Argument definitions

Argument Definitions

user_name

description: TODO: Temporary(?) for authentication testing.
type: string
pattern: ^\w+$
cmdFlags: --userName

test_mode

description: Activates the Beacon test setting, i.e. returning some random documents
type: boolean
cmdFlags: -t,--testMode
default: False

skip

description: Number of pages to be skipped.
type: integer
cmdFlags: --skip
default: 0

limit

type: integer
cmdFlags: -l,--limit
description: limit number of documents; a value of 0 sets to unlimited
default: 200
local: 0

paginate_results

description: Custom bycon parameter used for paginating results in some bycon services.
type: boolean
cmdFlags: --paginateResults
default: True

requested_granularity

description: The requested granularity of the beacon
type: string
pattern: ^\w+$
cmdFlags: --requestedGranularity
default: record

request_entity_path_id

description:

• data entry point, equal to the first REST path element in Beacon
• this only is used for command-line tests instead of the REST path value seen by the stack in web server mode
  type: string
  cmdFlags: --requestEntityPathId

response_entity_path_id

description:

• optional data delivery entry point, for {id} paths
• for command line (see above), but also potentially for selecting a special response entity in byconaut services (e.g. indviduals in /sampletable/)
  type: string
  cmdFlags: --responseEntityPathId

include_resultset_responses

type: string
cmdFlags: --includeResultsetResponses
description:

• include resultset responses, e.g. HIT, MISS
• kind of a holdover from Beacon pre-v1 but HIT & ALL might have some use in networks
  default: HIT

dataset_ids

type: array
items:
- type: string
cmdFlags: -d,--datasetIds
description: dataset ids

cohort_ids

type: array
items:
- type: string
cmdFlags: --cohortIds
description: cohort ids

filters

type: array
items:
- type: string
cmdFlags: --filters
description: prefixed filter values, comma concatenated; or objects in POST

filter_precision

type: string
cmdFlags: --filterPrecision
description: either start or exact for matching filter values
default: exact

filter_logic

type: string
cmdFlags: --filterLogic
description: Global for either OR or AND (translated to the MongoDB $and etc.). The Beacon protocol only knows AND.
default: AND

include_descendant_terms

type: boolean
cmdFlags: --includeDescendantTerms
description: global treatment of descendant terms
default: True

assembly_id

type: string
pattern: ^\w+?[\w\-\.]*?\w*?$
db_key: assembly_id
cmdFlags: --assemblyId
description: assembly id; currently not used in bycon's version

reference_name

type: string
db_key: location.sequence_id
pattern: ^\w+.*?\w?$
cmdFlags: --referenceName
description: chromosome

mate_name

type: string
db_key: adjoined_sequences.sequence_id
pattern: ^\w+.*?\w?$
cmdFlags: --mateName
description: chromosome

reference_bases

type: string
db_key: reference_sequence
pattern: ^[ACGTN]+$
cmdFlags: --referenceBases
description: reference bases

alternate_bases

type: string
db_key: sequence
pattern: ^[ACGTN]+$
cmdFlags: --alternateBases
description: alternate bases

variant_type

type: string
db_key: variant_state.id
pattern: ^\w+[\w \-\:]\w+?$
cmdFlags: --variantType
description: variant type, e.g. DUP

start

type: array
db_key: location.start
items:
- type: integer
- pattern: ^\d+?$
cmdFlags: --start
description: genomic start position

end

type: array
db_key: location.end
items:
- type: integer
- pattern: ^\d+?$
cmdFlags: --end
description: genomic end position

mate_start

type: integer
db_key: adjoined_sequences.start
pattern: ^\d+?$
cmdFlags: --mateStart
description: genomic start position of fusion partner breakpoint region

mate_end

type: integer
db_key: adjoined_sequences.end
pattern: ^\d+?$
cmdFlags: --MateEnd
description: genomic end position of fusion partner breakpoint region

variant_min_length

type: integer
db_key: info.var_length
pattern: ^\d+?$
cmdFlags: --variantMinLength
description: The minimal variant length in bases e.g. for CNV queries.

variant_max_length

type: integer
db_key: info.var_length
pattern: ^\d+?$
cmdFlags: --variantMaxLength
description: The maximum variant length in bases e.g. for CNV queries.

gene_id

type: string
pattern: ^\w+?(\w+?(\-\w+?)?)?$
db_key: None
cmdFlags: --geneId
description: gene id

aminoacid_change

type: string
db_key: molecular_attributes.aminoacid_changes
pattern: ^\w+?$
examples: V600E,M734V,G244A
cmdFlags: --aminoacidChange
description: Aminoacid alteration in 1 letter format

genomic_allele_short_form

type: string
db_key: identifiers.genomicHGVS_id
pattern: ^\w+.*\w$
examples: NC_000017.11:g.7674232C>G
cmdFlags: --genomicAlleleShortForm
description: Genomic HGVSId descriptor

variant_query_digests

type: array
db_key: None
items:
- type: string
- pattern: ^(?:chro?)?([12]?[\dXY]):(\d+?(?:-\d+?)?)(?:--(\d+?(?:-\d+?)?))?(?::([\w\:\>]+?))?$
cmdFlags: --variantQueryDigests
examples: 9:9000001-21975098--21967753-24000000:DEL
description: EXPERIMENTAL Variant query digest-style short form

variant_multi_pars

type: array
db_key: None
items:
- type: object
cmdFlags: --variantMultiPars
description: EXPERIMENTAL List of multiple variant queries, for POST

variant_internal_id

type: string
db_key: variant_internal_id
pattern: ^\w[\w\:\-\,]+?\w$
examples: 11:52900000-134452384:EFO_0030067
cmdFlags: --variantInternalId
description: An id value used for all variant instances of the same composition; a kind of digest

accessid

type: string
db_key: id
pattern: ^\w[\w\-]+?\w$
examples: b59857bc-0c4a-4ac8-804b-6596c6566494
cmdFlags: --accessid
description: An accessid for retrieving handovers etc.

file_id

type: string
pattern: ^\w[\w\-]+?\w$
examples: 90e19951-1443-4fa8-8e0b-6b5d8c5e45cc
cmdFlags: --fileId
description: A file id e.g. as generated by the uploader service

id

type: string
db_key: id
pattern: ^\w[\w\:\-\,]+?\w$
examples: pgxvar-5bab576a727983b2e00b8d32,pgxind-kftx25eh
cmdFlags: --id
description: An id; this parameter only makes sense for specific REST entry types

ids

type: array
items:
- type: string
- pattern: ^\w[\w:-]+\w$
cmdFlags: --ids
description: One or more ids; this parameter only makes sense for specific REST entry types

biosample_ids

type: array
items:
- type: string
- pattern: ^\w[\w:-]+\w$
byc_entity: biosample
cmdFlags: --biosampleIds
description: biosample ids

analysis_ids

type: array
items:
- type: string
- pattern: ^\w[\w:-]+\w$
byc_entity: analysis
cmdFlags: --analysisIds
description: analysis ids

individual_ids

type: array
items:
- type: string
- pattern: ^\w[\w:-]+\w$
byc_entity: individual
cmdFlags: --individualIds
description: subject ids

variant_ids

type: array
items:
- type: string
- pattern: ^\w[\w:-]+\w$
byc_entity: genomicVariant
cmdFlags: --variantIds
description: variant ids

debug_mode

type: boolean
cmdFlags: --debugMode
description: debug setting
default: False

show_help

type: boolean
cmdFlags: --showHelp
description: specific help display
default: False

test_mode_count

type: integer
cmdFlags: --testModeCount
description: setting the number of documents reurned in test mode
default: 5

output

type: string
cmdFlags: --output
description: For defining a special output format, mostly for byconaut services use. Examples:

• cnvstats, for analyses, to present some CNV statistics
• pgxseg, using the .pgxseg variant file format
• text, for some services to deliver a text table instead of JSON
• in byconaut for the target database when copying...

include_handovers

type: boolean
default: True
cmdFlags: --includeHandovers
description: only used for web requests & testing

method

type: string
cmdFlags: --method
description: special method
default: None

group_by

type: string
cmdFlags: --groupBy
description: group parameter e.g. for subset splitting
default: text

mode

type: string
cmdFlags: -m,--mode
description: mode, e.g. file type

update

type: boolean
cmdFlags: -u,--update
description: update existing records - might be deprecated; only used for publications
default: False

force

type: boolean
cmdFlags: --force
description: force mode, e.g. for update or insert (cmd line)
default: False

inputfile

type: string
cmdFlags: -i,--inputfile
description: a custom file to specify input data, usually tab-delimited with special header

outputdir

type: string
cmdFlags: --outputdir
description: output directory where supported (cmd line)

outputfile

type: string
cmdFlags: -o,--outputfile
description: output file where supported (cmd line)

min_number

type: integer
cmdFlags: --minNumber
description: minimal number, e.g. for collations, where supported
default: 0

delivery_keys

type: array
items:
- type: string
cmdFlags: --deliveryKeys
description: delivery keys to force only some parameters in custom exporters

collation_types

type: array
items:
- type: string
cmdFlags: --collationTypes
description: selected collation types, e.g. "EFO"

genome_binning

type: string
default: 1Mb
cmdFlags: --genomeBinning
description: one of the predefined genome binning keys - default 1Mb

cyto_bands

type: string
pattern: ^(?:chro?)?([12]?[\dXY])([pq](?:(?:ter)|(?:cen)|(?:[1-4](?:\d(?:\.\d\d*?)?)?)?))?\-?([pq](?:(?:cen)|(?:ter)|(?:[1-4](?:\d(?:\.\d\d*?)?)?)?))?$
db_key: None
cmdFlags: --cytoBands
description: cytobands, e.g. 8q21q24.1

chro_bases

type: string
pattern: ^(chro?)?([12]?[\dXY])\:(\d+?)(\-(\d+?))?$
db_key: None
cmdFlags: --chroBases
description: only for the cytoband converter ... e.g. 8:0-120000000

city

type: string
cmdFlags: -c,--city
description: only for the geolocations...

geo_latitude

type: number
cmdFlags: --geoLatitude
description: only for the geolocations...

geo_longitude

type: number
cmdFlags: --geoLongitude
description: only for the geolocations...

geo_distance

type: integer
cmdFlags: --geoDistance
description: only for the geolocations...

plot_pars

type: string
cmdFlags: --plotPars
description: plot parameters in form par=value concatenated by ::

plot_type

type: string
cmdFlags: --plotType
description: plot type (histoplot, samplesplot, arrayplot - more?)
default: None