lynx startup helper

Author: Ryan Calvin Barron

examples/Lynx/README.md

@@ -16,3 +16,8 @@
     ```ssh USER@HOST -L 8501:localhost:8501```
 6. Have fun!
 
+
+
+## OPTIONAL STARTUP
+
+zsh ./start_lynx.sh  -p  ../Full\ TELF\ Pipeline/single_block_examples/example_results/semantic_HNMFk_collection_slurm_option/07_SemanticHNMFk

examples/Lynx/settings.json

@@ -0,0 +1,8 @@
+{
+	"VIEW_TYPE":"Document Analysis",
+	"DOCUMENT_FILE_START_WITH":"best_50_docs_in_",
+	"ROOT_NAME":"Root",
+	"TEXT_COLUMN":"clean_title_abstract",
+	"ATTRIBUTE_COLUMN":"slic_authors",
+	"ATTRIBUTE_COLUMN_SPLIT_BY":";"
+}

examples/Lynx/start_lynx.sh

@@ -0,0 +1,180 @@
+#!/usr/bin/env sh
+# -------------------------------------------------------------
+# T-ELF / TELF launcher (zsh/bash/sh compatible)
+# - CDs to a directory that CONTAINS "TELF/" so:
+#     streamlit run TELF/applications/Lynx/frontend/main.py
+#   works and the app finds TELF/projects correctly.
+# - Copies each -p project into TELF/projects/
+# - ALSO copies a settings.json that sits NEXT TO THIS SCRIPT
+#   into each destination project (backs up existing one).
+#
+# Usage:
+#   ./start_lynx.sh
+#   ./start_lynx.sh -p "../Full TELF Pipeline/.../07_SemanticHNMFk"
+#   ./start_lynx.sh -p /abs/path/ProjA -p "../rel path/ProjB"
+#   ./start_lynx.sh --ssh user@host --port 8501
+#   ./start_lynx.sh --no-copy
+# -------------------------------------------------------------
+
+set -eu
+
+PORT=8501
+SSH_TARGET=""
+COPY_PROJECTS=1
+PROJECTS=""
+
+# --- parse args (POSIX)
+while [ $# -gt 0 ]; do
+  case "$1" in
+    -p|--project)
+      [ $# -ge 2 ] || { echo "Missing value for $1" >&2; exit 1; }
+      PROJECTS="${PROJECTS}${PROJECTS:+
+}$2"
+      shift 2
+      ;;
+    --ssh)
+      [ $# -ge 2 ] || { echo "Missing value for $1" >&2; exit 1; }
+      SSH_TARGET="$2"
+      shift 2
+      ;;
+    --port)
+      [ $# -ge 2 ] || { echo "Missing value for $1" >&2; exit 1; }
+      PORT="$2"
+      shift 2
+      ;;
+    --no-copy)
+      COPY_PROJECTS=0
+      shift
+      ;;
+    -h|--help)
+      echo "Usage: $0 [-p PATH]... [--ssh USER@HOST] [--port N] [--no-copy]"
+      exit 0
+      ;;
+    *)
+      echo "Unknown arg: $1" >&2
+      exit 1
+      ;;
+  esac
+done
+
+# ---- resolve script dir robustly (works in zsh/bash/sh)
+case "$0" in
+  /*) SCRIPT_PATH="$0" ;;
+  *)  SCRIPT_PATH="$(pwd)/$0" ;;
+esac
+SCRIPT_DIR=$(cd "$(dirname -- "$SCRIPT_PATH")" 2>/dev/null && pwd -P)
+SETTINGS_SRC="$SCRIPT_DIR/settings.json"
+
+# ---- find a repo root that CONTAINS a TELF/ directory
+# Try common layouts:
+#   <prefix>/TELF/...
+#   <prefix>/T-ELF/TELF/...
+find_repo_root() {
+  CUR="$SCRIPT_DIR"
+  i=0
+  while [ $i -le 6 ]; do
+    if [ -d "$CUR/TELF" ]; then
+      echo "$CUR"; return 0
+    fi
+    if [ -d "$CUR/T-ELF/TELF" ]; then
+      echo "$CUR/T-ELF"; return 0
+    fi
+    if [ -d "$CUR/../TELF" ]; then
+      echo "$(cd "$CUR/.." && pwd -P)"; return 0
+    fi
+    CUR=$(cd "$CUR/.." 2>/dev/null && pwd -P)
+    i=$((i+1))
+  done
+  echo ""
+}
+
+REPO_ROOT="$(find_repo_root)"
+if [ -z "$REPO_ROOT" ]; then
+  echo "Error: couldn't locate a directory that contains 'TELF/' starting from: $SCRIPT_DIR" >&2
+  exit 1
+fi
+
+TELF_DIR="$REPO_ROOT"
+APP_REL="TELF/applications/Lynx/frontend/main.py"
+APP_ABS="$REPO_ROOT/$APP_REL"
+PROJECTS_DIR="$TELF_DIR/projects"
+
+if [ ! -f "$APP_ABS" ]; then
+  echo "Error: Streamlit app not found at: $APP_ABS" >&2
+  exit 1
+fi
+
+# Ensure projects dir
+mkdir -p "$PROJECTS_DIR"
+
+# Resolve a user-supplied directory (relative to current working dir; handles spaces)
+resolve_dir() {
+  _p="$1"
+  case "$_p" in
+    /*) ABS="$_p" ;;
+    *)  ABS="$(pwd)/$_p" ;;
+  esac
+  if cd "$ABS" 2>/dev/null; then
+    pwd -P
+    cd - >/dev/null 2>&1 || true
+    return 0
+  fi
+  return 1
+}
+
+copy_settings_into() {
+  _dest="$1"
+  if [ -f "$SETTINGS_SRC" ]; then
+    if [ -f "$_dest/settings.json" ]; then
+      mv -f "$_dest/settings.json" "$_dest/settings.json.bak"
+    fi
+    cp -f "$SETTINGS_SRC" "$_dest/settings.json"
+    echo "  -> settings.json copied into '$(basename -- "$_dest")' (backup: settings.json.bak if existed)"
+  else
+    echo "  -> Warning: settings.json not found next to the script at: $SETTINGS_SRC (skipping settings copy)" >&2
+  fi
+}
+
+# Copy projects (if any)
+if [ "$COPY_PROJECTS" -eq 1 ] && [ -n "$PROJECTS" ]; then
+  echo "$PROJECTS" | while IFS= read -r src_raw; do
+    [ -n "$src_raw" ] || continue
+    if ! src_abs="$(resolve_dir "$src_raw")"; then
+      echo "Warning: project path not found: $src_raw (skipping)" >&2
+      continue
+    fi
+    base_name=$(basename -- "$src_abs")
+    dest="$PROJECTS_DIR/$base_name"
+    echo "Copying '$src_raw' -> '$dest' ..."
+    rm -rf -- "$dest"
+    if command -v rsync >/dev/null 2>&1; then
+      rsync -a --delete "$src_abs"/ "$dest"/
+    else
+      mkdir -p "$dest"
+      cp -R -- "$src_abs"/. "$dest"/
+    fi
+    # Always drop the local settings.json into the copied project
+    copy_settings_into "$dest"
+  done
+fi
+
+# Optional SSH port forward
+if [ -n "$SSH_TARGET" ]; then
+  echo "Starting SSH tunnel: localhost:$PORT -> $SSH_TARGET:localhost:$PORT"
+  if ! ssh -N -f -L "$PORT:localhost:$PORT" "$SSH_TARGET"; then
+    echo "Warning: SSH port forward failed; continuing without it." >&2
+  fi
+fi
+
+# Check streamlit
+if ! command -v streamlit >/dev/null 2>&1; then
+  echo "Error: 'streamlit' not found on PATH. Activate your env or 'pip install streamlit'." >&2
+  exit 1
+fi
+
+# CD to the repo root so the *relative* Streamlit path works
+cd "$REPO_ROOT"
+echo "Working directory: $(pwd -P)"
+echo "Ensured: $(pwd -P)/TELF/projects"
+echo "Launching: streamlit run $APP_REL --server.port $PORT"
+exec streamlit run "$APP_REL" --server.port "$PORT"