Parameter: UseAPIToken

Required: Yes, if using API Token

Parameter: LocalWorkingPath

Default: Environment.GetFolderPath(Environment.SpecialFolder.CommonApplicationData)\ProteinMetrics\AutomationServer

Folder location to store temporary files generated and then deleted during uploads.

The default value will be used if the customer value is not specified or accessible.

Parameter: BaseDir

Required: On prem only

This is a required parameter for OnPrem only. This is the NAS mount drive.

This setting in Windows must match its counterpart in App Server’s base_dir in Linux.

Example:

"BaseDir": "C:"

This parameter is required for Watcher. To run the executable as a Watcher, set it as:

"AutomatedMode": "BuildWflw",

In this mode, samples, workflow templates and other inputs are used to generate workflows in the directory defined by the Output parameter (see the Configure the Watcher section below).

Parameter: WriteLastScan

Default: false

If true, last scan time will be auto-created / updated by the program and written to the configuration file.

Note: when set to true, the LastScanTime line should be removed (along with the comma after “WriteLastScan”: true) before restarting the service.

The unit is second. The Automation will check for new data using time stamp setup in Modified After or LastScanTime. However, sometimes NAS data is not immediately available for cloud instance to be picked up. The delta window makes the Modified After orLastScanTime more tolerant in such cases. If there is data with timestamp 12-20-22 11:50 AM, data will not be uploaded using “Modified After”: “2022-12-20 12:30:00”.

Data will be uploaded using the following, given a 3600 second or 1 hour delta effectively checking the file against 12-20-22 11:30 AM.

“RollingWindowDelta": 3600,

"Modified After": "2022-12-20 12:30:00"

If no value is specified, no delta window will be applied.

Example:“RollingWindowDelta”: 3600

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)

Parameter: SubFolderLevel

Default: 1

Parameter: WflwOutputDir

Required: Yes

Parameter: Sequence

Required: Yes

Parameter: SampleProteinCSV

Required: No

Parameter: AutomationTrigger

Required: No

When ProcessEntireFolder is true, a more precise way to trigger the Watcher is to use an automation trigger file.

A sub-folder will be processed if and only if the filename designated as the AutomationTrigger is present in the folder.

Example: "AutomationTrigger": "WatersmabEnd.raw"