These are system-level setting and can be configured only by a "Super Administrator" user.
Steps to configure the settings:
- Log in as a user with 'Super Administrator' role
- Click on 'Settings' card from the home page
- Search the desired property using 'Search' box OR
- 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:
- With 'Enabled' and 'Disabled' options- Using these options user can enable/disabled the property
- Without 'Enabled' and 'Disabled' options- User can specify any desired values
Module: Administrative
| Added in | Property | Description | Possible Values |
|---|---|---|---|
| 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 |
**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
| Property | Description | Possible 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 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 |
Module: Biospecimen
| Property | Description | Possible Values |
|---|---|---|
| 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 |
Module: Catalog
| Property | Description | Possible Values |
|---|---|---|
| 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 |
Module: Common
| Property | Description | Possible Values |
|---|---|---|
| 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 between 20 to 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 | A maximum number of records that can be pre-validated before importing to the database. | 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 | |
| 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 |
Module: Email
| Property | Description | Possible Values |
|---|---|---|
| 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. |
Module: Notifications
| Added in | Property | Description | Possible 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 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 |
Module: Query
| Property | Description | Possible Values |
|---|---|---|
| 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 |
Module: Training
| Property | Description | Possible Values |
|---|---|---|
| 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 | http://help.openspecimen.org/containers |
| Collection Protocol | Link to training materials on how to manage collection protocols | http://help.openspecimen.org/collection |
| 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 | http://help.openspecimen.org/collection-protocol |
| Distribution Protocol | Link to training materials on how to manage distribution protocols | http://help.openspecimen.org/distribution |
| Form | Link to training materials on how to manage custom forms and fields | http://help.openspecimen.org/forms |
| 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 | http://help.openspecimen.org/institute |
| Job | Link to training materials on how to manage custom jobs | http://help.openspecimen.org/jobs |
| 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 | http://help.openspecimen.org/orders |
| Print Rules Setup | Link to training materials on how to create and manage specimen label print rules | http://help.openspecimen.org/print-label |
| Query | Link to training materials on how to query for data (reporting) | http://help.openspecimen.org/query |
| Role | Link to training materials on how to manage roles | http://help.openspecimen.org/roles |
| Shipping and Tracking | Link to training materials on how to manage specimen shipments | http://help.openspecimen.org/shipment |
| 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 |