Source Config

This YAML file sets properties for the ingest of a single file type from a within a Source.

Paths are relative to the directory from which you execute Koza.

Source Configuration Properties

Required properties
`name`	Name of the data ingest, as `<data source>_<type_of_ingest>`, ex. `hpoa_gene_to_disease`
`files`	List of files to process

`node_properties`	List of node properties to include in output
`edge_properties`	List of edge properties to include in output
Note	Either node or edge properties (or both) must be defined in the primary config yaml for your transform

Optional properties
`file_archive`	Path to a file archive containing the file(s) to process Supported archive formats: zip, gzip
`format`	Format of the data file(s) (CSV or JSON)
`sssom_config`	Configures usage of SSSOM mapping files
`depends_on`	List of map config files to use
`metadata`	Metadata for the source, either a list of properties, or path to a `metadata.yaml`
`transform_code`	Path to a python file to transform the data
`transform_mode`	How to process the transform file
`global_table`	Path to a global translation table file
`local_table`	Path to a local translation table file
`field_type_map`	Dict of field names and their type (using the FieldType enum)
`filters`	List of filters to apply
`json_path`	Path within JSON object containing data to process
`required_properties`	List of properties that must be present in output (JSON only)

CSV-Specific Properties
`delimiter`	Delimiter for csv files (Required for CSV format)
Optional CSV Properties
`columns`	List of columns to include in output (CSV only)
`header`	Header row index for csv files
`header_delimiter`	Delimiter for header in csv files
`header_prefix`	Prefix for header in csv files
`comment_char`	Comment character for csv files
`skip_blank_lines`	Skip blank lines in csv files

Metadata Properties

Metadata is optional, and can be defined as a list of properties and values, or as a path to a metadata.yaml file, for example - metadata: "./path/to/metadata.yaml".
Remember that the path is relative to the directory from which you execute Koza.

Metadata Properties
name	Name of data source, ex. "FlyBase"
description	Description of data/ingest
ingest_title	*Title of source of data, map to biolink name
ingest_url	*URL to source of data, Maps to biolink iri
provided_by	`<data source>_<type_of_ingest>`, ex. `hpoa_gene_to_disease` (see config propery "name")
rights	Link to license information for the data source

*Note: For more information on ingest_title and ingest_url, see the infores catalog

Composing Configuration from Multiple Yaml Files

Koza's custom YAML Loader supports importing/including other yaml files with an !include tag.

For example, if you had a file named standard-columns.yaml:

- "column_1"
- "column_2"
- "column_3"
- "column_4": "int"

Then in any ingests you wish to use these columns, you can simply !include them:

columns: !include "./path/to/standard-columns.yaml"

Next Steps: Mapping and Additional Data