-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathapplication.yml
146 lines (137 loc) · 6.19 KB
/
application.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
spring:
autoconfigure:
exclude:
- org.springframework.boot.autoconfigure.mongo.MongoAutoConfiguration
- org.springframework.boot.autoconfigure.data.mongo.MongoDataAutoConfiguration
- org.springframework.boot.autoconfigure.data.mongo.MongoRepositoriesAutoConfiguration
mvc:
async:
request-timeout: -1
data:
mongodb:
database: # Mongo Database Name
uri: # Mongo Database connection URL
datasource:
url: # MySQL Database connection URL
username:
password:
driver-class-name: com.mysql.cj.jdbc.Driver
jpa:
show-sql: false
hibernate:
naming:
physical-strategy: org.hibernate.boot.model.naming.PhysicalNamingStrategyStandardImpl
use-new-id-generator-mappings: false
rabbitmq:
host: # RabbitMQ host
username: # RabbitMQ user
password: # RabbitMQ password
port: # RabbitMQ port
listener:
direct:
prefetch: 25
simple:
prefetch: 25
servlet:
multipart:
max-file-size: 20GB
max-request-size: 20GB
location: ${app.tempDirPath}
server:
tomcat:
max-http-form-post-size: 50MB
max-swallow-size: 50MB
logging:
file:
name: logs/application_logs.txt
level:
org.springframework.data.mongodb.core.convert.QueryMapper: ERROR # Disable to avoid mapping log population.
app:
processId: # Id to register the submission task
retrySubmission: # Boolean flag to enable/disable automatic retrying of staled submissions
checkFilesPath: true # Boolean flag to enable/disable files path allowed character check.
enablePropertiesLog: # Boolean flag to enable/disable displaying the application properties on start
consumers: # Number of processing queue consumers.
maxConsumers: # Max number of processing queue consumers.
instanceBaseUrl: # Instance base url e.g. http://server.ebi.ac.uk:5541
#subBasePath: # Allows to allocate submissions under different base path. Commented to avoid empty string binding.
submissionTask:
enabled: # Whether the submission tasks should be executed in the cluster
jarLocation: # the submitter task jar location.
javaLocation: # The path to the java installation
singleJobMode: # Whether to execute all submission in a single cluster job
configFilePath: # the submitter task application.yml file location.
taskMemoryMgb: # Amount of memory (in MB) to be allocated for the submission processing tasks
taskCores: # Number of cores to be allocated for the submission processing tasks
taskMinutes: # Maximum number of minutes to execute the submission processing tasks
cluster:
enabled: # Whether the cluster jobs should be triggered remotely
default: # Default cluster mode. Valid values: LSF | SLURM
user: # cluster user
key: # cluster ssh key path.
lsfServer: # LSF cluster sever
slurmServer: # SLURM cluster sever
logsPath: # path to place the logs of the dispatched jobs
wrapperPath: # path to place the command wrapper script
fire:
host: # FIRE host
username: # FIRE user
password: # FIRE password
version: # FIRE version
tempDirPath: # Absolute path to the temp folder for FIRE storage
s3:
accessKey: # FIRE s3 access key
secretKey: # FIRE s3 access key
region: # Fire s3 region
endpoint: # Fire s3 region
bucket: # Fire s3 region
retry:
maxAttempts: # Maximum retry attempts
initialInterval: # Initial waiting interval time in ms
multiplier: # Multiplier for the waiting interval
maxInterval: # Maximum interval duration
security:
captchaKey: # Captcha validation token
checkCaptcha: # Boolean flag to enable/disable captcha key checking
tokenHash: # Token used for hash authentication
environment: # Current application execution environment
requireActivation: # Indicates whether a new user need activation before being used
preventFileDeletion: # Indicates wheter or not to prevent public submission non pagetab file delitions
instanceKeys:
dev: # Instance key for the submission tool DEV environment
beta: # Instance key for the submission tool BETA environment
prod: # Instance key for the submission tool PROD environment
filesProperties:
defaultMode: # The default mode to create user folder. Valid values are: NFS, FTP
filesDirPath: # Absolute path to the folder to be used for the user/groups files
magicDirPath: # Absolute path to create user magic folder for dropbox simple access
ftpDirPath: # Absolute path of the FTP-IN folder in NFS
ftpRootPath: # Root path to find the user files in the FTP-IN folder. If blank, root level FTP-IN will be used
ftpUser: # FTP user
ftpPassword: # FTP password
ftpUrl: # FTP url without port
ftpPort: # FTP port
persistence:
enableFire: # Boolean flag to indicate whether the files are stored on FIRE if true or NFS if false
concurrency: # Number of files processed concurrently
includeSecretKey: # Boolean flag to indicate whether the secret key should be added to the private submission path
nfsReleaseMode: # Method used to release files for NFS submissions. Valid values are: MOVE, HARD_LINKS
privateSubmissionsPath: # Absolute path to the folder to be used as storage for private submissions
publicSubmissionsPath: # Absolute path to the folder to be used as storage for public submissions
requestFilesPath: # Absolute path to the folder where request files are stored
tempDirPath: # Absolute path to the folder used to generate temporary files
mongo:
execute-migrations: # Boolean flag to enable/disable the execution of mongo migrations
migration-package: # Mongo migrations package
validator:
euToxRiskValidationApi: # EU-ToxRisk validation API
notifications:
requestQueue: # Queue used to handle request stages
requestRoutingKey: # Submission request messages routing key
errorNotificationsEnabled: # Boolean flag to enable/disable the Slack error notifications
doi:
endpoint: # DOI registration endpoint
uiUrl: # The BioStudies UI URL which will be associated to the DOI record
email: # E-Mail to get the DOI processing notifications
user: # User for the DOI service
password: # Password for the DOI service