Add details and script to mount isilon for Way Lab

.pre-commit-config.yaml

@@ -14,6 +14,9 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
+        args:
+          # ignore for "school of medicine" abbreviation
+          ["-L","SOM"]
   - repo: https://github.com/executablebooks/mdformat
     rev: 0.7.17
     hooks:
@@ -24,3 +27,7 @@ repos:
     rev: v1.7.1
     hooks:
       - id: actionlint
+  - repo: https://github.com/koalaman/shellcheck-precommit
+    rev: v0.10.0
+    hooks:
+      - id: shellcheck

data_strategy.md

@@ -148,3 +148,25 @@ flowchart LR
 ```
 
 **Figure 2.** Raw data is received by the lab from Google Cloud Storage (GCS) project-specific buckets or a collaborator storage solution which is provided upfront. A lab member then transfers the data from the GCS bucket or collaborator storage solution to bandicoot (Isilon) so it may be used or shared within the lab. If the data need to be processed on HPC Alpine a lab member may decide to transfer the data to koala (PetaLibrary). Once HPC Alpine processing is complete the data are transferred back to bandicoot.
+
+## Using Isilon
+
+Leveraging Isilon involves the use of a computer system with access to the campus or virtual private network (VPN).
+Isilon can be used through a filesystem mount or through the S3-like API.
+The S3-like API requires you to email IT support at: ucd-oit-helpdesk@cuanschutz.edu
+Mounting an Isilon directory entails using operating system tools to help handle authentication and persistence.
+__Special note: the username provided when authenticating is your CU Anschutz enterprise username.__
+
+- __MacOS:__ [`mount_smbfs`](https://man.freebsd.org/cgi/man.cgi?mount_smbfs) is shipped with MacOS automatically and can be used to setup a connection to Isilon directories.
+  For example: `mount_smbfs "$SHARE" "$MOUNT_POINT"`
+- __Linux:__ [`cifs-utils`](https://wiki.samba.org/index.php/LinuxCIFS_utils) can be used in conjunction with `mount` to help setup a connection to Isilon directories.
+  For example: `mount -t cifs "$SHARE" "$MOUNT_POINT" -o username="$CIFS_USERNAME",domainauto`
+  Note: `domainauto` is important for ensuring the connection to CU Anschutz shares.
+
+### Connection script
+
+Please feel free to use the following script to automatically help setup your mount point to the Way Lab specific mount point on CU Anschutz Isilon: `bandicoot`.
+
+```shell
+curl https://raw.githubusercontent.com/WayScience/playbooks/refs/heads/main/internal/mount_bandicoot.sh | sh
+```

internal/mount_bandicoot.sh

@@ -0,0 +1,104 @@
+#!/usr/bin/env sh
+# shellcheck shell=sh
+# ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
+# mount_bandicoot.sh
+#
+# This script creates a local mount point and mounts a CIFS/Samba share
+# at //data.ucdenver.pvt/dept/SOM/DBMI/Bandicoot into ~/mnt/bandicoot.
+# It auto-detects macOS vs. Linux, installs cifs-utils on Linux if needed,
+# verifies VPN/network access, and works under any POSIX shell
+# (sh, bash, zsh, dash, etc.).
+# ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
+
+set -eu
+# -e: exit immediately on any error
+# -u: treat unset variables as an error
+
+# Remote share location (UNC path)
+SHARE="//data.ucdenver.pvt/dept/SOM/DBMI/Bandicoot"
+# Local directory where the share will be mounted
+MOUNT_POINT="$HOME/mnt/bandicoot"
+
+# ────────────────────────────────────────────────────────────────────────────
+# 1) Ensure the mount directory exists
+# ────────────────────────────────────────────────────────────────────────────
+if [ ! -d "$MOUNT_POINT" ]; then
+    echo "→ Creating mount point directory: $MOUNT_POINT"
+    mkdir -p "$MOUNT_POINT"
+    # mkdir -p will also create any missing parent directories
+fi
+
+# ────────────────────────────────────────────────────────────────────────────
+# 2) Extract host from the UNC path and verify network/VPN access
+# ────────────────────────────────────────────────────────────────────────────
+# Strip leading '//' and everything after the first '/'
+HOST="${SHARE#//}"
+HOST="${HOST%%/*}"
+echo "→ Checking network reachability to $HOST..."
+# Try a single ping with 1s timeout; adjust flags if your ping differs
+if ! ping -c 1 -W 1 "$HOST" >/dev/null 2>&1; then
+    echo "✗ Unable to reach $HOST. Please ensure you're connected to VPN or network." >&2
+    exit 1
+fi
+
+# ────────────────────────────────────────────────────────────────────────────
+# 3) Detect operating system and perform mount
+# ────────────────────────────────────────────────────────────────────────────
+OS="$(uname)"
+case "$OS" in
+    Darwin)
+        # macOS branch
+        echo "→ Detected macOS (Darwin). Using mount_smbfs."
+        #
+        # mount_smbfs is the built-in macOS SMB client.
+        # It will prompt you for credentials if required,
+        # or use your current login keychain.
+        #
+        mount_smbfs "$SHARE" "$MOUNT_POINT"
+        ;;
+
+    Linux)
+        # Linux branch
+        echo "→ Detected Linux. Verifying cifs-utils (mount.cifs) is installed..."
+        #
+        # mount.cifs is provided by the cifs-utils package.
+        # If it's missing, we detect your package manager and install it.
+        #
+        if ! command -v mount.cifs >/dev/null 2>&1; then
+            echo "→ cifs-utils not found. Attempting installation..."
+            if command -v apt-get >/dev/null 2>&1; then
+                echo "   • Using apt-get to install cifs-utils"
+                sudo apt-get update
+                sudo apt-get install -y cifs-utils
+            elif command -v yum >/dev/null 2>&1; then
+                echo "   • Using yum to install cifs-utils"
+                sudo yum install -y cifs-utils
+            else
+                echo "✗ Unsupported package manager. Please install cifs-utils manually." >&2
+                exit 1
+            fi
+        fi
+
+        # Prompt the user for their CIFS username
+        printf "Isilon/CIFS username (CU Anschutz username): " >/dev/tty
+        read -r CIFS_USERNAME </dev/tty  # read from the terminal, not the script pipe
+        if [ -z "$CIFS_USERNAME" ]; then
+            echo "✗ Username cannot be empty." >&2
+            exit 1
+        fi
+        # Mount the share with domainauto for automatic domain selection
+        sudo mount -t cifs "$SHARE" "$MOUNT_POINT" \
+            -o username="$CIFS_USERNAME",domainauto
+        ;;
+
+    *)
+        # Unsupported OS
+        echo "✗ Unsupported operating system: $OS" >&2
+        exit 1
+        ;;
+esac
+
+# ────────────────────────────────────────────────────────────────────────────
+# 4) Success message
+# ────────────────────────────────────────────────────────────────────────────
+echo "✔ Successfully mounted $SHARE at $MOUNT_POINT"