nci-cidc-schemas 0.28.3__py2.py3-none-any.whl → 0.28.13__py2.py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cidc_schemas/__init__.py +1 -1
- cidc_schemas/ngs_pipeline_api/__init__.py +0 -1
- cidc_schemas/ngs_pipeline_api/wes/wes_output_API.py +1 -1
- cidc_schemas/prism/constants.py +7 -8
- cidc_schemas/prism/pipelines.py +2 -24
- cidc_schemas/schemas/artifacts/artifact_ibd.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_imzml.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_parquet.json +51 -0
- cidc_schemas/schemas/assays/atacseq_assay.json +4 -0
- cidc_schemas/schemas/assays/components/available_assays.json +34 -1
- cidc_schemas/schemas/assays/components/maldi_glycan_input.json +28 -0
- cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json +4 -0
- cidc_schemas/schemas/assays/components/ngs/rna/rna_analysis.json +10 -1
- cidc_schemas/schemas/assays/components/ngs_assay_core.json +2 -1
- cidc_schemas/schemas/assays/ctdna_assay.json +4 -0
- cidc_schemas/schemas/assays/cytof_assay.json +4 -0
- cidc_schemas/schemas/assays/cytof_assay_core.json +4 -0
- cidc_schemas/schemas/assays/elisa_assay.json +8 -4
- cidc_schemas/schemas/assays/hande_assay.json +18 -1
- cidc_schemas/schemas/assays/ihc_assay.json +9 -1
- cidc_schemas/schemas/assays/maldi_glycan_assay.json +72 -0
- cidc_schemas/schemas/assays/mibi_assay.json +4 -0
- cidc_schemas/schemas/assays/microbiome_assay.json +5 -1
- cidc_schemas/schemas/assays/mif_assay.json +10 -3
- cidc_schemas/schemas/assays/mihc_assay.json +4 -1
- cidc_schemas/schemas/assays/misc_data.json +9 -1
- cidc_schemas/schemas/assays/nanostring_assay.json +5 -1
- cidc_schemas/schemas/assays/nulisa_assay.json +4 -0
- cidc_schemas/schemas/assays/olink_assay.json +4 -0
- cidc_schemas/schemas/assays/olink_ht_assay.json +100 -0
- cidc_schemas/schemas/assays/rna_assay-v0.json +9 -0
- cidc_schemas/schemas/assays/scrnaseq_analysis.json +4 -0
- cidc_schemas/schemas/assays/scrnaseq_assay.json +4 -0
- cidc_schemas/schemas/assays/tcr_analysis.json +4 -0
- cidc_schemas/schemas/assays/tcr_assay.json +4 -0
- cidc_schemas/schemas/assays/tcrseq_rna_assay.json +64 -0
- cidc_schemas/schemas/assays/visium_analysis.json +4 -0
- cidc_schemas/schemas/assays/visium_assay.json +4 -0
- cidc_schemas/schemas/assays/wes_analysis.json +9 -1
- cidc_schemas/schemas/assays/wes_assay.json +25 -3
- cidc_schemas/schemas/assays/wes_tumor_only_analysis.json +9 -1
- cidc_schemas/schemas/clinical_data.json +8 -0
- cidc_schemas/schemas/shipping_core.json +3 -1
- cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json +6 -2
- cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json +16 -12
- cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json +9 -1
- cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json +32 -28
- cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json +9 -5
- cidc_schemas/schemas/templates/analyses/visium_analysis_template.json +11 -7
- cidc_schemas/schemas/templates/analyses/wes_analysis_template.json +9 -1
- cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json +9 -1
- cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json +6 -2
- cidc_schemas/schemas/templates/assays/clinical_data_template.json +8 -0
- cidc_schemas/schemas/templates/assays/ctdna_template.json +15 -11
- cidc_schemas/schemas/templates/assays/cytof_template.json +9 -4
- cidc_schemas/schemas/templates/assays/elisa_template.json +8 -4
- cidc_schemas/schemas/templates/assays/hande_template.json +10 -2
- cidc_schemas/schemas/templates/assays/ihc_template.json +8 -0
- cidc_schemas/schemas/templates/assays/maldi_glycan_template.json +143 -0
- cidc_schemas/schemas/templates/assays/mibi_template.json +8 -4
- cidc_schemas/schemas/templates/assays/microbiome_template.json +12 -8
- cidc_schemas/schemas/templates/assays/mif_template.json +8 -0
- cidc_schemas/schemas/templates/assays/mihc_template.json +6 -2
- cidc_schemas/schemas/templates/assays/misc_data_template.json +8 -0
- cidc_schemas/schemas/templates/assays/nanostring_template.json +10 -6
- cidc_schemas/schemas/templates/assays/nulisa_template.json +8 -4
- cidc_schemas/schemas/templates/assays/olink_ht_template.json +86 -0
- cidc_schemas/schemas/templates/assays/olink_template.json +8 -4
- cidc_schemas/schemas/templates/assays/rna_bam_template.json +9 -1
- cidc_schemas/schemas/templates/assays/rna_fastq_template.json +9 -1
- cidc_schemas/schemas/templates/assays/scrnaseq_template.json +8 -4
- cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json +9 -5
- cidc_schemas/schemas/templates/assays/tcr_fastq_template.json +10 -6
- cidc_schemas/schemas/templates/assays/tcrseq_rna_template.json +59 -0
- cidc_schemas/schemas/templates/assays/visium_template.json +13 -9
- cidc_schemas/schemas/templates/assays/wes_bam_template.json +8 -0
- cidc_schemas/schemas/templates/assays/wes_fastq_template.json +8 -0
- cidc_schemas/template.py +0 -4
- cidc_schemas/unprism.py +3 -3
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.13.dist-info}/METADATA +21 -15
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.13.dist-info}/RECORD +85 -76
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.13.dist-info}/WHEEL +1 -1
- cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json +0 -63
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.13.dist-info}/entry_points.txt +0 -0
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.13.dist-info}/licenses/LICENSE +0 -0
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.13.dist-info}/top_level.txt +0 -0
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@@ -16,6 +16,14 @@
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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"CIMAC Batch ID": {
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"merge_pointer": "0/batch_id",
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"type_ref": "assays/ihc_assay.json#properties/batch_id"
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},
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"CIDC Submission ID": {
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"merge_pointer": "0/optional_id",
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"type_ref": "assays/ihc_assay.json#properties/optional_id"
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},
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"slide scanner model": {
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"merge_pointer": "0/slide_scanner_model",
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"type_ref": "assays/ihc_assay.json#properties/slide_scanner_model"
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@@ -0,0 +1,143 @@
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{
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"title": "MALDI Glycan assay template",
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"description": "MALDI Glycan submission.",
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"prism_template_root_object_schema": "assays/maldi_glycan_assay.json",
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"prism_template_root_object_pointer": "/assays/maldi_glycan/0",
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"properties": {
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"worksheets": {
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"MALDI Glycan": {
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"prism_data_object_pointer": "/records/-",
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"preamble_rows": {
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"protocol identifier": {
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"merge_pointer": "3/protocol_identifier",
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"type_ref": "clinical_trial.json#properties/protocol_identifier"
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},
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"CIMAC Batch ID": {
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"merge_pointer": "0/batch_id",
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"type_ref": "assays/mibi_assay.json#properties/batch_id"
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},
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"CIDC Submission ID": {
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"merge_pointer": "0/optional_id",
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"type_ref": "assays/mibi_assay.json#properties/optional_id"
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},
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"assay creator": {
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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"molecular assignments file": {
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"merge_pointer": "0/molecular_assignments_file",
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{cimac batch id}/molecular_assignments.tsv",
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"is_artifact": 1,
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
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"metadata tsv": {
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"merge_pointer": "0/metadata_tsv",
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{cimac batch id}/metadata.tsv",
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"is_artifact": 1,
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"allow_empty": true
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}
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},
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"data_columns": {
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"Samples": {
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"cimac id": {
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"merge_pointer": "0/cimac_id",
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"type_ref": "sample.json#properties/cimac_id"
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},
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"ibd file": {
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"merge_pointer": "0/details/ibd_file",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{cimac batch id}/{cimac id}/ibd_file.ibd",
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
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"imzml file": {
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"merge_pointer": "0/details/imzml_file",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{cimac batch id}/{cimac id}/imzml_file.imzml",
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"type_ref": "assays/components/local_file.json#properties/file_path"
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"channels csv": {
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"merge_pointer": "0/details/channels_csv",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{cimac batch id}/{cimac id}/channels.csv",
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
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"tiff zip": {
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"merge_pointer": "0/details/tiff_zip",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{cimac batch id}/{cimac id}/tiff.zip",
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"type_ref": "assays/components/local_file.json#properties/file_path"
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}
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}
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}
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},
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"Antibodies": {
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"prism_data_object_pointer": "/antibodies/-",
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"data_columns":
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{
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"Antibodies":
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{
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"Channel id": {
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"merge_pointer": "0/channel_id",
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"type_ref": "assays/components/mibi_antibody.json#properties/channel_id"
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"Antibody name": {
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"merge_pointer": "0/antibody",
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"type_ref": "assays/components/antibody.json#properties/antibody"
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},
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"Clone": {
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"merge_pointer": "0/clone",
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"type_ref": "assays/components/antibody.json#properties/clone",
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"allow_empty": true
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"Company": {
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"merge_pointer": "0/company",
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"type_ref": "assays/components/antibody.json#properties/clone",
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"allow_empty": true
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"Scicrunch rrid": {
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"merge_pointer": "0/scicrunch_rrid",
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"type_ref": "assays/components/mibi_antibody.json#properties/scicrunch_rrid",
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"allow_empty": true
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"Uniprot accession number": {
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"merge_pointer": "0/uniprot_accession_number",
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"type_ref": "assays/components/mibi_antibody.json#properties/uniprot_accession_number",
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"allow_empty": true
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"Lot number": {
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"merge_pointer": "0/lot_num",
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"type_ref": "assays/components/antibody.json#properties/lot_num",
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"allow_empty": true
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"Dilution": {
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"merge_pointer": "0/dilution",
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"type_ref": "assays/components/mibi_antibody.json#properties/dilution",
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"allow_empty": true
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"Concentration value": {
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"type_ref": "assays/components/mibi_antibody.json#properties/concentration_value",
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"allow_empty": true
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"Concentration units": {
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"merge_pointer": "0/concentration_units",
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"type_ref": "assays/components/mibi_antibody.json#properties/concentration_units",
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"allow_empty": true
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"Conjugated catalog number": {
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"merge_pointer": "0/cat_num",
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"type_ref": "assays/components/antibody.json#properties/cat_num",
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"allow_empty": true
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"Conjugated tag": {
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"merge_pointer": "0/conjugated_tag",
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"type_ref": "assays/components/mibi_antibody.json#properties/conjugated_tag",
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"allow_empty": true
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}
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"CIDC Submission ID": {
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"assay creator": {
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"metadata tsv": {
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"gcs_uri_format": "{protocol identifier}/mibi/{cimac batch id}/metadata.tsv",
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"gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/he_file.{he file type}",
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"gcs_uri_format": "{protocol identifier}/mibi/{cimac batch id}/{cimac id}/{roi id}/he_file.{he file type}",
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"Roi description": {
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"gcs_uri_format": "{protocol identifier}/mibi/{cimac batch id}/{cimac id}/{roi id}/{mibi ome tiff file name}.ome.tiff"
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"CIDC Submission ID": {
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"CIMAC Batch ID": {
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"CIDC Submission ID": {
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"merge_pointer": "0/optional_id",
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"type_ref": "assays/misc_data.json#properties/optional_id"
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"data_columns": {
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@@ -15,20 +15,24 @@
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"CIDC Submission ID": {
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@@ -43,7 +47,7 @@
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@@ -56,7 +60,7 @@
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|
@@ -0,0 +1,86 @@
|
|
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1
|
+
{
|
|
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|
+
"title": "Olink HT assay template",
|
|
3
|
+
"description": "Olink HT submission.",
|
|
4
|
+
"prism_template_root_object_schema": "assays/olink_ht_assay.json",
|
|
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|
+
"prism_template_root_object_pointer": "/assays/olink_ht/0",
|
|
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|
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|
|
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|
+
"worksheets": {
|
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|
+
"Olink HT": {
|
|
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|
+
"prism_data_object_pointer": "/records/-",
|
|
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|
+
"preamble_rows": {
|
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|
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|
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|
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|
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|
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|
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|
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},
|
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"assay creator": {
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
|
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},
|
|
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|
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"CIMAC Batch ID": {
|
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|
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"merge_pointer": "0/batch_id",
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"type_ref": "assays/mibi_assay.json#properties/batch_id"
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+
},
|
|
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|
+
"CIDC Submission ID": {
|
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|
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"merge_pointer": "0/optional_id",
|
|
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"type_ref": "assays/mibi_assay.json#properties/optional_id"
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},
|
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"Panel": {
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},
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|
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"Assay panel lot": {
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|
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"type": "string"
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},
|
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"study-level combined file": {
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"merge_pointer": "0/study_level_combined_file",
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"gcs_uri_format": "{protocol identifier}/olink_ht/{cimac batch id}/study_level_combined_file.parquet",
|
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"is_artifact": 1,
|
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
|
|
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|
+
"Study-level combined npx manager version": {
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"merge_pointer": "0/study_level_combined_npx_manager_version",
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"type": "string"
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+
},
|
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"batch-level combined file": {
|
|
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"merge_pointer": "0/batch_level_combined_file",
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+
"gcs_uri_format": "{protocol identifier}/olink_ht/{cimac batch id}/batch_level_combined_file.parquet",
|
|
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"is_artifact": 1,
|
|
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|
+
"type_ref": "assays/components/local_file.json#properties/file_path"
|
|
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|
+
},
|
|
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|
+
"Batch-level combined npx manager version": {
|
|
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|
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"merge_pointer": "0/batch_level_combined_npx_manager_version",
|
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+
"type": "string"
|
|
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|
+
}
|
|
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|
+
},
|
|
56
|
+
"data_columns": {
|
|
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|
+
"Olink HT Details": {
|
|
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|
+
"cimac id": {
|
|
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|
+
"merge_pointer": "0/cimac_id",
|
|
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|
+
"type_ref": "sample.json#properties/cimac_id"
|
|
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|
+
},
|
|
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|
+
"npx run file": {
|
|
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|
+
"merge_pointer": "0/npx_run_file",
|
|
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|
+
"is_artifact": 1,
|
|
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|
+
"type_ref": "assays/components/local_file.json#properties/file_path",
|
|
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|
+
"gcs_uri_format": "{protocol identifier}/olink_ht/{cimac batch id}/{cimac id}/npx_run_file.parquet"
|
|
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+
},
|
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|
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"instrument": {
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|
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|
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"merge_pointer": "0/instrument",
|
|
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|
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"type": "string"
|
|
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|
+
},
|
|
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|
+
"npx manager version": {
|
|
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|
+
"merge_pointer": "0/npx_manager_version",
|
|
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|
+
"type": "string"
|
|
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|
+
},
|
|
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|
+
"comments": {
|
|
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|
+
"merge_pointer": "0/comments",
|
|
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|
+
"type": "string",
|
|
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|
+
"allow_empty": true
|
|
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|
+
}
|
|
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|
+
}
|
|
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|
+
}
|
|
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}
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@@ -16,10 +16,14 @@
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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-
"
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"CIMAC Batch ID": {
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"merge_pointer": "0/batch_id",
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"type_ref": "assays/olink_assay.json#definitions/batch/properties/batch_id"
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},
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"CIDC Submission ID": {
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"merge_pointer": "0/optional_id",
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"type_ref": "assays/olink_assay.json#definitions/batch/properties/optional_id"
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},
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"panel": {
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"merge_pointer": "0/panel",
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"type_ref": "assays/olink_assay.json#definitions/batch/properties/panel"
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@@ -46,7 +50,7 @@
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"description": "Relative path to a combined NPX file containing all samples for this upload only.",
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"merge_pointer": "0/combined/npx_file",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/olink/batch_{batch
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"gcs_uri_format": "{protocol identifier}/olink/batch_{cimac batch id}/combined_npx.xlsx",
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"extra_metadata": true,
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"allow_empty": true
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@@ -66,7 +70,7 @@
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"npx file": {
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"merge_pointer": "0/files/assay_npx",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/olink/batch_{batch
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"gcs_uri_format": "{protocol identifier}/olink/batch_{cimac batch id}/chip_{chip barcode}/assay_npx.xlsx",
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"extra_metadata": true,
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"description": "NPX file name on a user's computer."
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@@ -74,7 +78,7 @@
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"raw ct file": {
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"merge_pointer": "0/files/assay_raw_ct",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/olink/batch_{batch
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"gcs_uri_format": "{protocol identifier}/olink/batch_{cimac batch id}/chip_{chip barcode}/assay_raw_ct.csv",
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"description": "Raw CT file name on a user's computer."
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},
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@@ -17,6 +17,14 @@
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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"CIMAC Batch ID": {
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+
"merge_pointer": "0/batch_id",
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"type_ref": "assays/rna_assay-v0.json#properties/batch_id"
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},
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+
"CIDC Submission ID": {
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"merge_pointer": "0/optional_id",
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"type_ref": "assays/rna_assay-v0.json#properties/optional_id"
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},
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"enrichment method": {
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"merge_pointer": "0/enrichment_method",
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"type_ref": "assays/rna_assay-v0.json#properties/enrichment_method"
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@@ -75,4 +83,4 @@
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}
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}
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}
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-
}
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+
}
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@@ -17,6 +17,14 @@
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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20
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+
"CIMAC Batch ID": {
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+
"merge_pointer": "0/batch_id",
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+
"type_ref": "assays/rna_assay-v0.json#properties/batch_id"
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+
},
|
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+
"CIDC Submission ID": {
|
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25
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+
"merge_pointer": "0/optional_id",
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"type_ref": "assays/rna_assay-v0.json#properties/optional_id"
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+
},
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"enrichment method": {
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"merge_pointer": "0/enrichment_method",
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"type_ref": "assays/rna_assay-v0.json#properties/enrichment_method"
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@@ -79,4 +87,4 @@
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}
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}
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}
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}
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+
}
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@@ -20,10 +20,14 @@
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20
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|
"merge_pointer": "0/assay_creator",
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"type_ref": "assays/scrnaseq_assay.json#properties/assay_creator"
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},
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-
"
|
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+
"CIMAC Batch ID": {
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|
"merge_pointer": "0/batch_id",
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|
"type_ref": "assays/scrnaseq_assay.json#properties/batch_id"
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|
},
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+
"CIDC Submission ID": {
|
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+
"merge_pointer": "0/optional_id",
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|
+
"type_ref": "assays/scrnaseq_assay.json#properties/optional_id"
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|
+
},
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"azimuth reference": {
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|
"merge_pointer": "0/azimuth_reference",
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|
"type_ref": "assays/components/scrnaseq_preamble.json#properties/azimuth_reference",
|
|
@@ -48,7 +52,7 @@
|
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|
},
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|
"sample metadata csv": {
|
|
50
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|
"merge_pointer": "0/samples_metadata_csv",
|
|
51
|
-
"gcs_uri_format": "{protocol identifier}/scrnaseq/{batch id}/samples_metadata.csv",
|
|
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|
+
"gcs_uri_format": "{protocol identifier}/scrnaseq/{cimac batch id}/samples_metadata.csv",
|
|
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|
"is_artifact": 1,
|
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"type_ref": "assays/components/local_file.json#properties/file_path"
|
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|
}
|
|
@@ -70,13 +74,13 @@
|
|
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|
"Read 1": {
|
|
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"merge_pointer": "0/details/read_1_file",
|
|
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|
"is_artifact": 1,
|
|
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|
-
"gcs_uri_format": "{protocol identifier}/scrnaseq/{batch id}/{cimac id}/read_1.gz",
|
|
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|
+
"gcs_uri_format": "{protocol identifier}/scrnaseq/{cimac batch id}/{cimac id}/read_1.gz",
|
|
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|
"type_ref": "assays/components/local_file.json#properties/file_path"
|
|
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|
},
|
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|
"Read 2": {
|
|
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|
"merge_pointer": "0/details/read_2_file",
|
|
78
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|
"is_artifact": 1,
|
|
79
|
-
"gcs_uri_format": "{protocol identifier}/scrnaseq/{batch id}/{cimac id}/read_2.gz",
|
|
83
|
+
"gcs_uri_format": "{protocol identifier}/scrnaseq/{cimac batch id}/{cimac id}/read_2.gz",
|
|
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|
"type_ref": "assays/components/local_file.json#properties/file_path"
|
|
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|
},
|
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|
"library yield ng": {
|