3.0.0 • Published 5 years ago

@datafire/warwick_ac_uk_enterobase v3.0.0

Weekly downloads
1
License
MIT
Repository
github
Last release
5 years ago

@datafire/warwick_ac_uk_enterobase

Client library for Enterobase-API

Installation and Usage

npm install --save @datafire/warwick_ac_uk_enterobase
let warwick_ac_uk_enterobase = require('@datafire/warwick_ac_uk_enterobase').create({
  username: "",
  password: ""
});

.then(data => {
  console.log(data);
});

Description

API for EnteroBase (http://enterobase.warwick.ac.uk)

EnteroBase is a user-friendly online resource, where users can upload their own sequencing data for de novo assembly by a stream-lined pipeline. The assemblies are used for calling MLST and wgMLST patterns, allowing users to compare their strains to publically available genotyping data from other EnteroBase users, GenBank and classical MLST databases.

Click here to find how to get and use an API token: http://bit.ly/1TKlaOU

Actions

api.v2.0.get

Top level information about EnteroBase databases

warwick_ac_uk_enterobase.api.v2.0.get({}, context)

Input

  • input object
    • prefix string: Database prefix, e.g. SAL for Salmonella
    • name string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively
    • description string: Database description

Output

Output schema unknown

api.v2.0.login.get

Login endpoint, refresh your API token

warwick_ac_uk_enterobase.api.v2.0.login.get({}, context)

Input

  • input object
    • username string: EnteroBase username
    • password string: EnteroBase Password

Output

Output schema unknown

api.v2.0.lookup.get

Generic endpoint for lookup list of barcodes

warwick_ac_uk_enterobase.api.v2.0.lookup.get({}, context)

Input

  • input object
    • barcode string: Unique barcode for Traces records, e.g. SAL_AA0001AA_ST

Output

Output schema unknown

api.v2.0.lookup.barcode.get

Generic endpoint for lookup of barcodes

warwick_ac_uk_enterobase.api.v2.0.lookup.barcode.get({
  "barcode": ""
}, context)

Input

  • input object
    • barcode required string: Unique barcode for Traces records, e.g. SAL_AA0001AA_ST

Output

Output schema unknown

api.v2.0.lookup.barcode.post

Generic endpoint for lookup of barcodes

warwick_ac_uk_enterobase.api.v2.0.lookup.barcode.post({
  "barcode": ""
}, context)

Input

  • input object
    • body object
      • barcode string
    • barcode required string: Unique barcode for Traces records, e.g. SAL_AA0001AA_ST

Output

Output schema unknown

api.v2.0.database.assemblies.get

Genome assemblies

warwick_ac_uk_enterobase.api.v2.0.database.assemblies.get({
  "database": ""
}, context)

Input

  • input object
    • orderby string: Field to order by. Default: barcode
    • only_fields array
    • barcode array: Unique barcode for Traces records, __AS e.g. SAL_AA0001AA_AS
    • n50 integer
    • top_species string
    • uberstrain string
    • version integer
    • limit integer: Number of results per page
    • reldate integer
    • offset integer: Cursor position in results
    • assembly_status string
    • sortorder string: Order of search results: asc or desc
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.assemblies.barcode.get

Genome assemblies

warwick_ac_uk_enterobase.api.v2.0.database.assemblies.barcode.get({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • assembly_status string
      • barcode array
        • items string
      • limit integer
      • n50 integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • reldate integer
      • sortorder string
      • top_species string
      • uberstrain string
      • version integer
    • barcode required string: Unique barcode for Traces records, __AS e.g. SAL_AA0001AA_AS
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.assemblies.barcode.post

Genome assemblies

warwick_ac_uk_enterobase.api.v2.0.database.assemblies.barcode.post({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • assembly_status string
      • barcode array
        • items string
      • limit integer
      • n50 integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • reldate integer
      • sortorder string
      • top_species string
      • uberstrain string
      • version integer
    • barcode required string: Unique barcode for Traces records, __AS e.g. SAL_AA0001AA_AS
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.assemblies.barcode.put

Genome assemblies

warwick_ac_uk_enterobase.api.v2.0.database.assemblies.barcode.put({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • assembly_status string
      • barcode array
        • items string
      • limit integer
      • n50 integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • reldate integer
      • sortorder string
      • top_species string
      • uberstrain string
      • version integer
    • barcode required string: Unique barcode for Traces records, __AS e.g. SAL_AA0001AA_AS
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.schemes.get

Genotyping schemes

warwick_ac_uk_enterobase.api.v2.0.database.schemes.get({
  "database": ""
}, context)

Input

  • input object
    • orderby string: Field to order by. Default: barcode
    • scheme_name string
    • created string
    • lastmodified string
    • barcode array: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • label string
    • only_fields array
    • version integer
    • limit integer: Number of results per page
    • sortorder string: Order of search results: asc or desc
    • offset integer: Cursor position in results
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.schemes.barcode.get

Genotyping schemes

warwick_ac_uk_enterobase.api.v2.0.database.schemes.barcode.get({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • barcode array
        • items string
      • created string
      • label string
      • lastmodified string
      • limit integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • scheme_name string
      • sortorder string
      • version integer
    • barcode required string: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.schemes.barcode.post

Genotyping schemes

warwick_ac_uk_enterobase.api.v2.0.database.schemes.barcode.post({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • barcode array
        • items string
      • created string
      • label string
      • lastmodified string
      • limit integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • scheme_name string
      • sortorder string
      • version integer
    • barcode required string: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.schemes.barcode.put

Genotyping schemes

warwick_ac_uk_enterobase.api.v2.0.database.schemes.barcode.put({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • barcode array
        • items string
      • created string
      • label string
      • lastmodified string
      • limit integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • scheme_name string
      • sortorder string
      • version integer
    • barcode required string: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.straindata.get

Strain data

warwick_ac_uk_enterobase.api.v2.0.database.straindata.get({
  "database": ""
}, context)

Input

  • input object
    • comment string
    • secondary_sample_accession string
    • my_strains boolean
    • offset integer: Cursor position in results
    • serotype string
    • n50 integer
    • county string
    • only_fields array
    • postcode string
    • lab_contact string
    • substrains boolean
    • custom_fields string
    • city string
    • strain_name string
    • collection_date integer
    • collection_month integer
    • reldate integer
    • continent string
    • source_details string
    • version integer
    • latitude number
    • email string
    • source_niche string
    • barcode array: Unique barcode for Traces records, __AS e.g. SAL_AA0001AA_AS
    • uberstrain string
    • sortorder string: Order of search results: asc or desc
    • collection_year integer
    • orderby string: Field to order by. Default: strain barcode
    • assembly_status string
    • source_type string
    • country string
    • region string
    • longitude number
    • sample_accession string
    • limit integer: Number of results per page
    • top_species string
    • collection_time string
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.strains.get

Strain metadata

warwick_ac_uk_enterobase.api.v2.0.database.strains.get({
  "database": ""
}, context)

Input

  • input object
    • comment string
    • secondary_sample_accession string
    • antigenic_formulas string
    • my_strains boolean
    • serotype string
    • county string
    • only_fields array
    • postcode string
    • lab_contact string
    • substrains boolean
    • city string
    • strain_name string
    • collection_date integer
    • collection_month integer
    • reldate integer
    • continent string
    • source_details string
    • version integer
    • latitude number
    • assembly_barcode string
    • source_niche string
    • barcode array: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • uberstrain string
    • sortorder string: Order of search results: asc or desc
    • offset integer: Cursor position in results
    • collection_year integer
    • orderby string: Field to order by. Default: barcode
    • return_all boolean
    • source_type string
    • country string
    • region string
    • longitude number
    • sample_accession string
    • limit integer: Number of results per page
    • collection_time string
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.strains.barcode.get

Strain metadata

warwick_ac_uk_enterobase.api.v2.0.database.strains.barcode.get({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • antigenic_formulas string
      • assembly_barcode string
      • barcode array
        • items string
      • city string
      • collection_date integer
      • collection_month integer
      • collection_time string
      • collection_year integer
      • comment string
      • continent string
      • country string
      • county string
      • lab_contact string
      • latitude number
      • limit integer
      • longitude number
      • my_strains boolean
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • postcode string
      • region string
      • reldate integer
      • return_all boolean
      • sample_accession string
      • secondary_sample_accession string
      • serotype string
      • sortorder string
      • source_details string
      • source_niche string
      • source_type string
      • strain_name string
      • substrains boolean
      • uberstrain string
      • version integer
    • barcode required string: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.strains.barcode.post

Strain metadata

warwick_ac_uk_enterobase.api.v2.0.database.strains.barcode.post({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • antigenic_formulas string
      • assembly_barcode string
      • barcode array
        • items string
      • city string
      • collection_date integer
      • collection_month integer
      • collection_time string
      • collection_year integer
      • comment string
      • continent string
      • country string
      • county string
      • lab_contact string
      • latitude number
      • limit integer
      • longitude number
      • my_strains boolean
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • postcode string
      • region string
      • reldate integer
      • return_all boolean
      • sample_accession string
      • secondary_sample_accession string
      • serotype string
      • sortorder string
      • source_details string
      • source_niche string
      • source_type string
      • strain_name string
      • substrains boolean
      • uberstrain string
      • version integer
    • barcode required string: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.strains.barcode.put

Strain metadata

warwick_ac_uk_enterobase.api.v2.0.database.strains.barcode.put({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • antigenic_formulas string
      • assembly_barcode string
      • barcode array
        • items string
      • city string
      • collection_date integer
      • collection_month integer
      • collection_time string
      • collection_year integer
      • comment string
      • continent string
      • country string
      • county string
      • lab_contact string
      • latitude number
      • limit integer
      • longitude number
      • my_strains boolean
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • postcode string
      • region string
      • reldate integer
      • return_all boolean
      • sample_accession string
      • secondary_sample_accession string
      • serotype string
      • sortorder string
      • source_details string
      • source_niche string
      • source_type string
      • strain_name string
      • substrains boolean
      • uberstrain string
      • version integer
    • barcode required string: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.strainsversion.get

Strain previous metadata

warwick_ac_uk_enterobase.api.v2.0.database.strainsversion.get({
  "database": ""
}, context)

Input

  • input object
    • comment string
    • secondary_sample_accession string
    • antigenic_formulas string
    • my_strains boolean
    • serotype string
    • county string
    • only_fields array
    • postcode string
    • lab_contact string
    • substrains boolean
    • city string
    • strain_name string
    • collection_date integer
    • collection_month integer
    • reldate integer
    • continent string
    • source_details string
    • version integer
    • latitude number
    • assembly_barcode string
    • source_niche string
    • barcode array: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • uberstrain string
    • sortorder string: Order of search results: asc or desc
    • offset integer: Cursor position in results
    • collection_year integer
    • orderby string: Field to order by. Default: barcode
    • return_all boolean
    • source_type string
    • country string
    • region string
    • longitude number
    • sample_accession string
    • limit integer: Number of results per page
    • collection_time string
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.traces.get

Traces (sequence-reads) metadata

warwick_ac_uk_enterobase.api.v2.0.database.traces.get({
  "database": ""
}, context)

Input

  • input object
    • orderby string: Field to order by. Default: barcode
    • barcode array: Unique barcode for Traces records, __TR e.g. SAL_AA0001AA_TR
    • only_fields array
    • limit integer: Number of results per page
    • sortorder string: Order of search results: asc or desc
    • offset integer: Cursor position in results
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.traces.barcode.get

Traces (sequence-reads) metadata

warwick_ac_uk_enterobase.api.v2.0.database.traces.barcode.get({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • barcode array
        • items string
      • limit integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • sortorder string
    • barcode required string: Unique barcode for Traces records, __TR e.g. SAL_AA0001AA_TR
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.traces.barcode.post

Traces (sequence-reads) metadata

warwick_ac_uk_enterobase.api.v2.0.database.traces.barcode.post({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • barcode array
        • items string
      • limit integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • sortorder string
    • barcode required string: Unique barcode for Traces records, __TR e.g. SAL_AA0001AA_TR
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.traces.barcode.put

Traces (sequence-reads) metadata

warwick_ac_uk_enterobase.api.v2.0.database.traces.barcode.put({
  "barcode": "",
  "database": ""
}, context)

Input

  • input object
    • body object
      • barcode array
        • items string
      • limit integer
      • offset integer
      • only_fields array
        • items string
      • orderby string
      • sortorder string
    • barcode required string: Unique barcode for Traces records, __TR e.g. SAL_AA0001AA_TR
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.scheme.alleles.get

Alleles data 

warwick_ac_uk_enterobase.api.v2.0.database.scheme.alleles.get({
  "locus": "",
  "scheme": "",
  "database": ""
}, context)

Input

  • input object
    • allele_id string
    • seq string
    • barcode array: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • reldate integer
    • locus required string
    • only_fields array
    • limit integer
    • offset integer
    • scheme required string
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.scheme.loci.get

Loci 

warwick_ac_uk_enterobase.api.v2.0.database.scheme.loci.get({
  "scheme": "",
  "database": ""
}, context)

Input

  • input object
    • barcode array: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • locus string
    • only_fields array
    • create_time string
    • limit integer
    • offset integer
    • scheme_query string
    • scheme required string
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

api.v2.0.database.scheme.sts.get

ST profile data

warwick_ac_uk_enterobase.api.v2.0.database.scheme.sts.get({
  "scheme": "",
  "database": ""
}, context)

Input

  • input object
    • st_id string
    • scheme_query string
    • show_alleles boolean
    • barcode array: Unique barcode for Strain records, _ e.g. SAL_AA0001AA
    • only_fields array
    • limit integer
    • reldate integer
    • offset integer
    • scheme required string
    • database required string: Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively

Output

Output schema unknown

Definitions

This integration has no definitions

datafire
@infinitebrahmanuniverse/nolb-_datafire_w@everything-registry/sub-chunk-222@zalastax/nolb-_datafire_w
3.0.0

5 years ago