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Discovery Environment - Data Management

DE Basics Walkthrough

• Log in at https://de.cyverse.org/

Data Window

• Open the data window and upload a file:

• Create a new text file and share it with someone in the class:

• Download the shared file.

Using metadata in the DE

• Using metadata in the DE :

• Search for data in the DE:

• Try a simple search for the word “maize”
• Try an advanced search for attribute = subject and value = maize

• Other options to be covered on Tuesday:

  • bulk metadata application
  • metadata templates

Advanced Metadata Usage

The Data Commons provides advanced metadata features in the Discovery Environment, including:

• metadata templates

Exercise: - Open the DE - Apply a Plant Ontology template to a folder. - Apply an ontology term to a file or folder.

• bulk metadata application

Exercise: 1. Copy the B123 file to your home directory - Using icommands:

$ icd /iplant/home/$username
$ icp -r /iplant/home/rwalls/B123 B123
$ ils

• In the DE:

• create a folder in your home directory called B123
• Move into B123
• Upload >> Import from URL…
• paste each of the URLs below into a slot. This must be done in two batches.

https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/012.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/123.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/234.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/345.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/456.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/567.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/678.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/789.txt
https://raw.githubusercontent.com/CyVerse-learning-materials/foss-2020/master/slides/B123/Rice_metadata.csv

2. Apply metadata - In the DE apply the DE apply metadata to the contents of B123

• Browse to B123
• View the metadata for one of the files using the Metadata menu or the three dots (it should be blank)
• View the contents of the file Rice_metadata.csv
• Browse back to your home directory
• Check the box next to B123
• Select Metadata > Apply Bulk Metadata
• Select the file B123/Rice_metadata.csv
• Browse back to B123
• View the metadata of the different files in the directory

3. Advanced search - Click on the search magnifying glass - Click + - Change File Name to Metadata - Under Attribute, type treatment, under Value type cold - Hit Search

Additional resources

• DE Guide
• DE Manual
• Using CyVerse for a shared project

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Fix or improve this documentation:

• On Github: Github Repo Link
• Send feedback: Tutorials@CyVerse.org

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