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  • l-sanfilippo/bielefeld-ce-bi-tec-temp
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......@@ -3,13 +3,20 @@ venv
.vscode
__pycache__
.venv
code/biblib-master
node_modules
versions
code
.vite
app.py
unused.py
unused-css-master
my-chart-test
other
dist
src/components/resources
code/test.bib
.DS_Store
code/test file gitignore.txt
src/.DS_Store
vite.config.js.timestamp-1732367750130-6d00136194c2.mjs
vite.config.js.timestamp-1733161862061-488217339257e.mjs
# Voraussetzungen
#- Python 3.x
#- bibtexparser (Installieren Sie es mit `pip install bibtexparser`)
# use like: python3 cit.py -i bibtex.bib -s 1
import re
problemlist = []
def main():
print("Starting program...")
try:
import bibtexparser
except ImportError:
print("The package 'bibtexparser' is not installed. Install with: pip install bibtexparser")
exit(1)
try:
import argparse
except ImportError:
print("The package 'argparse' is not installed.")
exit(1)
try:
import re
except ImportError:
print("The package 're' is not installed.")
exit(1)
try:
#reading command line input and parsing it
parser = argparse.ArgumentParser(
prog='HTML Citations',
description='create acessible HTML Citations from bib files')
parser.add_argument('-i','--input', required=True, help="path to source bib")
parser.add_argument('-s','--startnumber', required=True, help="number from which to start numbering")
args = parser.parse_args()
print("Source: " + args.input)
except argparse.ArgumentError as e:
print(f"Argument parsing error: {e}")
except Exception as e:
print(f"An unexpected error occurred: {e}")
print("Reading file...")
#reading and parsing the file
try:
with open(args.input, 'r') as file:
file_content = file.read()
print("Parsing file...")
try:
library = bibtexparser.loads(file_content)
#opening output file
try:
with open('output.txt', 'w') as out:
length = len(library.entries)
print("found " + str(length) + " entries")
ran = range(length)
startnum = int(args.startnumber);
count = 0;
#processing every entry and writing the dictionary for it
for x in ran:
print("\n Initializing empty dictionary for entry "+ str(startnum+count) + "...")
dictio = {}
en_x = library.entries[x]
print("Filling dictionary for entry "+ str(startnum+count) + "")
for key, value in en_x.items():
key_low = key.lower()
dictio[key_low] = value
print("Checking Entry type of "+ str(startnum+count) + "")
if en_x['ENTRYTYPE'] == "article":
articleHTML(dictio, (startnum+count), out)
elif en_x['ENTRYTYPE'] == "misc":
miscHTML(dictio, (startnum+count), out)
elif en_x['ENTRYTYPE'] == "book":
bookHTML(dictio, (startnum+count), out)
elif en_x['ENTRYTYPE'] == "inbook":
bookHTML(dictio, (startnum+count), out)
count += 1;
except Exception as e:
print(f"An unexpected error occurred: {e} in line 85")
except Exception as e:
print(f"An unexpected error occurred: {e} in line 87")
except FileNotFoundError:
print(f"Error: The file '{args.input}' was not found. line 89")
if len(problemlist)>0:
print("- - - - - - - - - - - - - - - - - ")
print("REMAINING ERRORS:")
for p in problemlist:
print(p)
else:
print("DONE")
def makeauthors(authors, out):
print("Starting on authors...")
authors = authors.replace("\n", " ").replace(" and ", "|").strip() # "and" durch "|" ersetzen und Whitespace entfernen
autlist = authors.split("|")
# Maximale Anzahl der anzuzeigenden Autoren
max_authors = 7
out.write("\t<span property=\"schema:author\" typeof=\"schema:Person\">\n") # Tag für Autoren öffnen
#print(autlist)
for i, a in enumerate(autlist):
try:
a = a.strip() # Whitespace entfernen
# Nachnamen und Vornamen aufteilen
if ',' in a:
s = a.split(", ")
last = s[0].strip() # Nachname
first_names = s[1].strip() if len(s) > 1 else ''
# Initialen für Vornamen erstellen
initials = '. '.join([n[0] for n in first_names.split()]) + '.' if first_names else ''
name = f"{last}, {initials}" if initials else f"{last}, "
else:
s = a.split()
last = s[-1].strip() # Nachname
first = '. '.join([n[0] for n in s[:-1]]) + '.' # Initialen der Vornamen
name = f"{last}, {first}"
# Schreibe den Namen in die Ausgabedatei
if i < max_authors:
out.write(f"\t\t<span property=\"schema:Name\"> {name}</span>\n")
# Wenn wir den 6. Autor erreicht haben, schreibe "et al." nach dem 6. Autor
if i == max_authors:
out.write("\t\t<span property=\"schema:Name\"> et al.</span>\n")
break # Stoppe die Schleife, nachdem "et al." hinzugefügt wurde
except Exception as e:
print(f"An unexpected error occurred: {e} see " + a)
out.write("\t</span>\n") # Tag für Autoren schließen
def articleHTML(dictio, x, out):
print("Writing html code for article "+ str(x) + "...")
out.write("{/*<!-- Citation num " + str(x) + "--> */}" + "\n")
out.write("<li typeof=\"schema:ScolarlyArticle\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
print("Just a sec, separating authors...")
authors = dictio['author']
print("giving authors...")
makeauthors(authors, out)
# out.write("\t" +"</span>"+ "\n")
title = dictio['title'].replace('{', '').replace('}', '')
out.write("\t" + "<span property=\"schema:name\">&nbsp;"+ title + "</span>. "+ "\n")
out.write("\t" +"<i property=\"schema:publisher\" typeof=\"schema:Organization\"> "+ dictio['journal'] +"</i>"+ "\n")
out.write("\t" +"<b property=\"issueNumber\" typeof=\"PublicationIssue\"> "+dictio['volume']+"</b>"+ "\n")
print("Getting pages...")
try:
pages = dictio['pages']
if pages is not None and len(pages) > 0:
# Überprüfen, ob die Seitenangabe nur aus Zahlen und Bindestrichen besteht
if '-' in pages or '' in pages or '--' in pages or '–' in pages:
pag = re.split('--|-|–|–', pages)
begin = pag[0].strip()
end = pag[1].strip()
print("- in pages")
out.write("\t" + ",&nbsp;<span property=\"schema:pageBegin\"> "+ begin +"</span>-<span property=\"schema:pageEnd\">"+ end + "</span>&nbsp;"+ "\n")
else:
if re.match(r'^\d+(-\d+)?$', pages): # Check for typical numeric page ranges
out.write("\t" + "<span property=\"schema:pageBegin\">"+ pages +"</span>&nbsp;"+ "\n")
else:
# Seitenangabe ist nicht numerisch, als fehlend behandeln
print(f"Non-numeric page information detected ('{pages}'). Treating as missing.")
problemlist.append(f"Non-numeric page info at entry {x}")
else:
print("Sorry, no page information")
problemlist.append("Check for missing page info at " + str(x))
except KeyError:
print("Sorry, no page information")
problemlist.append("Check for missing page info at " + str(x))
year = dictio['year']
out.write("\t" +"(<time property=\"schema:datePublished\" datatype=\"xsd:gYear\" dateTime=\" " + year + "\">"+year+"</time>)."+ "\n")
try:
doi = dictio['doi']
out.write("\t" +"<a className=\"doi\" href=\"https://doi.org/"+doi+"\"> doi: "+doi+"</a>"+ "\n")
except KeyError as e:
print("Sorry, no doi information")
problemlist.append("Check for missing doi info at " + str (x))
out.write("</li>" + "\n"+ "\n")
def miscHTML(dictio, x, out):
print("Writing html code for entry "+ str(x) + "...")
out.write("{/*<!-- Citation num " + str(x) + "--> */}" + "\n")
out.write("<li typeof=\"schema:WebPage\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
out.write("\t" + "<span property=\"schema:author\" typeof=\"schema:Organisation\">"+ "\n")
aut = dictio['author']
out.write("\t" + "\t" +"<span property=\"schema:Name\"> " + aut + "</span>."+ "\n")
out.write("\t" +"</span>"+ "\n")
out.write("\t" + "<span property=\"schema:name\">"+dictio['title']+ ".</span>"+ "\n")
out.write("\t" +"<i property=\"schema:publisher\" typeof=\"schema:Organization\">"+ dictio['howpublished'] +"</i>"+ "\n")
year = dictio['year']
out.write("\t" +"&nbsp;(<time property=\"schema:datePublished\" datatype=\"xsd:gYear\" dateTime=\"" + year + "\">"+year+"</time>)."+ "\n")
out.write("</li>" + "\n"+ "\n")
def bookHTML(dictio, x, out):
print("Writing html code for entry "+ str(x) + "...")
out.write("{/*<!-- Citation num " + str(x) + "--> */}" + "\n")
out.write("<li typeof=\"schema:Book\" role=\"doc-biblioentry\" property=\"schema:citation\" id=\"desc-" + str(x) + "\">"+ "\n")
# out.write("\t" + "<span property=\"schema:author\" typeof=\"schema:Organisation\">"+ "\n")
print("Just a sec, separating authors...")
if 'author' in dictio:
authors = dictio['author']
elif 'editor' in dictio:
authors = dictio['editor']
makeauthors(authors, out)
# out.write("\t" + "\t" +"<span property=\"schema:Name\"> " + aut + "</span>."+ "\n")
# out.write("\t" +"</span>"+ "\n")
if 'title' in dictio:
out.write("\t" + "<span property=\"schema:name\">&nbsp;"+dictio['title']+ ".</span>"+ "\n")
elif 'booktitle' in dictio:
out.write("\t" + "<span property=\"schema:name\">&nbsp;"+dictio['booktitle']+ ".</span>"+ "\n")
else:
print(f"No title or booktitle found for entry {x}")
problemlist.append(f"Check for missing title or booktitle at entry {x}")
out.write("\t" +"<i property=\"schema:publisher\" typeof=\"schema:Organization\">&nbsp;"+ dictio['publisher'] +"</i>"+ "\n")
year = dictio['year']
out.write("\t" + "&nbsp;(<time property=\"schema:datePublished\" datatype=\"xsd:gYear\" dateTime=\"" + year + "\">"+year+"</time>)."+ "\n")
out.write("</li>" + "\n"+ "\n")
main()
import biblib.bib
import biblib.messages
import biblib.algo
from biblib import FileBibDB
import argparse
import sys
import re
fileDb = biblib.FileBibDB('test.bib', mode='r')
<!doctype html>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<link
rel="shortcut icon"
href="https://static.igem.wiki/teams/5247/logos-team/precyse-no-slogan.png"
type="image/x-icon"
rel="icon" type="image/png" sizes="32x32"
href="https://static.igem.wiki/teams/5247/logos-team/precyse-no-slogan.ico"
/>
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<!-- <script type="text/javascript" defer src="./assets/js/mapscript.js" charset="utf-8">
</script> -->
<!-- <script type="module" src="https://2024.igem.wiki/bielefeld-cebitec/mapscript.js"></script> -->
<title>Bielefeld-CeBiTec - iGEM 2024</title>
</head>
<body>
......
# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
# dependencies
/node_modules
/.pnp
.pnp.js
# testing
/coverage
# production
/build
# misc
.DS_Store
.env.local
.env.development.local
.env.test.local
.env.production.local
npm-debug.log*
yarn-debug.log*
yarn-error.log*
# Getting Started with Create React App
This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
## Available Scripts
In the project directory, you can run:
### `npm start`
Runs the app in the development mode.\
Open [http://localhost:3000](http://localhost:3000) to view it in your browser.
The page will reload when you make changes.\
You may also see any lint errors in the console.
### `npm test`
Launches the test runner in the interactive watch mode.\
See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
### `npm run build`
Builds the app for production to the `build` folder.\
It correctly bundles React in production mode and optimizes the build for the best performance.
The build is minified and the filenames include the hashes.\
Your app is ready to be deployed!
See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
### `npm run eject`
**Note: this is a one-way operation. Once you `eject`, you can't go back!**
If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own.
You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it.
## Learn More
You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
To learn React, check out the [React documentation](https://reactjs.org/).
### Code Splitting
This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting)
### Analyzing the Bundle Size
This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size)
### Making a Progressive Web App
This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app)
### Advanced Configuration
This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration)
### Deployment
This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment)
### `npm run build` fails to minify
This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify)
This diff is collapsed.
{
"name": "my-chart-test",
"version": "0.1.0",
"private": true,
"dependencies": {
"@testing-library/jest-dom": "^5.17.0",
"@testing-library/react": "^13.4.0",
"@testing-library/user-event": "^13.5.0",
"chart.js": "^4.4.3",
"react": "^18.3.1",
"react-chartjs-2": "^5.2.0",
"react-dom": "^18.3.1",
"react-scripts": "5.0.1",
"web-vitals": "^2.1.4"
},
"scripts": {
"start": "react-scripts start",
"build": "react-scripts build",
"test": "react-scripts test",
"eject": "react-scripts eject"
},
"eslintConfig": {
"extends": [
"react-app",
"react-app/jest"
]
},
"browserslist": {
"production": [
">0.2%",
"not dead",
"not op_mini all"
],
"development": [
"last 1 chrome version",
"last 1 firefox version",
"last 1 safari version"
]
}
}
my-chart-test/public/favicon.ico

3.78 KiB

<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="theme-color" content="#000000" />
<meta
name="description"
content="Web site created using create-react-app"
/>
<link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
<!--
manifest.json provides metadata used when your web app is installed on a
user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
-->
<link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
<!--
Notice the use of %PUBLIC_URL% in the tags above.
It will be replaced with the URL of the `public` folder during the build.
Only files inside the `public` folder can be referenced from the HTML.
Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
work correctly both with client-side routing and a non-root public URL.
Learn how to configure a non-root public URL by running `npm run build`.
-->
<title>React App</title>
</head>
<body>
<noscript>You need to enable JavaScript to run this app.</noscript>
<div id="root"></div>
<!--
This HTML file is a template.
If you open it directly in the browser, you will see an empty page.
You can add webfonts, meta tags, or analytics to this file.
The build step will place the bundled scripts into the <body> tag.
To begin the development, run `npm start` or `yarn start`.
To create a production bundle, use `npm run build` or `yarn build`.
-->
</body>
</html>
my-chart-test/public/logo192.png

5.22 KiB

my-chart-test/public/logo512.png

9.44 KiB

{
"short_name": "React App",
"name": "Create React App Sample",
"icons": [
{
"src": "favicon.ico",
"sizes": "64x64 32x32 24x24 16x16",
"type": "image/x-icon"
},
{
"src": "logo192.png",
"type": "image/png",
"sizes": "192x192"
},
{
"src": "logo512.png",
"type": "image/png",
"sizes": "512x512"
}
],
"start_url": ".",
"display": "standalone",
"theme_color": "#000000",
"background_color": "#ffffff"
}
# https://www.robotstxt.org/robotstxt.html
User-agent: *
Disallow:
.App {
text-align: center;
}
.App-logo {
height: 40vmin;
pointer-events: none;
}
@media (prefers-reduced-motion: no-preference) {
.App-logo {
animation: App-logo-spin infinite 20s linear;
}
}
.App-header {
background-color: #282c34;
min-height: 100vh;
display: flex;
flex-direction: column;
align-items: center;
justify-content: center;
font-size: calc(10px + 2vmin);
color: white;
}
.App-link {
color: #61dafb;
}
@keyframes App-logo-spin {
from {
transform: rotate(0deg);
}
to {
transform: rotate(360deg);
}
}
import logo from './logo.svg';
import './App.css';
function App() {
return (
<div className="App">
<header className="App-header">
<img src={logo} className="App-logo" alt="logo" />
<p>
Edit <code>src/App.js</code> and save to reload.
</p>
<a
className="App-link"
href="https://reactjs.org"
target="_blank"
rel="noopener noreferrer"
>
Learn React
</a>
</header>
</div>
);
}
export default App;
import { render, screen } from '@testing-library/react';
import App from './App';
test('renders learn react link', () => {
render(<App />);
const linkElement = screen.getByText(/learn react/i);
expect(linkElement).toBeInTheDocument();
});
body {
margin: 0;
font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto', 'Oxygen',
'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans', 'Helvetica Neue',
sans-serif;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
code {
font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New',
monospace;
}
import React from 'react';
import ReactDOM from 'react-dom/client';
import './index.css';
import App from './App';
import reportWebVitals from './reportWebVitals';
const root = ReactDOM.createRoot(document.getElementById('root'));
root.render(
<React.StrictMode>
<App />
</React.StrictMode>
);
// If you want to start measuring performance in your app, pass a function
// to log results (for example: reportWebVitals(console.log))
// or send to an analytics endpoint. Learn more: https://bit.ly/CRA-vitals
reportWebVitals();
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