add build step

Dockerfile

@@ -20,7 +20,23 @@ RUN sed -i "s/'_headers'/'headers'/" /usr/local/lib/python3.9/site-packages/revp
 
 WORKDIR /primerdriver
 
-ENTRYPOINT gunicorn primerx.wsgi -b 0.0.0.0:$PORT --log-file - --reload
+ENTRYPOINT python manage.py migrate && gunicorn primerx.wsgi -b 0.0.0.0:$PORT --log-file - --reload
+
+FROM base as make-linux
+
+RUN apt-get update
+RUN apt-get install upx-ucl libgfortran-10-dev libquadmath0 -y
+
+ENV PYTHONDONTWRITEBYTECODE 1
+
+COPY requirements.dev.txt /tmp/requirements.dev.txt
+COPY requirements.txt /tmp/requirements.txt
+
+RUN pip install --no-cache-dir -r /tmp/requirements.dev.txt
+
+WORKDIR /primerdriver
+
+ENTRYPOINT [ "sh", "build.sh" ]
 
 FROM node:16-alpine as build
 

README.md

@@ -9,20 +9,24 @@
 
 You can access and download the CLI from the 
 [releases page](https://github.com/kvdomingo/primerdriver/releases). 
-Extract the files to your local machine and run the program via
+Run the program in a terminal using
 ```shell
-python -m primerdriver
+primerdriver -h
 ```
 
-This will automatically run the help program, which can also be accessed 
-by passing a `-h` flag. For first-time users, the program can be run in 
-interactive mode by passing the `-i` flag. This will walk you through 
-each option step-by-step. Batch design can be performed by 
-including [`primerdriver.py`](pdcli/primerdriver.py) as part of a shell script.
+This will run the help program. For first-time users, the program can be run in 
+interactive mode by passing the `-i` flag:
+```shell
+primerdriver -i
+```
+
+This will walk you through each option step-by-step.
+Batch design can be performed by including
+[`primerdriver`](primerdriver/__main__.py) as part of a shell script.
 
 ## Web application
-For a more interactive experience, the updated web application can be 
-accessed via https://primerdriver.vercel.app.
+For a more interactive experience, visit the 
+[web application](https://primerdriver.kvdstudio.app).
 
 ## Documentation
 The documentation is available at https://kvdomingo.github.io/primerdriver/.
@@ -44,7 +48,7 @@ A step by step series of examples that tell you how to get a
 development environment running
 
 1. Clone and extract the repo.
-2. Install backend dependencies:
+2. Create a virtual environment and install backend dependencies:
 ```shell
 pip install -r requirements.dev.txt
 ```
@@ -59,14 +63,20 @@ docker compose up --build
 Wait a few minutes for all the containers to start, then access the 
 local server in your browser at http://localhost:8000.
 
+### Building from source
+Run the script:
+```shell
+./build.sh
+```
+
 ### Deployment
-```bash
-> git add .
-> git commit -m <DESCRIPTIVE_COMMIT_MESSAGE>
-> git push origin <GITHUB_BRANCH>
+```shell
+git add .
+git commit -m "DESCRIPTIVE_COMMIT_MESSAGE"
+git push origin your_feature_branch
 ```
 
-where `GITHUB_BRANCH` should summarize the changes you are implementing 
+where `your_feature_branch` should summarize the changes you are implementing 
 (e.g., `feature/implementing-xxxx-feature`, `bugfix/crush-critical-yyyy-bug`).
 
 
@@ -77,7 +87,7 @@ where `GITHUB_BRANCH` should summarize the changes you are implementing
 - **Carlo M. Lapid** - Project Adviser - [Email](mailto:[email protected])
 
 ## Versioning
-This project complies with [SemVer](https://semver.org) for versioning. Fo
+This project complies with [SemVer](https://semver.org) for versioning. For
 all available versions, see 
 [tags](https://github.com/kvdomingo/primerdriver/tags).
 

build.py

@@ -0,0 +1,5 @@
+from primerdriver.__main__ import main
+
+
+if __name__ == "__main__":
+ main()

build.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+pyinstaller --clean -F --name primerdriver build.py

docker-compose.yml

@@ -20,3 +20,11 @@ services:
  env_file: ./web/app/.env
  volumes:
  - ./web:/web
+
+ make-linux:
+ build:
+ context: .
+ target: make-linux
+ image: kvdomingo/primerdriver-makelinux:latest
+ volumes:
+ - .:/primerdriver

primerdriver/__main__.py

@@ -4,8 +4,22 @@
 from .output_handler import *
 
 
+@logger.catch
 def main():
- parser = ArgumentParser()
+ print(
+ f"""
+ ---. .------------.
+ ||||\\ /||||||||||||||\\ 
+ Primer · Driver
+\\|||||||||||/ \\||||||| 
+ `---------` `------
+ 
+PrimerDriver v{version}
+(c) 2020 Kenneth V. Domingo & Numeriano Amer E. Gutierrez
+ """
+ )
+
+ parser = ArgumentParser(prog="primerdriver")
  parser.add_argument(
  "-M",
  "--mode",
@@ -29,7 +43,7 @@ def main():
  if args.interactive:
  args_dict = interactive_handler()
  else:
- args_dict = singleCommand_handler(args)
+ args_dict = single_command_handler(args)
 
  res = PrimerDesign(**args_dict)
  if args_dict["mode"].upper() == "CHAR":
@@ -41,7 +55,7 @@ def main():
  interactive_saver(res.df)
  else:
  if res.savename is not None:
- singleCommand_saver(res, res.df, res.savename)
+ single_command_saver(res, res.df, res.savename)
 
  return 0
 

primerdriver/checks.py

@@ -47,7 +47,7 @@ def __init__(self, sequence):
  self.sequence = sequence.upper()
 
  def check_sequence_length(self, length_range):
- if len(self.sequence) >= length_range[0] and len(self.sequence) <= length_range[1]:
+ if length_range[0] <= len(self.sequence) <= length_range[1]:
  return True
  else:
  return False

primerdriver/input_handler.py

@@ -1,15 +1,11 @@
-from .primerclass import *
+from .primer_design import *
 from .version import __version__
 from Bio import SeqIO
-from Bio.Seq import Seq
-from Bio.Alphabet import IUPAC
-from Bio.SeqRecord import SeqRecord
-
 
 version = str(__version__)
 
 
-def singleCommand_handler(args):
+def single_command_handler(args):
  args_dict = dict()
  args_dict["mode"] = args.mode
  if args.save:
@@ -67,14 +63,6 @@ def singleCommand_handler(args):
 
 def interactive_handler():
  args_dict = dict()
- print("")
- print(" ---. .------------.")
- print(" ||||\ /||||||||||||||\ ")
- print(" Primer · Driver")
- print(" \|||||||||||/ \||||||| ")
- print(" `---------` `------" "\n")
- print(f"PrimerDriver v{version}")
- print("(c) 2020 Kenneth V. Domingo & Numeriano Amer E. Gutierrez\n")
  args_dict["mode"] = input("Enter primer mode [dna/pro/char]: ")
  if args_dict["mode"].upper() == "DNA":
  args_dict["sequence"] = input("Enter DNA sequence: ")

primerdriver/output_handler.py

@@ -1,3 +1,4 @@
+from loguru import logger
 from pandas import concat
 from datetime import datetime
 from Bio import SeqIO
@@ -43,10 +44,10 @@ def interactive_saver(df):
  df = concat([*df])
  df.to_json(savename, indent=4)
  else:
- print("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json")
+ logger.error("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json")
 
 
-def singleCommand_saver(res, df, savename):
+def single_command_saver(res, df, savename):
  if savename.endswith(".csv"):
  df = concat([*df])
  df.to_csv(savename)
@@ -78,5 +79,5 @@ def singleCommand_saver(res, df, savename):
  df = concat([*df])
  df.to_json(savename, indent=4)
  else:
- print("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json")
+ logger.error("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json")
  return 1

primerdriver/primerclass.py → primerdriver/primer_design.py

@@ -1,9 +1,8 @@
-from warnings import warn
-from json import load, loads
+from loguru import logger
+from json import loads
 from pandas import DataFrame
 from tabulate import tabulate
 from numpy import array
-from Bio.Seq import Seq
 from .checks import *
 
 
@@ -153,7 +152,7 @@ def characterize_primer(self, sequence, mutation_type, replacement, mismatched_b
  if index - 1 < self.print_buffer:
  print("\n", tabulate(array([col, dat]).T, headers=[f"Primer {index}"], tablefmt="orgtbl"), sep="")
  elif index - 1 == self.print_buffer:
- print("\nToo many results; truncating output...")
+ logger.info("Too many results; truncating output...")
  dat = array([dat])
  df = DataFrame(data=dat, columns=col, index=[index])
  self.df = df

primerdriver/tests.py

@@ -1,7 +1,7 @@
 import io
 from contextlib import redirect_stdout
 from django.test import TestCase
-from .primerclass import *
+from .primer_design import *
 
 
 class CharacterizeTestCase(TestCase):

primerdriver/version.py

@@ -3,6 +3,6 @@
 
 __version__ = VersionInfo(
  major=1,
- minor=1,
- patch=1,
+ minor=2,
+ patch=0,
 )

primerx/jinja2.py

@@ -1,4 +1,3 @@
-import os
 from django.templatetags.static import static
 from django.urls import reverse
 from django.conf import settings
@@ -20,7 +19,7 @@ def environment(**options):
  "settings": settings,
  "static": static,
  "url": reverse,
- "web_version": f'(web {os.environ["HEROKU_RELEASE_VERSION"]})' if settings.ON_HEROKU else "",
+ "web_version": __version__,
  }
  )
  return env

primerx/settings.py

@@ -91,7 +91,12 @@
 # Database
 # https://docs.djangoproject.com/en/3.0/ref/settings/#databases
 
-DATABASES = {}
+DATABASES = {
+ "default": {
+ "ENGINE": "django.db.backends.sqlite3",
+ "NAME": BASE_DIR / "db.sqlite3",
+ }
+}
 
 # Password validation
 # https://docs.djangoproject.com/en/3.0/ref/settings/#auth-password-validators

requirements.dev.txt

@@ -1,5 +1,6 @@
 black
 django-revproxy
+pyinstaller
 Sphinx==3.5.1
 sphinxcontrib-applehelp==1.0.2
 sphinxcontrib-devhelp==1.0.2

requirements.txt

@@ -11,10 +11,11 @@ django-cors-headers==3.8.0
 django-heroku==0.3.1
 djangorestframework==3.12.4
 docutils==0.16
-gunicorn==20.0.4
+gunicorn==20.1.0
 idna==2.10
 imagesize==1.2.0
 Jinja2==2.11.3
+loguru
 MarkupSafe==1.1.1
 numpy==1.20.1
 packaging==20.9

sdm/views.py

@@ -3,15 +3,18 @@
 from rest_framework import status
 from rest_framework.views import APIView
 from rest_framework.response import Response
+from rest_framework.permissions import AllowAny
 from django.conf import settings
-from primerdriver.primerclass import PrimerDesign
+from primerdriver.primer_design import PrimerDesign
 from primerdriver.checks import PrimerChecks
 from primerdriver.version import __version__
 
 BASE_DIR = settings.BASE_DIR
 
 
 class PrimerDriverAPIView(APIView):
+ permission_classes = [AllowAny]
+
  def post(self, request):
  data = request.data
  checks = PrimerChecks(data["sequence"])
@@ -34,16 +37,20 @@ def post(self, request):
 
 
 class VersionView(APIView):
+ permission_classes = [AllowAny]
+
  def get(self, request):
  return Response(
  data={
  "program_version": str(__version__),
- "web_version": f'(web {os.environ.get("HEROKU_RELEASE_VERSION")})' if settings.ON_HEROKU else "",
+ "web_version": str(__version__),
  }
  )
 
 
 class ExpressionSystemsView(APIView):
+ permission_classes = [AllowAny]
+
  def get(self, request):
  return Response(
  {

web/app/src/components/Station.js

@@ -11,7 +11,7 @@ import Results from "./menu/Result";
 const styles = {
  appContainer: {
  boxShadow: "none",
- overflow: "scroll",
+ overflow: "auto",
  height: "100vh",
  },
 };