Updating docs and adding db

Author: jwbear

.readthedocs.yaml

@@ -4,7 +4,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Python settings and pip install
 python:

DashML/GUI/DT.py

@@ -133,7 +133,7 @@ def validate_inputs_and_collect_errors(self):
 
         # Check required text fields
         sequence_txt = self.sequence_input.text().strip()
-        if not re.fullmatch(r"^[ACGTU]+$", sequence_txt, re.IGNORECASE):
+        if not re.fullmatch(r"^[ACGTUacgtu]+$", sequence_txt, re.IGNORECASE):
             errors.append("Sequence nucleotides must be ACGTU.")
 
         # Check required text fields
@@ -152,12 +152,9 @@ def validate_inputs_and_collect_errors(self):
 
         # Check secondary structure and experiment consistency
         secondary = self.secondary_input.text().strip()
-        if not re.fullmatch(r"^[().]+$", secondary):
-            errors.append("[red]Error: Secondary structure must contain only '.', '(', and ')' characters.[/red]")
-
         experiment = self.experiment_input.text().strip()
 
-        if secondary:
+        if secondary != '':
             if not re.fullmatch(r"^[().]+$", secondary):
                 errors.append("Secondary structure must be in valid dot-bracket notation (only '.', '(', ')').")
 
@@ -169,7 +166,7 @@ def validate_inputs_and_collect_errors(self):
 
         # Check if experiment is given without secondary (if needed)
         if experiment and not secondary:
-            errors.append("If specifying an experiment, a secondary structure must also be provided.")
+            errors.append("If specifying an experiment, a secondary control structure must also be provided.")
 
         return errors
 

DashML/UI/DT_CLI.py

@@ -1,6 +1,8 @@
 import sys, re
 import traceback
 import readline
+import contextlib
+import io
 import cmd
 import configparser
 import os
@@ -28,18 +30,30 @@
     readline.parse_and_bind("set editing-mode emacs")
 
 
-# Configure libedit on macOS (if needed)
+
+def safe_bind(binding):
+    try:
+        readline.parse_and_bind(binding)
+    except Exception:
+        pass
+
 if 'libedit' in readline.__doc__:
-    readline.parse_and_bind("bind ^I rl_complete")
-    readline.parse_and_bind("bind ^A beginning-of-line")
-    readline.parse_and_bind("bind ^E end-of-line")
-    readline.parse_and_bind("bind ^K kill-line")
-    readline.parse_and_bind("bind ^Y yank")
-    readline.parse_and_bind("bind ^P previous-history")
-    readline.parse_and_bind("bind ^N next-history")
+    # Only use *known valid* libedit commands
+    safe_bind("bind ^I rl-complete")
+    safe_bind("bind ^A ed-move-to-beg")
+    safe_bind("bind ^E ed-move-to-end")
+    safe_bind("bind ^K ed-kill-line")
+    safe_bind("bind ^P ed-prev-history")
+    safe_bind("bind ^N ed-next-history")
 else:
-    # GNU readline (Linux or correctly installed on macOS)
-    readline.parse_and_bind("tab: complete")
+    # GNU readline
+    safe_bind("tab: complete")
+    safe_bind("Control-a: beginning-of-line")
+    safe_bind("Control-e: end-of-line")
+    safe_bind("Control-k: kill-line")
+    safe_bind("Control-y: yank")
+    safe_bind("Control-p: previous-history")
+    safe_bind("Control-n: next-history")
 
 init(autoreset=True)
 
@@ -256,20 +270,21 @@ def handle_seq_add(self, args):
 
             sequence = opts.sequence
             # Validate that the sequence contains only valid RNA characters
-            if not re.fullmatch(r"^[ACGU]+$", sequence.upper()):
+            if not re.fullmatch(r"^[ACGTUacgtu]+$", sequence):
                 console = Console()
-                console.print("[red]Error: Sequence must contain only A, C, G, or U characters.[/red]")
+                console.print("[red]Error: Sequence must contain only A, C, G, T, or U characters.[/red]")
                 return
 
             secondary = opts.secondary
-            # Check that secondary structure is valid dot-bracket notation
-            if not re.fullmatch(r"^[().]+$", secondary):
-                console.print("[red]Error: Secondary structure must contain only '.', '(', and ')' characters.[/red]")
-                return
 
             # Validate secondary structure length
             if secondary:
 
+                if not re.fullmatch(r"^[().]+$", secondary):
+                    console.print("[red]Error: Secondary structure must contain only '.', '(', and ')' characters.[/red]")
+                    return
+
+
                 # Check secondary structure length
                 if len(secondary) != len(sequence):
                     console.print(
@@ -280,7 +295,7 @@ def handle_seq_add(self, args):
                 # Check that experiment is not blank
                 if not opts.experiment.strip():
                     console.print(
-                        "[red]Error: Experiment ID must be provided when a secondary structure is specified.[/red]"
+                        "[red]Error: Control experiment must be provided when a secondary structure is specified.[/red]"
                     )
                     return
 

DashML/db/__init__.py

@@ -0,0 +1,25 @@
+services:
+  db:
+    image: mariadb:10.11.5
+    restart: always
+    environment:
+      MARIADB_ROOT_PASSWORD: ${DB_ROOT_PASSWORD:-root}
+      MARIADB_DATABASE: ${DB_NAME:-dtuser_DASH}
+      MARIADB_USER: ${DB_USER:-dtuser}
+      MARIADB_PASSWORD: ${DB_PASSWORD:-dtpass}
+      MARIADB_GENERAL_LOG: 1
+      MARIADB_GENERAL_LOG_FILE: /var/lib/mysql/general.log
+    ports:
+      - "3307:3306"
+    volumes:
+      # Persistent DB volume
+      - db_datad:/var/lib/mysql
+
+      # SQL init script, extracted at runtime or fallback to local dev copy
+      - ${INIT_SQL_PATH:-./DashML/db/init.sql}:/docker-entrypoint-initdb.d/init.sql
+
+      # MariaDB config file, extracted at runtime or fallback to local dev copy
+      - ${MY_CNF_PATH:-./DashML/db/my.cnf}:/etc/mysql/conf.d/my.cnf
+
+volumes:
+  db_datad:

DashML/db/docker-compose.yml

@@ -0,0 +1,100 @@
+import os
+import argparse
+import pathlib
+import tempfile
+import shutil
+import sys
+import subprocess
+import importlib.resources as pkg_resources
+
+PACKAGE_NAME = "DashML"
+DB_SUBDIR = "db"
+INIT_SQL_NAME = "init.sql"
+COMPOSE_FILE = "docker-compose.yml"
+
+
+def check_docker_access():
+    # Check if docker is installed
+    if not shutil.which("docker"):
+        print("❌ Docker is not installed or not in PATH.")
+        sys.exit(1)
+
+    try:
+        subprocess.run(["docker", "info"], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, check=True)
+    except subprocess.CalledProcessError:
+        print("❌ Docker is running but your user lacks permission to access the Docker daemon.")
+        print("➡️  Try running:")
+        print("    sudo usermod -aG docker $USER")
+        print("    newgrp docker  # or log out and back in")
+        sys.exit(1)
+    except Exception as e:
+        print(f"❌ Unexpected error trying to access Docker: {e}")
+        sys.exit(1)
+
+
+
+def extract_resource(filename):
+    tmp_dir = pathlib.Path(tempfile.mkdtemp(prefix="dashml_"))
+    output_path = tmp_dir / filename
+
+    with pkg_resources.files(f"{PACKAGE_NAME}.{DB_SUBDIR}").joinpath(filename).open("rb") as src:
+        with open(output_path, "wb") as dst:
+            shutil.copyfileobj(src, dst)
+
+    return output_path
+
+
+def run_docker_compose(command_args, extra_env=None):
+    compose_path = pathlib.Path(__file__).parent.parent / DB_SUBDIR / COMPOSE_FILE
+
+    if not compose_path.exists():
+        print(f"❌ Could not find docker-compose.yml at {compose_path}")
+        return
+
+    env = os.environ.copy()
+    if extra_env:
+        env.update(extra_env)
+
+    cmd = ["docker", "compose", "-f", str(compose_path)] + command_args
+    subprocess.run(cmd, env=env)
+
+def main():
+    check_docker_access()
+
+    parser = argparse.ArgumentParser(prog="dt_db", description="DashML DB manager")
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    subparsers.add_parser("up", help="Start the database container")
+    subparsers.add_parser("reset", help="Warning: Deletes the data!")
+    subparsers.add_parser("down", help="Stop and remove the container")
+    subparsers.add_parser("logs", help="Show container logs")
+    subparsers.add_parser("status", help="Show container status")
+
+    args = parser.parse_args()
+
+    if args.command == "up":
+        init_sql_path = extract_resource("init.sql")
+        my_cnf_path = extract_resource("my.cnf")
+
+        print(f"📦 Using init.sql: {init_sql_path}")
+        print(f"⚙️  Using my.cnf:   {my_cnf_path}")
+
+        run_docker_compose(["up", "--build", "-d"], {
+            "INIT_SQL_PATH": str(init_sql_path),
+            "MY_CNF_PATH": str(my_cnf_path)
+        })
+
+    elif args.command == "down":
+        run_docker_compose(["down"])
+
+    elif args.command == "del":
+        run_docker_compose(["down", "-v"])
+
+    elif args.command == "logs":
+        run_docker_compose(["logs"])
+
+    elif args.command == "status":
+        run_docker_compose(["ps"])
+
+    else:
+        parser.print_help()