# csv

Convert CSV files with custom column allocations

### Command line usage

```
/*^babelfsh
csv
   [--help] [--path PATH] [--url URL] [--delimiter DELIMITER]
   [--csv-quote CSV_QUOTE] [--csv-escape CSV_ESCAPE] [--skip-empty-lines]
   [--charset CHARSET] [--line-ending LINE_ENDING] [--headers HEADERS]
   [--concept-filter CONCEPT_FILTER] --code-column CODE_COLUMN
   --display-column DISPLAY_COLUMN [--definition-column DEFINITION_COLUMN]
   [--allow-missing-code-column] [--property-mapping PROPERTY_MAPPING]
   [--no-filter-duplicates]
   [--split-code-and-display-using SPLIT_CODE_AND_DISPLAY_USING]
^babelfsh*/
```

### Command line argument reference

|                                                         Argument name                                                        | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
| :--------------------------------------------------------------------------------------------------------------------------: | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
|      <p><code>--code-column CODE\_COLUMN</code></p><p><code>--cc CODE\_COLUMN</code></p><p><strong>Required</strong></p>     | Name of the column containing the codes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| <p><code>--display-column DISPLAY\_COLUMN</code></p><p><code>--dc DISPLAY\_COLUMN</code></p><p><strong>Required</strong></p> | Name of the column containing the display names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
|                                                 `--allow-missing-code-column`                                                | Allow missing code column in CSV file (these rows are filtered out, useful for mapping source files that mainly define a ConceptMap). This is opt-in, i.e. default=false                                                                                                                                                                                                                                                                                                                                                                                                                        |
|                              <p><code>--charset CHARSET</code></p><p><code>-c CHARSET</code></p>                             | The charset of the file, with the name from java.nio.charset.Charset: Big5, Big5-HKSCS, CESU-8, EUC-JP, EUC-KR, ... See <https://docs.oracle.com/javase/8/docs/technotes/guides/intl/encoding.doc.html>                                                                                                                                                                                                                                                                                                                                                                                         |
|                 <p><code>--concept-filter CONCEPT\_FILTER</code></p><p><code>--cf CONCEPT\_FILTER</code></p>                 | Filter concepts based on the values in the CSV file. Supported operators with supported case-insensitive keywords in parentheses: EQUALS ('=', '==', 'equals'), NOT\_EQUALS ('!=', '<>', 'not-equals', 'not\_equals'), NOT\_BLANK ('not-blank', 'not\_blank'), BLANK ('blank')                                                                                                                                                                                                                                                                                                                  |
|                                                   `--csv-escape CSV_ESCAPE`                                                  | Escape character used in the CSV file. Default is double quote (")                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
|                                                    `--csv-quote CSV_QUOTE`                                                   | Quote character used in the CSV file. Default is double quote (")                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
|                                            `--definition-column DEFINITION_COLUMN`                                           | Name of the column containing the definitions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                           <p><code>--delimiter DELIMITER</code></p><p><code>-d DELIMITER</code></p>                          | Delimiter used in the CSV file. Default is comma (,)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
|                             <p><code>--headers HEADERS</code></p><p><code>--hd HEADERS</code></p>                            | List of headers to use, provided as a JSON list. If not provided, headers will be read from the file. Example: \["header1", "header2"]                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
|                                       <p><code>--help</code></p><p><code>-h</code></p>                                       | show this help message and exit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
|                      <p><code>--line-ending LINE\_ENDING</code></p><p><code>--le LINE\_ENDING</code></p>                     | Line ending used in the CSV file, default                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
|                       <p><code>--no-filter-duplicates</code></p><p><code>--filter-duplicates</code></p>                      | Filter duplicate concepts based on code and display name. If collisions occur, this will result in an error. Default false (all duplicates are treated as errors).                                                                                                                                                                                                                                                                                                                                                                                                                              |
|     <p><code>--path PATH</code></p><p><code>--file PATH</code></p><p><code>-p PATH</code></p><p><code>-f PATH</code></p>     | Path to the CSV file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
|              <p><code>--property-mapping PROPERTY\_MAPPING</code></p><p><code>--pm PROPERTY\_MAPPING</code></p>              | Mapping of additional properties to columns in the CSV file. The property mapping is a JSON array of objects, where each object has the following properties: \<column>: the name of the column in the CSV file; \<code>: the code of the property in the FHIR CodeSystem; \<required>: whether the property is required (true or false, default false); \<mapper>: a mapper specification (see below)Example: {"column": "my\_column", "required": true, "property": "my\_property", "mapper": {"id": "boolean", "arguments": {"1": "true", "0": "false"}}}Supported property mappers: boolean |
|                                 <p><code>--skip-empty-lines</code></p><p><code>-s</code></p>                                 | Skip empty lines in the CSV file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
|                                 `--split-code-and-display-using SPLIT_CODE_AND_DISPLAY_USING`                                | If specified, split code and display columns using this separator. Default is not to split.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
|                                    <p><code>--url URL</code></p><p><code>-u URL</code></p>                                   | URL to the CSV file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |


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