Site Configuration
This page details all of the options that can be configured in the miso.properties file. When setting up MISO, you
should go through this file in detail, ensuring that the settings all make sense for your site. Options marked with a *
are required. Others may be omitted, or commented out by placing a # at the start of the line.
Storage directories
miso.baseDirectory*
Base directory for MISO to store things in. Logs, and possibly other items will be created here by MISO. This is also
where MISO will look for the additional security.properties and submission.properties configuration files. An
absolute path should be specified.
miso.fileStorageDirectory*
Directory for storing any files uploaded to MISO. An absolute path should be specified.
miso.submissionStorageDirectory*
Directory for writing ENA submission files to. An absolute path should be specified.
General settings
miso.instanceName
A name to display in the header of every page. This is especially useful if you have multiple MISO instances, such as staging and production. Example below.
miso.timeCorrection.uiZone*
Time zone for the user interface. Times will be displayed in this time zone, and input will be taken in this time zone.
A full timezone name should be specified. e.g. Canada/Eastern. See 'TZ database name' column here:
https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
miso.fiscalYearStartMonth
Month (1-12) of fiscal year beginning. If specified, advanced search by fiscal year and quarter will be enabled.
miso.bugUrl
URL for users to report problems. If set, a "Report a problem" link will be added to the header of every page (see above image). The link will also appear on error pages. This could be used to link to
- Your internal issue tracker
- An email address if provided in the form
mailto:address@domain.com
Note that there is also a "Chat" link in the header that goes to the MISO users Gitter, where users can ask questions.
miso.newOptionSopUrl
URL of your SOP for adding new options such as scientific names, kits, and indices to MISO. If specified, a message and link will be shown at the top of several list pages under the Misc and Configuration menus.
miso.detailed.sample.enabled*
Set true to use detailed sample mode, or false for plain sample mode. Changing this setting after you have created
any samples is not supported as the data is not compatible between modes. Changing between plain and detailed sample
mode requires starting over with a fresh database.
See the User Manual for more information about detailed sample mode:
miso.autoGenerateIdentificationBarcodes*
Set false if your items already have barcodes assigned by some other system. Set true to have MISO generate and
assign barcodes for items you create.
Issue tracker
miso.issuetracker.tracker
If an issue tracker is configured, issues related to projects and runs will be displayed in MISO. The only valid setting
is jira, though support for other issue trackers may be added in the future. If specified, the
miso.issuetracker.jira.baseUrl and either the JIRA OAuth or HTTP Basic authentication properties (see below) must also
be set.
miso.issuetracker.jira.baseUrl
URL for JIRA.
miso.issuetracker.jira.oAuthConsumerKey
Consumer key to use for OAuth authentication to JIRA.
miso.issuetracker.jira.oAuthConsumerSecret
Consumer secret to use for OAuth authentication to JIRA.
miso.issuetracker.jira.oAuthSignatureMethod
Signature method to use for OAuth authentication to JIRA.
miso.issuetracker.jira.httpBasicAuthUsername
Username to use for HTTP basic authentication to JIRA.
miso.issuetracker.jira.httpBasicAuthPassword
Password to use for HTTP basic authentication to JIRA.
Email Notifications
These settings are used for sending transfer notifications and may be used for other notifications in the future.
miso.smtp.host
FQDN of SMTP server to send mail through. If host is unspecified, notifications will not be available.
miso.smtp.port
Port to use for sending email via SMTP. Defaults to 25 if not specified.
miso.smtp.ssl
Whether or not to use SSL for SMTP (true/false). Defaults to false if unspecified.
miso.smtp.username
Username for SMTP authentication. Authentication will not be performed if unspecified.
miso.smtp.password
Password for SMTP authentication. Authentication will not be performed if unspecified.
miso.smtp.fromAddress
Email address to display for sender of outgoing mail.
miso.smtp.fromName
Name to display for sender of outgoing mail. Defaults to "MISO" if unspecified.
miso.smtp.holdMinutes
Minimum number of minutes to wait before sending notifications. This allows time for the user to catch mistakes and revise the data or cancel the notification before it is sent. Defaults to 60 if unspecified.
miso.smtp.throttleMinutes
Defines the time window for throttling outgoing email. Defaults to 60 (minutes) if unspecified.
miso.smtp.throttleLimit
Number of emails that can be sent within the throttle window. Defaults to 25 if unspecified.
miso.smtp.internalDomain
Emails to this domain, if specified, will be considered internal. Internal emails will contain links to MISO entries.
miso.internalBaseUrl
MISO base URL (e.g. "https://miso.example.org"), used for generating links in emails to internal recipients. If unspecified, emails will not contain links to MISO entries.
Naming Schemes
MISO Naming Schemes are used to validate and generate entity String fields. They are used for all name fields, some
alias fields, and project codes.
miso.naming.scheme*
May be default, oicr, or v2, which have the default configurations shown below. The naming scheme can optionally
be customized further using the other miso.naming... properties as detailed below. Only the default scheme supports
plain sample mode. For detailed sample mode, v2 is recommended.
| default | oicr | v2 | |
|---|---|---|---|
| Name Generator | DefaultNameGenerator | DefaultNameGenerator | DefaultNameGenerator |
| Name Validator | DefaultNameValidator | DefaultNameValidator | DefaultNameValidator |
| Sample Alias Generator | none | OicrSampleAliasGenerator | V2SampleAliasGenerator |
| Sample Alias Validator | DefaultSampleAliasValidator | OicrSampleAliasValidator | V2SampleAliasValidator |
| Library Alias Generator | DefaultLibraryAliasGenerator | OicrLibraryAliasGenerator | V2LibraryAliasGenerator |
| Library Alias Validator | DefaultLibraryAliasValidator | OicrLibraryAliasValidator | V2LibraryAliasValidator |
| Library Aliquot Alias Generator | DefaultLibraryAliquotAliasGenerator | OicrLibraryAliquotAliasGenerator | V2LibraryAliquotAliasGenerator |
| Library Aliquot Alias Validator | DefaultLibraryAliquotAliasValidator | OicrLibraryAliasValidator | V2LibraryAliquotAliasValidator |
| Project Code Validator | AllowAnythingValidator | OicrProjectCodeValidator | OicrProjectCodeValidator |
| Configurable components | all | none | none |
miso.naming.generator.nameable.name
Change the generator for all entity names.
| Option | Example |
|---|---|
| default | SAM1 |
| classname | SampleImpl1 |
miso.naming.generator.sample.alias
Change the generator for sample aliases.
| Option | Example | Note |
|---|---|---|
| oicr | PROJ_0001_Ad_P_nn_1-1 | for use with DetailedSample only |
| v2 | PROJ_0001_02_SG03_04 | for use with DetailedSample only |
miso.naming.generator.library.alias
Change the generator for library aliases.
| Option | Example | Note |
|---|---|---|
| default | XX_LYY-1 | XX and YY taken from sample alias - depends on sample alias passing default validator with default regex |
| oicr | PROJ_0001_Ad_P_PE_300_WG | For use with DetailedSample only. Depends on sample alias passing oicr validator |
| v2 | PROJ_0001_02_LB05 | For use with DetailedSample only. Depends on tissue alias passing v2 validator |
miso.naming.generator.libraryaliquot.alias
Change the generator for library aliquot aliases.
| Option | Example | Note |
|---|---|---|
| default | XX_LYY-1 | This generator just copies the library's alias |
| oicr | PROJ_0001_Ad_P_PE_300_WG | For use with DetailedSample only. Depends on sample alias passing oicr validator |
| v2 | PROJ_0001_02_LB05-06 | For use with DetailedSample only. Depends on library alias passing v2 validator |
miso.naming.validator.nameable.name
Change the validator for all entity names.
| Option | Detail | Allow null | Allow duplicates | Custom Regex | Custom Duplication |
|---|---|---|---|---|---|
| default | Matches 'default' generator, or custom regex | no | no | yes | yes |
| allowany | Only checks that the name is not null | no | yes | no | no |
miso.naming.validator.sample.alias
Change the validator for sample aliases.
| Option | Detail | Allow null | Allow duplicates | Custom Regex | Custom Duplication |
|---|---|---|---|---|---|
| default | Default regex: ([A-z0-9]+)_S([A-z0-9]+)_(.*) |
no | no | yes | no |
| allowany | Only checks that the alias is not null | no | yes | no | no |
| oicr | Matches 'oicr' generator | no | no | no | no |
| v2 | Matches 'v2' generator | no | no | no | no |
miso.naming.validator.library.alias
Change the validator for library aliases.
| Option | Detail | Allow null | Allow duplicates | Custom Regex | Custom Duplication |
|---|---|---|---|---|---|
| default | Matches 'default' generator | no | no | yes | no |
| allowany | Only checks that the alias is not null | no | yes | no | no |
| oicr | Matches 'oicr' generator | no | no | no | no |
| v2 | Matches 'v2' generator | no | no | no | no |
miso.naming.validator.libraryaliquot.alias
Change the validator for library aliquot aliases.
| Option | Detail | Allow null | Allow duplicates | Custom Regex | Custom Duplication |
|---|---|---|---|---|---|
| default | Matches 'default' generator | no | yes | yes | yes |
| allowany | Only checks that the alias is not null | no | yes | no | no |
| oicr | Matches 'oicr' generator | no | no | no | no |
| v2 | Matches 'v2' generator | no | no | no | no |
miso.naming.validator.project.code
Change the validator for project codes.
| Option | Detail | Allow null | Allow duplicates | Custom Regex | Custom Duplication |
|---|---|---|---|---|---|
| allowany | Optional field, no format specified | yes | yes | no | no |
| oicr | 3-5 characters, CAPS and numbers only | no | no | no | no |
Custom regex
If a validator accepts custom regex, it can be configured via <base property>.regex. e.g.
miso.naming.validator.nameable.name.regex:.* to allow any name. A custom validator must be specified for this property
to be enabled - the naming scheme’s default validator will not be altered.
Custom duplication
If a validator accepts custom duplication, that can be configured via <base property>.duplicates. e.g.
miso.naming.validator.library.alias.duplicates:true to allow duplicate library aliases. A custom validator must be
specified for this property to be enabled - the naming scheme’s default validator will not be altered.
Secondary Naming Scheme
It is possible to configure a second naming scheme using the same properties above, except replacing naming with naming2,
e.g. miso.naming2.scheme=v2. When two naming schemes are configured, an extra field called "Use Secondary Naming Scheme"
is shown on the Edit Project page. If unselected, the primary naming scheme will be used for the project; if selected, the
secondary scheme is used instead. The secondary scheme will only ever be used for items that are tied to a single project. This
includes samples, libraries, and library aliquots. Other items, such as pools, boxes, and studies will always use the primary
naming scheme. When using two naming schemes, it is ideal to use the same name generator (nameable.name) in both in order
to maintain consistent names throughout MISO.
If you are switching to a new naming scheme and want it to be the default for new projects, you can make your current naming scheme secondary and the new one primary. Set all existing projects to use the secondary naming scheme, and they will continue to use the old scheme. This way, you don't have to select "Use Secondary Naming Scheme" for every new project.
Integration
miso.taxonLookup.enabled
Defaults to false if unspecified. If set to true, the NCBI taxon lookup service will be used to validate scientific
names.
miso.runscanner.urls
URLs of Run Scanners to use for populating and updating runs. Multiple Run Scanners can be specified separated by using a space to separate.
miso.runscanner.interval
Interval in milliseconds to poll Run Scanner(s). Defaults to 300000 (5 minutes) if unspecified;
miso.visionmate.servers
Config for VisionMate bulk barcode scanners. Enter in format <name>:<IP address>:<port>. Multiple scanners may be
specified by using a comma to separate.
Example: Lab 1 Scanner:192.168.0.120:8000,Lab 2 Scanner:192.168.0.121:8000
miso.project.report.links
Config for links to external project report services to display on Edit Project page. Enter in format
<link text>|<URI with placeholders>. Placeholders can be any of {id}, {name}, {code}. Multiple reports can
be specified by using a double backslash to separate.
Example: miso.project.report.links: External Project Link|http://example.com/{id}\\Another Project Link|http://example.com/project/{name}
For a project with ID 123 and name "PRO123," this will create an "External Project Link" link to
http://example.com/123 and an "Another Project Link" link to http://example.com/project/PRO123.
miso.run.report.links
Config for links to external run report services to display on Edit Run page. Enter in format
<PlatformTypes>|<link text>|<URI with placeholders>. Multiple platform types can be specified by separating with
commas. Placeholders can be any of {id}, {name}, {alias}. Multiple reports can be specified by using a double
backslash to separate.
Example: miso.run.report.links: Illumina,PacBio|Generic Run Report|http://example.com/{id}\\Illumina|Illumina Run Report|http://example.com/illumina/{alias}
For an Illumina run with ID 456 and alias "200723_D00789_0123_BCEHPCANXX," this will create a "Generic Run Report" link
to http://example.com/456 and an "Illumina Run Report" link to
http://example.com/illumina/200723_D00789_0123_BCEHPCANXX.
A PacBio run will only have the "Generic Run Report" link.
Bulk Table Customization
miso.defaults.sample.bulk.scientificname
Default scientific name to use when creating samples. Note that projects specify a reference genome and reference genomes may specify a default scientific name, which will override this setting.
miso.display.library.bulk.libraryalias
Defaults to true if unspecified. Set to false to hide the alias column when bulk creating/editing libraries. Only do
this if library aliases are always generated by MISO and you do not want to see them.
miso.display.library.bulk.description
Defaults to true if unspecified. Set to false to hide the description column when bulk creating/editing libraries.
miso.display.library.bulk.volume
Defaults to true if unspecified. Set to false to hide the volume column when bulk creating/editing libraries.
Index Checking
miso.pools.strictIndexChecking
Defaults to false if unspecified. If set to true, library aliquots with duplicate or near-duplicate indices cannot
be added to pools.
miso.pools.error.index.mismatches
Maximum number of mismatches to consider a duplicate index error. Defaults to 1 if unspecified.
miso.pools.error.index.mismatches.message
Error label to display for duplicate indices. Defaults to "DUPLICATE INDICES" if unspecified.
miso.pools.warning.index.mismatches
Maximum number of mismatches to consider a near-duplicate index warning. Defaults to 2 if unspecified.
miso.pools.warning.index.mismatches.message
Warning label to display for near-duplicate indices. Defaults to "Near-Duplicate Indices" if unspecified.