nci-cidc-schemas 0.27.21__tar.gz → 0.27.24__tar.gz
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- {nci_cidc_schemas-0.27.21/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.27.24}/PKG-INFO +1 -1
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/__init__.py +1 -1
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/prism/constants.py +48 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_html.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_mtx.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_out.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_rds.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_stats.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_tab.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_tiff.json +51 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/artifacts/artifact_txt.json +51 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/available_assays.json +11 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/available_ngs_analyses.json +22 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/assays/components/visium_input.json +60 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/assays/components/visium_preamble.json +27 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/assays/scrnaseq_analysis.json +102 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/assays/visium_analysis.json +62 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/assays/visium_assay.json +68 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/sample.json +1 -1
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json +232 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/templates/analyses/visium_analysis_template.json +103 -0
- nci_cidc_schemas-0.27.24/cidc_schemas/schemas/templates/assays/visium_template.json +150 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +2 -1
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24/nci_cidc_schemas.egg-info}/PKG-INFO +1 -1
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/nci_cidc_schemas.egg-info/SOURCES.txt +16 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/cidc_test_data/analysis_data.py +402 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/cidc_test_data/assay_data.py +135 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/LICENSE +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/MANIFEST.in +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/README.md +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/cli.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/constants.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/json_validation.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/metaschema/strict_meta_schema.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/migrations.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2 +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/prism/__init__.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/prism/core.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/prism/extra_metadata.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/prism/merger.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/prism/pipelines.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/aliquot.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_bam.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_bam_bai.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_bed.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_bigwig.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_binary.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_clinical_csv.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_clinical_docx.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_cncf.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_cns.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_csv.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_fastq_gz.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_fcs.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_file.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_gz.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_h5ad.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_image.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_jpg.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_json.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_junction.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_log.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_maf.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_narrowPeak.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_npx.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_ome_tiff.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_pdf.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_png.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_rcc.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_rdata.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_tbi.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_text.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_tsv.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_vcf.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_vcf_gz.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_xlsx.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_yaml.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/artifacts/artifact_zip.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/atacseq_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/antibody.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/assay_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/composite_image.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/controls.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/enrichment_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/excluded_samples.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/hande_local_file.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/image.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/imaging/mif_entry.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/imaging/mif_export.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/imaging/mif_input.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/imaging/mif_roi.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/imaging_data.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/local_file.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/mapping.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/mibi_antibody.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/mif_antibody.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/mihc_antibody.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/mihc_input.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/multiple_local_files.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/fusion.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/microbiome.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/msisensor.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/neoantigen.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/rna_level1_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/rseqc.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/salmon.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/star.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs/rna/trust4.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs_assay_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/ngs_assay_record.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/reads_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/reads_with_index.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/scrnaseq_input.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/components/scrnaseq_preamble.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/ctdna_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/cytof_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/cytof_assay_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/elisa_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/hande_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/ihc_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/mibi_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/microbiome_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/mif_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/mihc_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/misc_data.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/nanostring_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/olink_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/rna_assay-v0.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/rna_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/scrnaseq_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/tcr_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/tcr_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/wes_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/wes_assay.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/wes_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/assays/wes_tumor_only_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/clinical_data.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/clinical_trial.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/participant.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/shipping_core.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/clinical_data_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/ctdna_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/cytof_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/elisa_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/hande_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/ihc_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/mibi_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/microbiome_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/mif_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/mihc_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/misc_data_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/nanostring_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/olink_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/rna_bam_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/rna_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/scrnaseq_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/tcr_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/wes_bam_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/assays/wes_fastq_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/h_and_e_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/pbmc_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/plasma_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/template.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/template_reader.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/template_writer.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/unprism.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/cidc_schemas/util.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/nci_cidc_schemas.egg-info/dependency_links.txt +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/nci_cidc_schemas.egg-info/entry_points.txt +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/nci_cidc_schemas.egg-info/not-zip-safe +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/nci_cidc_schemas.egg-info/requires.txt +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/nci_cidc_schemas.egg-info/top_level.txt +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/requirements.txt +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/setup.cfg +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/setup.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/__init__.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/conftest.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/constants.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.1.csv +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.1.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.2.bom.csv +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.2.csv +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.2.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.3.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinical_test_file.docx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinicaltrial_examples/CT_1.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinicaltrial_examples/CT_1PA_multiWES.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinicaltrial_examples/CT_cytof_with_analysis.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinicaltrial_examples/CT_ihc.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/clinicaltrial_examples/CT_minimal.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/date_examples.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/elisa_test_file.1.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/elisa_test_file.2.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/hande_err_template.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/olink/invalid_olink_assay_1_NPX.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/olink/olink_assay_1_NPX.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/olink/olink_assay_2_NPX.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/olink/olink_assay_combined.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/pbmc_invalid.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/pbmc_manifest_valid.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/1.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/a.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/b.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/c.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/d1/3.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/d1/d2/2.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/invalid_ref.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/target-templates/atacseq_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/target-templates/rna_level1_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/target-templates/wes_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/tiny_invalid_manifest.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/data/tiny_valid_manifest.xlsx +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/__init__.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/cidc_test_data/__init__.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/cidc_test_data/manifest_data.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/cidc_test_data/utils.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/schema/test_schema.json +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/test_cidc_data_model.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/test_constants.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/test_core.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/test_extra_metadata.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/test_merger.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/prism/test_pipelines.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_artifacts.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_assays.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_clinicaltrial_examples.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_json_validation.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_migrations.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_schemas.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_strict_meta_schema.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_template.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_template_reader.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_template_writer.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_templates.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_trial_core.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_unprism.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/test_util.py +0 -0
- {nci_cidc_schemas-0.27.21 → nci_cidc_schemas-0.27.24}/tests/utils/test_template_generator.py +0 -0
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our scrnaseq_analysis documentation here. These are the files (and folder structure) that are expected in the gcloud
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"data_format": {
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"description": "Data format.",
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"const": "HTML"
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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},
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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"uploaded_timestamp": {
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},
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"file_size_bytes": {
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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"mergeStrategy": "objectMerge"
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}
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@@ -0,0 +1,51 @@
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "mtx_artifact",
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"title": "MTX Artifact",
|
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"type": "object",
|
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"description": "Information about a MTX file.",
|
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"additionalProperties": false,
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"properties": {
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"data_format": {
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"description": "Data format.",
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"const": "MTX"
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},
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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},
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
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"uploaded_timestamp": {
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},
|
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"file_size_bytes": {
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
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"crc32c_hash": {
|
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
|
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"facet_group": {
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}
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},
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"allOf": [
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|
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"mergeStrategy": "objectMerge"
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}
|
|
@@ -0,0 +1,51 @@
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{
|
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"$schema": "metaschema/strict_meta_schema.json#",
|
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"$id": "out_artifact",
|
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"title": "OUT Artifact",
|
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"type": "object",
|
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|
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"description": "Information about a OUT file.",
|
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"additionalProperties": false,
|
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"properties": {
|
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"data_format": {
|
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"description": "Data format.",
|
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"const": "OUT"
|
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},
|
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
|
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"artifact_creator": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
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},
|
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
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"file_name": {
|
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"$ref": "artifacts/artifact_core.json#properties/file_name"
|
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},
|
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"object_url": {
|
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
|
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"uploaded_timestamp": {
|
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
|
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"file_size_bytes": {
|
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
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},
|
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
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|
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"crc32c_hash": {
|
|
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
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},
|
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
|
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"artifact_category": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
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},
|
|
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"facet_group": {
|
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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}
|
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},
|
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"allOf": [
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{
|
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|
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],
|
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|
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}
|
|
@@ -0,0 +1,51 @@
|
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|
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{
|
|
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|
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"$schema": "metaschema/strict_meta_schema.json#",
|
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|
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"$id": "rds_artifact",
|
|
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|
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"title": "RDS Artifact",
|
|
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"type": "object",
|
|
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|
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"description": "Information about a rds file.",
|
|
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|
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"additionalProperties": false,
|
|
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|
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"properties": {
|
|
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|
+
"data_format": {
|
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|
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"description": "Data format.",
|
|
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|
+
"const": "RDS"
|
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|
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},
|
|
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|
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"upload_placeholder": {
|
|
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
|
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},
|
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"artifact_creator": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
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},
|
|
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|
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
|
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|
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
|
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|
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"file_name": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/file_name"
|
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|
+
},
|
|
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|
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"object_url": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/object_url"
|
|
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|
+
},
|
|
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|
+
"uploaded_timestamp": {
|
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|
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
|
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|
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},
|
|
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|
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"file_size_bytes": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
|
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|
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},
|
|
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|
+
"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
|
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|
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"crc32c_hash": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
|
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|
+
},
|
|
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|
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
|
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|
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"artifact_category": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
|
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|
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},
|
|
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|
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"facet_group": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
|
|
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|
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}
|
|
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|
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},
|
|
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|
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"allOf": [
|
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{
|
|
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|
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"$ref": "artifacts/artifact_core.json"
|
|
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|
+
}
|
|
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|
+
],
|
|
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|
+
"mergeStrategy": "objectMerge"
|
|
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|
+
}
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
{
|
|
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|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "stats_artifact",
|
|
4
|
+
"title": "Stats Artifact",
|
|
5
|
+
"type": "object",
|
|
6
|
+
"description": "Information about a STATS file.",
|
|
7
|
+
"additionalProperties": false,
|
|
8
|
+
"properties": {
|
|
9
|
+
"data_format": {
|
|
10
|
+
"description": "Data format.",
|
|
11
|
+
"const": "STATS"
|
|
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|
+
},
|
|
13
|
+
"upload_placeholder": {
|
|
14
|
+
"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
|
|
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|
+
},
|
|
16
|
+
"artifact_creator": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
|
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|
+
},
|
|
19
|
+
"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
|
20
|
+
"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
|
21
|
+
"file_name": {
|
|
22
|
+
"$ref": "artifacts/artifact_core.json#properties/file_name"
|
|
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|
+
},
|
|
24
|
+
"object_url": {
|
|
25
|
+
"$ref": "artifacts/artifact_core.json#properties/object_url"
|
|
26
|
+
},
|
|
27
|
+
"uploaded_timestamp": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
|
|
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|
+
},
|
|
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|
+
"file_size_bytes": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
|
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|
+
},
|
|
33
|
+
"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
|
34
|
+
"crc32c_hash": {
|
|
35
|
+
"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
|
36
|
+
},
|
|
37
|
+
"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
|
38
|
+
"artifact_category": {
|
|
39
|
+
"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
|
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|
+
},
|
|
41
|
+
"facet_group": {
|
|
42
|
+
"$ref": "artifacts/artifact_core.json#properties/facet_group"
|
|
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|
+
}
|
|
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|
+
},
|
|
45
|
+
"allOf": [
|
|
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|
+
{
|
|
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|
+
"$ref": "artifacts/artifact_core.json"
|
|
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|
+
}
|
|
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|
+
],
|
|
50
|
+
"mergeStrategy": "objectMerge"
|
|
51
|
+
}
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
{
|
|
2
|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "tab_artifact",
|
|
4
|
+
"title": "TAB Artifact",
|
|
5
|
+
"type": "object",
|
|
6
|
+
"description": "Information about a TAB file.",
|
|
7
|
+
"additionalProperties": false,
|
|
8
|
+
"properties": {
|
|
9
|
+
"data_format": {
|
|
10
|
+
"description": "Data format.",
|
|
11
|
+
"const": "TAB"
|
|
12
|
+
},
|
|
13
|
+
"upload_placeholder": {
|
|
14
|
+
"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
|
|
15
|
+
},
|
|
16
|
+
"artifact_creator": {
|
|
17
|
+
"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
|
18
|
+
},
|
|
19
|
+
"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
|
20
|
+
"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
|
21
|
+
"file_name": {
|
|
22
|
+
"$ref": "artifacts/artifact_core.json#properties/file_name"
|
|
23
|
+
},
|
|
24
|
+
"object_url": {
|
|
25
|
+
"$ref": "artifacts/artifact_core.json#properties/object_url"
|
|
26
|
+
},
|
|
27
|
+
"uploaded_timestamp": {
|
|
28
|
+
"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
|
|
29
|
+
},
|
|
30
|
+
"file_size_bytes": {
|
|
31
|
+
"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
|
32
|
+
},
|
|
33
|
+
"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
|
34
|
+
"crc32c_hash": {
|
|
35
|
+
"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
|
36
|
+
},
|
|
37
|
+
"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
|
38
|
+
"artifact_category": {
|
|
39
|
+
"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
|
40
|
+
},
|
|
41
|
+
"facet_group": {
|
|
42
|
+
"$ref": "artifacts/artifact_core.json#properties/facet_group"
|
|
43
|
+
}
|
|
44
|
+
},
|
|
45
|
+
"allOf": [
|
|
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|
+
{
|
|
47
|
+
"$ref": "artifacts/artifact_core.json"
|
|
48
|
+
}
|
|
49
|
+
],
|
|
50
|
+
"mergeStrategy": "objectMerge"
|
|
51
|
+
}
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
{
|
|
2
|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "tiff_artifact",
|
|
4
|
+
"title": "Tiff Artifact",
|
|
5
|
+
"type": "object",
|
|
6
|
+
"description": "Information about a tiff file.",
|
|
7
|
+
"additionalProperties": false,
|
|
8
|
+
"properties": {
|
|
9
|
+
"data_format": {
|
|
10
|
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"description": "Data format.",
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"const": "TIFF"
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},
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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},
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
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"uploaded_timestamp": {
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
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"file_size_bytes": {
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
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"crc32c_hash": {
|
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
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"artifact_category": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
|
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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}
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},
|
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"allOf": [
|
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{
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"$ref": "artifacts/artifact_core.json"
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}
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],
|
|
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"mergeStrategy": "objectMerge"
|
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}
|
|
@@ -0,0 +1,51 @@
|
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|
+
{
|
|
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|
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"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "txt_artifact",
|
|
4
|
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"title": "Txt Artifact",
|
|
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|
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"type": "object",
|
|
6
|
+
"description": "Information about a txt file.",
|
|
7
|
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"additionalProperties": false,
|
|
8
|
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"properties": {
|
|
9
|
+
"data_format": {
|
|
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|
+
"description": "Data format.",
|
|
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+
"const": "TXT"
|
|
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+
},
|
|
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|
+
"upload_placeholder": {
|
|
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+
"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
|
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|
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},
|
|
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"artifact_creator": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
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+
},
|
|
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
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"file_name": {
|
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
|
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"object_url": {
|
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"$ref": "artifacts/artifact_core.json#properties/object_url"
|
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},
|
|
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"uploaded_timestamp": {
|
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
|
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"file_size_bytes": {
|
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
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},
|
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
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|
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"crc32c_hash": {
|
|
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
|
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"artifact_category": {
|
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
|
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},
|
|
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|
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"facet_group": {
|
|
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
|
|
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}
|
|
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},
|
|
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|
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"allOf": [
|
|
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{
|
|
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|
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"$ref": "artifacts/artifact_core.json"
|
|
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|
+
}
|
|
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|
+
],
|
|
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|
+
"mergeStrategy": "objectMerge"
|
|
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|
+
}
|
|
@@ -141,6 +141,17 @@
|
|
|
141
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|
"idRef": "batch_id"
|
|
142
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|
}
|
|
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|
},
|
|
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|
+
"visium": {
|
|
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|
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"type": "array",
|
|
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|
+
"description": "Visium",
|
|
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|
+
"items": {
|
|
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|
+
"$ref": "assays/visium_assay.json"
|
|
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|
+
},
|
|
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|
+
"mergeStrategy": "arrayMergeById",
|
|
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|
+
"mergeOptions": {
|
|
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|
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"idRef": "batch_id"
|
|
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|
+
}
|
|
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|
+
},
|
|
144
155
|
"nanostring": {
|
|
145
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|
"type": "array",
|
|
146
157
|
"description": "Nanostring",
|
|
@@ -35,6 +35,28 @@
|
|
|
35
35
|
"mergeOptions": {
|
|
36
36
|
"idRef": "batch_id"
|
|
37
37
|
}
|
|
38
|
+
},
|
|
39
|
+
"scrnaseq_analysis": {
|
|
40
|
+
"type": "array",
|
|
41
|
+
"description": "Analysis for Assay for scRNA.",
|
|
42
|
+
"items": {
|
|
43
|
+
"$ref": "assays/scrnaseq_analysis.json"
|
|
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|
+
},
|
|
45
|
+
"mergeStrategy": "arrayMergeById",
|
|
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|
+
"mergeOptions": {
|
|
47
|
+
"idRef": "batch_id"
|
|
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|
+
}
|
|
49
|
+
},
|
|
50
|
+
"visium_analysis": {
|
|
51
|
+
"type": "array",
|
|
52
|
+
"description": "Analysis for Assay for visium.",
|
|
53
|
+
"items": {
|
|
54
|
+
"$ref": "assays/visium_analysis.json"
|
|
55
|
+
},
|
|
56
|
+
"mergeStrategy": "arrayMergeById",
|
|
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|
+
"mergeOptions": {
|
|
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|
+
"idRef": "batch_id"
|
|
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|
+
}
|
|
38
60
|
}
|
|
39
61
|
}
|
|
40
62
|
}
|
|
@@ -0,0 +1,60 @@
|
|
|
1
|
+
{
|
|
2
|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "visium_input",
|
|
4
|
+
"title": "Visium Input Files and Data",
|
|
5
|
+
"type": "object",
|
|
6
|
+
"description": "Visium assay input files and data",
|
|
7
|
+
"inheritableBase": true,
|
|
8
|
+
"properties": {
|
|
9
|
+
"lane": {
|
|
10
|
+
"description": "Lane used for this run from 1-9",
|
|
11
|
+
"type": "integer",
|
|
12
|
+
"exclusiveMinimum": 0,
|
|
13
|
+
"maximum": 9
|
|
14
|
+
},
|
|
15
|
+
"read_1_fastq_gz": {
|
|
16
|
+
"$ref": "artifacts/artifact_gz.json"
|
|
17
|
+
},
|
|
18
|
+
"read_2_fastq_gz": {
|
|
19
|
+
"$ref": "artifacts/artifact_gz.json"
|
|
20
|
+
},
|
|
21
|
+
"loupe_alignment_file": {
|
|
22
|
+
"$ref": "artifacts/artifact_json.json"
|
|
23
|
+
},
|
|
24
|
+
"slide_serial_code": {
|
|
25
|
+
"type": "string",
|
|
26
|
+
"description": "Visium slide serial number"
|
|
27
|
+
},
|
|
28
|
+
"slide_capture_area": {
|
|
29
|
+
"type": "string",
|
|
30
|
+
"description": "Visium capture area identifier"
|
|
31
|
+
},
|
|
32
|
+
"library_yield_ng": {
|
|
33
|
+
"description": "Resulting yield (in ng) from library construction.",
|
|
34
|
+
"type": "number"
|
|
35
|
+
},
|
|
36
|
+
"dv200": {
|
|
37
|
+
"description": "The percentage of fragments > 200 nucleotides. (0-1)",
|
|
38
|
+
"type": "number",
|
|
39
|
+
"minimum": 0,
|
|
40
|
+
"maximum": 1
|
|
41
|
+
},
|
|
42
|
+
"brightfield_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
43
|
+
"dark_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
44
|
+
"colorized_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
45
|
+
"cytassist_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
46
|
+
"dapi_index": {
|
|
47
|
+
"type": "integer",
|
|
48
|
+
"description": "Index of DAPI channel (1-indexed) of fluorescence image."
|
|
49
|
+
},
|
|
50
|
+
"comments": {
|
|
51
|
+
"type": "string",
|
|
52
|
+
"description": "Comments on visium run"
|
|
53
|
+
}
|
|
54
|
+
},
|
|
55
|
+
"required": [
|
|
56
|
+
"lane",
|
|
57
|
+
"read_1_fastq_gz",
|
|
58
|
+
"read_2_fastq_gz"
|
|
59
|
+
]
|
|
60
|
+
}
|
|
@@ -0,0 +1,27 @@
|
|
|
1
|
+
{
|
|
2
|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "visium_preamble",
|
|
4
|
+
"title": "Visium Preamble",
|
|
5
|
+
"description": "Preamble information in a visium assay",
|
|
6
|
+
"type": "object",
|
|
7
|
+
"inheritableBase": true,
|
|
8
|
+
"properties": {
|
|
9
|
+
"spatial_gene_expression_platform": {
|
|
10
|
+
"description": "Visium spatial gene expression platform",
|
|
11
|
+
"type": "string",
|
|
12
|
+
"enum": [
|
|
13
|
+
"Visium Spatial Gene Expression for FFPE",
|
|
14
|
+
"Visium CytAssist Spatial Gene Expression for FFPE",
|
|
15
|
+
"Visium HD Spatial Gene Expression for FFPE"
|
|
16
|
+
]
|
|
17
|
+
},
|
|
18
|
+
"human_transcriptome_probe_set_version": {
|
|
19
|
+
"description": "Visium human transcriptome probe set version",
|
|
20
|
+
"type": "string",
|
|
21
|
+
"enum": [
|
|
22
|
+
"Visium Human Transcriptome Probe Set v1.0",
|
|
23
|
+
"Visium Human Transcriptome Probe Set v2.0"
|
|
24
|
+
]
|
|
25
|
+
}
|
|
26
|
+
}
|
|
27
|
+
}
|