From fd65d506460be43af3d80674db6d3e12022a9c91 Mon Sep 17 00:00:00 2001
From: j-uranic <117292295+j-uranic@users.noreply.github.com>
Date: Thu, 21 Mar 2024 09:59:23 -0400
Subject: [PATCH] Juranic/histology dirschema update (#1314)

* Update histology-v2.yaml

Add qptiff to /raw/images/

* Update CHANGELOG.md

Update Histology directory schema

* Docs: Update histology docs

---------

Co-authored-by: Juan Puerto <=>
---
 CHANGELOG.md                                                    | 1 +
 docs/histology/current/index.md                                 | 2 +-
 src/ingest_validation_tools/directory-schemas/histology-v2.yaml | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7578d64c4..ecc4341c7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@
 - Update Histology with links
 - Update GeoMx NGS directory schema
 - Ported murine from SenNet
+- Update Histology directory schema
 
 ## v0.0.17
 
diff --git a/docs/histology/current/index.md b/docs/histology/current/index.md
index 00c48f36e..37a3780db 100644
--- a/docs/histology/current/index.md
+++ b/docs/histology/current/index.md
@@ -37,7 +37,7 @@ Related files:
 | <code>extras\/microscope_settings\.json</code> |  | **[QA/QC]** A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk <help@hubmapconsortium.org> if help is required in generating this document. |  |
 | <code>raw\/.*</code> | ✓ | Raw data files for the experiment. |  |
 | <code>raw\/images\/.*</code> | ✓ | Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file. |  |
-| <code>raw\/images\/[^\/]+\.(?:xml&#124;scn&#124;vsi&#124;ndpi&#124;svs&#124;czi&#124;tiff)</code> | ✓ | Raw microscope file for the experiment |  |
+| <code>raw\/images\/[^\/]+\.(?:xml&#124;scn&#124;vsi&#124;ndpi&#124;svs&#124;czi&#124;tiff&#124;qptiff)</code> | ✓ | Raw microscope file for the experiment |  |
 | <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. |  |
 | <code>lab_processed\/images\/.*</code> | ✓ | Processed image files |  |
 | <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> (example: <code>lab_processed/images/HBM892.MDXS.293.ome.tiff</code>) | ✓ | OME-TIFF files (multichannel, multi-layered) produced by the microscopy experiment. If compressed, must use loss-less compression algorithm. See the following link for the set of fields that are required in the OME TIFF file XML header. <https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0> |  |
diff --git a/src/ingest_validation_tools/directory-schemas/histology-v2.yaml b/src/ingest_validation_tools/directory-schemas/histology-v2.yaml
index d11b1d59a..684117d41 100644
--- a/src/ingest_validation_tools/directory-schemas/histology-v2.yaml
+++ b/src/ingest_validation_tools/directory-schemas/histology-v2.yaml
@@ -22,7 +22,7 @@ files:
     required: True
     description: Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file.
   -
-    pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff)
+    pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff|qptiff)
     required: True
     description: Raw microscope file for the experiment
     is_qa_qc: False