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wrote a source_config doc and working on a source_file_config doc
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kevinschaper committed Aug 17, 2021
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40 changes: 40 additions & 0 deletions docs/source.md
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### Source (aka metadata.yaml)

The Source File provides metadata for the description of the dataset and the list of Source Files to be ingested

#### Example
name: 'xenbase'

dataset_description:
ingest_title: 'Xenbase'
ingest_url: 'https://xenbase.org'
description: 'Xenbase: The Xenopus Model Organism Knowledgebase'
rights: 'https://www.xenbase.org/other/static-xenbase/citingMOD.jsp'

source_files:
- 'gene-information.yaml'
- 'gene-to-phenotype.yaml'
- 'gene-literature.yaml'

#### Properties

<dl>
<dt>name</dt>
<dd>The name of this ingest</dd>

<dt>dataset_description.ingest_title</dt>
<dd>The title of the ingest</dd>

<dt>dataset_description.ingest_url</dt>
<dd>Homepage of ingest organization</dd>

<dt>dataset_description.description</dt>
<dd>Description of organization</dd>

<dt>dataset_description.rights</dt>
<dd>URL for a page describing data usage policies</dd>

<dt>source_files</dt>
<dd>List of [Source Files](http://example.com#link-to-source-file-doc)</dd>

</dl>
33 changes: 33 additions & 0 deletions docs/source_file.md
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### Source File

This YAML file sets properties for the ingest of a single file type from a within a [Source](http://example.com?link-to-source).

#### Example

name: 'gene-to-phenotype'

format: 'json'

files:
- './data/PHENOTYPE_RGD.json.gz' # "https://fms.alliancegenome.org/download/PHENOTYPE_RGD.json.gz"
- './data/PHENOTYPE_MGI.json.gz' # "https://fms.alliancegenome.org/download/PHENOTYPE_MGI.json.gz"
- './data/PHENOTYPE_WB.json.gz' # "https://fms.alliancegenome.org/download/PHENOTYPE_WB.json.gz"
- './data/PHENOTYPE_HUMAN.json.gz' # "https://fms.alliancegenome.org/download/PHENOTYPE_HUMAN.json.gz"

json_path:
- 'data'

depends_on:
- './mingestibles/maps/alliance-gene.yaml'

node_properties:
- 'id'
- 'category'
- 'provided_by'

edge_properties:
- 'id'
- 'subject'
- 'predicate'
- ...

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