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Omics Dashboard

The Omics Dashboard is accessed by clicking on Omics on the left panel of PHC. The dashboard shows the status of all Omics Tests and associated data records within a project. It consists of a page header with buttons for access to useful functions, Data Records showing the status of file ingestion, and a Recent Events table listing file ingestion events from the last 90 days.

Omics Dashboard header:

The blue header of the Omics Dashboard includes buttons for easy access to useful functions including:

  • Help: Connects you to the User Guide page related to this part of the UI
  • Download CLI: Takes you to the GitHub page of LifeOmic's CLI.
  • Rest API: Links to the LifeOmic docs and explains about the API using the REST architectural style to manipulate resources within the platform.
  • Add Omics Data button: Takes you to the Omics Add Data page of PHC.

Omics Dashboard

Data Records

Data Records show the ingestion status of the following genomic data file types:

  • Copy Number Variants
  • Structural Variants
  • Short Variants
  • BAM files: These are mapping files that show the raw data of the variants mapped to the genome.
  • RNA Expression

The number beside each status tells how many files are in that grouping.

  • Active: These variants have been successfully ingested and indexed in the genomics database.
  • Indexing: These files are in the process of ingestion (clock icon).
  • Failed: The file ingestion has failed (possible causes of the failure include a software issue at LifeOmic, an issue with the file, or incompatible file structure to name a few).

The status words (active, indexing, failed) are active filters, meaning you can click on them to see which files are in that status. For example, click on indexing to open a page showing all files that are indexing. On this filtered view, you can click the clear all button next to Filters to remove the filters and show a complete list of files (see clip below).

Ingest status

Failed Ingestion

Sometimes a file fails to be ingested and indexed. Possible causes of the failure include a software issue at LifeOmic, an issue with the file, or incompatible file structure.

Note

A failed ingestion will automatically retry the process four times.

For Enterprise level accounts, users with the appropriate ABAC privilege can initiate a retry of the ingestion. However, may only be beneficial if the user has changed something in the data to possibly fix the error, it may not be worth trying the manual retry as the PHC automatically retries several times for the user.

Access Control

This procedure requires createData>Access privileges. To grant privileges, see Access Control.

  1. Navigate to the project.
  2. Select Automation from the left side panel of the UI. Automation
  3. Select Tasks: A list of all run tasks will populate in the table. Rerun
  4. Filter on Executor Error.
  5. Hover over one of the failed tasks in the table. The quick tools that show up on the right of the screen has an option to rerun the task. Click on the rerun task icon to initiate a rerun.

Cancel a test ingestion

Test files in "queued" status of ingestion can be canceled by users with the appropriate ABAC permissions to stop the ingestion.

Access Control

This procedure requires deleteData>Access privileges. To grant privileges, see Access Control.

To stop a file ingestion:

  1. Navigate to the project.
  2. Select Automation from the left side panel of the UI.
  3. Select Tasks: A list of all run tasks will populate in the table.
  4. Hover your cursor on a test in queue. The quick tools will appear to your right.
  5. Click the Stop Run icon. A message in the top right corner states the task is being cancelled.

Stop run

Recent Events

The Recent Events table shows only events from the last 90 days. Some of this information is also viewable in Tests, located in the Omics tab of the left panel of PHC.

Recent Events

The Recent Events table includes:

  • Event Time: In the above example, this is the time the test was created
  • Subject: Subject identifier generated by LifeOmic
  • Resource: The Resource is a combination of the Test Name(Test Type). The user defines that naming when ingesting the genomic data
  • Message: In the example above, the test was created

Table results can be filtered using the dropdown menu:

  • All Tests: Shows all tests (successfully ingested, attempting ingestion, and unsuccessfully ingested)
  • Errors: Shows tests that have failed ingestion
  • Info: Shows all tasks which have completed successfully

Last update: 2021-06-24