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Here are some tasks that a SHRINE system administrator may need to do from time to time.
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Handling Lockout (Lockout was replaced with better obfuscation and the DSA in 1.22, will be removed in 1.26)
In SHRINE, when a user runs too many queries that return the same result from a site's Adapter, that user will be locked out from that site. This will usually show itself in the form of an AdapterLockoutException coming back from a site when executing a query.
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For an explanation on what values can be used whenever [duration]
is mentioned, refer to this document: shrine.conf SHRINE's Configuration File - SHRINE 1.22.3shrine.conf#Durations
- Hub Timeout
- Where: shrine.conf, hub { maxQueryWaitTime {
[duration]
} } - Default:
minutes = 4.5
- Explanation: How long the SHRINE Hub will wait to collect responses before it gives up and sends out what it has. In a standard single-hub network with many nodes, this value only needs to be set at the central hub. To ensure smooth operation, this value should be lower than the QEP Timeout at other nodes.
- Where: shrine.conf, hub { maxQueryWaitTime {
- QEP Timeout
- Where: shrine.conf, queryEntryPoint { maxQueryWaitTime {
[duration]
} } - Default:
minutes = 5
- Explanation: How long a SHRINE Query Entry Point will wait for a response from a hub/broadcaster before giving up. If this timeout is reached, the user will see an error in their SHRINE webclient containing "Futures timed out". To ensure smooth operation, this value should be higher than the Hub Timeout at the central hub.
- Where: shrine.conf, queryEntryPoint { maxQueryWaitTime {
- i2b2 PM Timeout
- Where: shrine.conf, pmEndpoint { timeout {
[duration]
} } (also present in steward.conf and dashboard.conf) - Default:
seconds = 10
- Explanation: How long SHRINE will wait for a response from the i2b2 PM before timing out. This is typically a low value, but if i2b2 is experiencing performance issues and users are having trouble logging in to SHRINE, this timeout should be increased.
- Where: shrine.conf, pmEndpoint { timeout {
- i2b2 CRC Timeout
- Where: shrine.conf, adapter { crcEndpoint { timeout {
[duration]
} } } - Default:
seconds = 1
- Explanation: How long a SHRINE Adapter will wait for a response to an i2b2 query before timing out. This value is typically superseded by the Webclient Timeout value provided by the incoming query message.
- Where: shrine.conf, adapter { crcEndpoint { timeout {
- Webclient Query Timeout
- Where: SHRINE Webclient, click on green checkmark icon in the upper-right corner of the Query Tool panel
- Default: 180 (seconds)
- Explanation: How long the a SHRINE Webclient adapter will wait for a response to a query it sends to the CRC. Each message sent by the webclient will contain a
<result_waittime_ms>
element in its request based on this value. The particulars of this threshold vary wildly, but the general outcome is that query results will contain responses of "Results not available" for nodes that did not respond in time. Due to the potential long-running nature of complex i2b2 queries, this value should be somewhat high. However, it should be lower than a network's Hub Timeout (and thus, also lower than the QEP Timeout).
- Webclient Idle Timeout
- Where: The webclient will logout a user due to inactivity
- Explanation: The user will be warned with the pop-up shown below after 25 minutes of inactivity and will be logged out after 30 minutes if they do not click "ok".
- Webclient Cell Loading Timeout
- Where: i2b2_config_data.js, adapter { loginTimeout: (duration in seconds) }
- Default: 120 (seconds)
Explanation: The webclient will notify the user that loading the cells is taking too long and gives the user the option to continue waiting or to discontinue loading cells.
Timeouts in I2B2
- I2B2 Setfinder Timeout settings
- When a setfinder query is run, the CRC needs to know how long the query should remain in the small, medium or large queue before it will timeout and move on to the next queue. This length of time is defined in the Setfinder JMS Queue transaction timeout properties section of the crc.properties file. More details can be found here:http://community.i2b2.org/wiki/display/getstarted/10.4.4.2.3+Setfinder+Query+-+Timeout+Properties
FR Repository Cell Timeout
Where: ontology.properties, edu.harvard.i2b2.ontology.ws.fr.timeout = (duration in seconds)
Default: 1000 (seconds)
Explanation: A timeout for Ontology cell to communication with the File Repository. More details found here: http://community.i2b2.org/wiki/display/getstarted/9.4.3.3+File+Repository+Cell+Properties