From ca70913c5b8d1819a1b9a804b5f1f27093762bf5 Mon Sep 17 00:00:00 2001
From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com>
Date: Thu, 4 May 2023 11:00:34 -0700
Subject: [PATCH 1/2] update amp-ad config options

- remove app url
- change annotations link to metadata dictionary
- make templates and required columns match dccvalidator config
---
 inst/config.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/inst/config.yml b/inst/config.yml
index 3b7d8bb..534ae2d 100644
--- a/inst/config.yml
+++ b/inst/config.yml
@@ -43,7 +43,7 @@ dev:
 
 amp-ad:
   app_url: "https://shinypro.synapse.org/users/awilliams/dccmonitor/"
-  annotations_link: "https://shinypro.synapse.org/users/nkauer/amp-ad-metadata-dictionary/"
+  annotations_link: "https://www.synapse.org/#!Synapse:syn25878249"
   consortium_fileview: "syn21448475"
   samples_table: "syn21578908"
   annotations_storage: "syn21698384"
@@ -78,6 +78,7 @@ amp-ad:
       ATACseq: "syn22024364"
       autorad: "syn22087295"
       immunoassay: "syn22117582"
+      rnaSeq: "syn12973256"
       proteomics: "syn12973255"
       single cell RNAseq: "syn21018360"
       wholeGenomeSeq: "syn21018358"
@@ -101,11 +102,17 @@ amp-ad:
       - "grant"
       - "fileFormat"
       - "parent"
+      - "path"
     individual:
       - "individualID"
+      - "species"
+      - "sex"
     biospecimen:
       - "individualID"
       - "specimenID"
+      - "organ"
+      - "tissue:
+      - "assay"
     assay:
       - "specimenID"
 

From 628bd408764f5787dbc6cbcbda25f7e75446183e Mon Sep 17 00:00:00 2001
From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com>
Date: Thu, 4 May 2023 11:53:22 -0700
Subject: [PATCH 2/2] fix missing "

---
 inst/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/config.yml b/inst/config.yml
index 534ae2d..6ba24ff 100644
--- a/inst/config.yml
+++ b/inst/config.yml
@@ -111,7 +111,7 @@ amp-ad:
       - "individualID"
       - "specimenID"
       - "organ"
-      - "tissue:
+      - "tissue"
       - "assay"
     assay:
       - "specimenID"