These lessons give step by step instructions for using Visual Studio
Code (abbreviated "vscode") to develop CWL workflows on Arvados.

1. Set up SSH
1. Install vscode and necessary extensions, then use vscode to connect to an Arvados shell node for development
1. Register a workflow, run it on workbench, and view the log
1. Upload input, run a workflow on it, and view the output
1. Register a workflow with default inputs
1. Run a workflow without registering it

## 1. SSH Setup

1. (Windows only) Install Git for Windows [https://git-scm.com/download/win](https://git-scm.com/download/win)
   1. Choose "64-bit Git for Windows Setup".  It does not require admin privileges to install.
   1. Hit "Next" a bunch of times to accept the defaults
   1. The most important things is that "install git bash" and "install OpenSSH" are enabled (this is the default).
   1. At the end of the installation, you can launch tick a box to git bash directly.
   1. Open "Git Bash" (installed in the "Git" folder of the start menu)
1. (All operating systems) Starting from bash shell (on MacOS or Linux you will open "Terminal")
   1. Shell: Run `ssh-keygen`
      1. Hit enter to save to a default location
      1. You can choose to protect the key with a password, or just hit enter for no password.
   1. Shell: Look for a message like `Your public key has been saved
      in /c/Users/MyUsername/.ssh/id_rsa.pub` (Windows git bash
      example, on MacOS or Linux this will probably start with `/Users` or `/home`)
      1. Shell: Run `cat /c/Users/MyUsername/.ssh/id_rsa.pub`
   1. Shell: Use the pointer to highlight and copy the lines starting
      with `ssh-rsa …` up to the next blank line.  Right click and
      select "Copy"
1. Open Arvados workbench 2.  If necessary, go to the user menu and
   select "Go to Workbench 2"
   1. Workbench: Go to `SSH keys` in the user menu
   1. Workbench:Click `+Add new ssh key`
   1. Workbench: Paste the key into `Public key` and enter something for `name`
   1. Workbench: Go to `Virtual Machines` in the user menu
   1. Workbench: Highlight and copy the value in in the `Command line` column.
1. At the git bash command line
   1. Shell: paste the `ssh shell…` command line you got from workbench.
   1. Shell: type "yes" if it asks `Are you sure you want to continue connecting`.
   1. Note: it can take up to two minutes for the SSH key to be copied to
      the shell node.  If you get "Permission denied" the first time, wait 60
      seconds and try again.
   1. Shell: You should now be logged into the Arvados shell node.
   1. Shell: Log out by typing `exit`

## 2. VSCode setup

1. Install [Visual Studio Code](https://code.visualstudio.com/) and start it up
1. Vscode: On the left sidebar, select `Extensions` ![](images/Extensions.png)
   1. In `Search Extensions in Marketplace` enter "remote development".
   1. Choose and install the "Remote Development" extension pack from Microsoft
1. Vscode: On the left sidebar, choose `Remote Explorer` ![](images/RemoteExplorer.png)
   1. At the top of the Remote Explorer panel choose `SSH targets` ![](images/SSHTargets.png)
   1. Click `Add New` ![](images/AddNew.png)
   1. Enter the `ssh shell…` command line you used in the previous section, step 1.4.1
      1. If it asks you `Select SSH configuration file to update` choose the first one in the list.
   1. Right click the newly added ssh target in the list and select “connect to host in current window`
   1. If it asks `Select platform of the remote host` select `Linux`.
1. Vscode: On the left sidebar, go back to `Extensions` ![](images/Extensions.png)
   1. Search for "benten", then look for `CWL (Rabix/Benten)` and click `Install`
   1. On the information page for `CWL (Rabix/Benten)`
      1. If you see a warning `Install the extension on 'SSH: ...' to enable` then click the button `Install in SSH: ...`
   1. You should now see a message `Extension is enabled on 'SSH: ...' and disabled locally.`
1. Vscode: On the left sidebar, choose `Explorer` ![](images/Explorer.png)
   1. Select `Clone Repository` and enter [https://github.com/arvados/arvados-vscode-cwl-training](https://github.com/arvados/arvados-vscode-cwl-training), then click `Open`
   1. If asked `Would you like to open the cloned repository?` choose `Open`
1. Go to Arvados Workbench
   1. Workbench: In the user menu, select `Current token`
   1. Workbench: Click on `Copy to Clipboard`.
   1. Workbench: You should see a notification `Token copied to clipboard`.
   1. Go to Vscode
   1. Vscode: Click on the `Terminal` menu
   1. Vscode: Click `Run Task…`
   1. Vscode: Select `Configure Arvados`
   1. Vscode: Paste text into the `Current API_TOKEN and API_HOST from Workbench` prompt
   1. Vscode: This will create files called `API_HOST` and `API_TOKEN`

## 3. Register & run a workflow

1. Vscode: Click on the `lesson1/main.cwl` file
   1. Click on the `Terminal` menu
   1. Click `Run Task…`
   1. Select `Register or update CWL workflow on Arvados Workbench`
   1. This will create a file called `WORKFLOW_UUID`
1. Workbench: Go to `+NEW` and select `New project`
   1. Enter a name for the project like "Lesson 1"
   1. You should arrive at the panel for the new project
1. Workbench: With `Lesson 1` selected
   1. Click on `+NEW` and select `Run a process`
   1. Select `CWL training lesson 1` from the list and click `Next`
   1. Enter a name for this run like `First training run`
   1. Enter a message (under `#main/message`) like "Hello world"
   1. Click `Run process`
   1. This should take you to a panel showing the workflow run status
1. Workbench: workflow run status panel
   1. Wait for the badge in the upper right to say `Completed`
   1. In the lower panel, double click on the `echo` workflow step
   1. This will take you to the status panel for the `echo` step
   1. Click on the three vertical dots in the top-right corner next to `Completed`
   1. Choose `Log`
   1. This will take you to the log viewer panel
   1. Under `Event Type` choose `stdout`
   1. You should see your message

## 4. Working with input and output files

1. Vscode: Click on the `lesson2/main.cwl` file
   1. Click on the `Terminal` menu
   1. Click `Run Task…`
   1. Select `Register or update CWL workflow on Arvados Workbench`
1. Go to your desktop
   1. Right click on the desktop, select `New > Text Document`
   1. Name the file `message`
   1. Enter a message like "Hello earth" and save
1. Workbench: Go to `+NEW` and select `New project`
   1. Enter a name for the project like "Lesson 2"
   1. You should arrive at the panel for the new project
1. Arvados workbench: With `Lesson 2` project selected
   1. Click on +NEW and select `New collection`
   1. For Collection Name enter "my message"
   1. Drag and drop `message.txt` into the browser
   1. Click `Create a collection`
   1. The file should be uploaded and then you will be on the collection page
1. Workbench: Select the `Lesson 2` project
   1. Click on `+NEW` and select `Run a process`
   1. Select `CWL training lesson 2` from the list and click `Next`
   1. Enter a name for this run like "Second training run"
   1. Click on `#main/message`
   1. A selection dialog box will appear
   1. Navigate to the collection you created in step (4.4.4) and choose `message.txt`
   1. Click `Run process`
   1. This should take you to a panel showing the workflow run status
1. Workbench: workflow run status panel
   1. Wait for the process to complete
   1. Click on the dot menu
   1. Choose `Outputs`
   1. Right click on `reverse.txt`
   1. Click on `Open in new tab`
   1. The results should be visible in a new browser tab.

## 5. Register a workflow with default inputs

The default value for the `message` parameter will taken from the `lesson3/defaults.yaml` file

1. Vscode: Click on the `lesson3/main.cwl` file
   1. Click on the `Terminal` menu
   1. Click `Run Task…`
   1. Select `Register or update CWL workflow on Arvados Workbench`
1. Workbench: Go to `+NEW` and select `New project`
   1. Enter a name for the project like "Lesson 3"
   1. You should arrive at the panel for the new project
1. Workbench: With `Lesson 3` selected
   1. Click on `+NEW` and select `Run a process`
   1. Select `CWL training lesson 3` from the list and click `Next`
   1. Enter a name for this run like "Third training run"
   1. The `#main/message` parameter will be pre-filled with your default value.  You can choose to change it or use the default.
   1. Click `Run process`
   1. This should take you to the status page for this workflow
   1. The greeting will appear in the `Log` of the `echo` task, which
      can be found the same way as described earlier in section 3.

## 6. Run a workflow without registering it

The `message` parameter will be taken from the file `lesson4/main-input.yaml`.  This is useful during development.

1. Workbench: Go to `+NEW` and select `New project`
   1. Enter a name for the project like "Lesson 4"
   1. You should arrive at the panel for the new project
   1. Click on `Additional info` in the upper right to expand the `info` panel
   1. Under `Project UUID` click the `Copy to clipboard` button
1. Vscode: Select the file `lesson4/main.cwl`
   1. Click on the `Terminal` menu
   1. Click `Run Task…`
   1. Select `Set Arvados project UUID`
   1. Paste the project UUID from workbench at the prompt
1. Vscode: Select the file `lesson4/main.cwl`
   1. Click on the `Terminal` menu
   1. Click `Run Task…`
   1. Select `Run CWL workflow on Arvados`
1. Vscode: In the bottom panel select the `Terminal` tab
   1. In the upper right corner of the Terminal tab select `Task - Run CWL Workflow` from the drop-down
   1. Look for logging text like `submitted container_request zzzzz-xvhdp-0123456789abcde`
   1. Highlight and copy the workflow identifier (this the string containing `-xvhdp-` in the middle)
   1. The results of this run will appear in the terminal when the run completes.
1. Workbench: Paste the workflow identifier into the search box
   1. This will take you to the status page for this workflow


## Notes

If you need to change something about the environment of the user on
the remote host (for example, the user has been added to a new unix
group) you need to restart the vscode server that runs on the remote
host.  Do this in vscode:

ctrl+shift+p: `Remote-SSH: Kill VS Code Server on Host`

This is because the vscode server remains running on the remote host
even after you disconnect, so exiting/restarting vscode on the desktop
has no effect.