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removing data_file props from file nodes
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cgmeyer committed Jun 14, 2024
1 parent ca3c474 commit 7039b0f
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Showing 7 changed files with 42 additions and 8 deletions.
6 changes: 6 additions & 0 deletions gdcdictionary/schemas/aligned_reads_file.yaml
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Expand Up @@ -104,6 +104,12 @@ properties:
# - Amplicon
# - Other

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

read_groups:
$ref: "_definitions.yaml#/to_many"
core_metadata_collections:
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14 changes: 6 additions & 8 deletions gdcdictionary/schemas/aligned_reads_index_file.yaml
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Expand Up @@ -50,25 +50,23 @@ properties:
term:
$ref: "_terms.yaml#/data_category"
type: string
# enum:
# - Sequencing Data
# - Sequencing Reads
# - Raw Sequencing Data

data_type:
term:
$ref: "_terms.yaml#/data_type"
type: string
# enum: [ "Aligned Reads Index" ]

data_format:
term:
$ref: "_terms.yaml#/data_format"
type: string
# enum:
# - BAI
# - CRAI

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

aligned_reads_files:
$ref: "_definitions.yaml#/to_one"
core_metadata_collections:
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6 changes: 6 additions & 0 deletions gdcdictionary/schemas/annotation.yaml
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Expand Up @@ -122,6 +122,12 @@ properties:
maximum: 24
minimum: 0

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

sift_image_quality_index:
description: A score of image quality based on the SIFT annotation software.
enum:
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6 changes: 6 additions & 0 deletions gdcdictionary/schemas/clinical_file.yaml
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Expand Up @@ -77,6 +77,12 @@ properties:
description: "The text term describing the file format of the supplementary file, for example, PDF, XLSX, JPEG, PNG, TSV, etc."
type: string

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

core_metadata_collections:
description: The submitter_id or id of the core_metadata_collection to which the supplementary file belongs, i.e., a link to a record in the parent node.
$ref: "_definitions.yaml#/to_many"
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6 changes: 6 additions & 0 deletions gdcdictionary/schemas/image_file.yaml
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Expand Up @@ -92,6 +92,12 @@ properties:
- "Poor image quality"
- "Not Reported"

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

series_instance_uid:
description: >
Formal identifier for this image or other content.
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6 changes: 6 additions & 0 deletions gdcdictionary/schemas/unaligned_reads_file.yaml
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Expand Up @@ -69,6 +69,12 @@ properties:
$ref: "_terms.yaml#/experimental_strategy"
type: string

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

read_groups:
$ref: "_definitions.yaml#/to_many"
core_metadata_collections:
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6 changes: 6 additions & 0 deletions gdcdictionary/schemas/variant_call_file.yaml
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Expand Up @@ -76,6 +76,12 @@ properties:
$ref: "_terms.yaml#/experimental_strategy"
type: string

object_ids:
description: The list of file identifiers (object_ids, DRS URIs, or data GUIDs, etc.) for the file(s), if applicable.
type: array
items:
type: string

variant_calling_workflow_type: # from BDC germline_mutation_calling_workflow node
description: The workflow used to call germline mutations from sequencing reads, e.g., HaplotypeCaller.
type: string
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