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Introduction

Deployment

Multi-Node Cluster

See  NDS-312 - Getting issue details... STATUS

Single-Node Development Instance

None

NDS Labs UI

Account Views

Register View

  • fill out and submit request account form
    • user should receive an e-mail from the server to verify your e-mail
  • click the link in your e-mail
    • user should receive an e-mail from the server informing you that your account is awaiting approval
    • support should receive an e-mail asking them to approve or deny this account
  • approve an account: “This account has been approved.”
    • user should receive an e-mail from the server informing them that they can now log in
  • deny an account: “This account has been denied.”
    • user should receive an e-mail from the server informing them that their request has been denied, and that they should contact support with further questions
  • attempt to sign up again using the same username and/or same e-mail
    • API / UI server should not allow this (HTTP 409 + validation message)

Login View

  • failed login
  • successful login

Reset Password View

  • reset password while logged in
  • reset password while logged out
  • reset password with nonexistent e-mail
  • reset password with unverified e-mail
  • reset password with unapproved account

Contact Us View

  • support links
  • enter feedback of each type:
    • help
    • bug
    • wish
    • comment

Spec Views

Catalog View

See  NDS-386 - Getting issue details... STATUS

  • search for apps
  • documentation link
    • view json
    • copy to clipboard
  • clone a spec
    • edit cloned spec
    • delete cloned spec
  • import spec
  • install imported spec
    • add button
    • view button
  • attempt to edit / delete imported spec while an instance of it exists

Add / Edit Spec View

  • Details Tab
  • Dependencies Tab
  • Environment Tab
  • Data Tab
  • Ports Tab
  • Resource Limits Tab
  • Development Tab 

Application Views

Dashboard View

See  NDS-318 - Getting issue details... STATUS

  • Launch file manager
  • Install an application
  • Start the application
  • Navigate to endpoint
  • Log view
  • Config view
  • Console view
  • Stop the application
  • Unlock the application
  • Start the application once more
  • Navigate to endpoint
  • Stop the application again
  • Remove the application

Add / Edit Service View

  • Environment Tab
  • Data Tab
  • Docker Tab

Console View

  • ls -al /home/username
  • try with many services, including different base images:
    • centos
    • ubuntu
    • alpine
    • debian
    • others?

NDS Labs Services

In general:

  • Install service
  • Add any optional plugins
  • Start service
  • Navigate to its endpoint link
  • Perform any necessary setup procedures
  • Perform an adequate test of the system's most basic of functionality
    • Uploads / Downloads
    • Collection viewing
    • Visualizations
    • Plugins
    • etc

Clowder + MongoDB + RabbitMQ + Elasticsearch

See  NDS-320 - Getting issue details... STATUS

  • Add Clowder app
  • Configure Elasticsearch plugin service
  • Configure Toolserver plugin service
  • Configure PlantCV extractor plugin service
    • RabbitMQ plugin should be added automatically
  • Start Clowder app
  • Navigate to its endpoint
  • Create an account by verifying your e-mail address
  • Login to Clowder
  • Create a Dataset
  • Upload PlantCV test image(s) to the Dataset
  • Verify that extractors ran (logs)
  • View metadata extraction results (Clowder should have attached the results in their UI)

Dataverse + PostgreSQL + Rserve + Solr + iRODS + TwoRavens

See  NDS-321 - Getting issue details... STATUS

  • Add Dataverse app
  • Configure TwoRavens plugin
  • Configure Dataverse iCAT plugin
  • Login using the default dataverseAdmin/admin username and password
  • From this interface, you can create dataverses, add users, groups, permissions, etc.
  • For now, we'll simply upload a file
  • Select "Add Data+" > New Dataset
  • Fill in required fields and select "Select files to add"
  • Upload the test/test.csv file
  • Select "Save dataset"
  • Note that the file is converted to "Tabular" format and the "Explore" button is now enabled. Explore is the link to the TwoRavens service.
  • Select "Explore", which will open the TwoRavens interface in a new tab or window
  • The TwoRavens interface should display a network of variables.

DSpace + PostgreSQL

See 

  • Add Dspace app
  • Configure Postgres plugin service
    • Database Name=dspace
    • Username=dspace
  • Configure Dspace service
    • set email address
    • Set password as Postgres password
  • Launch
    • Login using admin email and password
  • Create community > Test (select "Return" after creation)
  • Select community "Test" link
  • Create collection "Test" (select "Return after creation)
  • Select collection 'Test" link
  • Submissions > start a new submission
    • Complete the submission process, including file upload
  • Browse by title, confirm your submission is available and file can be downloaded

Fedora Commons

Girder + MongoDB

  1. Add Girder app
    • You should be brought to the Dashboard view, with the Girder header(s) expanded
    • You should see MongoDB under the services list
  2. Start Girder app
    • You should see the Girder application begin its startup process
  3. Once the endpoint comes up, click the endpoint link
    • You should be brought to the Girder web interface
  4. At the top-right of the Girder UI, choose "Register"
  5. Enter some information about your desired account and click "Register"
  6. On the left side, choose "Admin Console", then choose "Assetstores"
  7. Create a new File System assetstore with the following:
    • Name = "assetstore"
    • Root Path = "/assetstore"
  8. On the left side, click "Collections" and create a new Collection
    • Your new collection should contain a folder named "Private"
  9. Click "Private" and click the green button at the top-right
  10. Choose one or more files to upload items into this Collection and click "Start Upload"
    • You should see you files appear in the Collection on the UI
  11. Click the name of your newly uploaded file
    • Your browser should download the selected file
  12. Several interesting plugins for different use cases exist, although I did not dive into each of them:
    • Jobs: long-running services
    • Metadata Extraction: sounds familiar
    • Several other plugins

iQvoc

  • Add iQvoc app
  • Start iQvoc app
  • Navigate to its endpoint
  • Login admin@iqvoc / admin
  • Add new collection

Kibana + Logstash + Elasticsearch (ELK)

See  NDS-318 - Getting issue details... STATUS

OntoWiki

  • Login as Admin (no password)
  • Select Edit >Create Knowledge Base
  • TItle: Test
  • "Import RDF from web"
  • Select "Create Knowledge Base"
  • Enter URL when prompted: https://raw.github.com/AKSW/aksw.org/master/site/data.rdf
  • Confirm "Navigation" now contains classes Organization, Document, Person, Object.

OwnCloud + MySQL

  1. If you're not already running your own instance of NDS Labs, check out our Setup Documentation.
  2. Navigate your browser to http://YOUR_IP:30000 (create a project if necessary) and log in.
  3. You should now see "ownCloud" listed with the other services on the left side of the page.
  4. Click the + button beside "ownCloud" and step through the wizard to configure ownCloud:
    • Choose a name your stack appropriately and click Next.
    • Now, select MySQL as an optional service and click Next.
    • The wizard will now prompt you to enter passwords necessary for MySQL, as specified by the "Config" in the spec above. Because we specified "isPassword" above, you can click the button on the right to generate a secure random password.
      • Clicking Advanced Configuration will also allow you to set the database and username that MySQL will use, if want to change the default values.
    • Choose a size to use for the volumes that will attach to these services.
      • The numbers of the top-right of the colored panel will allow you to switch between the volume requirements for this stack, if more than one exist.
      • You will be asked to create one volume each for ownCloud and MySQL.
      • If previous volumes matching these services exist, and are not currently attached to another service, the wizard will offer to reuse them.
    • Confirm that your stack looks correct and click Confirm.
    • You will see your new "ownCloud" stack appear in the Stacks tab of the UI.
  5. Click the name of the stack to expand the accordion and show a more fine-grained status.
    • You will see MySQL listed beneath the ownCloud in te Service List.
  6. Click the "Launch Stack" button at the bottom-right of the pane.
  7. Wait for the stack to start.
    • NOTE: this may take several minutes the first time, as Docker will pull the image before running it.
  8. Once the stack has started, navigate to its endpoint by click the link to the right of the service name.
  9. A new tab will open, where you will be taken to the ownCloud self-installation web interface.
    • Enter the username and password that you would like to use for the ownCloud administrator.
    • During the setup, be sure to expand the "Storage & database".
    • Choose MySQL / MariaDB to specify your MySQL instance details.
    • You will be prompted to enter the database, username, and password that you specified while configuring MySQL, as well as the address of the running instance.
      • Back at the NDS Labs interface, click the Config button to the right of the service name under your ownCloud stack.
      • The database, username, and password are listed under "Environment".
      • The address where ownCloud can reach MySQL is listed under "Endpoints" as the "Internal Address".
      • NOTE: This MySQL instance is not exposed to the public internet, so there is no "External Address" listed.
    • Once you have entered the details of the running MySQL instance, click Finish Setup.
  10. You should then be brought to your ownCloud instance's home page, where you will be able to upload new files and view existing files existing on the attached volume.
  11. Upload a test file somewhere into ownCloud using the + button at the top-left of the screen.
  12. To verify that MySQL is receiving updates from ownCloud, let's find a reference to the file you just uploaded in the MySQL database.
    • Jump over to your terminal and execute docker ps | grep mysql to locate the running MySQL container and grab its container id.
    • Execute docker exec -it <container id> mysql -u owncloud -p and enter the MySQL password for the "owncloud" user. This will drop you into the container at the mysql shell.
      • Click the Config button to the right of the service name under your ownCloud stack and copy / paste the MySQL password into the prompt.
    • Execute the following query to verify that your new file upload was persisted to MySQL select path from owncloud.oc_filecache order by path;.
    • You should see all of your files, including the newly-uploaded file, ordered by file path and listed in the output.

WebProtege

  • Add WebProtege app
  • Start WebProtege app
    • the service can take a long time to become ready
  • Navigate to its endpoint
    • the JavaScript can take a long time to load
  • Sign up, then sign-in
  • Create project "test"
  • Select "test" project link
  • Select Classes > Create > "test"

System Services

Chisel

    • Download the Chisel client
    • Add and start RabbitMQ, note internal IP and port
    • Add and start Chisel server, note endpoint URL
    • Copy the command from the Chisel server logs and run your client. For example

       

       

      ./chisel client --auth=demo:password http://141.142.210.150:30540/ localhost:15672:10.0.0.25:15672
      2016/08/22 12:49:48 client: Connecting to ws://141.142.210.150:30540/
      2016/08/22 12:49:48 client: Fingerprint 79:1b:29:80:ad:33:f7:bf:17:5a:8a:00:7e:d8:25:20
      2016/08/22 12:49:48 client: Connected (Latency 1.930073ms)

       

       

    • Open your browser to localhost:15672
    • Voila, you are tunneled in.

Cloud Commander (File Manager)

  • Press the "Manage Files" button in the NDS Labs UI navbar
  • File Manager application should be added and started automatically for you
    • Once the endpoint appears, you should be automatically directed to its endpoint url
  • You will be dropped at the CloudCommander UI, where you can modify the current user's Home directory

Docker

Jenkins

  • Add Jenkins app
  • Start Jenkins app
  • Retrieve the admin password from the logs
  • Navigate to its endpoint
  • Create a new job
  • Set SCM type to “Git” and point at the Git repository containing the code you would like to build
  • Add any build steps you want to execute – as a simple test, you can choose “Execute shell” to execute the “ls –al” command
  • Click "Apply" / "Save", then build the new job – you should see your new build job appear in the queue on the left
  • Click the "Build Now" to view details about it and click “Console Output” to watch the console output your build

IDEs

Cloud9

  • Add Cloud9 app
  • Start Cloud9
  • Import code snippet
  • Run code snippet
  • Place a breakpoint
  • Enable debugger
  • Debug code snippet

Jupyter

  • Add Jupyter app
  • Start Jupyter
  • Retrieve password from logs
  • Navigate to its endpoint
  • Import script into notebook
  • Evaluate the cell containing you script

pyCharm

  • Add pyCharm stack
  • Start pyCharm
  • Navigate to its endpoint
  • On first open, you will be prompted to import and accept a license.
  • Once opened, create a new project
  • Create a new file "Hello.py"

     

    class Hello:
     def f(self):
     print("NDS-342")
  • Right click and run and debug the application.
  • In the bottom left corner, select the grey box and open a terminal
  • Close the browser window and reopen the endpoint link – you should be just where you started
  • Select File > Exit – you will be shown an Xpra Conncet page (I need to do something with this if we're satisfied with the PyCharm/Xpra container). Close it.
  • Reopen the endpoint link, you should be taken to the opened IDE

Rstudio

  • Add Rstudio app
  • Start Rstudio

Low-level Services

Overview:

  • Install Elasticsearch
    • Ingress should link to endpoint
    • Endpoint should link to a service
  • Start Elasticsearch
    • API server should spawn a replication controller
    • Replication controller should spawn a pod
    • Service should round-robin requests to pods whose labels match and are "Ready"
  • curl the hostname given in the ingress rule

Elasticsearch

  • Install Elasticsearch 2.0
  • Start Elasticsearch 2.0
  • curl the hostname given in the ingress rule
    • ingress should link to port 9200 of the pod

RabbitMQ

  • Install RabbitMQ
  • Start RabbitMQ
  • curl the hostname given in the ingress rule
    • ingress should link to port 15672 of the pod

Databases

  • Same as above, but maybe insert some data?

MongoDB

  • Install MongoDB
  • Start MongoDB
  • curl the hostname given in the ingress rule
    • ingress should link to port 27017 of the pod

MySQL

  • Install MySQL
  • Start MySQL
  • curl the hostname given in the ingress rule
    • ingress should link to port 3306 of the pod

PostgreSQL

  • Install PostgreSQL
  • Start PostgreSQL
  • curl the hostname given in the ingress rule
    • ingress should link to port 5432 of the pod
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