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logging:
level:
cz.mendelu.dnaAnalyser: INFO
file:
name: "./logs/app.log"
max-size: "1MB"
# Profiles config
spring:
profiles:
active: pgsql, dev
servlet:
multipart:
max-file-size: 2048MB
max-request-size: 2048MB
datasource:
# Datasource are define separetly in profiles:
# - h2: for embedded h2 database, for testing mainly
# - pgsql: for postgres database, witch is default option
# Spring actuator config
management:
endpoints:
web:
base-path: /api/management
exposure:
include: configprops, env, flyway, health, httptrace, info, mappings, scheduledtasks, logfile
enabled-by-default: true
# info data publish by spring boot actuator
info:
app:
version: @gitVersion@
assemblyDate: @assemblyDate@
analysis: # List of implemented analysis and
g4hunter: true
p53predictor: true
g4killer: true
rloopr: true
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limits:
multipart:
maxFileSize: ${spring.servlet.multipart.max-file-size}
maxRequestSize: ${spring.servlet.multipart.max-request-size}
# This is module configuration.
email:
smtp: localhost
port: 25
from: palindrome@ibp.cz
disabled: false
batch:
asynchronous: true
# threadPoolSize is positive number (1 - x) for exact number of working threads
# or -1, then command: Executors.newWorkStealingPool(); is used for determinate optimal number of threads.
threadPoolSize: -1
sequence:
dir: ./db/sequence
# This sequences are add to each new user
defaults: >
24a8e29b-ec11-4116-8719-34c00c25a5d7,
c0a8b159-2f02-4be9-8714-a27712c5cbb2,
df7d3c96-bed4-4bb0-b758-ce04d77da676,
78a4e97d-8eb4-42cf-a5df-bacd5ca61646,
eb50a995-a044-4f33-8ffa-5b184750b120,
50a722e2-7814-4e82-9621-f1f30cc985fe,
9a8e796b-1372-493d-8326-6769338d378b
ncbi:
## Configuring access to the NCBI database
# Do not change this configuration unless you know exactly what you are doing.
# Access url, default: "ncbi.url = http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
# Database of nucleotide, default: "db = nuccore"
db: nuccore
# Return mode, default: "retmode = text"
retmode: text
# Return type, default: "rettype = fasta"
rettypefasta: fasta
# Return type for featue, default: "rettype = ft"
rettypefeature: ft
# Time-limited approach permits the download source of once every X milliseconds. NCBI recommends that users post
# no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM
# Eastern time during weekdays.
# That value determines the minimum time (ms) between two accesses to the NCBI. default: "restriction_timing = 1000"
restriction-timing: 1000
security:
jwt:
header: Authorization
secret: secret
expiration: 604800
importDefaultUsers: true
management:
swagger: enabled
# This is analyse configuration.
analyse:
dir: ./db/analyse
datasource:
# String "analyse-id" will be replace by real analyse uuid.
url: jdbc:h2:file:${analyse.dir}/analyse-id;DB_CLOSE_ON_EXIT=FALSE
username:
password:
driverClassName: org.h2.Driver
# Swagger 2 generator configuration
swagger2:
info:
title: Bioinformatics REST API
description: API to access REST interfaces
license: TODO
licenseUrl: TODO
termsOfServiceUrl: TODO
version: 3.0.0
contact:
name: Ing. Jan Kolomazník, Ph.D.
url:
email: xkoloma1@mendelu.cz
javamelody:
# JavaMelody autoconfiguration
enabled: true
spring-monitoring-enabled: true
# Initialization parameters for JavaMelody (optional)
# See: https://github.com/javamelody/javamelody/wiki/UserGuide#6-optional-parameters
init-parameters:
# log http requests:
log: true