added VM specific code

VM/install.sh

@@ -0,0 +1,122 @@
+#!/bin/bash
+DOCKER_GPG=/etc/apt/keyrings/docker.gpg
+ apt-get install -y --no-install-recommends \
+        curl \
+        dbus-x11 \
+        feh \
+        firefox \
+        fluxbox \
+        fonts-wqy-microhei \
+        geany \
+        gtk2-engines-murrine \
+        gvfs-backends \
+        jq \
+        language-pack-gnome-zh-hant \
+        language-pack-zh-hant \
+        libbz2-dev \
+        libgl1-mesa-dri \
+        liblzma-dev \
+        libssl1.0 \
+        libwebkit2gtk-4.0 \
+        mesa-utils \
+        nano \
+        nemo \
+        net-tools \
+        openssh-server \
+        pwgen \
+        python3-pyqt5 \
+        python3-pyqt5.qtsvg \
+        python3-pyqt5.qtwebkit \
+        rsync \
+        ttf-ubuntu-font-family \
+        wget \
+        xdg-utils \
+        lxterminal \
+        xvfb \
+        zlib1g-dev \
+        zenity
+  git clone https://github.com/Biodepot/Biodepot-workflow-builder
+  cp -r Biodepot-workflow-builder/orange3 /orange3
+  cp -r Biodepot-workflow-builder/orangePatches /orangePatches
+apt-get install -y \
+        build-essential \
+        python3-dev \
+        python3-pip \
+    && python3 -m pip install --upgrade \
+        pip==20.0.1 \
+        setuptools \
+        wheel 
+ cd / && pip3 install -r orange3/requirements-gui.txt 
+         beautifulsoup4 \
+         docker \
+         pysam 
+ pip3 install -e orange3
+
+apt-get install -y --no-install-recommends gnupg 
+mkdir -p /etc/apt/keyrings && curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o $DOCKER_GPG 
+arch=$(dpkg --print-architecture) \
+     && codename=$(awk -F= '/CODENAME/ {print $2;exit}' /etc/os-release) \
+     && echo "deb [arch=$arch signed-by=$DOCKER_GPG] https://download.docker.com/linux/ubuntu $codename stable" > \
+         /etc/apt/sources.list.d/docker.list \
+     && apt-get update \
+     && apt-get install -y --no-install-recommends \
+         containerd.io \
+         docker-ce \
+         docker-ce-cli
+ pip3 install --user jsonpickle
+ cp -r Biodepot-workflow-builder/widgets widgets
+ cp -r Biodepot-workflow-builder/biodepot biodepot
+ cp -r Biodepot-workflow-builder/coreutils coreutils
+
+ apt-get install -y xorg 
+ cp -r Biodepot-workflow-builder/scripts/generate_setup.sh /usr/local/bin/generate_setup.sh
+ chmod +x /usr/local/bin/generate_setup.sh
+ pip3 install -e /biodepot
+ curl -L "https://github.com/docker/compose/releases/download/1.23.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose \
+     && chmod +x /usr/local/bin/docker-compose
+ sed -i 's/"Orange Canvas"/"Bwb"/' /orange3/Orange/canvas/config.py
+ rm -rf ~/.fluxbox
+ cp -r Biodepot-workflow-builder/fluxbox_config ~/.fluxbox
+ cp -r Biodepot-workflow-builder/user_config/* ~/. 
+ cp /orangePatches/schemeedit.py /orange3/Orange/canvas/document/schemeedit.py
+ cp /orangePatches/canvasmain.py /orange3/Orange/canvas/application/canvasmain.py
+ cp /orangePatches/widgetsscheme.py /orange3/Orange/canvas/scheme/widgetsscheme.py
+ cp /orangePatches/signalmanager.py /orange3/Orange/canvas/scheme/signalmanager.py
+ cp /orangePatches/link.py /orange3/Orange/canvas/scheme/link.py
+ cp /orangePatches/signals.py /orange3/Orange/widgets/utils/signals.py
+ cp /orangePatches/linkitem.py /orange3/Orange/canvas/canvas/items/linkitem.py
+ cp /orangePatches/__main__.py /orange3/Orange/canvas/__main__.py
+ cp /orangePatches/discovery.py /orange3/Orange/canvas/registry/discovery.py
+
+cp Biodepot-workflow-builder/scripts/startBwb.sh /usr/local/bin/startBwb.sh
+cp Biodepot-workflow-builder/scripts/startSingleBwb.sh /usr/local/bin/startSingleBwb.sh
+cp Biodepot-workflow-builder/scripts/runDockerJob.sh /usr/local/bin/runDockerJob.sh
+cp Biodepot-workflow-builder/scripts/startScheduler.sh /usr/local/bin/startScheduler.sh
+cp Biodepot-workflow-builder/scripts/build_workflow_containers.sh /usr/local/bin/build_workflow_containers.sh
+cp Biodepot-workflow-builder/scripts/whiteListToolDock.py /usr/local/bin/whiteListToolDock.py
+cp Biodepot-workflow-builder/scripts/addWorkflowsToToolDock.py /usr/local/bin/addWorkflowsToToolDock.py
+cp Biodepot-workflow-builder/scripts/addWidgetToToolDock.sh /usr/local/bin/addWidgetToToolDock.sh
+cp Biodepot-workflow-builder/scripts/removeWidgetFromToolDock.sh /usr/local/bin/removeWidgetFromToolDock.sh
+cp Biodepot-workflow-builder/scripts/generate_setup.sh /usr/local/bin/generate_setup.sh
+cp -r Biodepot-workflow-builder/executables /usr/local/bin/executables
+groupadd ftpaccess
+cp Biodepot-workflow-builder/sshd_config /etc/ssh/sshd_config
+cp Biodepot-workflow-builder/startSftp.sh /usr/local/bin/startSftp.sh
+cp Biodepot-workflow-builder/scripts/findResolution.sh /usr/local/bin/findResolution.sh
+
+cp -r Biodepot-workflow-builder/workflows /workflows
+cp -r Biodepot-workflow-builder/notebooks /notebooks
+cp -r Biodepot-workflow-builder/templates /templates
+cp -r Biodepot-workflow-builder/icons /icons
+cp -r Biodepot-workflow-builder/tutorialFiles /tutorialFiles
+cp Biodepot-workflow-builder/serverSettings.json /biodepot
+
+cp Biodepot-workflow-builder/startup.sh /
+cp Biodepot-workflow-builder/nginx.conf /etc/nginx/sites-enabled/default
+
+#cp Biodepot-workflow-builder/ config files for dev tools
+cp -r Biodepot-workflow-builder/dev-files/geany/ /root/.config/
+cp -r Biodepot-workflow-builder/VM/xorg.conf /etc/X11/xorg.conf
+cp -r Biodepot-workflow-builder/VM/*.sh /usr/local/bin/
+cp Biodepot-workflow-builder/VM/menu /root/.fluxbox/menu
+cp .fluxbox/bwb.svg /orange3/Orange/canvas/icons/.

VM/menu

@@ -0,0 +1,28 @@
+# Generated by fluxbox-generate_menu
+#
+# If you read this it means you want to edit this file manually, so here
+# are some useful tips:
+#
+# - You can add your own menu-entries to ~/.fluxbox/usermenu
+#
+# - If you miss apps please let me know and I will add them for the next
+#   release.
+#
+# - The -r option prevents removing of empty menu entries and lines which
+#   makes things much more readable.
+#
+# - To prevent any other app from overwriting your menu
+#   you can change the menu name in ~/.fluxbox/init to:
+#     session.menuFile: ~/.fluxbox/my-menu
+[begin] (Applications)
+[encoding] {UTF-8}
+  [exec] (Bwb) {/usr/local/bin/startBwb.sh} </root/.fluxbox/bwb256.png>
+  [exec] (Bwb-debug) {/bin/bash -c 'export XENVIRONMENT=.Xresources; lxterminal -e startBwb.sh orange-canvas -l 4'} </root/.fluxbox/bwb256.png>
+  [exec] (Files) {dbus-launch nemo}
+  [exec] (Resize) {/usr/local/bin/resize.sh}
+  [exec] (Terminal) {/bin/bash -c 'export XENVIRONMENT=.Xresources; lxterminal'}
+  [exec] (geany) {geany}
+  [exec] (firefox) {firefox}
+  [exec] (Quit) {quit_desktop.sh}
+  [endencoding]
+[end]

VM/quit_desktop.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+# Find the Xorg process for the current user
+XORG_PID=$(ps -u "$USER" -o pid,cmd | grep -E 'Xorg|X ' | grep -v grep | awk '{print $1}')
+
+# Check if Xorg process was found
+if [ -z "$XORG_PID" ]; then
+    zenity --info --text="No Xorg process found for user $USER. Exiting."
+    exit 1
+fi
+
+# Prompt the user for confirmation using zenity
+if zenity --question --text="Are you sure you want to terminate your X11 session?"; then
+    # User clicked "Yes"
+    zenity --info --text="Terminating Xorg process (PID: $XORG_PID)..."
+    kill "$XORG_PID"
+
+    # Verify if the process is still running, and if so, forcefully kill it
+    if ps -p "$XORG_PID" > /dev/null; then
+        zenity --warning --text="Process did not terminate gracefully. Forcing termination..."
+        kill -9 "$XORG_PID"
+    fi
+    zenity --info --text="Xorg process terminated."
+    stty echo
+else
+    # User clicked "No"
+    zenity --info --text="Operation canceled by the user."
+fi

VM/resize.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+# Get all unique modes (resolutions) from the first column of xrandr output
+modes=$(xrandr | awk '{ print $1 }' | grep '^[0-9]*x[0-9]*$' | sort -u)
+
+# Check if we found any modes
+if [ -z "$modes" ]; then
+    zenity --error --text="No available screen resolutions found."
+    exit 1
+fi
+
+# Display the unique list of available modes in zenity
+selected_mode=$(echo "$modes" | zenity --list --title="Select Screen Resolution" \
+  --text="Choose a screen resolution" \
+  --column="Resolution" --width=300 --height=400)
+
+# Check if the user pressed cancel or didn't select a mode
+if [ -z "$selected_mode" ]; then
+    echo "No resolution selected. Exiting."
+    exit 1
+fi
+
+# Prompt the user to select an output if multiple displays are connected
+outputs=$(xrandr | grep " connected" | awk '{ print $1 }')
+output_count=$(echo "$outputs" | wc -l)
+
+if [ "$output_count" -gt 1 ]; then
+    # Let the user choose an output if more than one is connected
+    selected_output=$(echo "$outputs" | zenity --list --title="Select Display Output" \
+      --text="Choose a display output to apply the resolution" \
+      --column="Output" --width=300 --height=200)
+
+    # Check if the user pressed cancel or didn't select an output
+    if [ -z "$selected_output" ]; then
+        echo "No display output selected. Exiting."
+        exit 1
+    fi
+else
+    # Use the single output if only one display is connected
+    selected_output="$outputs"
+fi
+
+# Apply the selected resolution to the chosen output using xrandr
+if xrandr --output "$selected_output" --mode "$selected_mode" 2>/dev/null; then
+    zenity --info --text="Resolution set to $selected_mode on $selected_output successfully."
+else
+    zenity --error --text="Failed to set resolution. $selected_mode may not be supported on $selected_output."
+    exit 1
+fi
+
+# Check if the background image path is stored in ~/.fehbg
+if [ -f ~/.fehbg ]; then
+    # Source ~/.fehbg to reapply the same background image
+    source ~/.fehbg
+else
+    zenity --warning --text="No existing background image found to reapply."
+fi

VM/xorg.conf

@@ -0,0 +1,18 @@
+Section "Monitor"
+    Identifier "Monitor0"
+    Option "PreferredMode" "1920x1080"
+EndSection
+
+Section "Screen"
+    Identifier "Screen0"
+    Device "Card0"
+    Monitor "Monitor0"
+    SubSection "Display"
+        Modes "1920x1080"
+    EndSubSection
+EndSection
+
+Section "Device"
+    Identifier "Card0"
+    Driver "intel" # or "modesetting" or your specific driver
+EndSection

coreutils/DockerClient.py

@@ -10,6 +10,21 @@
 import time
 from pathlib import Path
 #runScheduler.sh ['b2b72d36270f4200a9e', '/tmp/docker.b2b72d36270f4200a9e.json', '8', '8096']
+def detect_container():
+    # Check for Docker-specific markers
+    if (os.path.isfile("/.dockerenv")):
+        return True
+
+    # Check for Apptainer/Singularity-specific markers
+    if (
+        os.environ.get("APPTAINER_NAME") or
+        os.environ.get("SINGULARITY_NAME") or
+        os.path.isdir("/.singularity.d") or
+        os.path.isfile("/.apptainer")
+    ):
+        return True
+    return False
+
 def breakpoint(title=None, message=None):
     QtGui.QMessageBox.warning(title,'',message)
 class ConsoleProcess:
@@ -259,21 +274,25 @@ def __init__(self, url, name):
         self.url = url
         self.name = name
         self.cli = APIClient(base_url=url)
-        command = "awk -F'/containers/|/resolv.conf' '$2!=\"\" {print $2; exit}' /proc/self/mountinfo"
-        outputString=str(subprocess.check_output(
-                command,
-                shell=True,
-                universal_newlines=True,
-            ))
-        if outputString:
-            self.bwb_instance_id = outputString.splitlines()[0]
-        else:
+        self.isContainer = detect_container()
+        self.bwb_instance_id = None
+        if(self.isContainer):   
+            command = "awk -F'/containers/|/resolv.conf' '$2!=\"\" {print $2; exit}' /proc/self/mountinfo"
             outputString=str(subprocess.check_output(
-                "cat /proc/self/mountinfo | grep -oP '(?<=docker/containers/).*?(?=/resolv)'",
-                shell=True,
-                universal_newlines=True,
-            ))
-            self.bwb_instance_id = outputString.strip()
+                    command,
+                    shell=True,
+                    universal_newlines=True,
+                ))
+            if outputString:
+                self.bwb_instance_id = outputString.splitlines()[0]
+            else:
+                outputString=str(subprocess.check_output(
+                    "cat /proc/self/mountinfo | grep -oP '(?<=docker/containers/).*?(?=/resolv)'",
+                    shell=True,
+                 universal_newlines=True,
+                ))
+                self.bwb_instance_id = outputString.strip()
+
         print(self.bwb_instance_id)
         self.bwbMounts = {}
         self.shareMountPoint={};
@@ -283,6 +302,7 @@ def __init__(self, url, name):
         self.logFile = None
         self.schedulerStarted = False
 
+
     def getClient(self):
         return self.cli
 
@@ -510,6 +530,9 @@ def findShareMountPoint(self,overwrite=False):
 
         #check if mountpoint variable exists
     def findVolumeMappings(self):
+        if not self.isContainer:
+            self.bwbMounts["/data"] = "/data"
+            return
         for c in self.cli.containers():
             container_id = c["Id"]
             if container_id == self.bwb_instance_id:
@@ -527,6 +550,8 @@ def findNextFlowSelfMounts(self):
         return mountString
 
     def to_best_host_directory(self, path, returnNone=False):
+        if not detect_container():
+            return path
         sys.stderr.write("bwbMounts are {}\n".format(self.bwbMounts))
         if self.bwbMounts == {}:
             self.findVolumeMappings()