Update steps for simpler arvados config

[arvados-vscode-cwl-training.git] / README.md

diff --git a/README.md b/README.md
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 These lessons give step by step instructions for using Visual Studio
 These lessons give step by step instructions for using Visual Studio

-Code to develop CWL workflows on Arvados.
-
-1. Install & set up ssh client on Windows
-1. Install vscode and relevant extensions
-1. Use vscode to connect to an arvados shell node for development
-1. Create an simple command line tool, run it, and view the log
-1. Upload input, create a command line tool to process it, and view the output
-
-# Windows SSH Setup
-
-Linux and MacOS users can skip this step.
-
-1. Install git for windows https://git-scm.com/download/win
-1. Open git bash
-1. Run “ssh-keygen”
-1. Look for “Your public key has been saved in /c/Users/MyUsername/.ssh/id_rsa.pub”
-1. Run “cat /c/Users/MyUsername/.ssh/id_rsa.pub”
-1. Copy the lines starting with “ssh-rsa …”
-1. Open Arvados workbench
-1. Go to “SSH keys” in the user menu
-1. Click + Add new ssh key
-1. Paste the key into “Public key” and enter something for “name”
-1. At the git bash command line, run “ssh shell…” and say “yes” if it asks “do you want to continue connecting”
-1. You should be logged into the Arvados shell node.
-1. Log out by typing “exit”
-
-# VSCode setup
-
-1. Install vscode https://code.visualstudio.com/ and start it up
-1. Vscode: go to “Extensions”
-   1. search for “remote development” and install the Remote Development extension pack from Microsoft
-1. Vscode: On the left side bar, choose “Remote explorer”
-   1. In the drop down, choose “SSH targets”
-   1. Click “Add new”
-   1. Enter the “ssh shell…” command line you used in step 1(j)
-   1. Right click the ssh target in the list and select “connect to host in current window”
-1. Vscode: go to “Extensions”
-   1. Search for “benten” and install “CWL (Rabix/Benten)”
-   1. Choose “Install extension on the remote ssh host”
-1. Vscode: On the left side bar, choose “Explorer”
-   1. Select “Clone Repository” and then enter “https://github.com/tetron/vscode-cwl-testing.git”
-   1. Choose “Open”
+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. Go to Arvados Workbench

-   1. Workbench: In the user menu, select “Current token”
-   1. Vscode: Click on the “Terminal” menu
-   1. Vscode: Click “Run Task…”
-   1. Vscode: Select “Configure Arvados”
-   1. Workbench: Copy the string following “ARVADOS_API_HOST=”
-   1. Vscode: Paste the string at the “Value for ARVADOS_API_HOST” prompt
-   1. Workbench: Copy the string following “ARVADOS_API_TOKEN=”
-   1. Vscode: Paste the string at the “Value for ARVADOS_API_TOKEN” prompt
-
-# 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. Workbench: Go to “+NEW” and select “New project”
-   1. Enter a name for the project like “Lesson 1”
+   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. 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. 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. This should take you to a panel showing the workflow run status
 1. Workbench: workflow run status panel

-   1. Click on the three vertical dots in the top-right corner
-   1. Choose “Log”
-   1. Under “event type” choose “stdout”
+   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
 
    1. You should see your message
 

-# Working with input and output files
+## 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. 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. Go to your desktop

-   1. Using a text editor such as notepad, create a file “message.txt”
-   1. Enter a message like “Hello world” and save
-1. Workbench: Go to “+NEW” and select “New project”
-   1. Enter a name for the project like “Lesson 2”
+   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. 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. Call the collection “my message”
-   1. Drag and drop “message.txt” into the browser
-   1. Click “Create a collection”
+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. 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. 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. A selection dialog box will appear

-   1. Navigate to the collection you created in step (13) and choose “message.txt”
-   1. Click “Run process”
+   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. 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 “Download”
-   1. Open the downloaded file.  It should have your results.
+   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.

 
 

-# Register a workflow with default inputs
+## 5. Register a workflow with default inputs

 
 

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

 
 

-1. Workbench: Go to “+NEW” and select “New project”
-   1. Enter a name for the project like “Lesson 3”
+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. 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. 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. 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.

 
 

-# Run a workflow without registering it
+## 6. Run a workflow without registering it

 
 

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