bio

Dockerfile

@@ -0,0 +1,91 @@
+# Choose a base image. Debian is a good choice due to pyenv
+FROM debian:latest
+
+# Update the package list and install necessary dependencies
+RUN apt-get update && apt-get install -y \
+    aptitude \
+    tmux vim-nox nano mc git curl termshark procps \
+    sudo iproute2 iputils-ping bridge-utils \
+    ifupdown udev make build-essential libssl-dev zlib1g-dev \
+    libbz2-dev libreadline-dev libsqlite3-dev wget llvm libncurses5-dev \
+    libncursesw5-dev xz-utils libffi-dev liblzma-dev \
+    sqlite3 default-libmysqlclient-dev pkg-config \
+    npm
+
+# Set password for root user (optional, for configuration)
+RUN echo 'root:rootpass' | chpasswd
+
+# Add a new user `user` with password `pass` and prepare the environment
+RUN useradd -m user && echo 'user:pass' | chpasswd && adduser user sudo
+
+# Switch to user `user`
+USER user
+WORKDIR /home/user
+
+# Install pyenv
+RUN git clone https://github.com/pyenv/pyenv .pyenv
+
+# Install pyenv-virtualenv
+RUN git clone https://github.com/pyenv/pyenv-virtualenv .pyenv/plugins/pyenv-virtualenv
+
+# Set environment variables
+ENV HOME  /home/user
+ENV PYENV_ROOT $HOME/.pyenv
+ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH
+
+# Add pyenv and pyenv-virtualenv configuration to .bashrc
+RUN echo 'export PYENV_ROOT="$HOME/.pyenv"' >> .bashrc
+RUN echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> .bashrc
+RUN echo 'eval "$(pyenv init -)"' >> .bashrc
+RUN echo 'eval "$(pyenv virtualenv-init -)"' >> .bashrc
+
+# Install Python 3.11 with --enable-shared
+RUN bash -i -c "source ~/.bashrc && env PYTHON_CONFIGURE_OPTS='--enable-shared' pyenv install 3.11"
+
+# Create a virtual environment p3.11
+RUN bash -i -c "source ~/.bashrc && pyenv virtualenv 3.11 p3.11"
+
+# Set p3.11 as the default virtual environment
+RUN bash -i -c "source ~/.bashrc && pyenv local p3.11"
+
+# Install Poetry
+RUN curl -sSL https://install.python-poetry.org | python3 -
+
+# Add Poetry path to PATH directly in the Dockerfile
+ENV PATH="$HOME/.local/bin:$PATH"
+
+# Install SQLAlchemy and MySQL adapter in the pyenv environment
+RUN bash -i -c "source ~/.bashrc && pyenv activate p3.11 && pip install \
+                        sqlalchemy mysqlclient mysql-connector-python\
+                        ipython numpy scipy matplotlib \
+                        biopython"
+
+# Copy the project into the image
+COPY --chown=user:user . /home/user/fapi
+COPY ./_confs/* ./
+
+# Set the working directory for installing dependencies
+WORKDIR /home/user/fapi
+
+# Install project dependencies with Poetry in the p3.11 environment
+RUN bash -i -c "source ~/.bashrc && pyenv activate p3.11 && poetry install"                                                  
+
+#RUN bash -i -c "source ~/.bashrc && poetry config virtualenvs.create false && poetry install"
+
+# Copy the .vimrc file
+#COPY --chown=user:user .vimrc /home/user/.vimrc
+
+# Install vim-plug using curl
+RUN curl -fLo ~/.vim/autoload/plug.vim --create-dirs \
+    https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
+
+# Install Vim plugins
+RUN vim +PlugInstall +qall
+
+# Run the application
+#CMD ["/bin/bash", "-c", "python entrypoint.py"]
+
+# Run Bash
+CMD ["/bin/bash"]
+
+

__build

@@ -0,0 +1 @@
+docker build -t fapi .

__docker-portainer

@@ -0,0 +1,4 @@
+docker volume create portainer_data
+
+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
+

__incus-proxy

@@ -0,0 +1 @@
+sudo incus config device add tri proxy-9443 proxy listen=tcp:0.0.0.0:9443 connect=tcp:0.0.0.0:9443

__n1

@@ -0,0 +1,8 @@
+docker run --rm \
+	-dit \
+	--privileged \
+	-p 9999:9999 \
+	-p 8888:8888 \
+	-v /home/user/work/py/fapi/fapi:/home/user/fapi \
+	--name f1 \
+	fapi

__run

@@ -0,0 +1 @@
+docker run --rm -dit -p $2:9999 --name $1 fapi

__run2

@@ -0,0 +1,2 @@
+#. ./__run2 mpabi 1111
+docker run --rm -dit -p $2:9999 --name $1 fapi bash

__tracked_files

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+./Dockerfile
+
+./php/Dockerfile
+./docker-compose.yaml
+
+./__build
+./__n1
+./__run
+./__run2
+./__uvicorn
+
+./__docker-portainer
+./__incus-proxy
+
+./_confs/.tmux.conf
+./_confs/.vimrc
+
+./app/schemas.py
+./app/models.py
+./app/main.py
+./app/database.py
+
+./pyproject.toml
+
+./static/script.js
+./static/style.css
+./static/index.html
+./static/vue.global.js
+
+./data/pET-28a(+).gb
+
+./entrypoint.py
+
+./__tracked_files

__uvicorn

@@ -0,0 +1 @@
+poetry run uvicorn --reload app.main:app --host 0.0.0.0 --port 9999

_confs/.tmux.conf

@@ -0,0 +1,14 @@
+set-option -g default-command "bash --login"
+
+# remap prefix to Control + a
+set -g prefix C-s
+# bind 'C-a C-a' to type 'C-a'
+bind C-s send-prefix
+unbind C-b
+
+# synchronize all panes in a window
+# don't use control S, too easily confused
+# with navigation key sequences in tmux (show sessions)
+unbind C-S
+bind C-Y set-window-option synchronize-panes
+

_confs/.vimrc

@@ -0,0 +1,163 @@
+call plug#begin()
+
+Plug 'tpope/vim-fugitive'
+Plug 'tpope/vim-commentary'
+Plug 'preservim/nerdtree', { 'on': 'NERDTreeToggle' }
+
+Plug 'jupyter-vim/jupyter-vim'
+Plug 'goerz/jupytext.vim'
+
+Plug 'ConradIrwin/vim-bracketed-paste'
+
+Plug 'rafi/awesome-vim-colorschemes'
+Plug 'flazz/vim-colorschemes'
+
+Plug 'neoclide/coc.nvim', {'branch': 'release'}
+
+Plug 'jpalardy/vim-slime'
+
+call plug#end()
+
+nnoremap <leader>n :NERDTreeFocus<CR>
+nnoremap <C-n> :NERDTree<CR>
+nnoremap <C-t> :NERDTreeToggle<CR>
+nnoremap <C-f> :NERDTreeFind<CR>
+
+
+" Run current file
+nnoremap <buffer> <silent> <localleader>R :JupyterRunFile<CR>
+nnoremap <buffer> <silent> <localleader>I :PythonImportThisFile<CR>
+
+" Change to directory of current file
+nnoremap <buffer> <silent> <localleader>d :JupyterCd %:p:h<CR>
+
+" Send a selection of lines
+nnoremap <buffer> <silent> <localleader>X :JupyterSendCell<CR>
+nnoremap <buffer> <silent> <localleader>E :JupyterSendRange<CR>
+nmap     <buffer> <silent> <localleader>e <Plug>JupyterRunTextObj
+vmap     <buffer> <silent> <localleader>e <Plug>JupyterRunVisual
+
+" Debugging maps
+nnoremap <buffer> <silent> <localleader>b :PythonSetBreak<CR>
+
+set backspace=indent,eol,start
+set mouse=r
+
+packadd termdebug
+let g:termdebug_wide=1
+let g:termdebugger='riscv32-esp-elf-gdb'
+
+
+" Disable compatibility with vi which can cause unexpected issues.
+set nocompatible
+
+" Enable type file detection. Vim will be able to try to detect the type of file in use.
+filetype on
+
+" Enable plugins and load plugin for the detected file type.
+filetype plugin on
+
+" Load an indent file for the detected file type.
+filetype indent on
+
+" Turn syntax highlighting on.
+syntax on
+
+" Add numbers to each line on the left-hand side.
+set number
+
+" Highlight cursor line underneath the cursor horizontally.
+set cursorline
+
+" Highlight cursor line underneath the cursor vertically.
+" set cursorcolumn
+
+" Set shift width to 4 spaces.
+set shiftwidth=4
+
+" Set tab width to 4 columns.
+set tabstop=4
+
+" Use space characters instead of tabs.
+set expandtab
+
+" Do not save backup files.
+set nobackup
+
+" Do not let cursor scroll below or above N number of lines when scrolling.
+set scrolloff=10
+
+" Do not wrap lines. Allow long lines to extend as far as the line goes.
+set nowrap
+
+" While searching though a file incrementally highlight matching characters as you type.
+set incsearch
+
+" Ignore capital letters during search.
+set ignorecase
+
+" 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
+
+" Show the mode you are on the last line.
+set showmode
+
+" Show matching words during a search.
+set showmatch
+
+" Use highlighting when doing a search.
+set hlsearch
+
+" Set the commands to save in history default number is 20.
+set history=1000
+
+" Enable auto completion menu after pressing TAB.
+set wildmenu
+
+" 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
+

app/database.py

@@ -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())

app/main.py

@@ -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)
+

app/models.py

@@ -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")
+

app/schemas.py

@@ -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
+

data/pET-28a(+).gb

@@ -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
+//
+

docker-compose.yaml

@@ -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:
+

entrypoint.py

@@ -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")
+

php/Dockerfile

@@ -0,0 +1,2 @@
+FROM php:7.4.3-apache
+RUN docker-php-ext-install mysqli pdo pdo_mysql

pyproject.toml

@@ -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"

static/index.html

@@ -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>
+

static/script.js

@@ -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));
+}
+

static/style.css

@@ -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;
+}
+