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.

Instance Name Header

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 short names.

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 ShortName Validator AllowAnythingValidator OicrProjectShortNameValidator OicrProjectShortNameValidator
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.shortName

Change the validator for project short names.

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

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}, {shortName}. 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.

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.