bts:transplantationRecipientSpecies"
-    }, {
-      "@id" : "bts:transplantationRecipientTissue"
-    }, {
-      "@id" : "bts:experimentalCondition"
-    }, {
-      "@id" : "bts:experimentalTimepoint"
-    }, {
-      "@id" : "bts:runType"
-    }, {
-      "@id" : "bts:libraryPrep"
-    }, {
-      "@id" : "bts:genePerturbed"
-    }, {
-      "@id" : "bts:comments"
-    } ],
-    "sms:displayName" : "GenomicsAssayTemplateExtended"
   }, {
     "rdfs:subClassOf" : [ {
       "@id" : "bts:Template"
diff --git a/modules/Template/Template.yaml b/modules/Template/Template.yaml
index 05ba6560..b079c5c7 100644
--- a/modules/Template/Template.yaml
+++ b/modules/Template/Template.yaml
@@ -292,6 +292,36 @@ classes:
     annotations:
       requiresComponent: ''
       required: false
+
+    GenomicsAssayTemplateExtended:
+      is_a: SequencingDataTemplate
+      description: >
+        Genomics assay template but with additional fields for gene perturbation parameters, experimental conditions and time points.
+      slots:
+      - Component
+      - Filename
+      - resourceType
+      - progressReportNumber
+      - dataType
+      - assay
+      - platform
+      - individualID
+      - parentSpecimenID
+      - isXenograft
+      - transplantationType
+      - transplantationRecipientSpecies
+      - transplantationRecipientTissue
+      - runType
+      - libraryPrep
+      - experimentalCondition
+      - experimentalTimepoint
+      - genePerturbed
+      - genePerturbationTechnology
+      - genePerturbationType
+      - comments
+      annotations:
+        requiresComponent: ''
+        required: false
   
   ProteomicsAssayTemplate:
     is_a: AssayDataTemplate
@@ -336,35 +366,6 @@ classes:
       requiresComponent: ''
       required: false
   
-  GenomicsAssayTemplateExtended:
-    is_a: SequencingDataTemplate
-    description: >
-      Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties 
-      for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points.
-    slots:
-    - Component
-    - Filename
-    - resourceType
-    - progressReportNumber
-    - dataType
-    - assay
-    - platform
-    - individualID
-    - parentSpecimenID
-    - isXenograft
-    - transplantationType
-    - transplantationRecipientSpecies
-    - transplantationRecipientTissue
-    - experimentalCondition
-    - experimentalTimepoint
-    - runType
-    - libraryPrep
-    - genePerturbed
-    - comments
-    annotations:
-      requiresComponent: ''
-      required: false
-  
   WESTemplate:
     is_a: AssayDataTemplate
     description: Template for describing raw data from Whole Exome Sequencing (WES)