OpenSpecimen System Settings

Active User Login Days Criteria

A number of days elapsed since the last login before the user is considered as inactive. This is only used to calculate active users in dashboard. 

90

Print Distribution Labels

Additional label can be printed during distribution. This can be used as a de-identified label for specimens when distributed to researchers. 

Enabled/ Disabled

Relabel Shipment Specimens

Enable to allow editing of specimen labels when shipments are received as receiving sites might have a different label that they want to use. 

Enabled/ Disabled

Download Labels Print File

Enable or disable downloading of specimen labels print integration data file. When enabled, a CSV file containing the specimens data to be printed on labels (stickers) is downloaded to the user computer. When disabled, the CSV file is not downloaded. This can be used to test print rules or if integration is not possible, this file can be manually fed to the printer.

Enabled/ Disabled

DP Expiry Reminder

A number of days prior to distribution protocol expiry when email notification should be sent to the PI.

30

Repeat DP Expiry Reminder

A number of days after which email notification should be repeated for distribution protocol expiry.

E.g. If the values for DP Expiry reminder and Repeat DP expiry Reminder are set as 30 and 5, it will send 1 email every 5 days for 30 days prior to expiry. In total, it will send 6 notifications.

5

Order Specimens UI Limit

Maximum number of specimens whose details can be edited at the time of distribution using UI. This is useful for creating large orders like 1000s of specimens. Displaying large number of specimens on the order details page might take time and memory. To avoid this, you can restrict the number of specimens to display.

100

V5.0

Order Custom Fields Form

Identifier of custom form to be used as default custom fields form for distribution orders.

V5.0

Store List Max Retries

The maximum number of attempts to execute store list before marking the store list as permanently failed.

5

V5.0

Store List Retry Interval

The time interval in hours to elapse between retry of failed store list executions.

24

v4.1

System LockDown**

To stop users from using OpenSpecimen except for Super Admins

NOTE: This is useful to prevent users from login/performing any task when data to be migrated on the servers and the label autogeneration or MPI autogeneration is to turned off till the data is migrated.

Enabled/ Disabled

User Sign Up

Enable or disable users sign up feature. If admins do not want outside users to sign up to their instance and user accounts are always directly created by admins, this can be disabled.

Enabled/ Disabled

Inactive Account

The number of days of inactivity before the user account is locked. Setting to 0 will ensure the account is never get locked.

60

Failed Login Attempts

The number of consecutive failed logins that are allowed before the user account is locked.

5

Default Domain

The user domain to be pre-selected for authentication on the user sign-in page.

openspecimen

Device Verification

Enable device verification using OTP.

Disabled

Forgot Password

Allow or prevent users who have forgotten their passwords to set a new password by using the 'Forgot Password' feature.

Enabled/ Disabled

Concurrent Logins Limit

Maximum number of concurrent login sessions allowed per user. When not specified or zero, unlimited concurrent login sessions are allowed.

0

Notify Failed Logins

Enable to notify users and admins whenever an unsuccessful login attempt is made.

Enabled

Two Factor Authentication

Enable or disable two factor authentication using OTP. For more details, refer to the wiki page

Disabled

Password Age

The number of days before passwords expire. Setting to 0 will ensure that password never expires.

365, 90, etc

Password Complexity

Regular expression specifying complexity requirements that user passwords must meet. For example - pattern for at least one capital letter, one small letter, one number, and should be a minimum of 8 characters long.

((?=.*\d)(?=.*[a-z])(?=.*[A-Z]).{8,20})

Password Complexity Description

User-friendly description of password complexity requirements.

Tip: Password should contain at least 1 uppercase letter, 1 lowercase letter, 1 number and should be minimum 8 characters long

Password History

The number of unique passwords before an old password can be reused.

5

SAML authentication

Enable single sign-on using SAML based identity provider

Enabled/ Disabled

Single Logout

Enable single logout using SAML based identity provider.

Enabled/ Disabled

Session Timeout (minutes)

Minutes of inactiveness after which a user is automatically logged out.

60

IP Address Validation

Check whether requests are made from the same IP address to which the login token was issued.

Enabled/ Disabled

Add Participant on No Match

Allow or disallow users to add new participants when lookup yields no matching participants in two-step registration workflow.

Enabled/ Disabled

Aliquot Label Format 

The system-level format for aliquot labels.

%PSPEC_LABEL%.%PSPEC_UID%

Coordinator Role

Name of the role that is assigned to coordinators. When specified, coordinators cannot update participants, visits, and specimens if any of the specimens underneath them are in a received state.

CP Coding

Enable or disable short codes for collection protocol, events, and specimen requirements. Needed for barcoding.

Enabled/ Disabled

CP Expiry Reminder

Number of days prior to collection protocol expiry when email notification should be sent to the PI, coordinators, and CP site coordinators.

30

Repeat CP Expiry Reminder

Number of days after which email notification should be repeated for collection protocol expiry. E.g. If the values for CP Expiry reminder and Repeat CP expiry Reminder are set as 30 and 5, it will send 1 email every 5 days for 30 days prior to expiry. In total, it will send 6 notifications.

5

CP SOP Document

System-level collection protocol SOP document

SOP Documents Directory

Folder on the server to store collection protocol SOP documents

CP SOP Link

System-level collection protocol SOP document link

Consent Document Print Template

HTML template to use for printing the consent documents.

Specimen Barcoding

Enable or disable barcoding support for Specimen

Enabled/ Disabled

External Participant Sites

A comma-separated list of site IDs or names from which participant details are sourced from the external databases like EPIC etc

Extract Text from SPR PDF Docs

Enable or disable extraction of text content from SPR PDF documents

Enabled/ Disabled

Image URL

URL pattern to use for rendering the specimen image links.

Imaging

Enable to allow users to view the specimen images.

Mandatory Aliquot Quantity

Enable to make aliquots quantity a mandatory field.

Enabled: You cannot add, collect, distribute, and return aliquots with blank quantity.

Disabled: You can add, collect, distribute, and return aliquots with blank quantity.

Max. Child Specimens(new in v10.1)

Maximum number of child specimens that can be created from a parent specimen.

Default value 100

Specimens Update UI Limit

Maximum number of specimens that can be updated at a time using UI. The default value is 100.

MPI Format

Format for auto-generating master patient index (MPI).

The format should be like: Prefix + unique number + suffix

e.g MPI + %05d + ID ==> MPI00001ID

MPI Custom Generator

Custom Java class to auto-generate master patient index (MPI).

MPI RegEx Pattern

RegEx pattern to validate the master patient index (MPI).

e.g. The regEx pattern for an 8 digit number should be ^([0-9]{8})

MPI Custom Validator

Custom Java class to validate the master patient index (MPI).

Site-based Participant Access

Restrict access to participants based on the user's sites. By default, all participants within a protocol are displayed.

Enabled/ Disabled

Consent File Directory

Folder on the server to store participant consent files.

Participants Lookup Workflow

Spring bean name or fully qualified name of a class implementing customized matching participants lookup workflow. For example: bean: customisedLookup or class: com.krishagni.openspecimen.plugins.CustomisedLookup

UID Pattern

The pattern for participant unique identifier (UID)

UID Custom Validator

Custom validator for participant Unique ID field.

Survey Link Age

Number of days during which a survey link is valid.

Pending Specimens Display Interval

Pending specimens will be automatically hidden in specimen tree after specified number of days have elapsed since collection of parent specimen or visit.

60

If you add the value as '0', the pending specimens would be hidden immediately.

Shipment Received Quality

Regular expression for acceptable shipment received qualities.

Acceptable|Acceptable - Clotted

Specimens Sorting by Relationship Limit

Maximum number of specimens that can be sorted based on their relationship

250

Specimen Barcode Format (new in v5.0)

The system-level format for auto-generation of specimen barcodes.

%SYS_UID(n)%

Gel Image Directory

Folder on the server to store gel image files.

Specimen Label Printer Implementor

Name of the Java bean defined in the spring context for the implementor class

defaultSpecimenLabelPrinter

SPR De-identification

Name of the Spring bean implementing the customized logic of de-identifying surgical pathology reports.

SPR Directory

Folder on the server to store surgical pathology report files.

Staged Participants Retain Interval

Number of days to retain the details of a participant in the staging table

Anonymize Participants

Enable or disable features to anonymize the participant's PHI data.

Enabled/ Disabled

Path Reports

Enable or disable uploading of surgical pathology reports for a visit.

Enabled/ Disabled

CP Report

System-level collection protocol report settings. These settings are used when CP specific reporting settings are not specified

cp-report-settings.json

Specimen centric CP Report

System-level specimen centric collection protocol report settings. These settings are used when CP specific reporting settings are not specified. If this setting is also not specified then settings for regular CP reports is used

classpath:/com/krishagni/catissueplus/core/biospecimen/spmn-cp-report-settings.json

System Workflows

System-level participants and specimens list view configuration. This configuration is used when CP specific configuration is not specified

Two-Step Participant Registration

Enable or disable two-step participant registration workflow

Enabled/ Disabled

UID Mandatory

Enable participant's unique identifier field is mandatory

Enabled/ Disabled

Unique Specimen Barcode per CP

Enable or Disable uniqueness of Specimen barcodes at CP level. Enabling this setting ensures Specimen barcodes are unique only within Collection Protocol. Disabling this setting ensures no two specimen barcodes are the same throughout the system.

Enabled/ Disabled

Unique Specimen Label per CP

Enable or Disable uniqueness of Specimen labels at CP level. Enabling this setting ensures Specimen labels are unique only within Collection Protocol. Disabling this setting ensures no two specimen labels are the same throughout the system.

Enabled/ Disabled

Unplanned Visit Name Format

The system-level format for the unplanned visit names.

%PPI%_%SYS_UID%

Visit Label Print Rules

CSV file containing the conditions which decides the data to be printed as labels and which printer to use

Visit Label Printer Implementor

Name of the Java bean defined in the spring context for the implementor class

Specimens Collection Manifest

HTML template for generating specimens collection manifest at the visit level.

classpath:/com/krishagni/openspecimen/manifest/visit.html

Visits Lookup Workflow

Spring bean name or fully qualified name of a class implementing customized visits lookup workflow. For example: bean: customisedVisitsLookup or class: com.krishagni.openspecimen.plugins.CustomisedVisitsLookup

bean:stagedVisitsLookup

Visit Name Format

The system-level format for the planned visit names.

%PPI%_%EVENT_LABEL%_%SYS_UID%

Zero Out Specimen Quantity

Enable to set the available quantity of specimens to zero when they are disposed.

Enabled

CP Catalog Query

Identifier of the saved query to be used as a CP catalog query. This setting value is used when the CP specific catalog query is not specified

Specimen centric CP Catalog Query

Identifier of a saved query to be used as a catalog query for specimen centric CPs. If this setting is not specified then regular CP catalog query is used

Default Catalog

Identifier of catalog to be used as OpenSpecimen landing page

Application URL(added in v7.0)

Server URL to be used in the emails to end-users.

https://openspecimen.org

Container Specimens Report

Saved query to use for generating container specimens report

Data Directory

Data directory to store uploaded data

Long Date Format (added in v8.2)

Date format for displaying date fields in the view mode.

• Date: d or dd

• Month: M or MM or MMM

• Year: yyyy

• Further reference: Date and time formats

Short Date Format (added in v8.2)

Date format for parsing date field values in the data entry forms.

• Date: d or dd

• Month: M or MM or MMM

• Year: yyyy

• Further reference: Date and time formats

Deployment Environment

Any meaningful text that helps users distinguish between various OpenSpecimen deployment environments like test, dev, prod, demo, etc

Deployment Site Logo

Image file of the deployment site logo to be displayed on the OpenSpecimen navigation bar. The file size should be as below for best fit.

Height 1000px Width : 155px

Size: 20-40 kb

Deployment Site URL

Website URL to navigate users on clicking the deployment site logo

Default Distribution Report Query

Identifier of the saved query to be used as default distribution report query

Feedback To Developers

It gives an option for end-users to send feedback to developers.

Enabled/Disabled

Field Separator

A single character that specifies how records in the delimited text files should be split into fields. For example, CSV files use comma (,) as the field separator

Pre-validate Records Limit

Maximum number of records that can be pre-validated before importing to database. WARNING: Keep the limit below 15,000. With a higher limit, the system might become inaccessible to users.

10000

Locale

Locale in which the server has to be deployed. By default, it assumes the server's locale.

en_US, en_AU

Log Files Retain Period

A number of days to retain the log files after which they are deleted.

30

Shipment export report

Export Report format for all shipments

Container Shipment Report

Saved query to use for exporting the container shipment details. If not specified, shipment report is used.

Specimen Kit export report

Saved query to use for exporting details of specimen kit

Developer Email Address

Email address for end-users to email feedback on OpenSpecimen.

Toast Display Time

Duration, in seconds, for which the success or error notification toasts should be displayed.

5

Welcome Video Source

Add a welcome video to end-users during the sign-up process. E.g. from YouTube, Vimeo, etc

Welcome Video URL

URL for a welcome video

OpenSpecimen Email Address

The account from which the OpenSpecimen will send emails. E.g. openspecimen@mycenter.edu.

Account Password

Password for the OpenSpecimen email account.

Administrator Email Address

The email address of the OpenSpecimen administrator. It will be used to CC all emails.

Administrator Phone Number

Phone number of the OpenSpecimen administrator displayed in emails sent from OpenSpecimen. Users can call on this number to receive help, log support tickets, etc.

Email Authentication

Enable if email authentication is required for your email server.

Enabled/ Disabled

IT Administrator Email Address

The email address of the OpenSpecimen IT person, who will receive uncaught system errors notification

Email Server Hostname

Email server hostname.

Email Server Port

Email server port.

StartTLS

Enable if StartTLS is to be used for your email server.

v4.1

Email Notification

Enable or disable email notifications sent by OpenSpecimen. When disabled, no email notifications are sent irrespective of individual notification setting

Enabled/ Disabled

v4.1

Bulk Import Emails to Admin

Copy bulk import emails to administrator email ID as well.

Enabled/ Disabled

Expiring CP

Send reminder emails when the collection protocol is about to expire.

Enabled/ Disabled

Expiring DP

Send reminder emails when distribution protocol is about to expire.

Enabled/ Disabled

Order Distributed

Send an email when specimens are distributed.

Enabled/ Disabled

Query Data Exported

Send an email when the query interface has finished exporting the requested data.

Enabled/ Disabled

Query Folder Shared

Send an email when a query folder is shared with one or more users.

Enabled/ Disabled

Shipment Received

Send an email when specimens shipment is received at lab or storage site

Enabled/ Disabled

Shipment Shipped

Send an email when specimens are shipped.

Enabled/ Disabled

Cart Shared

Send an email when a cart is shared with one or more users.

Enabled/ Disabled

User-Created

Send an email when a new user is created.

Enabled/ Disabled

Distribution Protocol Created

Send an email when a new distribution protocol is created.

Enabled/ Disabled

User Signup Request

Send an email to the administrator when a new user signs up.

Enabled/ Disabled

User Password Changed

Send an email to the user when their password is changed.

Enabled/ Disabled

User Signup Rejected

Send an email when a signup request is rejected.

Enabled/ Disabled

User Role Updated

Send an email when users' role is updated.

Enabled/ Disabled

User Signup Approved

Send an email when a signup request is approved by the administrator.

Enabled/ Disabled

Default Result View Fields

List of field values to be displayed in the default query result view.

Concurrent Queries Limit

Maximum number of queries that are allowed to run simultaneously before rejecting new query execution requests

10

In-memory Records Limit

A maximum number of query records that are allowed to be cached in memory. When the limit is reached, excessive records are spooled to disk

100

Import Date and Time Formats

Link to a document describing date and time formats that can be used in bulk import input file

https://openspecimen.atlassian.net/wiki/x/MoAcB

Bulk Import Records

Link to training materials on how to bulk import records and available templates

https://openspecimen.atlassian.net/wiki/x/SIAcB

Container

Link to training materials on how to manage containers

Managing containers - OpenSpecimen - Confluence

Collection Protocol

Link to training materials on how to manage collection protocols

Biospecimen data entry - OpenSpecimen - Confluence

Collection Protocol Setup

Link to training materials on how to set up (create, update) collection protocols, events, specimen requirements, consents, label formats, and many more

Collection Protocol - OpenSpecimen - Confluence

Distribution Protocol

Link to training materials on how to manage distribution protocols

Specimen Distribution - OpenSpecimen - Confluence

Form

Link to training materials on how to manage custom forms and fields

Custom Forms - OpenSpecimen - Confluence

Q & A Forums

Link to Q & A forums site

http://forums.openspecimen.org

Online Help

Link to online software help

http://help.openspecimen.org

Institute

Link to training materials on how to manage institutes

Institutes and Sites - OpenSpecimen - Confluence

Job

Link to training materials on how to manage custom jobs

Jobs - OpenSpecimen - Confluence

Search URL

URL to use for showing results of users' online training manual search queries.

https://openspecimen.atlassian.net/wiki/dosearchsite.action?queryString=

Distribution Order

Link to training materials on how to distribute specimens to others

Specimen Distribution - OpenSpecimen - Confluence

Print Rules Setup

Link to training materials on how to create and manage specimen label print rules

Label printing configuration - OpenSpecimen - Confluence

Query

Link to training materials on how to query for data (reporting)

Reporting - OpenSpecimen - Confluence

Role

Link to training materials on how to manage roles

User Management - OpenSpecimen - Confluence

Shipping and Tracking

Link to training materials on how to manage specimen shipments

Shipment of Specimens - OpenSpecimen - Confluence

Site

Link to training materials on how to manage sites

http://help.openspecimen.org/sites

Gel

Link to training materials on how to manage gels

https://openspecimen.atlassian.net/wiki/x/2JQRBQ

Specimen Cart

Link to training materials on how to specimen carts

http://help.openspecimen.org/specimen-list

Training URL

Link to user manual and training videos portal

http://training.openspecimen.org

User

Link to training materials on how to manage users

http://help.openspecimen.org/user