Juranic/phenocycler dirschema updates (#1317)

* Update phenocycler-v2.yaml Remove /lab_processed/images/*.ome.tiff and /lab_processed/images/*OME-TIFF.channels.csv. Add /lab_processed/images/*QPTIFF.channels.csv * Update CHANGELOG.md Update Phenocycler directory schema * Docs: Update phenocycler documentation * Update phenocycler-v2.yaml Change lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson to lab_processed\/images\/[^\/]+tissue-boundary\.geojson * Docs: Update Phenocycler documentation and the example files for Phenocycler --------- Co-authored-by: Juan Puerto <=>
hubmapconsortium · Mar 27, 2024 · 000e112 · 000e112
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## v0.0.19 (in progress)
 - Directory validation changes for "shared" uploads
+- Update Phenocycler directory schema
 
 ## v0.0.18
 

diff --git a/docs/phenocycler/current/index.md b/docs/phenocycler/current/index.md
@@ -46,7 +46,6 @@ Related files:
 | <code>raw\/images\/phenocycler\/(?:CoverslipMask.tif&#124;FlowCellOverview.tif&#124;OverviewFL.tif&#124;SampleValMask.tif)</code> |  | Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. |
 | <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. |
 | <code>lab_processed\/images\/.*</code> | ✓ | This is a directory containing processed image files |
-| <code>lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson</code> |  | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
-| <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> | ✓ | OME-TIFF file (multichannel, multi-layered) produced by the 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>. It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling. |
-| <code>lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv</code> | ✓ | This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0> |
+| <code>lab_processed\/images\/[^\/]+tissue-boundary\.geojson</code> |  | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
+| <code>lab_processed\/images\/[^\/]*qptiff\.channels\.csv</code> | ✓ | This file provides essential documentation pertaining to each channel of the accommpanying QPTIFF. The file should contain one row per QPTIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1JikzRNyDErspgPSel4P9Y6gx6N_mrAGIMDcJZd8TucA/edit#gid=0> |
 
diff --git a/...ec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff b/...ec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff
diff --git a/...rocessed/images/OL9.ome-tiff.channels.csv → ..._processed/images/OL9.qptiff.channels.csv b/...rocessed/images/OL9.ome-tiff.channels.csv → ..._processed/images/OL9.qptiff.channels.csv
diff --git a/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml b/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml
@@ -60,16 +60,12 @@ files:
     required: True
     description: This is a directory containing processed image files
   -
-    pattern: lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson
+    pattern: lab_processed\/images\/[^\/]+tissue-boundary\.geojson
     required: False
     description: If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”.
     is_qa_qc: True
   -
-    pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
+    pattern: lab_processed\/images\/[^\/]*qptiff\.channels\.csv
     required: True
-    description: OME-TIFF file (multichannel, multi-layered) produced by the 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>. It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling.
-    is_qa_qc: False
-  -
-    pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
-    required: True
-    description: This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0>
+    description: This file provides essential documentation pertaining to each channel of the accommpanying QPTIFF. The file should contain one row per QPTIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1JikzRNyDErspgPSel4P9Y6gx6N_mrAGIMDcJZd8TucA/edit#gid=0>
+