Arvados » Arvados Workbench 2

_Note: these are not full use cases, simplified to just give more of the what and not a lot of the why or who.  We will be boiling these up into higher-level use cases.  This is more a list of items that should be included in all those higher-level use cases.  We want to not only ensure these use cases can be done in WB2 but the experience is equivalent or hopefully better in WB2 than in WB1._ 

h1. Use Cases for WB and Collections/Projects (Keep)

*Creating New Collections*

Summary: A users wants to make a collection in Arvados using the Workbench. 

Details:  Wants to make collection in from any of the data sources:

* From data already in an existing collection

* From a subset of files in an existing collection

* By combining files from different subsets of different collections

* By Uploading files from my desktop

* From the results of a already run workflow

* By downloading data from another source into a collection

*Annotating Collections*

Summary: User wants to annotate their collections with such details as sample

name, sample type, sequencing method, species, etc. 

Details:

* User wants to add annotations/metadata to existing collection

* User want to verify the added metadata to the collection

*Examining Collection Files* 

Summary:  User is viewing a collection and wants to examine the files and extract the data or metadata. 

Details:

* User wants to find certain files within the collection 

* (visually,using search (basic and advanced search using regexp, etc)

* User want to View or download certain files with the collection using a UI

*Sharing Collection Files* 

Summary:  User wants to share the Files in a Collection

Details:

* User wants make the collection available for downloading via ftp, s3 or other 3rd party application

* User wants to share the collection with others (by name) in their organization, others via a defined group, to everyone in their organization, or publicly.   Users want those they share the collection with to have: Read permission, Write permissions, Manage permissions

*Finding Existing Collections*

Summary: User want to find an existing collection

Details:  User wants to find the collection by one of the following ways:

* By Browsing to the project that contains the collection

* By searching the UUID of the project - and then looking through the items in the collection

* By searching the UUID of the collection

* By searching the collection name

* By searching the PDH

* By searching the collection metadata

* By searching for the workflow that produced it

* By a URL that can share that points to the project on WB

*Identifying Collections*

Summary: User needs to ID the collection for use as inputs to a workflow and/or inputs to a command using the API or CLI

Details:  

* User wants to find these specific file IDs

* User wants to get the collection UUID

* User wants to get the collection PDH

* User wants to get the collection metadata

*Editing an Existing Collection* 

Summary: User wants to modify a collection for use in their new project.

Details: 

* User will want to

* Copy over an existing collection to a new project

* Remove files in their collection to suit their needs for their new bioinformatics task. 

* Add files from either their desktop or from another collection into this new collection

* Editing the File Structure of An Existing Collection*

* Summary:  User wants to adjust the file structure of an existing collection to work better as an input to their analysis tools

* Details:  User will want to

* Remove files from folders to have them in all in a single flat directory

* Separate different subsets of files and place them in folders

* Verifying Correct Collection *

Summary: User wants to download data from a collection, and want to make sure the collect they found is the correct collection

Details:  User may want to check the following:

* UUID and/or PDH

* metadata

* file contents

* collection “version”

* lineage of the collection (i.e. if the collection was generated as the result of a workflow - which workflow created this collection)

*Creating Projects*

Summary: User is working in the Arvados Workbench and needs a new Arvados project for a new analysis project they are working on. 

Details: The user wants to do the following

* Create new project

* Create a subproject within the new project (e.g. For Testing vs Final Runs)

Name the project/subproject

Add description of the project

Add metadata to the project  

Extract UUID of Project for use in workflow inputs or various command line/SDK/API functionality. 

Copy a URL that can share to others that points to the project

Mark the projects as “favorites” to be able to it more easily

Moving or Creating Items within Project

Summary. A User wants to set up their project to do their work.  They want to move all relevant existing data and workflows as well as upload new data and create new registered workflows.  

Details: Users may want to:

Copy existing collections and register workflows into this project

Create new collections within the project

Create new registered workflows in that project

Run workflows in this projects having the output, logs and other created artifacts contained within this project

Archiving or Sharing a Project

Summary: Now that the work is finished and the user has the results they need.  They want to get the project ready for sharing with their organization, with those outside their organization or even possible publicly in a publication.  

Details: Users may want to

Clean up the project by removing old collections, logs, processes and subdirectories that are not necessary to keep. 

Edit the name or metadata for the project

Freeze the project

Share the project with others in their organization, to everyone in their organization, publicly.   These are possible configurations:

Others have read permission  

Others have write permissions

Others have manage permissions

Identifying an Existing Project

Summary: User needs to identify the correct project in which to run their workflow.  They think they found the correct project they want searching on the project name.  

Details: The user then may want to:

Find the UUID of the project

Examine aspects of the project to double check it is the project they want to use.  They might want to:

Check the contents of the project 

Check the project description 

User might want to see the history of the project (*not currently available)

User might want to see the metadata for the project

Check to see if the project is frozen

Finding a Project or Subproject

Summary: A user logs back into Arvados after a break and would like to find the project they were working on previously. 

Details:  Those users would may want to find this project by

Searching for UUID, metadata or the project name

Navigating through the project/subproject hierarchy to find the project

Skimming through projects marked as their “Favorites”

Look for projects owned or created by a specific user (* Not Currently available)

h1. Use Cases for WB and Workflows (Crunch)

Submitting Workflows to Arvados Without Command Line

Summary: User wants to submit a workflow to run on Arvados without having to use the command line. The workflow CWL file either lives in a git repository or on the user’s local machine or in a collection on Arvados.  (* Currently this is not available on WB)

Details: The user will want to indicate to Arvados which workflow they want to run and have Arvados 

Parse the CWL file and generate an interactive form to fill out with input values and then submit the workflow via Workbench

Upload a YML file of input values to upload or direct Arvados to an existing YML file in an Arvados collection and then submit the workflow via Workbench. 

Monitoring Submitted Workflows 

Summary: User submits a workflow to run on Arvados using the command line. They want to monitor the workflow that they submitted using the Arvados Workbench. 

Details: The User will want to

Find the running workflow

Through search

Via Project Navigation

Check the workflow’s current status

If run successfully, find output collection 

If run successfully, look at how long it took to run

If run successfully, estimate costs (* currently only available for CommandLine)

Debugging Workflows - Part I

Summary: User submits a workflow to run on Arvados using the command line. They find out that the workflow and it did not run not run successfully.   They want to figure out why it failed.  

Details: The User may wants to:

Examine logs

Examine inputs

Examine command

Examine CWL  (* CWL not yet available)

Check to see which docker container was used

Run crunch-run stats interactively on WB  (*Currently only available via the command line) or have those plots available on WB. 

Debugging Workflows - Part II

Summary:  A User is updating a workflow workflow and the workflow has now stops running after a series of changes.  The User needs to compare the new workflow to the old workflow to see why it failed.

Details:  The User may need to 

Examine old workflow runs and backtrack to see when was the workflow last working

Determine what is the difference between the last working workflow and the broken workflows main process . This could include comparing: Inputs, Command, Resource Allocation, Node Type, and Docker Image metadata.

Determine which steps (if any) were re-used from the working workflow

Determine which steps failed in the new workflows

Determine if any big differences between the different workflows steps

Look at information passed to the steps including Inputs, Command, Resource Allocation

Find and compare logs from the relevant workflow steps Compare Docker image metadata (docker image ID, name, version, dockerfile)

Need to compare compare crunch-run stats between jobs (*Currently only available via command line)

Integrating Git Commit Information with Submitted Workflow

User has been working on changes to an existing workflow.  They have been submitting workflows managed in a git repository.  The workflow stops working or returning different outputs. The User would like to 

Find the relevant git commit information for the commit version of the workflow run on Arvados that worked

Find the relevant git commit information for the version of the workflow that is returning different results or not working

Calculating Workflow Costs

Summary: A User ran a big job and is now worried about how much it cost to run.  Details: The user wants to

Find the container request UUID of the workflow  

Run the cost analyzer to see how much it cost to run the entire workflow 

(* Currently not available in WB)

Run the cost analyzer to see which step is costing the most money

(* Currently not available in WB)

See if it would be possible to run workflow on less expensive instances (using information now only possible from the command line)

Estimate how much would it cost to run another similar workflow

 (* Currently not available in Arvados)

Creating a Register Workflow Using Workbench

Summary: User wants to create a registered workflow interactively using the WB (* Only currently available using command line).

Details.  The user may want to:

Share registered workflow with others in their organization

Set default values for the workflow

Define the name, metadata and descriptive text for the register workflow

Finding a Registered Workflow

Summary: User wants to run a registered workflow created by their colleague. User needs to find this workflow.

Details: The user may want to find the workflow by

Name, metadata or unique identifier

A URL shared by the creator of the register workflow

Looking Inside “project” that contains all the available shared workflows

Specifying Inputs to a Registered Workflow

Summary:  User wants to use the WB to submit a registered workflow made by 

their collaque to run on Arvados .  

Details: The user wants to:

Specify the inputs for the register workflow to use

Use the default inputs (if provided)

Identify the project the workflow should “run” in (i.e. where the outputs, logs and other collections should be stored)

See details about which registered workflow they are running to help guide them with to provide the proper input (eg. Registered workflow , name, description, etc.)

Examining A Running Workflow

Summary: User notices that their workflow has been running a long time and wants to check up on it.They would like to figure out if workflow is hung or is progressing along.  If progressing, the user may want to try and figure out why the workflow is running slower than expected.

Details:  The User may want to examine the following on WB

Real time logs

Resources used

Steps run so far and their outputs/inputs

Real-time values of RAM, CPU usage etc currently 

(* Not available in WB)

 Rerunning Old Workflows  

Summary: A User has successfully run a workflow on Arvados using the command line and would like to rerun that old workflow. 

(*Not Currently Available in WB)

Details: User may want to specify:

New Inputs

New Resource Requirements

New Docker Container

 Canceling a Running or Queued Workflow

Summary: User has submitted a workflow to Arvados via the command line and releases that they accidentally used the wrong inputs or an outdated function that the workflow leverages.  They want to cancel the workflow before it wastes time and resources.

Details:  User would like to

Find the running workflow on WB

Have an easy (single-button) way to cancel workflow on WB

Have a way to verify that the workflow was canceled

Checking Workflow Inputs or Requirements

Summary: User is examining output results of a workflow and wants to remind themselves which input parameter they used for the model they ran in the workflow. 

Details:  User would like to

Trace output collection to process that created it (i.e. container)

Find and examine the inputs to the workflow or workflow step run in that container