bio
This commit is contained in:
mpabi
commit
40cc16cb4f
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@ -0,0 +1,91 @@
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# Choose a base image. Debian is a good choice due to pyenv
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FROM debian:latest
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# Update the package list and install necessary dependencies
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RUN apt-get update && apt-get install -y \
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aptitude \
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||||
tmux vim-nox nano mc git curl termshark procps \
|
||||
sudo iproute2 iputils-ping bridge-utils \
|
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ifupdown udev make build-essential libssl-dev zlib1g-dev \
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libbz2-dev libreadline-dev libsqlite3-dev wget llvm libncurses5-dev \
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||||
libncursesw5-dev xz-utils libffi-dev liblzma-dev \
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sqlite3 default-libmysqlclient-dev pkg-config \
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npm
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||||
# Set password for root user (optional, for configuration)
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RUN echo 'root:rootpass' | chpasswd
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|
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# Add a new user `user` with password `pass` and prepare the environment
|
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RUN useradd -m user && echo 'user:pass' | chpasswd && adduser user sudo
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# Switch to user `user`
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USER user
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WORKDIR /home/user
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|
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# Install pyenv
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RUN git clone https://github.com/pyenv/pyenv .pyenv
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|
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# Install pyenv-virtualenv
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RUN git clone https://github.com/pyenv/pyenv-virtualenv .pyenv/plugins/pyenv-virtualenv
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# Set environment variables
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ENV HOME /home/user
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ENV PYENV_ROOT $HOME/.pyenv
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ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH
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||||
# Add pyenv and pyenv-virtualenv configuration to .bashrc
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RUN echo 'export PYENV_ROOT="$HOME/.pyenv"' >> .bashrc
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||||
RUN echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> .bashrc
|
||||
RUN echo 'eval "$(pyenv init -)"' >> .bashrc
|
||||
RUN echo 'eval "$(pyenv virtualenv-init -)"' >> .bashrc
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|
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# Install Python 3.11 with --enable-shared
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RUN bash -i -c "source ~/.bashrc && env PYTHON_CONFIGURE_OPTS='--enable-shared' pyenv install 3.11"
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# Create a virtual environment p3.11
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RUN bash -i -c "source ~/.bashrc && pyenv virtualenv 3.11 p3.11"
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# Set p3.11 as the default virtual environment
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RUN bash -i -c "source ~/.bashrc && pyenv local p3.11"
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|
||||
# Install Poetry
|
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RUN curl -sSL https://install.python-poetry.org | python3 -
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|
||||
# Add Poetry path to PATH directly in the Dockerfile
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ENV PATH="$HOME/.local/bin:$PATH"
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|
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# Install SQLAlchemy and MySQL adapter in the pyenv environment
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RUN bash -i -c "source ~/.bashrc && pyenv activate p3.11 && pip install \
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sqlalchemy mysqlclient mysql-connector-python\
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ipython numpy scipy matplotlib \
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biopython"
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# Copy the project into the image
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COPY --chown=user:user . /home/user/fapi
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COPY ./_confs/* ./
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# Set the working directory for installing dependencies
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WORKDIR /home/user/fapi
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# Install project dependencies with Poetry in the p3.11 environment
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RUN bash -i -c "source ~/.bashrc && pyenv activate p3.11 && poetry install"
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#RUN bash -i -c "source ~/.bashrc && poetry config virtualenvs.create false && poetry install"
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# Copy the .vimrc file
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#COPY --chown=user:user .vimrc /home/user/.vimrc
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|
||||
# Install vim-plug using curl
|
||||
RUN curl -fLo ~/.vim/autoload/plug.vim --create-dirs \
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||||
https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
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# Install Vim plugins
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RUN vim +PlugInstall +qall
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# Run the application
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#CMD ["/bin/bash", "-c", "python entrypoint.py"]
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# Run Bash
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CMD ["/bin/bash"]
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@ -0,0 +1,4 @@
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docker volume create portainer_data
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docker run -d -p 8000:8000 -p 9443:9443 --name portainer --restart=always -v /var/run/docker.sock:/var/run/docker.sock -v portainer_data:/data portainer/portainer-ce:latest
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@ -0,0 +1 @@
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sudo incus config device add tri proxy-9443 proxy listen=tcp:0.0.0.0:9443 connect=tcp:0.0.0.0:9443
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@ -0,0 +1,8 @@
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docker run --rm \
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-dit \
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--privileged \
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-p 9999:9999 \
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-p 8888:8888 \
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-v /home/user/work/py/fapi/fapi:/home/user/fapi \
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--name f1 \
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fapi
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@ -0,0 +1,2 @@
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#. ./__run2 mpabi 1111
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docker run --rm -dit -p $2:9999 --name $1 fapi bash
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@ -0,0 +1,34 @@
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./Dockerfile
|
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||||
./php/Dockerfile
|
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./docker-compose.yaml
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./__build
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./__n1
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./__run
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./__run2
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./__uvicorn
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./__docker-portainer
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./__incus-proxy
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./_confs/.tmux.conf
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./_confs/.vimrc
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./app/schemas.py
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./app/models.py
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./app/main.py
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./app/database.py
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./pyproject.toml
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./static/script.js
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./static/style.css
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./static/index.html
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./static/vue.global.js
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./data/pET-28a(+).gb
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./entrypoint.py
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./__tracked_files
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@ -0,0 +1 @@
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poetry run uvicorn --reload app.main:app --host 0.0.0.0 --port 9999
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@ -0,0 +1,14 @@
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set-option -g default-command "bash --login"
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|
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# remap prefix to Control + a
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set -g prefix C-s
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# bind 'C-a C-a' to type 'C-a'
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bind C-s send-prefix
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unbind C-b
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|
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# synchronize all panes in a window
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# don't use control S, too easily confused
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# with navigation key sequences in tmux (show sessions)
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unbind C-S
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bind C-Y set-window-option synchronize-panes
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@ -0,0 +1,163 @@
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call plug#begin()
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||||
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||||
Plug 'tpope/vim-fugitive'
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Plug 'tpope/vim-commentary'
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Plug 'preservim/nerdtree', { 'on': 'NERDTreeToggle' }
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||||
|
||||
Plug 'jupyter-vim/jupyter-vim'
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||||
Plug 'goerz/jupytext.vim'
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||||
|
||||
Plug 'ConradIrwin/vim-bracketed-paste'
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||||
|
||||
Plug 'rafi/awesome-vim-colorschemes'
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||||
Plug 'flazz/vim-colorschemes'
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||||
|
||||
Plug 'neoclide/coc.nvim', {'branch': 'release'}
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||||
|
||||
Plug 'jpalardy/vim-slime'
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||||
call plug#end()
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||||
|
||||
nnoremap <leader>n :NERDTreeFocus<CR>
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nnoremap <C-n> :NERDTree<CR>
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nnoremap <C-t> :NERDTreeToggle<CR>
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||||
nnoremap <C-f> :NERDTreeFind<CR>
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||||
|
||||
|
||||
" Run current file
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||||
nnoremap <buffer> <silent> <localleader>R :JupyterRunFile<CR>
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||||
nnoremap <buffer> <silent> <localleader>I :PythonImportThisFile<CR>
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||||
|
||||
" Change to directory of current file
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nnoremap <buffer> <silent> <localleader>d :JupyterCd %:p:h<CR>
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||||
" Send a selection of lines
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||||
nnoremap <buffer> <silent> <localleader>X :JupyterSendCell<CR>
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nnoremap <buffer> <silent> <localleader>E :JupyterSendRange<CR>
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nmap <buffer> <silent> <localleader>e <Plug>JupyterRunTextObj
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vmap <buffer> <silent> <localleader>e <Plug>JupyterRunVisual
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||||
|
||||
" Debugging maps
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||||
nnoremap <buffer> <silent> <localleader>b :PythonSetBreak<CR>
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set backspace=indent,eol,start
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set mouse=r
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packadd termdebug
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let g:termdebug_wide=1
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let g:termdebugger='riscv32-esp-elf-gdb'
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|
||||
|
||||
" Disable compatibility with vi which can cause unexpected issues.
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set nocompatible
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|
||||
" Enable type file detection. Vim will be able to try to detect the type of file in use.
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filetype on
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||||
|
||||
" Enable plugins and load plugin for the detected file type.
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||||
filetype plugin on
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||||
|
||||
" Load an indent file for the detected file type.
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filetype indent on
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|
||||
" Turn syntax highlighting on.
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syntax on
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||||
|
||||
" Add numbers to each line on the left-hand side.
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set number
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|
||||
" Highlight cursor line underneath the cursor horizontally.
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set cursorline
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|
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" Highlight cursor line underneath the cursor vertically.
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" set cursorcolumn
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|
||||
" Set shift width to 4 spaces.
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set shiftwidth=4
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|
||||
" Set tab width to 4 columns.
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||||
set tabstop=4
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|
||||
" Use space characters instead of tabs.
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||||
set expandtab
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||||
|
||||
" Do not save backup files.
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||||
set nobackup
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||||
|
||||
" Do not let cursor scroll below or above N number of lines when scrolling.
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set scrolloff=10
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||||
|
||||
" Do not wrap lines. Allow long lines to extend as far as the line goes.
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set nowrap
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||||
|
||||
" While searching though a file incrementally highlight matching characters as you type.
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set incsearch
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||||
|
||||
" Ignore capital letters during search.
|
||||
set ignorecase
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||||
|
||||
" Override the ignorecase option if searching for capital letters.
|
||||
" This will allow you to search specifically for capital letters.
|
||||
set smartcase
|
||||
|
||||
" Show partial command you type in the last line of the screen.
|
||||
set showcmd
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||||
|
||||
" Show the mode you are on the last line.
|
||||
set showmode
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||||
|
||||
" Show matching words during a search.
|
||||
set showmatch
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||||
|
||||
" Use highlighting when doing a search.
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||||
set hlsearch
|
||||
|
||||
" Set the commands to save in history default number is 20.
|
||||
set history=1000
|
||||
|
||||
" Enable auto completion menu after pressing TAB.
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||||
set wildmenu
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||||
|
||||
" Make wildmenu behave like similar to Bash completion.
|
||||
set wildmode=list:longest
|
||||
|
||||
" There are certain files that we would never want to edit with Vim.
|
||||
" Wildmenu will ignore files with these extensions.
|
||||
set wildignore=*.docx,*.jpg,*.png,*.gif,*.pdf,*.pyc,*.exe,*.flv,*.img,*.xlsx
|
||||
|
||||
|
||||
" set colorscheme OceanicNext
|
||||
|
||||
|
||||
if !exists("g:slime_python_ipython")
|
||||
let g:slime_python_ipython = 1
|
||||
endif
|
||||
|
||||
let g:slime_target = "tmux"
|
||||
|
||||
" Run cell for vim-slime
|
||||
function! SendCell(pattern)
|
||||
let start_line = search(a:pattern, 'bnW')
|
||||
|
||||
if start_line
|
||||
let start_line = start_line + 1
|
||||
else
|
||||
let start_line = 1
|
||||
endif
|
||||
|
||||
let stop_line = search(a:pattern, 'nW')
|
||||
if stop_line
|
||||
let stop_line = stop_line - 1
|
||||
else
|
||||
let stop_line = line('$')
|
||||
endif
|
||||
|
||||
call slime#send_range(start_line, stop_line)
|
||||
endfunction
|
||||
|
||||
" Custom vim-slime mappings
|
||||
let g:slime_no_mappings = 1
|
||||
xmap <c-c><c-c> <Plug>SlimeRegionSend
|
||||
nmap <c-c><c-c> :<c-u>call SendCell('^#%%')<cr>
|
||||
nmap <c-c>v <Plug>SlimeConfig
|
||||
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
#%%
|
||||
from sqlalchemy import create_engine
|
||||
from sqlalchemy.ext.declarative import declarative_base
|
||||
from sqlalchemy.orm import sessionmaker
|
||||
|
||||
"""
|
||||
#SQLALCHEMY_DATABASE_URL = "sqlite:///./test.db" # SQLite
|
||||
engine = create_engine(
|
||||
SQLALCHEMY_DATABASE_URL, connect_args={"check_same_thread": False} # Opcja dla SQLite
|
||||
)
|
||||
"""
|
||||
|
||||
SQLALCHEMY_DATABASE_URL = "mysql+mysqlconnector://root:secret@172.18.0.2:3306/test" # Przykład dla MySQL
|
||||
engine = create_engine(
|
||||
SQLALCHEMY_DATABASE_URL,
|
||||
)
|
||||
|
||||
SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
|
||||
|
||||
Base = declarative_base()
|
||||
|
||||
|
||||
#%%
|
||||
from sqlalchemy import text
|
||||
|
||||
with engine.connect() as conn:
|
||||
result = conn.execute(text("select 'hello world'"))
|
||||
print(result.all())
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
from fastapi import FastAPI, Depends
|
||||
from fastapi.staticfiles import StaticFiles
|
||||
from sqlalchemy.orm import Session
|
||||
from .database import SessionLocal, engine
|
||||
from .models import Sequence, Feature
|
||||
from .database import Base
|
||||
|
||||
app = FastAPI()
|
||||
|
||||
Base.metadata.create_all(bind=engine)
|
||||
|
||||
def get_db():
|
||||
db = SessionLocal()
|
||||
try:
|
||||
yield db
|
||||
finally:
|
||||
db.close()
|
||||
|
||||
# Serwowanie plików statycznych
|
||||
app.mount("/static", StaticFiles(directory="static"), name="static")
|
||||
|
||||
@app.get("/sequences/")
|
||||
def read_sequences(skip: int = 0, limit: int = 10, db: Session = Depends(get_db)):
|
||||
sequences = db.query(Sequence).offset(skip).limit(limit).all()
|
||||
return sequences
|
||||
|
||||
@app.get("/features/")
|
||||
def read_features(skip: int = 0, limit: int = 10, db: Session = Depends(get_db)):
|
||||
features = db.query(Feature).offset(skip).limit(limit).all()
|
||||
return features
|
||||
|
||||
if __name__ == "__main__":
|
||||
import uvicorn
|
||||
uvicorn.run(app, host="0.0.0.0", port=9999)
|
||||
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
# app/models.py
|
||||
from sqlalchemy import Column, Integer, String, Text, ForeignKey
|
||||
from sqlalchemy.orm import relationship
|
||||
from .database import Base
|
||||
|
||||
class Sequence(Base):
|
||||
__tablename__ = "sequences"
|
||||
|
||||
id = Column(Integer, primary_key=True, index=True)
|
||||
name = Column(String, index=True)
|
||||
description = Column(String)
|
||||
sequence = Column(Text)
|
||||
|
||||
features = relationship("Feature", back_populates="sequence")
|
||||
|
||||
class Feature(Base):
|
||||
__tablename__ = "features"
|
||||
|
||||
id = Column(Integer, primary_key=True, index=True)
|
||||
type = Column(String, index=True)
|
||||
location = Column(String)
|
||||
sequence = Column(Text)
|
||||
qualifiers = Column(Text)
|
||||
|
||||
sequence_id = Column(Integer, ForeignKey('sequences.id'))
|
||||
sequence = relationship("Sequence", back_populates="features")
|
||||
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
from typing import List, Optional
|
||||
from pydantic import BaseModel, constr, conint
|
||||
|
||||
class AuthorCreate(BaseModel):
|
||||
name: constr(min_length=2, max_length=100)
|
||||
|
||||
class AuthorModel(BaseModel):
|
||||
id: int
|
||||
name: str
|
||||
|
||||
class Config:
|
||||
orm_mode = True
|
||||
|
||||
class BookCreate(BaseModel):
|
||||
title: constr(min_length=1, max_length=100)
|
||||
author_id: conint(gt=0)
|
||||
|
||||
class BookModel(BaseModel):
|
||||
id: int
|
||||
title: str
|
||||
author_id: int
|
||||
status: Optional[str] = None
|
||||
|
||||
class Config:
|
||||
orm_mode = True
|
||||
|
||||
class BookWithAuthor(BookModel):
|
||||
author: AuthorModel
|
||||
|
||||
|
|
@ -0,0 +1,194 @@
|
|||
LOCUS 40924_17796 5369 bp DNA circular SYN 14-OCT-2021
|
||||
DEFINITION synthetic circular DNA.
|
||||
ACCESSION .
|
||||
VERSION .
|
||||
KEYWORDS .
|
||||
SOURCE synthetic DNA construct
|
||||
ORGANISM synthetic DNA construct
|
||||
REFERENCE 1 (bases 1 to 5369)
|
||||
AUTHORS caoheibi
|
||||
TITLE Direct Submission
|
||||
REFERENCE 2 (bases 1 to 5369)
|
||||
AUTHORS .
|
||||
TITLE Direct Submission
|
||||
COMMENT SGRef: number: 1; type: "Journal Article"
|
||||
FEATURES Location/Qualifiers
|
||||
source 1..5369
|
||||
/mol_type="other DNA"
|
||||
/organism="synthetic DNA construct"
|
||||
terminator complement(26..73)
|
||||
/label=T7 terminator
|
||||
/note="transcription terminator for bacteriophage T7 RNA
|
||||
polymerase"
|
||||
CDS complement(140..157)
|
||||
/codon_start=1
|
||||
/label=6xHis
|
||||
/note="6xHis affinity tag"
|
||||
/translation="HHHHHH"
|
||||
CDS complement(207..239)
|
||||
/codon_start=1
|
||||
/label=T7 tag (gene 10 leader)
|
||||
/note="leader peptide from bacteriophage T7 gene 10"
|
||||
/translation="MASMTGGQQMG"
|
||||
CDS complement(243..260)
|
||||
/codon_start=1
|
||||
/label=thrombin site
|
||||
/note="thrombin recognition and cleavage site"
|
||||
/translation="LVPRGS"
|
||||
CDS complement(270..287)
|
||||
/codon_start=1
|
||||
/label=6xHis
|
||||
/note="6xHis affinity tag"
|
||||
/translation="HHHHHH"
|
||||
RBS complement(306..328)
|
||||
/label=RBS
|
||||
/note="efficient ribosome binding site from bacteriophage
|
||||
T7 gene 10 (Olins and Rangwala, 1989)"
|
||||
protein_bind complement(343..367)
|
||||
/label=lac operator
|
||||
/note="The lac repressor binds to the lac operator to
|
||||
inhibit transcription in E. coli. This inhibition can be
|
||||
relieved by adding lactose or
|
||||
isopropyl-beta-D-thiogalactopyranoside (IPTG)."
|
||||
promoter complement(368..386)
|
||||
/label=T7 promoter
|
||||
/note="promoter for bacteriophage T7 RNA polymerase"
|
||||
promoter 695..772
|
||||
/label=lacI promoter
|
||||
CDS 773..1852
|
||||
/codon_start=1
|
||||
/label=lacI
|
||||
/note="lac repressor"
|
||||
/translation="VKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
|
||||
NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
|
||||
EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
|
||||
EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
|
||||
MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
|
||||
YIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
|
||||
ALADSLMQLARQVSRLESGQ"
|
||||
protein_bind 1868..1889
|
||||
/label=CAP binding site
|
||||
/note="CAP binding activates transcription in the presence
|
||||
of cAMP."
|
||||
CDS 2664..2852
|
||||
/codon_start=1
|
||||
/label=rop
|
||||
/note="Rop protein, which maintains plasmids at low copy
|
||||
number"
|
||||
/translation="VTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
|
||||
DELYRSCLARFGDDGENL"
|
||||
misc_feature 2957..3099
|
||||
/label=bom
|
||||
/note="basis of mobility region from pBR322"
|
||||
rep_origin complement(3285..3873)
|
||||
/direction=LEFT
|
||||
/label=ori
|
||||
/note="high-copy-number ColE1/pMB1/pBR322/pUC origin of
|
||||
replication"
|
||||
CDS 3995..4807
|
||||
/codon_start=1
|
||||
/label=KanR
|
||||
/note="aminoglycoside phosphotransferase"
|
||||
/translation="MSHIQRETSCSRPRLNSNMDADLYGYKWARDNVGQSGATIYRLYG
|
||||
KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
|
||||
TAFQVLEEYPDSGENIVDALAVFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
|
||||
SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
|
||||
ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
|
||||
rep_origin complement(4903..5358)
|
||||
/direction=LEFT
|
||||
/label=f1 ori
|
||||
/note="f1 bacteriophage origin of replication; arrow
|
||||
indicates direction of (+) strand synthesis"
|
||||
ORIGIN
|
||||
1 atccggatat agttcctcct ttcagcaaaa aacccctcaa gacccgttta gaggccccaa
|
||||
61 ggggttatgc tagttattgc tcagcggtgg cagcagccaa ctcagcttcc tttcgggctt
|
||||
121 tgttagcagc cggatctcag tggtggtggt ggtggtgctc gagtgcggcc gcaagcttgt
|
||||
181 cgacggagct cgaattcgga tccgcgaccc atttgctgtc caccagtcat gctagccata
|
||||
241 tggctgccgc gcggcaccag gccgctgctg tgatgatgat gatgatggct gctgcccatg
|
||||
301 gtatatctcc ttcttaaagt taaacaaaat tatttctaga ggggaattgt tatccgctca
|
||||
361 caattcccct atagtgagtc gtattaattt cgcgggatcg agatctcgat cctctacgcc
|
||||
421 ggacgcatcg tggccggcat caccggcgcc acaggtgcgg ttgctggcgc ctatatcgcc
|
||||
481 gacatcaccg atggggaaga tcgggctcgc cacttcgggc tcatgagcgc ttgtttcggc
|
||||
541 gtgggtatgg tggcaggccc cgtggccggg ggactgttgg gcgccatctc cttgcatgca
|
||||
601 ccattccttg cggcggcggt gctcaacggc ctcaacctac tactgggctg cttcctaatg
|
||||
661 caggagtcgc ataagggaga gcgtcgagat cccggacacc atcgaatggc gcaaaacctt
|
||||
721 tcgcggtatg gcatgatagc gcccggaaga gagtcaattc agggtggtga atgtgaaacc
|
||||
781 agtaacgtta tacgatgtcg cagagtatgc cggtgtctct tatcagaccg tttcccgcgt
|
||||
841 ggtgaaccag gccagccacg tttctgcgaa aacgcgggaa aaagtggaag cggcgatggc
|
||||
901 ggagctgaat tacattccca accgcgtggc acaacaactg gcgggcaaac agtcgttgct
|
||||
961 gattggcgtt gccacctcca gtctggccct gcacgcgccg tcgcaaattg tcgcggcgat
|
||||
1021 taaatctcgc gccgatcaac tgggtgccag cgtggtggtg tcgatggtag aacgaagcgg
|
||||
1081 cgtcgaagcc tgtaaagcgg cggtgcacaa tcttctcgcg caacgcgtca gtgggctgat
|
||||
1141 cattaactat ccgctggatg accaggatgc cattgctgtg gaagctgcct gcactaatgt
|
||||
1201 tccggcgtta tttcttgatg tctctgacca gacacccatc aacagtatta ttttctccca
|
||||
1261 tgaagacggt acgcgactgg gcgtggagca tctggtcgca ttgggtcacc agcaaatcgc
|
||||
1321 gctgttagcg ggcccattaa gttctgtctc ggcgcgtctg cgtctggctg gctggcataa
|
||||
1381 atatctcact cgcaatcaaa ttcagccgat agcggaacgg gaaggcgact ggagtgccat
|
||||
1441 gtccggtttt caacaaacca tgcaaatgct gaatgagggc atcgttccca ctgcgatgct
|
||||
1501 ggttgccaac gatcagatgg cgctgggcgc aatgcgcgcc attaccgagt ccgggctgcg
|
||||
1561 cgttggtgcg gatatctcgg tagtgggata cgacgatacc gaagacagct catgttatat
|
||||
1621 cccgccgtta accaccatca aacaggattt tcgcctgctg gggcaaacca gcgtggaccg
|
||||
1681 cttgctgcaa ctctctcagg gccaggcggt gaagggcaat cagctgttgc ccgtctcact
|
||||
1741 ggtgaaaaga aaaaccaccc tggcgcccaa tacgcaaacc gcctctcccc gcgcgttggc
|
||||
1801 cgattcatta atgcagctgg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca
|
||||
1861 acgcaattaa tgtaagttag ctcactcatt aggcaccggg atctcgaccg atgcccttga
|
||||
1921 gagccttcaa cccagtcagc tccttccggt gggcgcgggg catgactatc gtcgccgcac
|
||||
1981 ttatgactgt cttctttatc atgcaactcg taggacaggt gccggcagcg ctctgggtca
|
||||
2041 ttttcggcga ggaccgcttt cgctggagcg cgacgatgat cggcctgtcg cttgcggtat
|
||||
2101 tcggaatctt gcacgccctc gctcaagcct tcgtcactgg tcccgccacc aaacgtttcg
|
||||
2161 gcgagaagca ggccattatc gccggcatgg cggccccacg ggtgcgcatg atcgtgctcc
|
||||
2221 tgtcgttgag gacccggcta ggctggcggg gttgccttac tggttagcag aatgaatcac
|
||||
2281 cgatacgcga gcgaacgtga agcgactgct gctgcaaaac gtctgcgacc tgagcaacaa
|
||||
2341 catgaatggt cttcggtttc cgtgtttcgt aaagtctgga aacgcggaag tcagcgccct
|
||||
2401 gcaccattat gttccggatc tgcatcgcag gatgctgctg gctaccctgt ggaacaccta
|
||||
2461 catctgtatt aacgaagcgc tggcattgac cctgagtgat ttttctctgg tcccgccgca
|
||||
2521 tccataccgc cagttgttta ccctcacaac gttccagtaa ccgggcatgt tcatcatcag
|
||||
2581 taacccgtat cgtgagcatc ctctctcgtt tcatcggtat cattaccccc atgaacagaa
|
||||
2641 atccccctta cacggaggca tcagtgacca aacaggaaaa aaccgccctt aacatggccc
|
||||
2701 gctttatcag aagccagaca ttaacgcttc tggagaaact caacgagctg gacgcggatg
|
||||
2761 aacaggcaga catctgtgaa tcgcttcacg accacgctga tgagctttac cgcagctgcc
|
||||
2821 tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
|
||||
2881 cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg
|
||||
2941 ttggcgggtg tcggggcgca gccatgaccc agtcacgtag cgatagcgga gtgtatactg
|
||||
3001 gcttaactat gcggcatcag agcagattgt actgagagtg caccatatat gcggtgtgaa
|
||||
3061 ataccgcaca gatgcgtaag gagaaaatac cgcatcaggc gctcttccgc ttcctcgctc
|
||||
3121 actgactcgc tgcgctcggt cgttcggctg cggcgagcgg tatcagctca ctcaaaggcg
|
||||
3181 gtaatacggt tatccacaga atcaggggat aacgcaggaa agaacatgtg agcaaaaggc
|
||||
3241 cagcaaaagg ccaggaaccg taaaaaggcc gcgttgctgg cgtttttcca taggctccgc
|
||||
3301 ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga
|
||||
3361 ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc
|
||||
3421 ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
|
||||
3481 agctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
|
||||
3541 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
|
||||
3601 aacccggtaa gacacgactt atcgccactg gcagcagcca ctggtaacag gattagcaga
|
||||
3661 gcgaggtatg taggcggtgc tacagagttc ttgaagtggt ggcctaacta cggctacact
|
||||
3721 agaaggacag tatttggtat ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt
|
||||
3781 ggtagctctt gatccggcaa acaaaccacc gctggtagcg gtggtttttt tgtttgcaag
|
||||
3841 cagcagatta cgcgcagaaa aaaaggatct caagaagatc ctttgatctt ttctacgggg
|
||||
3901 tctgacgctc agtggaacga aaactcacgt taagggattt tggtcatgaa caataaaact
|
||||
3961 gtctgcttac ataaacagta atacaagggg tgttatgagc catattcaac gggaaacgtc
|
||||
4021 ttgctctagg ccgcgattaa attccaacat ggatgctgat ttatatgggt ataaatgggc
|
||||
4081 tcgcgataat gtcgggcaat caggtgcgac aatctatcga ttgtatggga agcccgatgc
|
||||
4141 gccagagttg tttctgaaac atggcaaagg tagcgttgcc aatgatgtta cagatgagat
|
||||
4201 ggtcagacta aactggctga cggaatttat gcctcttccg accatcaagc attttatccg
|
||||
4261 tactcctgat gatgcatggt tactcaccac tgcgatcccc gggaaaacag cattccaggt
|
||||
4321 attagaagaa tatcctgatt caggtgaaaa tattgttgat gcgctggcag tgttcctgcg
|
||||
4381 ccggttgcat tcgattcctg tttgtaattg tccttttaac agcgatcgcg tatttcgtct
|
||||
4441 cgctcaggcg caatcacgaa tgaataacgg tttggttgat gcgagtgatt ttgatgacga
|
||||
4501 gcgtaatggc tggcctgttg aacaagtctg gaaagaaatg cataaacttt tgccattctc
|
||||
4561 accggattca gtcgtcactc atggtgattt ctcacttgat aaccttattt ttgacgaggg
|
||||
4621 gaaattaata ggttgtattg atgttggacg agtcggaatc gcagaccgat accaggatct
|
||||
4681 tgccatccta tggaactgcc tcggtgagtt ttctccttca ttacagaaac ggctttttca
|
||||
4741 aaaatatggt attgataatc ctgatatgaa taaattgcag tttcatttga tgctcgatga
|
||||
4801 gtttttctaa gaattaattc atgagcggat acatatttga atgtatttag aaaaataaac
|
||||
4861 aaataggggt tccgcgcaca tttccccgaa aagtgccacc tgaaattgta aacgttaata
|
||||
4921 ttttgttaaa attcgcgtta aatttttgtt aaatcagctc attttttaac caataggccg
|
||||
4981 aaatcggcaa aatcccttat aaatcaaaag aatagaccga gatagggttg agtgttgttc
|
||||
5041 cagtttggaa caagagtcca ctattaaaga acgtggactc caacgtcaaa gggcgaaaaa
|
||||
5101 ccgtctatca gggcgatggc ccactacgtg aaccatcacc ctaatcaagt tttttggggt
|
||||
5161 cgaggtgccg taaagcacta aatcggaacc ctaaagggag cccccgattt agagcttgac
|
||||
5221 ggggaaagcc ggcgaacgtg gcgagaaagg aagggaagaa agcgaaagga gcgggcgcta
|
||||
5281 gggcgctggc aagtgtagcg gtcacgctgc gcgtaaccac cacacccgcc gcgcttaatg
|
||||
5341 cgccgctaca gggcgcgtcc cattcgcca
|
||||
//
|
||||
|
||||
|
|
@ -0,0 +1,36 @@
|
|||
version: "3.7"
|
||||
services:
|
||||
|
||||
web-server:
|
||||
build:
|
||||
dockerfile: php/Dockerfile
|
||||
context: .
|
||||
restart: always
|
||||
volumes:
|
||||
- "./html/:/var/www/html/"
|
||||
ports:
|
||||
- "8080:80"
|
||||
|
||||
mysql-server:
|
||||
image: mysql:8.0.19
|
||||
restart: always
|
||||
environment:
|
||||
MYSQL_ROOT_PASSWORD: secret
|
||||
volumes:
|
||||
- mysql-data:/var/lib/mysql
|
||||
ports:
|
||||
- "3306:3306"
|
||||
|
||||
phpmyadmin:
|
||||
image: phpmyadmin/phpmyadmin:5.0.1
|
||||
restart: always
|
||||
environment:
|
||||
PMA_HOST: mysql-server
|
||||
PMA_USER: root
|
||||
PMA_PASSWORD: secret
|
||||
ports:
|
||||
- "5000:80"
|
||||
|
||||
volumes:
|
||||
mysql-data:
|
||||
|
||||
|
|
@ -0,0 +1,47 @@
|
|||
# entrypoint.py
|
||||
from Bio import SeqIO
|
||||
from sqlalchemy.orm import Session
|
||||
from app.database import engine, SessionLocal, Base
|
||||
from app.models import Sequence, Feature
|
||||
import json
|
||||
|
||||
# Tworzenie tabeli w bazie danych
|
||||
Base.metadata.create_all(bind=engine)
|
||||
|
||||
def get_db():
|
||||
db = SessionLocal()
|
||||
try:
|
||||
yield db
|
||||
finally:
|
||||
db.close()
|
||||
|
||||
def load_genbank_to_db(file_path: str):
|
||||
db = next(get_db())
|
||||
with open(file_path, 'r') as file:
|
||||
record = SeqIO.read(file, "genbank")
|
||||
|
||||
# Zapisz sekwencję do bazy danych
|
||||
sequence_data = Sequence(
|
||||
name=record.name,
|
||||
description=record.description,
|
||||
sequence=str(record.seq)
|
||||
)
|
||||
db.add(sequence_data)
|
||||
db.commit()
|
||||
|
||||
# Zapisz cechy (features) do bazy danych
|
||||
for feature in record.features:
|
||||
feature_data = Feature(
|
||||
type=feature.type,
|
||||
location=str(feature.location),
|
||||
sequence=str(record.seq[feature.location.start:feature.location.end]),
|
||||
qualifiers=json.dumps(feature.qualifiers),
|
||||
sequence_id=sequence_data.id
|
||||
)
|
||||
db.add(feature_data)
|
||||
db.commit()
|
||||
print(f"Loaded {file_path} to database.")
|
||||
|
||||
if __name__ == "__main__":
|
||||
load_genbank_to_db("data/pET-28+(a).gb")
|
||||
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
FROM php:7.4.3-apache
|
||||
RUN docker-php-ext-install mysqli pdo pdo_mysql
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
[tool.poetry]
|
||||
name = "app"
|
||||
version = "0.1.0"
|
||||
description = "Przykład aplikacji FastAPI z WebSockets i Flutter"
|
||||
authors = ["mpabi"]
|
||||
|
||||
[tool.poetry.dependencies]
|
||||
python = "^3.8"
|
||||
fastapi = "^0.85"
|
||||
websockets = "^12.0"
|
||||
sqlalchemy = "^2.0.26"
|
||||
strawberry-graphql = {extras = ["fastapi"], version = "^0.219.2"}
|
||||
mysqlclient = "^2.2.4"
|
||||
mysql-connector-python = "^8.3.0"
|
||||
|
||||
[tool.poetry.dev-dependencies]
|
||||
uvicorn = "^0.17.6"
|
||||
|
||||
[build-system]
|
||||
requires = ["poetry-core>=1.0.0"]
|
||||
build-backend = "poetry run pip install --no-deps ."
|
||||
build-frontend = "poetry run flutter build web"
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="UTF-8">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<title>Feature Viewer</title>
|
||||
<script src="/static/vue.global.js"></script>
|
||||
</head>
|
||||
<body>
|
||||
<div id="app">
|
||||
<h1>Feature Viewer</h1>
|
||||
<button @click="fetchSequences">Fetch Sequences</button>
|
||||
<button @click="fetchFeatures">Fetch Features</button>
|
||||
<div v-if="sequences.length">
|
||||
<h2>Sequences:</h2>
|
||||
<ul>
|
||||
<li v-for="sequence in sequences" :key="sequence.id">
|
||||
<p><strong>Name:</strong> {{ sequence.name }}</p>
|
||||
<p><strong>Description:</strong> {{ sequence.description }}</p>
|
||||
<p><strong>Sequence:</strong> {{ sequence.sequence }}</p>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div v-if="features.length">
|
||||
<h2>Features:</h2>
|
||||
<ul>
|
||||
<li v-for="feature in features" :key="feature.id">
|
||||
<p><strong>Type:</strong> {{ feature.type }}</p>
|
||||
<p><strong>Location:</strong> {{ feature.location }}</p>
|
||||
<p><strong>Sequence:</strong> {{ feature.sequence }}</p>
|
||||
<p><strong>Qualifiers:</strong> {{ feature.qualifiers }}</p>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<script>
|
||||
const { createApp } = Vue;
|
||||
|
||||
createApp({
|
||||
data() {
|
||||
return {
|
||||
sequences: [],
|
||||
features: []
|
||||
}
|
||||
},
|
||||
methods: {
|
||||
async fetchSequences() {
|
||||
try {
|
||||
const response = await fetch('/sequences/');
|
||||
this.sequences = await response.json();
|
||||
} catch (error) {
|
||||
console.error("There was an error fetching the sequences:", error);
|
||||
}
|
||||
},
|
||||
async fetchFeatures() {
|
||||
try {
|
||||
const response = await fetch('/features/');
|
||||
this.features = await response.json();
|
||||
} catch (error) {
|
||||
console.error("There was an error fetching the features:", error);
|
||||
}
|
||||
}
|
||||
}
|
||||
}).mount('#app');
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
const BASE_URL = 'http://qstack.pl:1111'; // Zaktualizuj zgodnie z konfiguracją Twojego serwera
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
loadAuthors();
|
||||
loadBooks();
|
||||
});
|
||||
|
||||
document.getElementById('addAuthorForm').addEventListener('submit', function(e) {
|
||||
e.preventDefault();
|
||||
const authorName = document.getElementById('authorName').value;
|
||||
fetch(`${BASE_URL}/authors/`, {
|
||||
method: 'POST',
|
||||
headers: { 'Content-Type': 'application/json' },
|
||||
body: JSON.stringify({ name: authorName }),
|
||||
})
|
||||
.then(response => response.json())
|
||||
.then(() => {
|
||||
loadAuthors(); // Ponowne ładowanie listy autorów po dodaniu nowego autora
|
||||
})
|
||||
.catch(error => console.error('Error:', error));
|
||||
});
|
||||
|
||||
document.getElementById('addBookForm').addEventListener('submit', function(e) {
|
||||
e.preventDefault();
|
||||
const bookTitle = document.getElementById('bookTitle').value;
|
||||
const bookAuthorId = document.getElementById('bookAuthorId').value;
|
||||
fetch(`${BASE_URL}/books/`, {
|
||||
method: 'POST',
|
||||
headers: { 'Content-Type': 'application/json' },
|
||||
body: JSON.stringify({ title: bookTitle, author_id: parseInt(bookAuthorId, 10) }),
|
||||
})
|
||||
.then(response => response.json())
|
||||
.then(() => {
|
||||
loadBooks(); // Ponowne ładowanie listy książek po dodaniu nowej książki
|
||||
})
|
||||
.catch(error => console.error('Error:', error));
|
||||
});
|
||||
|
||||
function loadAuthors() {
|
||||
fetch(`${BASE_URL}/authors/`)
|
||||
.then(response => response.json())
|
||||
.then(data => {
|
||||
const authorsSelect = document.getElementById('bookAuthorId');
|
||||
authorsSelect.innerHTML = '<option value="">Select an Author</option>'; // Dodaj domyślną opcję
|
||||
data.forEach(author => {
|
||||
const option = document.createElement('option');
|
||||
option.value = author.id;
|
||||
option.textContent = author.name;
|
||||
authorsSelect.appendChild(option);
|
||||
});
|
||||
})
|
||||
.catch(error => console.error('Error:', error));
|
||||
}
|
||||
|
||||
function loadBooks() {
|
||||
fetch(`${BASE_URL}/books/`)
|
||||
.then(response => response.json())
|
||||
.then(data => {
|
||||
const booksList = document.getElementById('booksList');
|
||||
booksList.innerHTML = '';
|
||||
data.forEach(book => {
|
||||
const listItem = document.createElement('li');
|
||||
listItem.textContent = `${book.title} - Author ID: ${book.author_id}`;
|
||||
booksList.appendChild(listItem);
|
||||
});
|
||||
})
|
||||
.catch(error => console.error('Error:', error));
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
body, html {
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
font-family: Arial, sans-serif;
|
||||
}
|
||||
|
||||
header, footer {
|
||||
background-color: #333;
|
||||
color: #fff;
|
||||
text-align: center;
|
||||
padding: 1rem 0;
|
||||
}
|
||||
|
||||
.container {
|
||||
display: flex;
|
||||
min-height: calc(100vh - 100px); /* Adjust based on header/footer height */
|
||||
}
|
||||
|
||||
.sidebar {
|
||||
width: 30%;
|
||||
padding: 20px;
|
||||
background-color: #f4f4f4;
|
||||
}
|
||||
|
||||
.content {
|
||||
flex-grow: 1;
|
||||
padding: 20px;
|
||||
}
|
||||
|
||||
form > * {
|
||||
display: block;
|
||||
margin-bottom: 10px;
|
||||
}
|
||||
|
||||
button {
|
||||
cursor: pointer;
|
||||
}
|
||||
|
||||
ul {
|
||||
list-style-type: none;
|
||||
padding-left: 0;
|
||||
}
|
||||
|
||||
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Reference in New Issue