Database setup

There are two types of BIGSdb database:

• sequence definition databases, containing

  • allele sequences and their identifiers

  • scheme data, e.g. MLST profile definitions

• isolate databases, containing

  • isolate provenance metadata

  • genome sequences

  • allele designations for loci defined in sequence definition databases.

These two databases are independent but linked. A single isolate database can communicate with multiple sequence definition databases and vice versa. Different access restrictions can be placed on different databases.

Databases are described in XML files telling BIGSdb everything it needs to know about them. Isolate databases can have any fields defined for the isolate table,allowing customisation of metadata - these fields are described in the XML file (config.xml) and must match the fields defined in the database itself.

Creating databases

There are templates available for the sequence definition and isolate databases. These are SQL scripts found in the sql directory.

To create a database, you will need to log in as the postgres user and use these templates. For example to create a new sequence definition database called bigsdb_test_seqdef, navigate to the sql directory and log in as the postgres user, e.g.

sudo su postgres

then

createdb bigsdb_test_seqdef
psql -f seqdef.sql bigsdb_test_seqdef

Create an isolate database the same way:

createdb bigsdb_test_isolates
psql -f isolatedb.sql bigsdb_test_isolates

The standard fields in the isolate table are limited to essential fields required by the system. To add new fields, you need to log in to the database and alter this table. For example, to add fields for country and year, first log in to the newly created isolate database as the postgres user:

psql bigsdb_test_isolates

and alter the isolate table:

ALTER TABLE isolates ADD country text;
ALTER TABLE isolates ADD year int;

Remember that any fields added to the table need to be described in the config.xml file for this database.

The xml directory of the software archive contains example XML files for sequence definition and isolate databases (rename these to config.xml). The isolates_config.xml file contains the minimum required isolate table fields and matches the isolate table that will be generated using the isolatedb.sql SQL script.

Database-specific configuration

Each BIGSdb database on a system has its own configuration directory, by default in /etc/bigsdb/dbases. The database has a short configuration name used to specify it in a web query and this matches the name of the configuration sub-directory, e.g. http://pubmlst.org/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_neisseria_isolates is the URL of the front page of the PubMLST Neisseria isolate database whose configuration settings are stored in /etc/bigsdb/dbases/pubmlst_neisseria_isolates. This database sub-directory contains a number of files (hyperlinks lead to the files used on the Neisseria database):

• config.xml - the database configuration file. Fields defined here correspond to fields in the isolate table of the database.

• banner.html - optional file containing text that will appear as a banner within the database index pages. HTML markup can be used within this text.

• header.html - HTML markup that is inserted at the top of all pages. This can be used to set up site-specific menubars and logos.

• footer.html - HTML markup that is inserted at the bottom of all pages.

• curate_header.html - HTML markup that is inserted at the top of all curator’s interface pages.

• curate_footer.html - HTML markup that is inserted at the bottom of all curator’s interface pages.

• profile_submit.html - HTML markup for text that is inserted in to the submission interface prior to profile submission finalization. This can be used to add specific instructions such as the requirement to make an isolate submission.

• allele_submit.html - HTML markup for text that is inserted in to the submission interface prior to allele submission finalization. This can be used to add specific instructions such as the requirement to attach Sanger trace files.

• registration_success.txt - Text file containing message content to be used in an automated E-mail when granting access to a user who has requested access to the database using the site-wide account system (where auto-registration is not enabled).

The header and footer files can alternatively be placed in the root directory of the web site, or in /etc/bigsdb, for site-wide use. If files exist in multiple locations, they are used in the following order of preference: database config directory > web root directory > /etc/bigsdb.

There are four additional files, site_header.html, site_footer.html, curate_site_header.html and curate_site_footer.html which are used when either bigsdb.pl or bigscurate.pl are called without a database configuration. These should be placed in the root directory of the web site or in /etc/bigsdb.

You can also add HTML meta attributes (such as a favicon) by including a file called meta.html in the database configuration directory. For example to set a favicon this file can contain something like the following:

<link rel="shortcut icon" href="/favicon.ico" type="image/ico" />

These attributes will appear in the <head> section of the HTML page.

XML configuration attributes used in config.xml

The following lists describes the attributes used in the config.xml file that is used to describe databases.

Isolate database XML attributes

Please note that database structure described by the field elements must match the physical structure of the database isolate table. Required attributes are in bold:

<db>

Top level element. Contains child elements: system and field.:

<system>

Any value set here can be overridden in a system.overrides file.

• authentication

  • Method of authentication: either ‘builtin’ or ‘apache’. See user authentication.

• db

  • Name of database on system.

• dbtype

  • Type of database: either ‘isolates’ or ‘sequences’.

• description

  • Description of database used throughout interface (see also ‘formatted_description’).

• align_limit

  • Overrides the sequence export record alignment limit in the Sequence Export plugin. Default: ‘200’.

• all_plugins

  • Enable all appropriate plugins for database: either ‘yes’ or ‘no’, default ‘no’.

• annotation

  • Semi-colon separated list of accession numbers with descriptions (separated by a |), eg. ‘AL157959|Z2491;AM421808|FAM18;NC_002946|FA 1090;NC_011035|NCCP11945;NC_014752|020-06’. Currently used only by Genome Comparator plugin.

• BLAST

  • Enable Blast plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the Blast plugin can be disabled by setting this attribute to ‘no’.

• BURST

  • Enable BURST plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the BURST plugin can be disabled by setting this attribute to ‘no’.

• cache_schemes

  • Enable automatic refreshing of scheme field caches when batch adding new isolates: either ‘yes’ or ‘no’, default ‘no’.

  • See scheme caching.

• CodonUsage

  • Enable Codon Usage plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the Codon Usage plugin can be disabled by setting this attribute to ‘no’.

• codon_usage_limit

  • Overrides the record limit for the Codon Usage plugin. Default: ‘500’.

• contig_analysis_limit

  • Overrides the isolate number limit for the Contig Export plugin. Default: ‘1000’.

• ContigExport

  • Enable contig export plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the contig export plugin can be disabled by setting this attribute to ‘no’.

• curate_config

  • The database configuration that should be used for curation if different from the current configuration. This is used when the submission system is being used so that curation links in the ‘Manage submissions’ pages for curators load the correct database configuration.

• curate_link

  • URL to curator’s interface, which can be relative or absolute. This will be used to create a link in the public interface dropdown menu.

• curate_path_includes

  • Partial path of the bigscurate.pl script used to curate the database. See user authentication.

• curate_script

  • Relative web path to curation script. Default ‘bigscurate.pl’ (version 1.11+).

  • This is only needed if automated submissions are enabled. If bigscurate.pl is in a different directory from bigsdb.pl, you need to include the whole web path, e.g. /cgi-bin/private/bigsdb/bigscurate.pl.

• curators_only

  • Set to ‘yes’ to prevent ordinary authenticated users having access to database configuration. This is only effective if read_access is set to ‘authenticated_users’. This may be useful if you have different configurations for curation and querying with some data hidden in the configuration used by standard users. Default ‘no’.

• daily_pending_submissions

  • Overrides the daily limit on pending submissions that a user can submit via the web submission system. Default: ‘15’.

• daily_rest_submissions_limit

  • Overrides the limit on number of submissions that can be made to the database via the RESTful interface. This is useful to prevent flooding of the submission system by aberrant scripts. Default: ‘100’.

• default_access

  • The default access to the database configuration, either ‘allow’ or ‘deny’. If ‘allow’, then specific users can be denied access by creating a file called ‘users.deny’ containing usernames (one per line) in the configuration directory. If ‘deny’ then specific users can be allowed by creating a file called ‘users.allow’ containing usernames (one per line) in the configuration directory. See default access.

• default_private_records

  • The default number of private isolate records that a user can upload. The user account must have a status of either ‘submitter’, ‘curator’, or ‘admin’. This value is used to set the private_quota field when creating a new user record (which can be overridden for individual users). Changing it will not affect the quotas of existing users. Default: ‘0’.

• default_seqdef_config

  • Isolate databases only: Name of the default seqdef database configuration used with this database. Used to automatically fill in details when adding new loci.

• default_seqdef_dbase

  • Isolate databases only: Name of the default seqdef database used with this database. Used to automatically fill in details when adding new loci.

• default_seqdef_script

  • Isolate databases only: URL of BIGSdb script running the seqdef database (default: ‘/cgi-bin/bigsdb/bigsdb.pl’).

• delete_retire_only

  • Set to ‘yes’ to retire the id of any isolate that is deleted. This prevents re-use of ids. This setting will override the global setting in bigsdb.conf.

• disable_updates

  • Set to ‘yes’ to prevent updates. This is useful when moving databases or temporarily running on a backup server.

• disable_update_message

  • Message shown when updates are disabled.

• eav_fields

  • Name to call sparsely-populated fields. Default: ‘secondary metadata’.

• eav_field_icon

  • Icon class from FontAwesome to use on isolate info page for sparsely- populated fields. Default ‘fas fa-microscope’.

• eav_groups

  • Comma-separated list of category names that sparsely-populated fields can be grouped in to. If this value is set, a category drop-down list will appear when adding or updating sparsely-populated fields. You can add an icon to appear by following the name with a pipe symbol (|) and an icon class from the FontAwesome library, e.g. ‘Vaccine reactivity|fas fa-syringe,Risk factors|fas fa-smoking’.

• export_limit

  • Overrides the default allowed number of data points (isolates x columns) to export. Default: ‘25000000’.

• fast_scan

  • Sets whether fast mode scanning is enabled via the web interface. This will scan all loci together, using exemplar sequences. In cases where multiple loci are being scanned this should be significantly faster than the standard locus-by-locus scan, but it will take longer for the first results to appear. Allele exemplars should be defined if you enable this option. Set to ‘yes’ to enable. Default: ‘no’.

• fieldgroup1 - fieldgroup10

  • Allows multiple fields to be queried as a group. Value should be the name of the group followed by a colon (:) followed by a comma-separated list of fields to group, e.g. identifiers:id,strain,other_name.

• formatted_description

  • Markdown formatted description of database. If set, this will be used throughout the HTML interface wherever formatting can be applied (main body of text) and overrides the value set in ‘db_description’. Currently only supports *italics* and **bold**.

• genepresence_record_limit

  • Overrides the record number limit (isolates x loci) for the Gene Presence plugin. Default: 500000 (this can also be set globally in bigsdb.conf).

• genepresence_taxa_limit

  • Overrides the isolate limit for the Gene Presence plugin. Default: 10000 (this can also be set globally in bigsdb.conf).

• GenomeComparator

  • Enable Genome Comparator plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the Genome Comparator plugin can be disabled by setting this attribute to ‘no’.

• genome_comparator_limit

  • Overrides the isolate number limit for the Genome Comparator plugin. Default: 1000 (this can also be set globally in bigsdb.conf).

• genome_comparator_max_ref_loci

  • Overrides the limit on number of loci allowed in a reference genome. Default: 10000.

• genome_comparator_threads

  • The number of threads to use for data gathering (BLAST, database queries) to populate data structure for Genome Comparator analysis. You should not set this to less than 2 as this will prevent job cancelling due to the way isolates are queued. Default: ‘2’.

• hide_unused_schemes

  • Sets whether a scheme is shown in a main results table if none of the isolates on that page have any data for the specific scheme: either ‘yes’ or ‘no’, default ‘no’.

• host

  • Host name/IP address of machine hosting isolate database, default ‘localhost’.

• itol_record_limit

  • Overrides the maximum number of records that can be included in an ITOL job. Default: 2000 (this can also be set globally in bigsdb.conf).

• itol_seq_limit

  • Overrides the maximum number of sequeneces (records x loci) that can be included in an ITOL job. Default: 100,000 (this can also be set globally in bigsdb.conf).

• job_priority

  • Integer with default job priority for offline jobs (default:5).

• job_quota

  • Integer with number of offline jobs that can be queued or currently running for this database.

• labelfield

  • Field that is used to describe record in isolate info page, default ‘isolate’.

• locus_aliases

  • Display locus aliases and use them in dropdown lists by default: must be either ‘yes’ or ‘no’, default ‘no’. This option can be overridden by a user preference.

• locus_superscript_prefix

  • Superscript the first letter of a locus name if it is immediately following by an underscore, e.g. f_abcZ would be displayed as fabcZ within the interface: must be either ‘yes’ or ‘no’, default ‘no’. This can be used to designate gene fragments (or any other meaning you like).

• maindisplay_aliases

  • Default setting for whether isolates aliases are displayed in main results tables: either ‘yes’ or ‘no’, default ‘no’. This setting can be overridden by individual user preferences.

• Microreact

  • Enable Microreact plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the Microreact plugin can be disabled by setting this attribute to ‘no’. Note that for the plugin to be active, a country field containing a defined list of allowed values and an integer year field must be defined in the isolates table.

• microreact_record_limit

  • Overrides the maximum number of records that can be included in a Microreact job. Default: 2000 (this can also be set globally in bigsdb.conf).

• microreact_seq_limit

  • Overrides the maximum number of sequences (records x loci) that can be included in an Microreact job. Default: 100,000 (this can also be set globally in bigsdb.conf).

• new_version

  • Set to ‘no’ to prevent copying field value when creating a new version of the isolate record.

• noshow

  • Comma-separated list of fields not to use in breakdown statistic plugins.

• no_publication_filter

  • Isolate databases only: Switches off display of publication filter in isolate query form by default: either ‘yes’ or ‘no’, default ‘no’.

• only_sets

  • Don’t allow option to view the ‘whole database’ - only list sets that have been defined: either ‘yes’ or ‘no’, default ‘no’.

• password

  • Password for access to isolates database, default ‘remote’.

• pcr_limit

  • Overrides the isolate number limit for the in silico PCR plugin. Default: ‘10000’.

• PhyloViz

  • Enable third party PhyloViz plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the PhyloViz plugin can be disabled by setting this attribute to ‘no’.

• port

  • Port number that the isolate host is listening on, default ‘5432’.

• privacy

  • Displays E-mail address for sender in isolate information page if set to ‘no’. Default ‘yes’.

• public_login

  • Optionally allow users to log in to a public database - this is useful as any jobs will be associated with the user and their preferences will also be linked to the account. Set to ‘no’ to disable. Default ‘yes’.

• query_script

  • Relative web path to bigsdb script. Default ‘bigsdb.pl’ (version 1.11+).

  • This is only needed if automated submissions are enabled. If bigsdb.pl is in a different directory from bigscurate.pl, you need to include the whole web path, e.g. /cgi-bin/bigsdb/bigsdb.pl.

• read_access

  • Describes who can view data: either ‘public’ for everybody or ‘authenticated_users’ for anybody who has been able to log in. Default ‘public’.

• recommended_schemes

  • Comma-separated list of recommended schemes to suggest to Genome Comparator users. If lots of schemes are defined, a user may be tempted to click ‘All loci’ and this may not be the best option. Populating this attribute, results in an additional list of preferred schemes that can be chosen.

• related_databases

  • Semi-colon separated list of links to related BIGSdb databases on the system. This should be in the form of database configuration name followed by a ‘|’ and the description, e.g. ‘pubmlst_neisseria_seqdef|Sequence and profile definitions’. This is used to populate the dropdown menu.

• remote_contigs

  • Optionally allow the use of remote contigs. These are stored in a remote BIGSdb database, accessible via the RESTful API. Set to ‘yes’ to enable.

• rest_kiosk

  • If ‘kiosk’ attribute is set, then the REST interface will be disabled for the configuration unless a value is set here. The only supported value currently is ‘sequenceQuery’ which will enable API routes for querying sequences.

• rMLSTSpecies

  • Enable rMLST Species identifier plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the plugin can be disabled by setting this attribute to ‘no’. Note that for the plugin to be active, a country field containing a defined list of allowed values and an integer year field must be defined in the isolates table.

• script_path_includes

  • Partial path of the bigsdb.pl script used to access the database. See user authentication.

• SeqbinBreakdown

  • Enable Sequence bin breakdown plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the plugin can be disabled by setting this attribute to ‘no’. Note that for the plugin to be active, a country field containing a defined list of allowed values and an integer year field must be defined in the isolates table.

• seqbin_size_threshold

  • Sets the size values in Mbp to enable for the seqbin filter.

  • Example: seqbin_size_threshold=”0.5,1,2,4”.

• seq_export_limit

  • Overrides the sequence export limit (records x loci) in the Sequence Export plugin. Default: ‘1000000’.

• sets

  • Use sets: either ‘yes’ or ‘no’, default ‘no’.

• set_id

  • Force the use of a specific set when accessing database via this XML configuration: Value is the name of the set.

• start_id

  • Defines the minimum record id to be used when uploading new isolate records. This can be useful when it is anticipated that two databases may be merged and it would be easier to do so if the id numbers in the two databases were different. Default: ‘1’.

• submissions

  • Enable automated submission system: either ‘yes’ or ‘no’, default ‘no’ (version 1.11+).

  • The curate_script and query_script paths should also be set, either in the bigsdb.conf file (for site-wide configuration) or within the system attribute of config.xml.

• submissions_deleted_days

  • Overrides the default number of days before closed submissions are deleted from the system. Default: ‘90’.

• TagStatus

  • Enable Tag status plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the plugin can be disabled by setting this attribute to ‘no’. Note that for the plugin to be active, a country field containing a defined list of allowed values and an integer year field must be defined in the isolates table.

• tblastx_tagging

  • Sets whether tagging can be performed using TBLASTX: either ‘yes’ or ‘no’, default ‘no’.

• total_pending_submissions

  • Overrides the total limit on pending submissions that a user can submit via the web submission system. Default: ‘20’.

• user

  • Username for access to isolates database, default ‘apache’.

• user_job_quota

  • Integer with number of offline jobs that can be queued or currently running for this database by any specific user - this parameter is only effective if users have to log in.

• user_projects

  • Sets whether authenticated users can create their own projects in order to group isolates: either ‘yes’ or ‘no’, default ‘no’.

• view

  • Database view containing isolate data, default ‘isolates’.

• views

  • Comma-separated list of views of the isolate table defined in the database. This is used to set a view for a set, or to restrict loci or schemes to a subset of isolate data.

• webroot

  • URL of web root, which can be relative or absolute. This is used to provide a hyperlinked item in the dropdown menu. Default ‘/’.

• webroot_label

  • Label text for the breadcrumb link defined by the webroot value. This can be formatted using Markdown. Currently only supports *italics* and **bold**.

<field>

Element content: Field name + optional list <optlist> of allowed values, e.g.:

<field type="text" required="no" length="40" maindisplay="no"
   web="http://somewebsite.com/cgi-bin/script.pl?id=[?]" optlist="yes">epidemiology
  <optlist>
   <option>carrier</option>
   <option>healthy contact</option>
   <option>sporadic case</option>
   <option>endemic</option>
   <option>epidemic</option>
   <option>pandemic</option>
  </optlist>
</field>

• type

  • Data type: int, text, float, bool, or date.

• comments * optional

  • Comments about the field. These will be displayed in the field description plugin and as tooltips within the curation interface.

• curate_only

  • Set to ‘yes’ to hide field unless logged-in user is a curator or admin.

• default

  • Default value. This will be entered automatically in the web form but can be overridden.

• dropdown

  • Select if you want this field to have its own dropdown filter box on the query page. If the field has an option list it will use the values in it, otherwise all values defined in the database will be included: ‘yes’ or ‘no’, default ‘no’. This setting can be overridden by individual user preferences.

• length

  • Length of field, default 12.

• log_delete

  • Sets if the field value will be recorded in the log table if the isolate is deleted. Set to ‘yes’ or ‘no’, default is ‘no’. The id and isolate name are always recorded if deletion is logged.

• maindisplay

  • Sets if field is displayed in the main table after a database search, ‘yes’ or ‘no’, default ‘yes’. This setting can be overridden by individual user preferences.

• max

  • Maximum value for integer and date types. Special values such as CURRENT_YEAR and CURRENT_DATE can be used.

• min

  • Minimum value for integer and date types.

• multiple

  • Sets if field allows multiple values to be set for it, ‘yes’ or ‘no’, default ‘no’. If set to ‘yes’, then the underlying field in the database must be an ARRAY type, e.g. text[].

• no_curate

  • Setting this will hide the field in the curator interface and prevent it from being manually modified. This is useful for fields that are populated by automated scripts or database triggers. Can be ‘yes’ or ‘no’, default ‘no’.

• no_submissions

  • Setting this will hide the field in the submission template. The field is still available if it is added back to the template manually.

• optlist

  • Sets if this field has a list of allowed values, default ‘no’. Surround each option with an <option> tag.

• regex

  • Regular expression used to constrain field values, e.g. regex=”^[A-Z].*$” forces the first letter of the value to be capitalized.

• required

  • Sets if data is required for this field, ‘yes’ or ‘no’, default ‘yes’.

• userfield

  • Select if you want this field to have its own dropdown filter box of users (populated from the users table): ‘yes’ or ‘no’, default ‘no’.

• web

  • URL that will be used to hyperlink field values. If [?] is included in the URL, this will be substituted for the actual field value.

Special values

The following special variables can be used in place of an actual value:

• CURRENT_DATE: current date in yyyy-mm-dd format

• CURRENT_YEAR: the 4 digit value of the current year

Sequence definition database XML attributes

Required attributes are in bold.

<db>

Top level element. Contains child element: system.

<system>

Any value set here can be overridden in a system.overrides file.

• authentication

  • Method of authentication: either ‘builtin’ or ‘apache’. See user authentication.

• db

  • Name of database on system.

• dbtype

  • Type of database: either ‘isolates’ or ‘sequences’.

• description

  • Description of database used throughout interface.

• align_limit

  • Overrides the sequence export record alignment limit in the Sequence Export plugin. Default: ‘200’.

• allele_comments

  • Enable comments on allele sequences: either ‘yes’ or ‘no’, default ‘no’.

  • This is not enabled by default to discourage the practice of adding isolate information to allele definitions (this sort of information belongs in an isolate database).

• allele_flags

  • Enable flags to be set for alleles: either ‘yes’ or ‘no’, default ‘no’.

• BURST

  • Enable BURST plugin: either ‘yes’ or ‘no’. If no value is set then the plugin will not be available unless the all_plugins attribute is set to ‘yes’. If the all_plugins attribute is set to ‘yes’, the BURST plugin can be disabled by setting this attribute to ‘no’.

• curate_config

  • The database configuration that should be used for curation if different from the current configuration. This is used when the submission system is being used so that curation links in the ‘Manage submissions’ pages for curators load the correct database configuration.

• curate_path_includes

  • Partial path of the bigscurate.pl script used to curate the database. See user authentication.

• curate_script

  • Relative web path to curation script. Default ‘bigscurate.pl’ (version 1.11+).

  • This is only needed if automated submissions are enabled. If bigscurate.pl is in a different directory from bigsdb.pl, you need to include the whole web path, e.g. /cgi-bin/private/bigsdb/bigscurate.pl.

• curators_only

  • Set to ‘yes’ to prevent ordinary authenticated users having access to database configuration. This is only effective if read_access is set to ‘authenticated_users’. This may be useful if you have different configurations for curation and querying with some data hidden in the configuration used by standard users. Default ‘no’.

• daily_pending_submissions

  • Overrides the daily limit on pending submissions that a user can submit via the web submission system. Default: ‘15’.

• daily_rest_submissions_limit

  • Overrides the limit on number of submissions that can be made to the database via the RESTful interface. This is useful to prevent flooding of the submission system by aberrant scripts. Default: ‘100’.

• delete_retire_only

  • Set to ‘yes’ to retire the id of any allele or profile that is deleted. This prevents re-use of ids. This setting will override the global setting in bigsdb.conf.

• diploid

  • Allow IUPAC 2-nuclotide ambiguity codes in allele definitions for use with diploid typing schemes: either ‘yes’ or ‘no’, default ‘no’.

• disable_seq_downloads

  • Prevent users or curators from downloading all alleles for a locus (admins always can). ‘yes’ or ‘no’, default ‘no’.

• exemplars

  • Use exemplar sequences in the BLAST caches used for the sequence query pages. This is useful on larger databases as it speeds up the query significantly. Exemplar alleles MUST be defined otherwise sequence queries will fail. ‘yes’ or ‘no’, default ‘no’.

• formatted_description

  • Markdown formatted description of database. If set, this will be used throughout the HTML interface wherever formatting can be applied (main body of text) and overrides the value set in ‘db_description’. Currently only supports *italics* and **bold**.

• isolate_database

  • The config name of the isolate database. This is used to provide a link to isolate submissions. You also need to set isolate_submissions=”yes”.

• isolate_submissions

  • Set to yes to provide a link to isolate submissions. The isolate_database attribute also needs to be set. Default: ‘no’.

• job_priority

  • Integer with default job priority for offline jobs (default:5).

• job_quota

  • Integer with number of offline jobs that can be queued or currently running for this database.

• kiosk

  • Set to a page name to restrict configuration to always start on this page, rather than an index page. This faciliates running in a cut-down kiosk mode that doesn’t allow access to all features. Currently only ‘sequenceQuery’ is supported.

• kiosk_allowed_pages

  • Comma-separated list of pages that the configuration is allowed to show, apart from the page set in the ‘kiosk’ attribute. Example for a sequence query configuration would be ‘sequenceTranslate’ to allow access to the translated sequence page following a query.

• kiosk_help

  • URL to context-sensitive help page.

• kiosk_locus

  • Restrict sequence query to a specific locus or scheme. Use either the locus primary name or ‘SCHEME_X’ where X is the scheme number.

• kiosk_no_genbank

  • Set to “yes” to hide the Genbank accesssion form element in kiosk mode.

• kiosk_no_upload

  • Set to “yes” to hide the sequence file upload in kiosk mode.

• kiosk_simple

  • Remove most explanatory text from kiosk page.

• kiosk_text

  • Alternative text to show on kiosk page.

• kiosk_title

  • Title text to use when running in kiosk mode.

• profile_submissions

  • Enable profile submissions (automated submission system): either ‘yes’ or ‘no’, default ‘no’ (version 1.11+).

  • To enable, you will also need to set submissions=”yes”. By default, profile submissions are disabled since generally new profiles should be accompanied by representative isolate data, and the profile can be extracted from that.

• public_login

  • Optionally allow users to log in to a public database - this is useful as any jobs will be associated with the user and their preferences will also be linked to the account. Set to ‘no’ to disable. Default ‘yes’.

• query_script

  • Relative web path to bigsdb script. Default ‘bigsdb.pl’ (version 1.11+).

  • This is only needed if automated submissions are enabled. If bigsdb.pl is in a different directory from bigscurate.pl, you need to include the whole web path, e.g. /cgi-bin/bigsdb/bigsdb.pl.

• read_access

  • Describes who can view data: either ‘public’ for everybody, or ‘authenticated_users’ for anybody who has been able to log in. Default ‘public’.

• related_databases

  • Semi-colon separated list of links to related BIGSdb databases on the system. This should be in the form of database configuration name followed by a ‘|’ and the description, e.g. ‘pubmlst_neisseria_isolates|Isolates’. This is used to populate the dropdown menu.

• script_path_includes

  • Partial path of the bigsdb.pl script used to access the database. See user authentication.

• seq_export_limit

  • Overrides the sequence export limit (records x loci) in the Sequence Export plugin. Default: ‘1000000’.

• sets

  • Use sets: either ‘yes’ or ‘no’, default ‘no’.

• set_id

  • Force the use of a specific set when accessing database via this XML configuration: Value is the name of the set.

• submissions

  • Enable automated submission system: either ‘yes’ or ‘no’, default ‘no’ (version 1.11+).

  • The curate_script and query_script paths should also be set, either in the bigsdb.conf file (for site-wide configuration) or within the system attribute of config.xml.

• submissions_deleted_days

  • Overrides the default number of days before closed submissions are deleted from the system. Default: ‘90’.

• total_pending_submissions

  • Overrides the total limit on pending submissions that a user can submit via the web submission system. Default: ‘20’.

• user_job_quota

  • Integer with number of offline jobs that can be queued or currently running for this database by any specific user - this parameter is only effective if users have to log in.

• webroot

  • URL of web root, which can be relative or absolute. This is used to provide a hyperlinked item in the dropdown menu. Default ‘/’.

• webroot_label

  • Label text for the breadcrumb link defined by the webroot value. This can be formatted using Markdown. Currently only supports *italics* and **bold**.

Over-riding global defaults set in bigsdb.conf

Certain values set in bigsdb.conf can be over-ridden by corresponding values set in a database-specific config.xml file. These can be set within the system tag like other attributes:

• query_script

  • Relative web path to bigsdb script.

• curate_script

  • Relative web path to curation script.

• prefs_db

  • The name of the preferences database.

• auth_db

  • The name of the authentication database.

• tmp_dir

  • Path to the web-accessible temporary directory.

• secure_tmp_dir

  • Path to the web-inaccessible (secure) temporary directory.

• ref_db

  • The name of the references database.

Over-riding values set in config.xml

Any attribute used in the system tag of the database config.xml file can be over-ridden using a file called system.overrides, placed in the same directory as config.xml. This is very useful as it allows you to set up multiple configs for a database, with the config.xml files symlinked so that any changes to one will be seen in each database configuration. An example of why you may wish to do this would be if you create separate public and private views of the isolate table that filters on some attribute. The system.overrides file uses key value pairs separated by = with the values quoted, e.g.

view="private"
read_access="authenticated_users"
description="Private view of database"

It is also possible to override the required or maindisplay attribute of a particular field using a file called field.overrides. The field.overrides file uses the format ‘field:attribute=”value”’ on each line, e.g.

date_received:required="yes"

Setting field validation rules

Sometimes it may be necessary to restrict the allowed values in one isolate field depending on the values submitted for another field. It is possible to do this using field validation rules. These combine one or more conditions which all have to match for validation to fail and an isolate record upload to be rejected.

An example of this may be if you have an age_year and an age_month field but you only want age_month to be populated if the subject is less than one year old. You can do this as follows.

As an admin, on the curator interface, click the ‘Field’ toggle to show the validation table links. Then click ‘Add’ on the ‘Validation conditions’ setting:

Add the following conditions separately:

• age_year > 0

• age_month NOT null

Now add a new ‘Validation rule’, by clicking ‘Add’ on the ‘Validation rules’ setting:

Here you just enter the message that will be returned when the validation fails:

Finally add the conditions to the rule by clicking ‘Add’ on the ‘Rule conditions’ setting:

Select the rule message and the condition from the dropdown boxes:

Make sure you do this for each of the conditions that have to match.

Validation checks are performed when adding or updating an isolate record, or when a user submits via the automated submission interface. Currently these checks are not enforced when doing a batch update.

Special condition values

Use the value null to indicate that the field is empty, e.g.

• age_month NOT null

Use a field name in square brackets to compare the value in that field, e.g. suppose you have two date fields, ‘date_sampled’ and ‘date_received’, and you want to ensure that ‘date_received’ is not before ‘date_sampled’. You can do this with the following condition:

• date_received < [date_sampled]

The two fields have to be of the same data type in order to be compared (you cannot compare a text field to an integer field for example).

Sparsely-populated fields

Commonly used isolate fields should be described in the config.xml file and included as columns within the isolates table. Sometimes, however, you may have a need to record information that is only likely to be found in a minority of records. This can be done more efficiently with the use of sparsely-populated fields. These are stored differently in the database (using an entity-attribute-value [EAV] model) but can still be searched and exported in a similar way to normal fields. There is no limit to the number of such fields that can be defined.

The default name for these fields is ‘secondary metadata’ and this is how they will be grouped in the interface. You can change this by setting the ‘eav_fields’ attribute in the system tag of config.xml. It is also possible to group these fields in to categories - these can be defined with a comma-separated list in the ‘eav_groups’ attribute in the system tag of config.xml.

You will need to be an admin to define sparely-populated fields. Make sure that the ‘Fields’ toggle is selected on the curators’ page. Click the add (+) button on the ‘Sparse fields’ function.

Fill in the form and click ‘Submit’.

Field options are:

• field

  • name of field

• value_format

  • date type - either integer, float, text, date or boolean.

• no_curate

  • Set to true to prevent user updates of fieldThis setting could be used if the value is calculated by an external script rather than entered by a curator.

• no_submissions

  • Set to true to prevent the field being listed in the submissions template.

• description

  • Tooltip text that will appear on curator forms.

• length

  • Restrict allowed length of value.

• option_list

  • Semi-colon separated list of allowed values.

• value_regex

  • Regular expression that can constrain allowed values.

• conditional_formatting

  • Semi-colon separated list of values - each consisting of the value, followed by a pipe character (|) and HTML to display instead of the value. If you need to include a semi-colon within the HTML, use two semi-colons (;;) otherwise it will be treated as the list separator.’

• html_link_text

  • This defines the text that will appear on an information link that will trigger a slide-in message (if defined int the next field). Default is ‘info’.

• html_message

  • This message will slide-in on the isolate information page when the field value is populated and the information link is clicked. Full HTML formatting is supported.

• min_value

  • Valid for number fields only.

• max_value

  • Valid for number fields only.

• field_order

  • Integer indicating the order that fields should be displayed. If this is not set they will appear alphabetically.

Kiosk mode

Kiosk mode allows you to run a cut-down interface that offers a single main functionality. Currently, only a sequence query page is supported. The interface is locked down so that only specified functionality is supported and data cannot be exported.

See the kiosk_* attributes in config.xml.

As an example, the following settings are used for the rMLST ‘Identify species’ tool at https://pubmlst.org/rmlst/. The database usually requires a user to log in, but this tool offers a restricted functionality without logging in.

kiosk="sequenceQuery"
kiosk_allowed_pages="sequenceTranslate"
kiosk_title="Identify species"
kiosk_locus="SCHEME_1"
kiosk_simple="yes"
kiosk_no_upload="no"
kiosk_no_genbank="no"
rest_kiosk="sequenceQuery"

When you go to this example kiosk page you see only the sequence query page and trying to access any other functionality is prevented.

The rest_kiosk attribute enables queries to also be performed using the RESTful API which will be similarly locked down.

User authentication

You can choose whether to allow Apache to handle your authentication or use built-in authentication.

Apache authentication

Using apache to provide your authentication allows a flexible range of methods and back-ends (see the Apache authentication HowTo for a start, or any number of tutorials on the web).

At its simplest, use a .htaccess file in the directory containing the bigscurate.pl (and bigsdb.pl for restriction of read-access) script or by equivalent protection of the directory in the main Apache server configuration. It is important to note however that, by default, any BIGSdb database can be accessed by any instance of the BIGSdb script (including one which may not be protected by a .htaccess file, allowing public access). To ensure that only a particular instance (protected by a specific htaccess directive) can access the database, the following attributes can be set in the system tag of the database XML description file:

• script_path_includes: the BIGSdb script path must contain the value set.

• curate_path_includes: the BIGSdb curation script path must contain the value set.

For public databases, the ‘script_path_includes’ attribute need not be set.

To use apache authentication you need to set the authentication attribute in the system tag of the database XML configuration to ‘apache’.

Built-in authentication

BIGSdb has its own built-in authentication, using a separate database to store password and session hashes. The advantages of using this over many forms of apache authentication are:

• Users are able to update their own passwords.

• Passwords are not transmitted over the Internet in plain text.

When a user logs in, the server provides a random one-time session variable and the user is prompted to enter their username and password. The password is encrypted within the browser using a Javscript one-way hash algorithm, and this is combined with the session variable and hashed again. This hash is passed to the server. The server compares this hash with its own calculated hash of the stored encrypted password and session variable that it originally sent to the browser. Implementation is based on perl-md5-login. Stored passwords are salted and hashed using bcrypt.

To use built-in authentication you need to set the authentication attribute in the system tag of the database XML configuration to ‘builtin’.

Setting up the admin user

The first admin user needs to be manually added to the users table of the database. Connect to the database using psql and add the following (changing details to suit the user).:

INSERT INTO users (id, user_name, surname, first_name, email, affiliation, status, date_entered,
datestamp, curator) VALUES (1, 'keith', 'Jolley', 'Keith', 'keith.jolley@zoo.ox.ac.uk',
'University of Oxford, UK', 'admin', 'now', 'now', 1);

If you are using built-in authentication, set the password for this user using the add_user.pl script. This hashes the password and stores this within the authentication database. Other users can be added by the admin user from the curation interface accessible from http://your_website/cgi-bin/private/bigscurate.pl?db=test_db (or wherever you have located your bigscurate.pl script).

Retrieving PubMed citations from NCBI

Publications listed in PubMed can be associated with individual isolate records, profiles, loci and sequences. Full citations for these are stored within a local reference database, enabling these to be displayed within isolate records and searching by publication and author. This local database is populated by a script that looks in BIGSdb databases for PubMed records not locally stored and then requests the full citation record from the PubMed database.

The script is called retrieve_pubmed_records.pl and can be found in the scripts/maintenance directory.

Simply run the script either as the ‘postgres’ user or an account that is allowed to connect as the postgres user.

This should be run periodically from a CRON job, e.g. every hour.

Configuring access to remote contigs

It is possible for isolate records to have contigs in an external BIGSdb database. These must be accessible via the RESTful API. The advantage of this is that it enables multiple isolate databases to use the same genome assemblies without having to duplicate the storage of those assemblies. If access to the external database requires authenticated access, OAuth settings can be set to enable contig retrieval.

To enable remote contigs, set the remote_contigs attribute in the <system> tag of config.xml, i.e.

remote_contigs = "yes"

Setting up authentication

A client key for the BIGSdb remote contig manager needs to be generated. This can be done using the create_client_credentials.pl script, e.g.

create_client_credentials.pl --a 'BIGSdb remote contig manager' --insert

This will generate a client id (key) and a client secret and add them to the authentication database.

You will then need to obtain an access token and access secret using the client key and secret with the get_oauth_access_token.pl script. You will need to enter the API database URI (e.g. http://rest.pubmlst.org/db/pubmlst_rmlst_isolates) and the web database URL (e.g. https://pubmlst.org/bigsdb?db=pubmlst_rmlst_isolates). You will then be prompted to follow a link and log in to the database with your user credentials. A verification code will be generated. You need to enter this in to the script when prompted. An access token and secret will be returned to you.

From the curators’ page, click the oauth credentials add link in the administrator settings. This function is normally hidden, so you may need to click the ‘Misc’ toggle to display it.

Populate the OAuth_credentials table with the client key/secret and access token/secret. You should also enter the root REST URI for the database (e.g. http://rest.pubmlst.org/db/pubmlst_rmlst_isolates).

Processing remote contigs

When remote contigs are first linked to a record, the sequences are downloaded in bulk (without their metadata). This allows the sequence lengths to be recorded as this is needed for various queries and outputs. The curator is then given an option to process the contigs, which involves downloading each contig individually to record metadata including the original designation and the sequence platform used. This may take a while so it may be preferable to perform this task offline. This can be done using the process_remote_contigs.pl script found in the scripts/automation directory. Options for using this script are shown below:

remote_contigs.pl --help
NAME
    process_remote_contigs.pl
    Download, check length and create checksum contigs stored as URIs

SYNOPSIS
    process_remote_contigs.pl --database NAME [options]

OPTIONS

--database NAME
    Database configuration name.

--exclude_isolates LIST
    Comma-separated list of isolate ids to ignore.

--exclude_projects LIST
    Comma-separated list of projects whose isolates will be excluded.

--help
    This help page.

--isolates LIST
    Comma-separated list of isolate ids to scan (ignored if -p used).

--isolate_list_file FILE
    File containing list of isolate ids (ignored if -i or -p used).

--min ID
    Minimum isolate id.

--max ID
    Maximum isolate id.

--projects LIST
    Comma-separated list of project isolates to scan.

--quiet
    Only display errors.