hubmapconsortium · gesinaphillips · Feb 6, 2024 · Jan 16, 2024 · Feb 2, 2024 · Feb 2, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,9 @@
 # Changelog
 
 ## v0.0.18 (in progress)
+
 - Update PhenoCycler directory schema
+- Update to prevent standalone child datasets in multi-assay upload
 
 ## v0.0.17
 

diff --git a/examples/dataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/README.md b/examples/dataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/README.md
@@ -2,7 +2,7 @@
 Upload Errors:
   Directory Errors:
     ? examples/dataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/upload/good-visium-assay-metadata.tsv,
-      column 'data_path', value ./Visium_9OLC_A4_S1
+      column 'data_path', value './Visium_9OLC_A4_S1'
     : examples/dataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/upload/Visium_9OLC_A4_S1 (as visium-no-probes-v2):
         Required but missing:
         - lab_processed\/.*.

diff --git a/...ataset-examples/bad-cedar-multi-assay-visium-unreferenced-parent-path/README.md b/...ataset-examples/bad-cedar-multi-assay-visium-unreferenced-parent-path/README.md
@@ -1,7 +1,7 @@
 ```
-Preflight: 'Multi-assay TSV examples/dataset-examples/bad-cedar-multi-assay-visium-unreferenced-parent-path/upload/bad-visium-extra-paths-assay-metadata.tsv
-  contains data paths that are not present in child assay TSVs. Data paths unique
-  to parent: ["./Visium_9OLC_I4_S3"].'
+Preflight: 'Path(s) in Visium (no probes) metadata TSV not present in component Histology:
+  {"./Visium_9OLC_I4_S3"}. Path(s) in Visium (no probes) metadata TSV not present
+  in component RNAseq: {"./Visium_9OLC_I4_S3"}.'
 Hint: 'If validation fails because of extra whitespace in the TSV, try:
 
   src/cleanup_whitespace.py --tsv_in original.tsv --tsv_out clean.tsv.'

diff --git a/...bad-cedar-multi-assay-visium-with-standalone-histology-bad-dir-schema/README.md b/...bad-cedar-multi-assay-visium-with-standalone-histology-bad-dir-schema/README.md
diff --git a/...stology-bad-dir-schema/MOCK_RESPONSE.json → ...h-standalone-histology/MOCK_RESPONSE.json b/...stology-bad-dir-schema/MOCK_RESPONSE.json → ...h-standalone-histology/MOCK_RESPONSE.json
diff --git a/...taset-examples/bad-cedar-multi-assay-visium-with-standalone-histology/README.md b/...taset-examples/bad-cedar-multi-assay-visium-with-standalone-histology/README.md
@@ -0,0 +1,6 @@
+```
+Preflight: 'Path(s) in Histology metadata TSV not present in parent: {"./dataset-1"}.'
+Hint: 'If validation fails because of extra whitespace in the TSV, try:
+
+  src/cleanup_whitespace.py --tsv_in original.tsv --tsv_out clean.tsv.'
+```
diff --git a/...histology-bad-dir-schema/README_ONLINE.md → ...ith-standalone-histology/README_ONLINE.md b/...histology-bad-dir-schema/README_ONLINE.md → ...ith-standalone-histology/README_ONLINE.md
diff --git a/...OLC_A4_S1/extras/microscope_hardware.json → ...OLC_A4_S1/extras/microscope_hardware.json b/...OLC_A4_S1/extras/microscope_hardware.json → ...OLC_A4_S1/extras/microscope_hardware.json
diff --git a/...essed/images/Visium.ome-tiff.channels.csv → ...essed/images/Visium.ome-tiff.channels.csv b/...essed/images/Visium.ome-tiff.channels.csv → ...essed/images/Visium.ome-tiff.channels.csv
diff --git a/...ocessed/images/Visium_90LC_A4_S1.ome.tiff → ...ocessed/images/Visium_90LC_A4_S1.ome.tiff b/...ocessed/images/Visium_90LC_A4_S1.ome.tiff → ...ocessed/images/Visium_90LC_A4_S1.ome.tiff
diff --git a/...load/Visium_9OLC_A4_S1/raw/empty_file.gpr → ...load/Visium_9OLC_A4_S1/raw/empty_file.gpr b/...load/Visium_9OLC_A4_S1/raw/empty_file.gpr → ...load/Visium_9OLC_A4_S1/raw/empty_file.gpr
diff --git a/...A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz → ...A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz b/...A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz → ...A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
diff --git a/...ad/Visium_9OLC_A4_S1/raw/fastq/empty_file → ...ad/Visium_9OLC_A4_S1/raw/fastq/empty_file b/...ad/Visium_9OLC_A4_S1/raw/fastq/empty_file → ...ad/Visium_9OLC_A4_S1/raw/fastq/empty_file
diff --git a/...isium_9OLC_A4_S1/raw/images/faketiff.tiff → ...isium_9OLC_A4_S1/raw/images/faketiff.tiff b/...isium_9OLC_A4_S1/raw/images/faketiff.tiff → ...isium_9OLC_A4_S1/raw/images/faketiff.tiff
diff --git a/...OLC_A4_S2/extras/microscope_hardware.json → ...OLC_A4_S2/extras/microscope_hardware.json b/...OLC_A4_S2/extras/microscope_hardware.json → ...OLC_A4_S2/extras/microscope_hardware.json
diff --git a/...essed/images/Visium.ome-tiff.channels.csv → ...essed/images/Visium.ome-tiff.channels.csv b/...essed/images/Visium.ome-tiff.channels.csv → ...essed/images/Visium.ome-tiff.channels.csv
diff --git a/...ocessed/images/Visium_90LC_A4_S1.ome.tiff → ...ocessed/images/Visium_90LC_A4_S1.ome.tiff b/...ocessed/images/Visium_90LC_A4_S1.ome.tiff → ...ocessed/images/Visium_90LC_A4_S1.ome.tiff
diff --git a/...load/Visium_9OLC_A4_S2/raw/empty_file.gpr → ...load/Visium_9OLC_A4_S2/raw/empty_file.gpr b/...load/Visium_9OLC_A4_S2/raw/empty_file.gpr → ...load/Visium_9OLC_A4_S2/raw/empty_file.gpr
diff --git a/...A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz → ...A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz b/...A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz → ...A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz
diff --git a/...ad/Visium_9OLC_A4_S2/raw/fastq/empty_file → ...ad/Visium_9OLC_A4_S2/raw/fastq/empty_file b/...ad/Visium_9OLC_A4_S2/raw/fastq/empty_file → ...ad/Visium_9OLC_A4_S2/raw/fastq/empty_file
diff --git a/...isium_9OLC_A4_S2/raw/images/faketiff.tiff → ...isium_9OLC_A4_S2/raw/images/faketiff.tiff b/...isium_9OLC_A4_S2/raw/images/faketiff.tiff → ...isium_9OLC_A4_S2/raw/images/faketiff.tiff
diff --git a/...OLC_I4_S1/extras/microscope_hardware.json → ...OLC_I4_S1/extras/microscope_hardware.json b/...OLC_I4_S1/extras/microscope_hardware.json → ...OLC_I4_S1/extras/microscope_hardware.json
diff --git a/...essed/images/Visium.ome-tiff.channels.csv → ...essed/images/Visium.ome-tiff.channels.csv b/...essed/images/Visium.ome-tiff.channels.csv → ...essed/images/Visium.ome-tiff.channels.csv
diff --git a/...ocessed/images/Visium_90LC_A4_S1.ome.tiff → ...ocessed/images/Visium_90LC_A4_S1.ome.tiff b/...ocessed/images/Visium_90LC_A4_S1.ome.tiff → ...ocessed/images/Visium_90LC_A4_S1.ome.tiff
diff --git a/...load/Visium_9OLC_I4_S1/raw/empty_file.gpr → ...load/Visium_9OLC_I4_S1/raw/empty_file.gpr b/...load/Visium_9OLC_I4_S1/raw/empty_file.gpr → ...load/Visium_9OLC_I4_S1/raw/empty_file.gpr
diff --git a/...I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz → ...I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz b/...I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz → ...I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
diff --git a/...ad/Visium_9OLC_I4_S1/raw/fastq/empty_file → ...ad/Visium_9OLC_I4_S1/raw/fastq/empty_file b/...ad/Visium_9OLC_I4_S1/raw/fastq/empty_file → ...ad/Visium_9OLC_I4_S1/raw/fastq/empty_file
diff --git a/...isium_9OLC_I4_S1/raw/images/faketiff.tiff → ...isium_9OLC_I4_S1/raw/images/faketiff.tiff b/...isium_9OLC_I4_S1/raw/images/faketiff.tiff → ...isium_9OLC_I4_S1/raw/images/faketiff.tiff
diff --git a/...gy-bad-dir-schema/upload/contributors.tsv → ...ndalone-histology/upload/contributors.tsv b/...gy-bad-dir-schema/upload/contributors.tsv → ...ndalone-histology/upload/contributors.tsv
diff --git a/...dataset-1/extras/microscope_hardware.json → ...dataset-1/extras/microscope_hardware.json b/...dataset-1/extras/microscope_hardware.json → ...dataset-1/extras/microscope_hardware.json
diff --git a/...cessed/annotations/segmentation-masks.csv → ...cessed/annotations/segmentation-masks.csv b/...cessed/annotations/segmentation-masks.csv → ...cessed/annotations/segmentation-masks.csv
diff --git a/...ab_processed/annotations/test-objects.csv → ...ab_processed/annotations/test-objects.csv b/...ab_processed/annotations/test-objects.csv → ...ab_processed/annotations/test-objects.csv
diff --git a/...d/annotations/test.segmentations.ome.tiff → ...d/annotations/test.segmentations.ome.tiff b/...d/annotations/test.segmentations.ome.tiff → ...d/annotations/test.segmentations.ome.tiff
diff --git a/...upload/dataset-1/lab_processed/empty-file → ...upload/dataset-1/lab_processed/empty-file b/...upload/dataset-1/lab_processed/empty-file → ...upload/dataset-1/lab_processed/empty-file
diff --git a/...dataset-1/lab_processed/images/empty-file → ...dataset-1/lab_processed/images/empty-file b/...dataset-1/lab_processed/images/empty-file → ...dataset-1/lab_processed/images/empty-file
diff --git a/...d/images/empty-file.ome-tiff.channels.csv → ...d/images/empty-file.ome-tiff.channels.csv b/...d/images/empty-file.ome-tiff.channels.csv → ...d/images/empty-file.ome-tiff.channels.csv
diff --git a/.../lab_processed/images/empty-file.ome.tiff → .../lab_processed/images/empty-file.ome.tiff b/.../lab_processed/images/empty-file.ome.tiff → .../lab_processed/images/empty-file.ome.tiff
diff --git a/...ema/upload/good-visium-assay-metadata.tsv → ...ogy/upload/good-visium-assay-metadata.tsv b/...ema/upload/good-visium-assay-metadata.tsv → ...ogy/upload/good-visium-assay-metadata.tsv
diff --git a/...upload/good-visium-histology-metadata.tsv → ...upload/good-visium-histology-metadata.tsv b/...upload/good-visium-histology-metadata.tsv → ...upload/good-visium-histology-metadata.tsv
diff --git a/...ma/upload/good-visium-rnaseq-metadata.tsv → ...gy/upload/good-visium-rnaseq-metadata.tsv b/...ma/upload/good-visium-rnaseq-metadata.tsv → ...gy/upload/good-visium-rnaseq-metadata.tsv
diff --git a/...taset-examples/good-cedar-multi-assay-visium-with-standalone-histology/MOCK_RESPONSE.json b/...taset-examples/good-cedar-multi-assay-visium-with-standalone-histology/MOCK_RESPONSE.json
diff --git a/...aset-examples/good-cedar-multi-assay-visium-with-standalone-histology/README.md b/...aset-examples/good-cedar-multi-assay-visium-with-standalone-histology/README.md
diff --git a/...amples/good-cedar-multi-assay-visium-with-standalone-histology/README_ONLINE.md b/...amples/good-cedar-multi-assay-visium-with-standalone-histology/README_ONLINE.md