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Configuration Settings

Download Labels Print FileThese are system-level setting and can be configured only by a "Super Administrator". 

Steps to configure the settings:

  1. Log in as a user with 'Super Administrator' role

  2. Click on 'Settings' card from the home page

  3. Search the desired property using 'Search' box OR
  4. Click on the desired module from the list and then click on the 'Property' that has to be configured



There are 2 types of properties:

  1. With 'Enabled' and 'Disabled' options- Using these options user can enable/disabled the property
  2. Without 'Enabled' and 'Disabled' options- User can specify any desired values


Module: Administrative 

Added inPropertyDescriptionPossible Values

Active User Login Days CriteriaA 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 LabelsAdditional 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 SpecimensEnable 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 FileEnable 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 ReminderA number of days prior to distribution protocol expiry when email notification should be sent to the PI.30

Repeat DP Expiry ReminderA number of days after which email notification should be repeated for distribution protocol expiry.5

Order Specimens UI LimitMaximum 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
V5.0Order Custom Fields FormIdentifier of custom form to be used as default custom fields form for distribution orders.
V5.0Store List Max RetriesThe maximum number of attempts to execute store list before marking the store list as permanently failed.5
V5.0Store List Retry IntervalThe 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 UpEnable 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

**Once System LockDown is 'Enabled' :

For users already logged in: They should get logged out and directed to the login page
On login to the system with user role other than Super Admin: the system should show the message as 'The system is locked down. Please contact the system administrator. (AUTH_SYSTEM_LOCKDOWN)'  

Module: Authentication 

PropertyDescriptionPossible Values
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 AttemptsThe number of consecutive failed logins that are allowed before the user account is locked.5
Default DomainThe user domain to be pre-selected for authentication on the user sign-in page.openspecimen
Device VerificationEnable device verification using OTP.Disabled
Forgot PasswordAllow or prevent users who have forgotten their passwords to set a new password by using the 'Forgot Password' feature.Enabled/ Disabled
Concurrent Logins LimitMaximum number of concurrent login sessions allowed per user. When not specified or zero, unlimited concurrent login sessions are allowed.0
Notify Failed LoginsEnable to notify users and admins whenever an unsuccessful login attempt is made.Enabled
Two Factor AuthenticationEnable or disable two factor authentication using OTP. For more details, refer to the wiki pageDisabled
Password AgeThe number of days before passwords expire. Setting to 0 will ensure that password never expires.365, 90, etc
Password ComplexityRegular 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 DescriptionUser-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 HistoryThe number of unique passwords before an old password can be reused.5
SAML authenticationEnable single sign-on using SAML based identity providerEnabled/ Disabled
Single LogoutEnable 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 ValidationCheck whether requests are made from the same IP address to which the login token was issued.Enabled/ Disabled


Module: Biospecimen 

PropertyDescriptionPossible Values
Add Participant on No MatchAllow 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 RoleName 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 CodingEnable or disable short codes for collection protocol, events, and specimen requirements. Needed for barcoding.Enabled/ Disabled
CP Expiry ReminderNumber of days prior to collection protocol expiry when email notification should be sent to the PI.30
Repeat CP Expiry ReminderNumber of days after which email notification should be repeated for collection protocol expiry.5
CP SOP DocumentSystem-level collection protocol SOP document
SOP Documents DirectoryFolder on the server to store collection protocol SOP documents
CP SOP LinkSystem-level collection protocol SOP document link
Consent Document Print TemplateHTML template to use for printing the consent documents.
Specimen BarcodingEnable or disable barcoding support for SpecimenEnabled/ Disabled
External Participant SitesA 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 DocsEnable or disable extraction of text content from SPR PDF documentsEnabled/ Disabled
Image URLURL pattern to use for rendering the specimen image links.
ImagingEnable to allow users to view the specimen images.
Mandatory Aliquot QuantityEnable 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.

Specimens Update UI LimitMaximum 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 GeneratorCustom 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 ValidatorCustom Java class to validate the master patient index (MPI).
Site-based Participant AccessRestrict access to participants based on the user's sites. By default, all participants within a protocol are displayed.Enabled/ Disabled
Consent File DirectoryFolder on the server to store participant consent files.
Participants Lookup WorkflowSpring 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 PatternThe pattern for participant unique identifier (UID)
UID Custom ValidatorCustom validator for participant Unique ID field.
Survey Link AgeNumber of days during which a survey link is valid.
Pending Specimens Display IntervalPending 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 QualityRegular expression for acceptable shipment received qualities.Acceptable|Acceptable - Clotted
Specimens Sorting by Relationship LimitMaximum number of specimens that can be sorted based on their relationship250
Specimen Barcode Format (new in v5.0)The system-level format for auto-generation of specimen barcodes.%SYS_UID(n)%
Gel Image DirectoryFolder on the server to store gel image files.
Specimen Label Printer ImplementorName of the Java bean defined in the spring context for the implementor classdefaultSpecimenLabelPrinter
SPR De-identificationName of the Spring bean implementing the customized logic of de-identifying surgical pathology reports.
SPR DirectoryFolder on the server to store surgical pathology report files.
Staged Participants Retain IntervalNumber of days to retain the details of a participant in the staging table
Anonymize ParticipantsEnable or disable features to anonymize the participant's PHI data.Enabled/ Disabled
Path ReportsEnable or disable uploading of surgical pathology reports for a visit.Enabled/ Disabled
CP ReportSystem-level collection protocol report settings. These settings are used when CP specific reporting settings are not specifiedcp-report-settings.json
Specimen centric CP ReportSystem-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 usedclasspath:/com/krishagni/catissueplus/core/biospecimen/spmn-cp-report-settings.json
System WorkflowsSystem-level participants and specimens list view configuration. This configuration is used when CP specific configuration is not specified
Two-Step Participant RegistrationEnable or disable two-step participant registration workflowEnabled/ Disabled
UID MandatoryEnable participant's unique identifier field is mandatoryEnabled/ Disabled
Unique Specimen Barcode per CPEnable 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 CPEnable 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 FormatThe system-level format for the unplanned visit names.%PPI%_%SYS_UID%
Visit Label Print RulesCSV file containing the conditions which decides the data to be printed as labels and which printer to use
Visit Label Printer ImplementorName of the Java bean defined in the spring context for the implementor class
Specimens Collection ManifestHTML template for generating specimens collection manifest at the visit level.classpath:/com/krishagni/openspecimen/manifest/visit.html
Visits Lookup WorkflowSpring bean name or fully qualified name of a class implementing customized visits lookup workflow. For example: bean: customisedVisitsLookup or class: com.krishagni.openspecimen.plugins.CustomisedVisitsLookupbean:stagedVisitsLookup
Visit Name FormatThe system-level format for the planned visit names.%PPI%_%EVENT_LABEL%_%SYS_UID%
Zero Out Specimen QuantityEnable to set the available quantity of specimens to zero when they are disposed.Enabled


Module: Catalog 

PropertyDescriptionPossible Values
CP Catalog QueryIdentifier 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 QueryIdentifier 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 CatalogIdentifier of catalog to be used as OpenSpecimen landing page


Module: Common 

PropertyDescriptionPossible Values
Application URL(added in v7.0)Server URL to be used in the emails to end-users.https://openspecimen.org
Container Specimens ReportSaved query to use for generating container specimens report
Data DirectoryData 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 EnvironmentAny meaningful text that helps users distinguish between various OpenSpecimen deployment environments like test, dev, prod, demo, etc


Deployment Site LogoImage file of the deployment site logo to be displayed on the OpenSpecimen navigation bar. The file size should be between 20 to 40 KB.


Deployment Site URLWebsite URL to navigate users on clicking the deployment site logo
Default Distribution Report QueryIdentifier of the saved query to be used as default distribution report query
Feedback To DevelopersIt gives an option for end-users to send feedback to developers.Enabled/Disabled
Field SeparatorA 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 LimitA maximum number of records that can be pre-validated before importing to the database.10000
LocaleLocale in which the server has to be deployed. By default, it assumes the server's locale.en_US, en_AU
Log Files Retain PeriodA number of days to retain the log files after which they are deleted.30
Shipment export reportExport Report format for all shipments
Specimen Kit export reportSaved query to use for exporting details of specimen kit
Developer Email AddressEmail address for end-users to email feedback on OpenSpecimen.
Toast Display TimeDuration, in seconds, for which the success or error notification toasts should be displayed.5
Welcome Video SourceAdd a welcome video to end-users during the sign-up process. E.g. from YouTube, Vimeo, etc
Welcome Video URLURL for a welcome video


Module: Email 

PropertyDescriptionPossible Values
OpenSpecimen Email AddressThe account from which the OpenSpecimen will send emails. E.g. openspecimen@mycenter.edu.
Account PasswordPassword for the OpenSpecimen email account.
Administrator Email AddressThe email address of the OpenSpecimen administrator. It will be used to CC all emails.
Administrator Phone NumberPhone 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 AuthenticationEnable if email authentication is required for your email server.Enabled/ Disabled
IT Administrator Email AddressThe email address of the OpenSpecimen IT person, who will receive uncaught system errors notification
Email Server HostnameEmail server hostname.
Email Server PortEmail server port.
StartTLSEnable if StartTLS is to be used for your email server.


Module: Notifications 

Added inPropertyDescriptionPossible Values
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 CPSend reminder emails when the collection protocol is about to expire.Enabled/ Disabled

Expiring DPSend reminder emails when distribution protocol is about to expire.Enabled/ Disabled

Order DistributedSend an email when specimens are distributed.Enabled/ Disabled

Query Data ExportedSend an email when the query interface has finished exporting the requested data.Enabled/ Disabled

Query Folder SharedSend an email when a query folder is shared with one or more users.Enabled/ Disabled

Shipment ReceivedSend an email when specimens shipment is received at lab or storage siteEnabled/ Disabled

Shipment ShippedSend an email when specimens are shipped.Enabled/ Disabled

Cart SharedSend an email when a cart is shared with one or more users.Enabled/ Disabled

User-CreatedSend an email when a new user is created.Enabled/ Disabled

Distribution Protocol CreatedSend an email when a new distribution protocol is created.Enabled/ Disabled

User Signup RequestSend an email to the administrator when a new user signs up.Enabled/ Disabled

User Password ChangedSend an email to the user when their password is changed.Enabled/ Disabled

User Signup RejectedSend an email when a signup request is rejected.Enabled/ Disabled

User Role UpdatedSend an email when users' role is updated.Enabled/ Disabled

User Signup ApprovedSend an email when a signup request is approved by the administrator.Enabled/ Disabled


Module: Query 

PropertyDescriptionPossible Values
Default Result View FieldsList of field values to be displayed in the default query result view.
Concurrent Queries LimitMaximum number of queries that are allowed to run simultaneously before rejecting new query execution requests10
In-memory Records LimitA maximum number of query records that are allowed to be cached in memory. When the limit is reached, excessive records are spooled to disk100

Module: Training

PropertyDescriptionPossible Values
Import Date and Time FormatsLink to a document describing date and time formats that can be used in bulk import input filehttps://openspecimen.atlassian.net/wiki/x/MoAcB
Bulk Import RecordsLink to training materials on how to bulk import records and available templateshttps://openspecimen.atlassian.net/wiki/x/SIAcB
ContainerLink to training materials on how to manage containershttp://help.openspecimen.org/containers
Collection ProtocolLink to training materials on how to manage collection protocolshttp://help.openspecimen.org/collection
Collection Protocol SetupLink to training materials on how to set up (create, update) collection protocols, events, specimen requirements, consents, label formats, and many morehttp://help.openspecimen.org/collection-protocol
Distribution ProtocolLink to training materials on how to manage distribution protocolshttp://help.openspecimen.org/distribution
FormLink to training materials on how to manage custom forms and fieldshttp://help.openspecimen.org/forms
Q & A ForumsLink to Q & A forums sitehttp://forums.openspecimen.org
Online HelpLink to online software helphttp://help.openspecimen.org
InstituteLink to training materials on how to manage instituteshttp://help.openspecimen.org/institute
JobLink to training materials on how to manage custom jobshttp://help.openspecimen.org/jobs
Search URLURL to use for showing results of users' online training manual search queries.https://openspecimen.atlassian.net/wiki/dosearchsite.action?queryString=
Distribution OrderLink to training materials on how to distribute specimens to othershttp://help.openspecimen.org/orders
Print Rules SetupLink to training materials on how to create and manage specimen label print ruleshttp://help.openspecimen.org/print-label
QueryLink to training materials on how to query for data (reporting)http://help.openspecimen.org/query
RoleLink to training materials on how to manage roleshttp://help.openspecimen.org/roles
Shipping and TrackingLink to training materials on how to manage specimen shipmentshttp://help.openspecimen.org/shipment
SiteLink to training materials on how to manage siteshttp://help.openspecimen.org/sites
GelLink to training materials on how to manage gelshttps://openspecimen.atlassian.net/wiki/x/2JQRBQ
Specimen CartLink to training materials on how to specimen cartshttp://help.openspecimen.org/specimen-list
Training URLLink to user manual and training videos portalhttp://training.openspecimen.org
UserLink to training materials on how to manage usershttp://help.openspecimen.org/user




Got feedback or spotted a mistake?

Leave a comment at the end of this page or email contact@krishagni.com