Use the file repository as a launching point for applying different tools to the data, especially "structured" data that can be imported to the database, for example, tabular spreadsheet data. Using the repository as a launching point, you can:
  • Create visualizations and SQL queries of selected data.
  • Import assay runs to an analysis dashboard.
  • Run an analysis on a genetic sequence file.
  • Pass the file to an R script sequence you define.
In the steps below, we will import data to use with analysis and visualization tools.

Import Data for Visualization

First, import some file you want to visualize. You can pick a file of interest to you, or follow this walkthrough using the sample file provided. When you "import" a file into LabKey Server, you add its contents to the database. This makes the data available to a wide variety of analysis/integration tools and dashboard environments inside LabKey Server. In the steps below we will import some data of interest and visualize it using an assay analysis dashboard.

  • Return to the main page of the File Repository folder.
  • In the Files web part, open the folder DataForImport.
  • Select the file Lab Results.xls.
  • Click Import Data.
  • Select Create New General Assay Design.
  • Click Import.
  • Enter a Name, for example "Preliminary Lab Data".
  • Select "Current Folder (File Repository)" as the Location.
  • Notice the import preview area below. Let's assume the inferred columns are correct and accept all defaults.
  • Click Begin Import, then Next to accept the default batch properties, then Save and Finish.
  • When the import completes, you see the "list" of runs, consisting of the one file we just imported.

  • To make it easier to access this data later, we can add a web part to show it:
    • Enter > Page Admin Mode.
    • Click the Start Page tab to return to the main folder page.
    • Add a Query web part.
      • Web Part Title: Enter "Preliminary Data" or whatever you would like the title to be.
      • Schema: Select "assay.General.Preliminary Lab Data" (or whatever you named your assay when you defined it above).
      • Click "Show the contents of a specific query and view."
      • Query: Select "Data."
      • Leave the default settings for View and the other remaining options.
      • Click Submit.
    • Scroll down to see your new data grid shown in a web part.
    • Click Exit Admin Mode.

Create a Box Plot

  • Explore the new Preliminary Data web part (or whatever name you gave your web part).
  • Select (Charts) > Create Chart.
  • Click Box.
  • Drag the column "Cohort" to the X Axis Categories box.
  • Drag the column "CD4+" to the Y Axis box.
  • Click Apply and you will see a box and whisker plot for the CD4+ levels of each cohort.
  • Explore more chart options via the Chart Type and Chart Layout buttons. Hover over the chart to reveal buttons in the upper right for exporting as PNG, PDF, or JavaScript. You can also return to the data grid and explore more visualization options on the (Reports and Charts) menu.


Congratulations, you've finished the File Repository tutorial and learned to manage files on your server.

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