[WIP] Adding for hosting in Docker

Dockerfile

@@ -0,0 +1,19 @@
+FROM ubuntu:22.04
+MAINTAINER Mingxun Wang "mwang87@gmail.com"
+
+RUN apt-get update && apt-get install -y build-essential libarchive-dev wget vim git-core
+
+# Install Mamba
+ENV CONDA_DIR /opt/conda
+RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O ~/miniforge.sh && /bin/bash ~/miniforge.sh -b -p /opt/conda
+ENV PATH=$CONDA_DIR/bin:$PATH
+
+# Adding to bashrc
+RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc
+
+# Creating conda env
+COPY environment.yml .
+RUN mamba env create -f environment.yml
+
+COPY . /app
+WORKDIR /app

Makefile

@@ -0,0 +1,17 @@
+server-compose-build-nocache:
+	docker-compose --compatibility build --no-cache
+
+server-compose-interactive:
+	docker-compose --compatibility build
+	docker-compose --compatibility -f docker-compose.yml -f docker-compose-dev.yml up
+
+server-compose:
+	docker-compose --compatibility build
+	docker-compose --compatibility -f docker-compose.yml -f docker-compose-dev.yml up -d
+
+server-compose-production:
+	docker-compose --compatibility build
+	docker-compose --compatibility -f docker-compose.yml up -d
+
+attach:
+	docker exec -i -t template-streamlit /bin/bash

docker-compose-dev.yml

@@ -0,0 +1,5 @@
+version: '3'
+services:
+  microspotter-streamlit:
+    ports:
+    - "5000:5000"

docker-compose.yml

@@ -0,0 +1,33 @@
+version: '3'
+services:
+  microspotter-streamlit:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    container_name: microspotter-streamlit
+    volumes:
+      - ./logs:/app/logs:rw
+    networks:
+      - default
+      - nginx-net
+    restart: unless-stopped
+    command: /app/run_server.sh
+    logging:
+      driver: json-file
+      options:
+        max-size: "10m"      # Maximum size of a single log file
+        max-file: "3"        # Maximum number of log files to keep (rotates after 3 files)
+    deploy:
+      resources:
+        limits:
+          memory: 8000M
+    environment:
+      VIRTUAL_HOST: microspotreader.gnps2.org
+      VIRTUAL_PORT: 5000
+      LETSENCRYPT_HOST: microspotreader.gnps2.org
+      LETSENCRYPT_EMAIL: mwang87@gmail.com
+
+networks:
+  nginx-net:
+    external:
+      name: nginx-net

environment.yml

@@ -2,124 +2,18 @@ name: microspotreader
 channels:
   - defaults
 dependencies:
-  - bzip2=1.0.8=he774522_0
-  - ca-certificates=2023.08.22=haa95532_0
-  - libffi=3.4.4=hd77b12b_0
-  - openssl=3.0.12=h2bbff1b_0
-  - pip=23.3=py311haa95532_0
-  - plotly=5.9.0=py311haa95532_0
-  - python=3.11.5=he1021f5_0
-  - setuptools=68.0.0=py311haa95532_0
-  - sqlite=3.41.2=h2bbff1b_0
-  - tk=8.6.12=h2bbff1b_0
-  - vc=14.2=h21ff451_1
-  - vs2015_runtime=14.27.29016=h5e58377_2
-  - wheel=0.41.2=py311haa95532_0
-  - xz=5.4.2=h8cc25b3_0
-  - zlib=1.2.13=h8cc25b3_0
+  - pip
+  - plotly=5.9.0
+  - python=3.11.5
+  - setuptools=68.0.0
+  - libglib
   - pip:
-      - altair==5.1.2
-      - ansi2html==1.8.0
-      - asttokens==2.4.1
-      - attrs==23.1.0
-      - backcall==0.2.0
-      - blinker==1.6.3
-      - cachetools==5.3.2
-      - certifi==2023.7.22
-      - charset-normalizer==3.3.1
-      - click==8.1.7
-      - colorama==0.4.6
-      - comm==0.1.4
-      - contourpy==1.1.1
-      - cycler==0.12.1
-      - dash==2.14.1
-      - dash-core-components==2.0.0
-      - dash-html-components==2.0.0
-      - dash-table==5.0.0
-      - debugpy==1.8.0
-      - decorator==5.1.1
-      - executing==2.0.0
-      - flask==3.0.0
-      - fonttools==4.43.1
-      - gitdb==4.0.11
-      - gitpython==3.1.40
-      - idna==3.4
-      - imagecodecs==2023.9.18
-      - imageio==2.31.6
-      - importlib-metadata==6.8.0
-      - ipykernel==6.27.0
-      - ipympl==0.9.3
-      - ipython==8.16.1
-      - ipython-genutils==0.2.0
-      - ipywidgets==8.1.1
-      - itsdangerous==2.1.2
-      - jedi==0.19.1
-      - jinja2==3.1.2
-      - jsonschema==4.19.1
-      - jsonschema-specifications==2023.7.1
-      - jupyter-client==8.6.0
-      - jupyter-core==5.5.0
-      - jupyter-dash==0.4.2
-      - jupyterlab-widgets==3.0.9
-      - kiwisolver==1.4.5
-      - lazy-loader==0.3
-      - llvmlite==0.42.0
-      - markdown-it-py==3.0.0
-      - markupsafe==2.1.3
-      - matplotlib==3.8.0
-      - matplotlib-inline==0.1.6
-      - mdurl==0.1.2
-      - nest-asyncio==1.5.8
-      - networkx==3.2
-      - numba==0.59.0
-      - numpy==1.26.1
-      - packaging==23.2
-      - pandas==2.1.2
-      - parso==0.8.3
-      - pexpect==4.8.0
-      - pickleshare==0.7.5
-      - pillow==10.0.1
-      - platformdirs==4.0.0
-      - prompt-toolkit==3.0.39
-      - protobuf==4.24.4
-      - psutil==5.9.6
-      - ptyprocess==0.7.0
-      - pure-eval==0.2.2
-      - pyarrow==13.0.0
-      - pydeck==0.8.1b0
-      - pygments==2.16.1
-      - pyopenms==3.1.0
-      - pyparsing==3.1.1
-      - python-dateutil==2.8.2
-      - pytz==2023.3.post1
-      - pywin32==306
-      - pyzmq==25.1.1
-      - referencing==0.30.2
-      - requests==2.31.0
-      - retrying==1.3.4
-      - rich==13.6.0
-      - rpds-py==0.10.6
-      - scikit-image==0.22.0
-      - scipy==1.11.3
-      - seaborn==0.13.2
-      - six==1.16.0
-      - smmap==5.0.1
-      - stack-data==0.6.3
-      - streamlit==1.31.1
-      - tenacity==8.2.3
-      - tifffile==2023.9.26
-      - toml==0.10.2
-      - toolz==0.12.0
-      - tornado==6.3.3
-      - traitlets==5.12.0
-      - typing-extensions==4.8.0
-      - tzdata==2023.3
-      - tzlocal==5.2
-      - urllib3==2.0.7
-      - validators==0.22.0
-      - watchdog==3.0.0
-      - wcwidth==0.2.8
-      - werkzeug==3.0.1
-      - widgetsnbextension==4.0.9
-      - zipp==3.17.0
-prefix: C:\Users\Nomis\anaconda3\envs\microspotreader
+    - streamlit
+    - matplotlib==3.8.0
+    - scipy==1.11.3
+    - pandas==2.1.2
+    - pyopenms==3.1.0
+    - numba==0.59.0
+    - seaborn==0.13.2
+    - scikit-image
+    - imagecodecs==2023.9.18

pages/1_Image_Analysis.py

@@ -6,7 +6,6 @@
 import src.streamlit.image_analysis as stim
 import streamlit as st
 from src.microspotreader import *
-from src.streamlit.DataStorage import DataStorage
 from src.streamlit.general import *
 
 # Sets up basic page layout

run.py

@@ -1,50 +1,8 @@
 from __future__ import annotations
 
-import io
 import os
 import sys
-import tempfile
-import zipfile
-from collections.abc import MutableSequence
-from copy import copy, deepcopy
-from dataclasses import dataclass, field
-from pathlib import Path
-from typing import TYPE_CHECKING
 
-import imageio.v3 as iio
-import matplotlib.patheffects as pe
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-import pyopenms as oms
-import seaborn as sns
-from matplotlib.patches import Patch
-from numba import njit
-from scipy.ndimage import gaussian_filter1d
-from scipy.signal import find_peaks, savgol_filter
-from scipy.stats import pearsonr
-from skimage.color import rgb2gray
-from skimage.draw import disk
-from skimage.feature import canny, peak_local_max
-from skimage.filters import threshold_otsu
-from skimage.filters.rank import equalize
-from skimage.morphology import (
-    binary_dilation,
-    binary_opening,
-    disk,
-    reconstruction,
-    remove_small_objects,
-    skeletonize,
-)
-from skimage.transform import (
-    hough_circle,
-    hough_circle_peaks,
-    hough_line,
-    hough_line_peaks,
-)
-from skimage.util import img_as_ubyte, invert
-
-import streamlit as st
 import streamlit.web.cli as stcli
 
 

run_server.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+source activate microspotreader
+streamlit run Microspot_Reader.py --server.port 5000 --server.address 0.0.0.0