ArrayServer.cfg for v12

From Array Suite Wiki

This is a comprehensive list of ArrayServer.cfg options. Options should be added to the proper section, indicated by [SectionName].

License section

Identified by [License] in configuration file. 

[License]
CompanyName=rockwellautomation
LicenseNumber=4
ExpirationDate=January 2, 2022
LicenseKey=40505124513131511

Option section

Identified by [Option] in configuration file. Options include:

Administrative Options


Analytical Server Options

Connection Options

Basic

Email Options

{{Tips|QIAGEN No longer provides an SMTP relay service via arrayserver.queue@qiagen.com. If your e-mail service supports Basic SMTP Authorization, you can add connection information into these fields to connect to your own server.

FTP Options

Proxy Options

Other connection options


Database Options

Directory Options

Sample, SampleSets, and Project Options


Logger Options

Starting from v12.3, the settings for the new logging functionality can be configured in ArrayServer.cfg in the [ Logger ] section. The settings are taken into account only after the server process is restarted. For more detais, see: OmicSoft Server logger settings page

Default URL Options

User Configuration Options

Genome Browser Options

Land

Cloud section

In the [Cloud] section:

Tips.png Also read ArrayServer Configuration with Cloud.


CloudFolder section

Mapped folders to Cloud should be listed here. For more information and examples, please see ArrayServer Configuration with Cloud.


CloudInstanceTag section

These parameters go in the [CloudInstanceTag] section, for labeling cloud instances for cost-control and tracking purposes. For more information, please see CloudInstanceTag.

CloudVolumeTag Section

These parameters go in the [CloudVolumeTag] section, for labeling cloud instances for cost-control and tracking purposes. For more information, please see CloudVolumeTag.


CFRPart11 section

In the [CFRPart11] section. Code of Federal Regulations Title 21, Part 11 specifies rules for electronic records. These parameters focus on password expiration and session timeout lengths. To be active, UserAuthorization must be set to True.

Land section

By default, land configuration file is a separate file, LandDataName.cfg, located in the $LandDirectory/LandDataName. However, user can also specify land directly in ArrayServer.cfg, identified by [Land] in the configuration file for each land data.

Tips.png Also read ArrayLand Configuration Options and LandDirectory

Filter section

Identified by the [Filter] section in configuration file.

  • Lists the meta data fields that can be used for filtering returned project searches, as well as criterion in the Custom tab for Add Criterion.
  • If the section is not specified, default fields will be returned ("Category", "Keywords", "PublishedBy", "PublishDate", "Organism", "StudyType", "Platform", "PlatformType", "PlatformOrganism", "PlatformTechnology", "SoftwareUsed, "Title").

Folder section

Identified by [Folder] section in configuration file.

  • Lists the folders that the user wants Array Server to monitor (for the client, they will be able to browse/search the files in the watched folders if they have read access to the files).
  • Each folder should be put on a separate line, and the format for each line is
  • for Windows single server configuration
FolderAlias=\\192.168.1.xxx\Data\TestDataSets
  • for Linux single server configuration,
FolderAlias=/media/Data/TestDataSets
  • for distributed server folder configuration (Master and Analytic servers).
FolderAlias=FullPathWindows | FullPathLinux | AnalyticalServerName
e.g DataTransfer=\\192.168.1.xxx\Data\DataTransfer|/media/Data/data_transfer|AnalyticServer1
In the example above, DataTransfer is the alias of the folder, and the Windows full path for the watched folder is "\\192.168.1.xxx\Data\DataTransfer", Linux full path is "/media/Data/data_transfer". The folder belongs to AnalyticServer1, which must be specified in the [AnalyticServers] section. The "ownership" of this folder can be used in some modules to redirect analysis to the appropriate analytic server.
  • Use Manage Users to specify folder permissions for read and write access.
  • It is not required to have both a Windows and Linux mapping, however, if this cannot be provided, the administrator should place instead an informative message that can be shown to the users, i.e
DataTransfer=\\192.168.1.xxx\Data\DataTransfer|No_Linux_Users_Folder_Mapped|AnalyticServer1

Tips.png Also read ArrayServer folder mapping and management


SearchProject section

Identified by [SearchProject] in configuration file.

Specifies the search project user interface tabs for the user. Each line in the section will specify either a branch of the category tree (e.g. Disease=Diseases) or a project meta data field (e.g. Organism and Platform).

For the first type of SearchProject tab, the format is “BranchAlias=BranchPath”. In the example above, Disease is the alias of the branch, and Diseases is the branch path. If the user would like to specify deeper levels of a branch, the user will need to use “\” to separate different levels (e.g. Location=CompanyName\By Location”).

For the second type of SearchProject tab, the meta data field must be either a Select type or a Combo InputType (it cannot be an "Input" InputType meta data field). The following user interface illustrates the concept.

SearchProjectTab.png


AnalyticServers

Used to specify the location, name, ServerProjects, and Users folder location of each Analytic folder.

Each server should have the following format: 

tcp://addressOfServer:port/RemoteServer | Name of Server | \\UsersFolderWindowsMapping | /UsersFolderLinuxMapping | \\ServerProjectsWindowsMapping | /ServerProjectsLinuxMapping | Server Description

An example is shown again below: 

tcp://192.168.1.128:8065/RemoteServer|WindowsServer|\\192.168.1.xxx\Data\Users|/home/omicsoft/fileserver/Data/Users|\\192.168.1.xxx\Data\ServerProjects|/home/omicsoft/fileserver/Data/ServerProjects
|server#1 description

A few points of note:

  • It is not required to have both a Windows and Linux mapping, however, if this cannot be provided, the administrator should place instead an informative message that can be shown to the users, i.e
tcp://192.168.1.128:8065/RemoteServer|LinuxServer|No_Windows_Users_Folder_Mapped|/home/omicsoft/fileserver/Data/Users|No_Windows_ServerProjects_Folder_Mapped|/home/omicsoft/fileserver/Data/ServerProjects
|server#1 description
  • The name of the analytic server will need to match exactly the name provided in the [AnalyticServers] of the associated server
  • If the administrator wishes to use the master server as an analytic server, this information must also be specified in the [AnalyticServers] section. If the server is not specified, it will not be available as an analytic server. If it is specified, the administrator must also specify the option AnalyticServerName in the Option section, and as above, the name must match.

Tips.png Also read Master Server and Analytic Server.


Database Backup section

In the [DBBackup] section. Copies essential databases (Users, UserGroups, Contrasts, Samples, Projects, Share, Lists, GenomeBrowser), keeping the two most recent versions. the Platforms and InferenceReports databases can be automatically regenerated when ArrayServer is started, so are not backed up.

Example: 

[DBBackup]
BackupDirectory=C:\__Working\ArrayServerHome Test\BACKUP
IntervalInDays=1
BackupStartTime=01:00


LDAP section

LDAP support is an add-on feature for OmicSoft Server; consult with your Account Manager to enable this feature.

The LDAP section should be generally be generated and updated via LDAP configuration in the Array Studio GUI, but some specialized parameters are only set in ArrayServer.cfg.

(Deprecated) Database

Sqlite is the supported database, but Oracle parameters are documented for reference, for customers who previously deployed integrating an Oracle-based database.

  • Provider: either Sqlite or Oracle or ODP (Windows ArrayServer only for direct ODP connection) (if Sqlite is specified the other options are ignored)
  • Server: specify the location of the Oracle server (IP address)
  • Port: specify the port of the Oracle server
  • DataSource: specify the name of the oracle database to be used
  • DataFileDirectory: species the location of the tablespace files
  • User: specify the oracle user to be used for accessing the database
  • Password: specify the password for the oracle user for accessing the database
  • UseSqliteForBigTables: set to True to use Sqlite for the larger tables (Inference Report, autofill, etc.). Set to True by default.

(Deprecated) NextBio section

This section is listed for reference, but NextBio integration is not currently supported. In the [NextBio] section. Specifies optional configuration for integration with NextBio.

Example: 

[NextBio]
AutoCompleteUrl=http://?????.nextbio.com/c/nbapi/autocomplete.api?v=0&apikey=???????????????????????
ApiUrl=http://????.nextbio.com/c/nbapi
ApiKey=?????????????????
OntologyUrl=https://????????.nextbio.com/ont
FtpUrl=snbftp.nextbio.com
FtpUser=??????????
FtpPassword=?????????
NextBioIntegration=True
FtpPort=22

Administrator can also add NextBio specific fields to the default.template file, which controls the meta data using NextBio ontology.


Updating ArrayServer.cfg

When an ArrayServer admin changes the contents of ArrayServer.cfg, changes will not be seen until ArrayServer is restarted.

Related Articles

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