schematic_cli_examples.ipynb

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   "source": [
    "## Schematic CLI examples"
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   "source": [
    "To read full documentation, please visit here: https://sage-schematic.readthedocs.io/en/develop/cli_reference.html\n",
    "\n",
    "To run the CLI commands in jupyter notebook, please add a code cell and add \"%%bash\" on top. For example: \n",
    "\n",
    "```\n",
    "%%bash\n",
    "schematic init --config ~/path/to/config.yml --auth service_account\n",
    "```"
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    "### Initalize schematic \n",
    "To get service account credentials:  \n",
    "* `schematic init --config ~/path/to/config.yml`"
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    "### Convert schema \n",
    "\n",
    "Convert schema from CSV version to JSON LD version \n",
    "\n",
    "* `schematic schema convert tests/data/example.model.csv`\n",
    "\n",
    "*Note*: by default, this save the JSON LD model to `'tests/data/example.model.jsonld'`\n",
    "\n",
    "You could also change the output location and output filename by doing: \n",
    "\n",
    "* `schematic schema convert tests/data/example.model.csv --output_json example.jsonld`\n"
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   "source": [
    "### Get manifests"
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    "Get an empty manifest as a CSV by using the example data model\n",
    "- `schematic manifest --config ~/path/to/config.yml get`\n",
    "\n",
    "Get an empty manifest as a google sheet by using the example data model\n",
    "- `schematic manifest --config ~/path/to/config.yml get --sheet_url`\n",
    "\n",
    "Get an existing manifest (syn28397250) and download it as a csv file (without customizing title)\n",
    "- `schematic manifest --config ~/path/to/config.yml get --dataset_id syn28268700 --data_type BulkRNA-seqAssay`\n",
    "\n",
    "*Note*: the dataset_id here has to be the parent folder syn id\n",
    "\n",
    "Get an existing manifest and download it as \"test.xlsx\"\n",
    "- `schematic manifest --config ~/path/to/config.yml get --output_xlsx 'test.xlsx' --dataset_id syn28268700`\n",
    "\n",
    "Get an existing manifest and download it as \"test.csv\"\n",
    "- `schematic manifest --config ~/path/to/config.yml get --output_csv 'test.csv' --dataset_id syn28268700`\n",
    "\n"
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   "source": [
    "## Validate manifest"
   ]
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    "Validate a manifest\n",
    "* For first time users, navigate to the root of schematic repo and run `great_expectation init`\n",
    "\n",
    "* `schematic model --config ~/path/to/config.yml validate --manifest_path tests/data/mock_manifests/Valid_Test_Manifest.csv --data_type MockComponent`"
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   "source": [
    "## Submit manifest"
   ]
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    "Submit a manifest as a table \n",
    "\n",
    "* `schematic model -c ~/path/to/config.yml submit -mp /path/to/Patient-Metadata-Manifest.csv -d syn23643250 -vc Patient -mrt table`\n"
   ]
  }
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