From 000e112b8013aee13fdb759b14ee0ccf27758253 Mon Sep 17 00:00:00 2001 From: j-uranic <117292295+j-uranic@users.noreply.github.com> Date: Wed, 27 Mar 2024 10:50:29 -0400 Subject: [PATCH] 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 <=> --- CHANGELOG.md | 1 + docs/phenocycler/current/index.md | 5 ++--- .../upload/global/lab_processed/images/OL9.ome.tiff | 0 ...ome-tiff.channels.csv => OL9.qptiff.channels.csv} | 0 .../directory-schemas/phenocycler-v2.yaml | 12 ++++-------- 5 files changed, 7 insertions(+), 11 deletions(-) delete mode 100644 examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff rename examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/{OL9.ome-tiff.channels.csv => OL9.qptiff.channels.csv} (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 09ed8718b..1c188a624 100644 --- 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 index 712f07576..2f41d4176 100644 --- a/docs/phenocycler/current/index.md +++ b/docs/phenocycler/current/index.md @@ -46,7 +46,6 @@ Related files: | raw\/images\/phenocycler\/(?:CoverslipMask.tif|FlowCellOverview.tif|OverviewFL.tif|SampleValMask.tif) | | Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. | | lab_processed\/.* | ✓ | Experiment files that were processed by the lab generating the data. | | lab_processed\/images\/.* | ✓ | This is a directory containing processed image files | -| lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson | | **[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”. | -| lab_processed\/images\/[^\/]+\.ome\.tiff | ✓ | 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. . 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. | -| lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv | ✓ | 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 | +| lab_processed\/images\/[^\/]+tissue-boundary\.geojson | | **[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”. | +| lab_processed\/images\/[^\/]*qptiff\.channels\.csv | ✓ | 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 | diff --git a/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff b/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff deleted file mode 100644 index e69de29bb..000000000 diff --git a/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome-tiff.channels.csv b/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.qptiff.channels.csv similarity index 100% rename from examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome-tiff.channels.csv rename to examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_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 index 94753580a..2101dc8b5 100644 --- 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. . 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 + 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 +