Merge pull request #50 from nleroy917/docker

Dockerize user interface

.dockerignore

@@ -0,0 +1,11 @@
+web/
+.env
+.venv
+venv
+env
+.vscode/
+benchmarks/
+R/
+scripts/
+sdk/
+tests/

docker-compose.yaml

@@ -0,0 +1,22 @@
+version: "3.8"
+
+services:
+  server:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - 8000:8000
+
+  client:
+    build:
+      context: web/
+      dockerfile: Dockerfile
+    ports:
+      - 3000:3000
+    environment:
+      - NEXT_PUBLIC_API_URL=http://server:8000
+
+networks:
+  optipyzer:
+    driver: bridge

optipyzer/db/interfaces.py

@@ -2,6 +2,7 @@
 from .models import Organism, AutocompleteOrganism, CodonUsage
 from ..const import AA_CODON_LIBRARY
 
+
 # not used unless the database connection
 # is required at the endpoint level
 def _get_db():
@@ -40,7 +41,6 @@ def calc_codon_usage(organism_id: int):
 
     # Iterate through each amino acid in the library, and pull data for it
     for aa in AA_CODON_LIBRARY:
-
         # Pull data for that particular amino acid and its codon preferences
         result = amino_acid_usage(organism_id, aa)
 
@@ -83,7 +83,6 @@ def amino_acid_usage(org_id: int, aa: str):
     a particular amino acid.
     """
     with SessionLocal() as db:
-
         # get list of codons
         codons = AA_CODON_LIBRARY[aa]
 

optipyzer/db/models.py

@@ -45,7 +45,6 @@ class AutocompleteOrganism(Base):
 
 
 class CodonUsage(Base):
-
     __tablename__ = "codon_usage"
 
     org_id = Column(Integer, primary_key=True)

optipyzer/response_models.py

@@ -1,6 +1,7 @@
 from typing import Dict, List
 from pydantic import BaseModel
 
+
 # model for an optimization result
 class OptimizationResult(BaseModel):
     query: str

scripts/load_autocomplete_data.py

@@ -28,7 +28,6 @@
 
 
 def reset_table(curs):
-
     try:
         # Drop table
         query = """ DROP TABLE autocomplete_data """
@@ -58,7 +57,6 @@ def reset_table(curs):
 
 
 def load_data(curs):
-
     # Get unqique species from database
     query = """SELECT * FROM ORGANISMS GROUP BY SPECIES"""
     curs.execute(query)
@@ -70,7 +68,6 @@ def load_data(curs):
     N = len(result)
     i = 1
     for row in result:
-
         # Update user
         print("Cleaned {}/{} rows".format(i, N))
         i += 1
@@ -107,7 +104,6 @@ def load_data(curs):
 
 
 def isolate_species(species_strain):
-
     # Split on spaces
     words = species_strain.split(" ")
 
@@ -121,7 +117,6 @@ def isolate_species(species_strain):
 
 
 def connect_to_db(db_file):
-
     # Attempt to connect to databse with specified file
     try:
         conn = sqlite3.connect(db_file)
@@ -134,7 +129,6 @@ def connect_to_db(db_file):
 
 
 if __name__ == "__main__":
-
     db_file = sys.argv[1]
 
     if not db_file:

sdk/tests/test_api.py

@@ -18,7 +18,6 @@ def protein_seq():
 
 
 def test_optimize_dna(api: optipyzer.API, dna_seq: str):
-
     result = api.optimize(
         seq=dna_seq,
         seq_type="dna",
@@ -30,7 +29,6 @@ def test_optimize_dna(api: optipyzer.API, dna_seq: str):
 
 
 def test_optimize_dna_with_pop_names(api: optipyzer.API, dna_seq: str):
-
     result = api.optimize(
         seq=dna_seq,
         seq_type="dna",
@@ -42,7 +40,6 @@ def test_optimize_dna_with_pop_names(api: optipyzer.API, dna_seq: str):
 
 
 def test_optimize_protein(api: optipyzer.API, protein_seq: str):
-
     result = api.optimize(
         seq=protein_seq,
         seq_type="protein",
@@ -54,7 +51,6 @@ def test_optimize_protein(api: optipyzer.API, protein_seq: str):
 
 
 def test_optimize_protein_with_pop_names(api: optipyzer.API, protein_seq: str):
-
     result = api.optimize(
         seq=protein_seq,
         seq_type="protein",

web/.dockerignore

@@ -0,0 +1,8 @@
+Dockerfile
+.dockerignore
+node_modules
+npm-debug.log
+README.md
+.next
+.git
+.env.local

web/Dockerfile

@@ -0,0 +1,59 @@
+FROM node:18-alpine AS base
+
+# Install dependencies only when needed
+FROM base AS deps
+# Check https://github.com/nodejs/docker-node/tree/b4117f9333da4138b03a546ec926ef50a31506c3#nodealpine to understand why libc6-compat might be needed.
+RUN apk add --no-cache libc6-compat
+WORKDIR /app
+
+# Install dependencies based on the preferred package manager
+COPY package.json yarn.lock* package-lock.json* pnpm-lock.yaml* ./
+RUN \
+  if [ -f yarn.lock ]; then yarn --frozen-lockfile; \
+  elif [ -f package-lock.json ]; then npm ci; \
+  elif [ -f pnpm-lock.yaml ]; then yarn global add pnpm && pnpm i --frozen-lockfile; \
+  else echo "Lockfile not found." && exit 1; \
+  fi
+
+
+# Rebuild the source code only when needed
+FROM base AS builder
+WORKDIR /app
+COPY --from=deps /app/node_modules ./node_modules
+COPY . .
+
+# Next.js collects completely anonymous telemetry data about general usage.
+# Learn more here: https://nextjs.org/telemetry
+# Uncomment the following line in case you want to disable telemetry during the build.
+# ENV NEXT_TELEMETRY_DISABLED 1
+
+RUN yarn build
+
+# If using npm comment out above and use below instead
+# RUN npm run build
+
+# Production image, copy all the files and run next
+FROM base AS runner
+WORKDIR /app
+
+ENV NODE_ENV production
+# Uncomment the following line in case you want to disable telemetry during runtime.
+# ENV NEXT_TELEMETRY_DISABLED 1
+
+RUN addgroup --system --gid 1001 nodejs
+RUN adduser --system --uid 1001 nextjs
+
+COPY --from=builder /app/public ./public
+
+# Automatically leverage output traces to reduce image size
+# https://nextjs.org/docs/advanced-features/output-file-tracing
+COPY --from=builder --chown=nextjs:nodejs /app/.next/standalone ./
+COPY --from=builder --chown=nextjs:nodejs /app/.next/static ./.next/static
+
+USER nextjs
+
+EXPOSE 3000
+
+ENV PORT 3000
+
+CMD ["node", "server.js"]

web/next.config.js

@@ -1,4 +1,5 @@
 module.exports = {
+  output: 'standalone',
   eslint: {
     dirs: ['src'],
   },

web/package.json

@@ -13,8 +13,7 @@
     "prettier:check": "prettier -c src",
     "format": "prettier -w src",
     "release": "standard-version",
-    "push-release": "git push --follow-tags origin main",
-    "postbuild": "next-sitemap"
+    "push-release": "git push --follow-tags origin main"
   },
   "dependencies": {
     "@headlessui/react": "^1.6.5",
@@ -26,10 +25,10 @@
     "axios": "^0.23.0",
     "clsx": "^1.1.1",
     "debounce-promise": "^3.1.2",
-    "next": "^12.1.0",
+    "next": "latest",
     "postcss": "^8.3.9",
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2",
+    "react": "^18.2.0",
+    "react-dom": "^18.2.0",
     "react-hook-form": "^7.17.4",
     "react-icons": "^4.3.1",
     "react-select": "^5.1.0"