csv_export

Export to CSV format operation

Synopsis

csv_export

Arguments:

ds: dataset name

filter: optional name of applying filter

conditions: optional list of applying condition descriptors

in JSON string representation

zone: optional :

[ list of zone settings
[
[0]: zone name, string
[1]: [ variants ], list of strings
[2]: false, add it if negation of condition is required
], ...
] in JSON string representation

schema: name of data schema

Returns:

Page in CSV format for download

Description

The request creates presentation of selected variants in CSV format.

This method is not a proper REST API call: it does not return a JSON object but file in CSV format.

Selection is defined by:

  • filter applies if either filter or conditions is set (see discussion here)

  • zone applies if zone is set - actual for workspaces only (see ws_list for details).

In current version of the system schemes are defined in source code of the server as solution items, so the list of it is fixed. The schema csv is supported for simple variant of export.

Export operations, this and export evaluate properly only a limited lists of records. The upper limit of coumt is visible in dataset descriptor as export-max-count property. In current settings this limit affects only for XL-datasets, since it equal to maximal size of WS-dataset. The User Interface needs to control this limit (or more low one) and disallow attemts of the final user to perform export operation over too long list of variants.

Available schemes in current version:

demo

gene(s), variant, gnomAD_AF

csv
chromosome, variant:

(chromosome|start|ref|alt)

xbr

ClinVar HGMD Coordinate Change MSQ Protein Change Polyphen2_HVAR Polyphen2_HDIV SIFT MUT TASTER FATHMM gnomAD_Overall_AF gnomAD_Overall_AF_Popmax gnomAD_Genomes_AF gnomAD_Exomes_AF gnomAD_Overall_Hom gnomAD_Overall_Hem QD FT ColorCode GTEx IGV gnomAD Samples GeneColored

Warning

List of schemes: move it to user documentation

See also

export