API Help Page

assets

GET

filename Name of the asset file to be served

Asset file used for the testing purposes

assets

HEAD

filename Name of the asset file to be served

Size of the asset file used for the testing purposes

static

GET

filename Name of the file to be served
token Secure token received after a successful login

Static content served from the server root folder (defined in the config file)

static

HEAD

filename Name of the file to be served
token Secure token received after a successful login

Size of the static content served from the server root folder (defined in the config file)

genome

GET

filename Name of the file to be served

Genome stored on the server

genome

HEAD

filename Name of the file to be served

Size of the genome stored on the server

temp

GET

id Unique id pointing to a file
token Secure token received after a successful login

Static file served via secure temporary URL

temp

HEAD

filename Filename in a folder with a temporary URL
id Unique id pointing to a folder
token Secure token received after a successful login

Size of the static file served via secure temporary URL

help

GET

endpoint Endpoint path the help is requested for. Help for all endpoints wiil be provided, if this parameter is ommited

Help page on the usage of the endpoints

file_location

GET

locus Locus for repeat expansion image
multiple_files Flag indicating that we expect a single file/list of files
path Returns an absolute path on the server, if set to 'absolute'
ps_url_id An id of a temporary URL pointing to a specific processed sample
return_if_missing Return file info, if the file is missing
token Secure token received after a successful login
type Format of the requested file(s)

Retrieve file location information for specific file types

processed_sample_path

GET

ps_id Processed sample id
token Secure token received after a successful login
type File type

Temporary URL leading to a specific project file (based on the processed sample id)

analysis_job_gsvar_file

GET

job_id Analysis job id
token Secure token received after a successful login

FileLocation object with the information about GSvar for the corresponding analysis job

analysis_job_last_update

GET

job_id Analysis job id
token Secure token received after a successful login

Date and time (in seconds) of the last log file modification for the specific analysis job

analysis_job_log

GET

job_id Analysis job id
token Secure token received after a successful login

Analysis job log file

project_file

PUT

ps_url_id An id of a temporary URL pointing to a specific processed sample
token Secure token received after a successful login

Update an existing project file (GSvar file)

ps_regions

GET

sys_id Processing system id
token Secure token received after a successful login

Processing system regions

ps_genes

GET

sys_id Processing system id
token Secure token received after a successful login

Processing system genes

secondary_analyses

GET

ps_name Processed sample name
token Secure token received after a successful login
type Analysis type

Secondary analyses list

rna_fusion_pics

GET

rna_id RNA id
token Secure token received after a successful login

List RNA fusion plots needed for a report

rna_expression_plots

GET

rna_id RNA id
token Secure token received after a successful login

List RNA expression plots needed for a report

current_client

GET

None

Information about the latest available desktop client application

notification

GET

None

Information for the users of the desktop client (i.e. updates, maintenance, potential downtimes)

qbic_report_data

POST

content QBic report data to be saved in a file
filename QBic data report file
id Location id of the QBic data report file
token Secure token received after a successful login

Save QBic data report files

low_coverage_regions

POST

bam_url_id An id of a temporary URL pointing to a BAM file
cutoff Cutoff value
roi Regions of interest
token Secure token received after a successful login

Calculates low coverage regions

avg_coverage_gaps

POST

bam_url_id An id of a temporary URL pointing to a BAM file
roi Regions of interest
token Secure token received after a successful login

Calculates average coverage for gaps

target_region_read_depth

POST

bam_url_id An id of a temporary URL pointing to a BAM file
roi Regions of interest
token Secure token received after a successful login

Calculates target region read depth used in germline report

multi_sample_analysis_info

POST

analyses List of available analyses
token Secure token received after a successful login

Creates a list of analysis names for multi-samples

upload

POST

ps_url_id An id of a temporary URL pointing to a specific processed sample
token Secure token received after a successful login

File upload to a folder on the server

variant_annotation

POST

token Secure token received after a successful login

Variant annotation by using megSAP

blat_search

GET

sequence sequence

BLAT search for a given sequence and genome

POST

name User name
password Password

Secure token generation, the token will be used to access protected resources and to perform certain API calls

session

GET

token Secure token to identify the session

Information about the session linked to the given token

validate_credentials

POST

name User name
password Password

Checks if provided GSvar credentials are valid

db_token

POST

token User name

Secure token generation for accessing the database credentials

ngsd_credentials

POST

dbtoken Secure token for the database credentials
secret Secret known to a client and to the server

Sends NGSD credentials to the GSvar client application

genlab_credentials

POST

dbtoken Secure token for the database credentials
secret Secret known to a client and to the server