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Prevent multiple dataset types in a single non-multi-assay upload #1298

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Feb 7, 2024
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Prevent multiple dataset types in a single non-multi-assay upload #1298

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checking assay types and counts earlier to fail out if repeated or di…
gesinaphillips Feb 6, 2024
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ran online tests
gesinaphillips Feb 6, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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- Update PhenoCycler directory schema
- Update to prevent standalone child datasets in multi-assay upload
- Update to prevent multiple dataset types in a non-multi-assay upload

## v0.0.17

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2 changes: 1 addition & 1 deletion examples/dataset-examples/bad-cedar-assay-histology/MOCK_RESPONSE.json
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{"Histology": {"args": ["wrong", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "DNA", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./dataset-1", "Yes", "H&E", "Progressive staining", "Yes", "No", "HTX Technologies", "SunCollect Sprayer", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "30", "e7475329-9a60-4088-8e34-19a3828e0b3b"], "response": {"assaytype": "h-and-e", "contains-pii": false, "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}}
{"Histology": {"args": ["wrong", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "DNA", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./dataset-1", "Yes", "H&E", "Progressive staining", "Yes", "No", "HTX Technologies", "SunCollect Sprayer", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "30", "e7475329-9a60-4088-8e34-19a3828e0b3b"], "response": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}}
2 changes: 1 addition & 1 deletion examples/dataset-examples/bad-cedar-dir-histology/MOCK_RESPONSE.json
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{"Histology": {"args": ["HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "DNA", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./dataset-1", "Yes", "H&E", "Progressive staining", "Yes", "No", "HTX Technologies", "SunCollect Sprayer", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "30", "e7475329-9a60-4088-8e34-19a3828e0b3b"], "response": {"assaytype": "h-and-e", "contains-pii": false, "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}}
{"Histology": {"args": ["HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "DNA", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./dataset-1", "Yes", "H&E", "Progressive staining", "Yes", "No", "HTX Technologies", "SunCollect Sprayer", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "30", "e7475329-9a60-4088-8e34-19a3828e0b3b"], "response": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}}
2 changes: 1 addition & 1 deletion examples/dataset-examples/bad-cedar-multi-assay-visium-bad-child-metadata/MOCK_RESPONSE.json
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{"Visium (no probes)": {"args": ["babf1e69-f0eb-479a-bdc5-b70199669675", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Visium (no probes)", "./contributors.tsv", "./Visium_9OLC_A4_S1", "42.25", "mm^2", "2375.9", "um^2", "4992", "100", "um", "A1", "24", "minute"], "response": {"assaytype": "visium-no-probes", "contains-pii": true, "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}}, "Histology": {"args": ["e7475329-9a60-4088-8e34-19a3828e0b3b", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "nucleic acid and protein", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "Yes", "H&E", "progressive staining", "Yes", "No", "Not applicable", "Not applicable", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "0.3"], "response": {"assaytype": "h-and-e", "contains-pii": false, "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "RNAseq": {"args": ["944e5fa0-f68b-4bdd-8664-74a3909429a9", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "RNAseq", "RNA", "No", "Illumina", "NovaSeq 6000", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "0", "Read 1 (R1)", "16", "16", "Read 1 (R1)", "12", "spot", "", "", "", "TSO: AAGCAGTGGTATCAACGCAGAGTACATGGG", "517", "176.834", "ng", "735.479", "ng", "61.584", "nM", "single-end", "16", "16", "10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184", "10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215", "SI-TT-D1", "No", "1448", "Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319", "28,10,10,90", "Penn-E.768", "", "", "", ""], "response": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}}
{"Visium (no probes)": {"args": ["babf1e69-f0eb-479a-bdc5-b70199669675", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Visium (no probes)", "./contributors.tsv", "./Visium_9OLC_A4_S1", "42.25", "mm^2", "2375.9", "um^2", "4992", "100", "um", "A1", "24", "minute"], "response": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}}, "Histology": {"args": ["e7475329-9a60-4088-8e34-19a3828e0b3b", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "nucleic acid and protein", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "Yes", "H&E", "progressive staining", "Yes", "No", "Not applicable", "Not applicable", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "0.3"], "response": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "RNAseq": {"args": ["944e5fa0-f68b-4bdd-8664-74a3909429a9", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "RNAseq", "RNA", "No", "Illumina", "NovaSeq 6000", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "0", "Read 1 (R1)", "16", "16", "Read 1 (R1)", "12", "spot", "", "", "", "TSO: AAGCAGTGGTATCAACGCAGAGTACATGGG", "517", "176.834", "ng", "735.479", "ng", "61.584", "nM", "single-end", "16", "16", "10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184", "10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215", "SI-TT-D1", "No", "1448", "Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319", "28,10,10,90", "Penn-E.768", "", "", "", ""], "response": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}}
2 changes: 1 addition & 1 deletion examples/dataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/MOCK_RESPONSE.json
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{"Visium (no probes)": {"args": ["babf1e69-f0eb-479a-bdc5-b70199669675", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Visium (no probes)", "./contributors.tsv", "./Visium_9OLC_A4_S1", "42.25", "mm^2", "2375.9", "um^2", "4992", "100", "um", "A1", "24", "minute"], "response": {"assaytype": "visium-no-probes", "contains-pii": true, "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}}, "Histology": {"args": ["e7475329-9a60-4088-8e34-19a3828e0b3b", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "nucleic acid and protein", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "Yes", "H&E", "progressive staining", "Yes", "No", "Not applicable", "Not applicable", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "0.3"], "response": {"assaytype": "h-and-e", "contains-pii": false, "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "RNAseq": {"args": ["944e5fa0-f68b-4bdd-8664-74a3909429a9", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "RNAseq", "RNA", "No", "Illumina", "NovaSeq 6000", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "0", "Read 1 (R1)", "16", "16", "Read 1 (R1)", "12", "spot", "", "", "", "TSO: AAGCAGTGGTATCAACGCAGAGTACATGGG", "517", "176.834", "ng", "735.479", "ng", "61.584", "nM", "single-end", "16", "16", "10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184", "10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215", "SI-TT-D1", "No", "1448", "Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319", "28,10,10,90", "Penn-E.768", "", "", "", ""], "response": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}}
{"Visium (no probes)": {"args": ["babf1e69-f0eb-479a-bdc5-b70199669675", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Visium (no probes)", "./contributors.tsv", "./Visium_9OLC_A4_S1", "42.25", "mm^2", "2375.9", "um^2", "4992", "100", "um", "A1", "24", "minute"], "response": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}}, "Histology": {"args": ["e7475329-9a60-4088-8e34-19a3828e0b3b", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "nucleic acid and protein", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "Yes", "H&E", "progressive staining", "Yes", "No", "Not applicable", "Not applicable", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "0.3"], "response": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "RNAseq": {"args": ["944e5fa0-f68b-4bdd-8664-74a3909429a9", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "RNAseq", "RNA", "No", "Illumina", "NovaSeq 6000", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "0", "Read 1 (R1)", "16", "16", "Read 1 (R1)", "12", "spot", "", "", "", "TSO: AAGCAGTGGTATCAACGCAGAGTACATGGG", "517", "176.834", "ng", "735.479", "ng", "61.584", "nM", "single-end", "16", "16", "10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184", "10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215", "SI-TT-D1", "No", "1448", "Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319", "28,10,10,90", "Penn-E.768", "", "", "", ""], "response": {"assaytype": "scRNAseq-10Genomics-v3", "contains-pii": true, "dataset-type": "RNAseq", "description": "scRNA-seq (10x Genomics v3)", "dir-schema": "rnaseq-v2", "primary": true, "vitessce-hints": []}}}
2 changes: 1 addition & 1 deletion ...ataset-examples/bad-cedar-multi-assay-visium-bad-dir-structure/README_ONLINE.md
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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\/.*.
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2 changes: 1 addition & 1 deletion examples/dataset-examples/bad-cedar-multi-assay-visium-missing-child/MOCK_RESPONSE.json
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{"Visium (no probes)": {"args": ["babf1e69-f0eb-479a-bdc5-b70199669675", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Visium (no probes)", "./contributors.tsv", "./Visium_9OLC_A4_S1", "42.25", "mm^2", "2375.9", "um^2", "4992", "100", "um", "A1", "24", "minute"], "response": {"assaytype": "visium-no-probes", "contains-pii": true, "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}}, "Histology": {"args": ["e7475329-9a60-4088-8e34-19a3828e0b3b", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "nucleic acid and protein", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "Yes", "H&E", "progressive staining", "Yes", "No", "Not applicable", "Not applicable", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "0.3"], "response": {"assaytype": "h-and-e", "contains-pii": false, "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "RNAseq": {"args": ["944e5fa0-f68b-4bdd-8664-74a3909429a9", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "RNAseq", "RNA", "No", "Illumina", "NovaSeq 6000", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "0", "Read 1 (R1)", "16", "16", "Read 1 (R1)", "12", "spot", "", "", "", "TSO: AAGCAGTGGTATCAACGCAGAGTACATGGG", "517", "176.834", "ng", "735.479", "ng", "61.584", "nM", "single-end", "16", "16", "10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184", "10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215", "SI-TT-D1", "No", "1448", "Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319", "28,10,10,90", "Penn-E.768", "", "", "", ""], "response": {"assaytype": "snRNAseq-10xGenomics-v3", "description": "snRNA-seq (10x Genomics v3)", "dir-schema": "scrnaseq-v2", "vitessce-hints": []}}}
{"Visium (no probes)": {"args": ["babf1e69-f0eb-479a-bdc5-b70199669675", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Visium (no probes)", "./contributors.tsv", "./Visium_9OLC_A4_S1", "42.25", "mm^2", "2375.9", "um^2", "4992", "100", "um", "A1", "24", "minute"], "response": {"assaytype": "visium-no-probes", "contains-pii": true, "dataset-type": "Visium (no probes)", "description": "Visium (No probes)", "dir-schema": "visium-no-probes-v2", "must-contain": ["Histology", "RNAseq"], "primary": true, "vitessce-hints": []}}, "Histology": {"args": ["e7475329-9a60-4088-8e34-19a3828e0b3b", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "Histology", "nucleic acid and protein", "No", "Zeiss Microscopy", "Axio Observer 7", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "Yes", "H&E", "progressive staining", "Yes", "No", "Not applicable", "Not applicable", "V11A19-078", "Snake-by-rows", "Right-and-down", "10", "120", "0.3"], "response": {"assaytype": "h-and-e", "contains-pii": false, "dataset-type": "Histology", "description": "H&E Stained Microscopy", "dir-schema": "histology-v2", "primary": true, "vitessce-hints": []}}, "RNAseq": {"args": ["944e5fa0-f68b-4bdd-8664-74a3909429a9", "HBM233.CGGG.482", "Visium_9OLC_A4_S1", "https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1", "RNAseq", "RNA", "No", "Illumina", "NovaSeq 6000", "24", "day", "", "", "./contributors.tsv", "./Visium_9OLC_A4_S1", "0", "Read 1 (R1)", "16", "16", "Read 1 (R1)", "12", "spot", "", "", "", "TSO: AAGCAGTGGTATCAACGCAGAGTACATGGG", "517", "176.834", "ng", "735.479", "ng", "61.584", "nM", "single-end", "16", "16", "10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184", "10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215", "SI-TT-D1", "No", "1448", "Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319", "28,10,10,90", "Penn-E.768", "", "", "", ""], "response": {"assaytype": "snRNAseq-10xGenomics-v3", "description": "snRNA-seq (10x Genomics v3)", "dir-schema": "scrnaseq-v2", "vitessce-hints": []}}}
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