Parameter: UseAPIToken

Required: Yes, if using API token

Parameter: ExecPath

Default: Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles)\ProteinMetrics\PMI-Byosphere-Client\Base

Parameter: AutomationConfigurationID

Required: Yes

Parameter: ConfirmFolderCanPacq

Default: false

CustomSettings is an array of custom codes. Custom code will be executed in the order they are listed. Parameter includes

• CustomCodeExePath, optional CustomCode, optional MetadataPath. This set is executed for each sample.
• CustomCodeExePathBefore, optional CustomCodeBefore, optional MetadataPathBefore. This set is executed before Automation starts scanning for new data.
• CustomCodeExePathAfter, optional CustomCodeAfter, optional MetadataPathAfter. This set is executed after Automation has processed current scan data.
• CustomCodeExePathAutomationTrigger, optional CustomCodeAutomationTrigger, optional MetadataPathAutomationTrigger. This set is executed for each Automation Trigger file.

MetadataPath can contain output from the custom code. Contact support@proteinmetrics.com for more information on integration with third party tools through custom codes.

Examples,

• First custom code executes python code,
• Second custom code executes python code with a parameter,
• Third example is an executable,
• Fourth example is an executable with a parameter and a metadata output path

"CustomSettings": [
{
"CustomCodeBeforeExePath": "python.exe",
"CustomCodeBefore": "PMIGetMetadata.py"
},
{
"CustomCodeAfterExePath": "python.exe",
"CustomCodeAfter": "\"D:\\Test Data\\PMIGetFasta.py\" --protein"
},
{
"CustomCodeAutomationTrigger": "GenedataIntegration.exe"
},
{
"CustomCodeExePath": "BioviaIntegration.exe",
"CustomCode": "-f",
"MetadataPath": "E:\\ProgramData\\ProteinMetrics\\BioviaMetadata"
}
],

Automation by default honors local folder hierarchy and will create a matching folder hierarchy in Byosphere. LocalInputRoot parameter allows user to define common path that will be skipped during Byosphere subfolder creation processor therefore redefine a root folder.

LocalInputRoot is case insensitive. LocalInputPath and LocalInputRoot are expected to have the same path format of Windows, Linux, or UNC path.

Examples in Linux or Windows filepath format:

LocalInputPath c:/a/b/z, LocalInputRoot c:/a/b => common path c:/a/b -> data will be uploaded to Output Folder > z

LocalInputPath c:/a/b, LocalInputRoot empty => no common path -> data will be uploaded to Output Folder > a > b

LocalInputPath c:ab, LocalInputRoot c:m => no common path -> data will be uploaded to Output Folder > a > b

LocalInputPath c:abz, LocalInputRoot c:abzy => common path c:/a/b/z -> data will be uploaded to Output Folder

Parameter: UserGroupSubfolderLevel (optional)

Default: 1

Specifies the level of LocalInputPath directory from where UserGroupIds should be applied when uploading folders.

When this parameter is not provided or its value is less than or equal to 1, UserGroupIds will be applied to all new folders.

Examples:

"LocalInputPath": "C:/a/b/c/d/e",

"UserGroupIds": "2,3"

Example 1:

"UserGroupSubfolderLevel ": 1

Result: User groups will be applied to all subfolders: a,b,c,d,e

Example 2:

"UserGroupSubfolderLevel ": 3

Result: User groups will be applied to the following subfolders: c,d,e

Example 3 (when LocalInputRoot is provided):

"LocalInputRoot": "C:/a/b/c",

"UserGroupSubfolderLevel ": 3

Result: User groups will be applied to the following subfolders: d,e (subfolder 'c' will not be uploaded due to LocalInputRoot value)