From c61a4acd46580143b5fb9f5242fecd784d5c7e00 Mon Sep 17 00:00:00 2001
From: j-uranic <117292295+j-uranic@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:18:42 -0500
Subject: [PATCH 1/3] Update publication-v2.yaml

Update to next-gen directory schema
---
 .../directory-schemas/publication-v2.yaml     | 23 +++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/ingest_validation_tools/directory-schemas/publication-v2.yaml b/src/ingest_validation_tools/directory-schemas/publication-v2.yaml
index 3042b8779..d753a9d56 100644
--- a/src/ingest_validation_tools/directory-schemas/publication-v2.yaml
+++ b/src/ingest_validation_tools/directory-schemas/publication-v2.yaml
@@ -1,9 +1,24 @@
 files:
-  -
-    pattern: 'TODO'
-    description: 'Directory structure not yet specified.'
-    required: True
   -
     pattern: extras\/.*
     required: True
     description: Folder for general lab-specific files related to the dataset. [Exists in all assays]
+  -
+    pattern: data\/.+
+    required: True
+    description: Supplementary data files for the publication. All files referenced by the Vitessce visualization configurations in the vignettes must be included in this directory.
+    example: data/file1.ext
+  -
+    pattern: vignettes\/.*
+    required: True
+    description: Subdirectory containing Vitessce visualization files and a description of those files.
+  -
+    pattern: vignettes\/vignette_\d+\/[^\/]+\.json
+    required: False
+    description: Vitessce visualization configuration files. One or more visualization configurations can be provided per vignette.
+    example: vignettes/vignette_01/file1.json
+  -
+    pattern: vignettes\/vignette_\d+\/description\.md
+    required: False
+    description: Description of the vignette and titles for the visualization configuration files.
+    example: vignettes/vignette_02/description.md

From 1dcc48422891eede64ccbcb3253200fcba26c4bc Mon Sep 17 00:00:00 2001
From: j-uranic <117292295+j-uranic@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:19:25 -0500
Subject: [PATCH 2/3] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a115bec15..ac0163422 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
 - Update CEDAR links for PhenoCycler & Histology
 - Refactor Upload to avoid validating the same contributors.tsv multiple times / running plugins over files multiple times
 - Add entry for segmentation-mask
+- Add Publication next-gen directory schema
 
 ## v0.0.16
 

From 1a3b63331e346098ec798975ef1e2d5407c946ae Mon Sep 17 00:00:00 2001
From: Juan Puerto <=>
Date: Fri, 19 Jan 2024 13:57:46 -0500
Subject: [PATCH 3/3] Docs: Update publication directory schema

---
 docs/publication/current/index.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/publication/current/index.md b/docs/publication/current/index.md
index 578491064..7d398c92a 100644
--- a/docs/publication/current/index.md
+++ b/docs/publication/current/index.md
@@ -28,6 +28,9 @@ Excel and TSV templates for this schema will be available when the draft next-ge
 
 | pattern | required? | description |
 | --- | --- | --- |
-| <code>TODO</code> | ✓ | Directory structure not yet specified. |
 | <code>extras\/.*</code> | ✓ | Folder for general lab-specific files related to the dataset. [Exists in all assays] |
+| <code>data\/.+</code> (example: <code>data/file1.ext</code>) | ✓ | Supplementary data files for the publication. All files referenced by the Vitessce visualization configurations in the vignettes must be included in this directory. |
+| <code>vignettes\/.*</code> | ✓ | Subdirectory containing Vitessce visualization files and a description of those files. |
+| <code>vignettes\/vignette_\d+\/[^\/]+\.json</code> (example: <code>vignettes/vignette_01/file1.json</code>) |  | Vitessce visualization configuration files. One or more visualization configurations can be provided per vignette. |
+| <code>vignettes\/vignette_\d+\/description\.md</code> (example: <code>vignettes/vignette_02/description.md</code>) |  | Description of the vignette and titles for the visualization configuration files. |