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README.md

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@@ -21,18 +21,10 @@ When poetry is installed run:
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# Workflow to update the model from:
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## [INCLUDE Schemasheets Google Sheets Project](https://docs.google.com/spreadsheets/d/1w6zDfz3_yrCjjrqfpXBGNmd0LZL4B03gr1KfzJtk5Cs/edit?usp=sharing)
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1. Pull latest changes from GSheets project and update the .tsv files located at src/data/sheets
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1. Run the Schematic JSON-LD transformer to generate the JSON-LD that Schematic will use to generate Manifests
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`cogs pull`
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2. Run the sheets2linkml command to push changes to the yaml model file located at src/linkml/include_linkml.yaml
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`sheets2linkml -o src/linkml/include_linkml.yaml src/data/sheets/*.tsv`
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3. Run the Schematic JSON-LD transformer to generate the JSON-LD that Schematic will use to generate Manifests
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`poetry run python src/schematic/json_transformer.py`
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`poetry run python src/schematic/schematic_json_transformer.py`
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4. Run Schematic configured to point at the generated json-ld at src/schematic/include_schematic_linkml.jsonld
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`schematic manifest --config /Users/putmanti/CODE/schematic/schematic/config.yml get -s`
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`schematic manifest --config */schematic/config.yml get -s`

project/excel/include_schema.xlsx

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project/jsonld/include_schema.context.jsonld

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{
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"_comments": "Auto generated from include_schema.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-11-08T08:52:32\n Schema: include-schema\n metamodel version: 1.7.0\n model version: None\n \n id: https://w3id.org/include\n description: \n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
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"_comments": "Auto generated from include_schema.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-11-09T12:04:48\n Schema: include-schema\n metamodel version: 1.7.0\n model version: None\n \n id: https://w3id.org/include\n description: \n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
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"@context": {
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"include": "https://w3id.org/include/",
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"linkml": "https://w3id.org/linkml/",

project/jsonld/include_schema.jsonld

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"source_file": "include_schema.yaml",
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"source_file_date": "2022-11-08T07:44:49",
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"source_file_size": 433,
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"generation_date": "2022-11-08T08:52:33",
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"generation_date": "2022-11-09T12:04:49",
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"@type": "SchemaDefinition",
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"@context": [
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"project/jsonld/include_schema.context.jsonld",

project/owl/include_schema.owl.ttl

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project/shacl/include_schema.shacl.ttl

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src/data/json_compare.py

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src/data/old_json_transform/old.Assay.manifest.csv

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src/data/old_json_transform/old.Assay.schema.json

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src/data/old_json_transform/old.Biospecimen.manifest.csv

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