PASTA-ELN | The favorite ELN for experimental scientists

:warning: Users: all documentation can be found at Github-pages

This page / area is for developers and contains some helpful information for them

Developers: Windows

How to start Pasta ELN

• Anaconda
  • python -m pasta_eln.gui
  • DOES NOT WORK "pastaELN"

Installation location:

• Default installation
  • C:\Users...\AppData\Local\Programs\Python\Python311\Scripts
  • C:\Users...\AppData\Local\Programs\Python\Python311\Lib\site-packages\pasta_eln
• Anaconda
  • C:\Users...\anaconda3\envs...\Scripts>
  • C:\Users...\anaconda3\envs...\Lib\site-packages\pasta_eln

Reinstall /retry windows installation

• uninstall couchdb in Settings
• remove directories
  • C:\Program Files\Apache CouchDB
  • C:\Users....\AppData\Local\Programs\Python [If deleted python]
  • Pasta-Folder in Documents
• remove Users....pastaELN.json
• remove shortcut on Windows desktop
• restart Windows
• python -m pasta_eln.gui
• go through steps and wait for restart
• after restart go to System->Configuration (ctrl-0) ->Setup-> start again
  • or have a separate button for that

Create an installer using pyInstaller

• Anacoda -> new environment and install "pip install pyinstaller" and dependencies
• In terminal
  • cd Documents\PastaELN_src: all files in pasta-eln
  • pyinstaller pastaELN.py -F
• File is in /dist/ folder

Developers: Linux

Installation location:

• Default
  • /usr/local/lib/python3.10/dist-packages/pasta_eln

Restart installation

rm .pastaELN.json pastaELN.log
rm -rf pastaELN/PastasExampleProject pastaELN/StandardOperatingProcedures
sudo snap stop couchdb
sudo snap remove couchdb

Test couchDB running

• CouchDB at HTTP! http://127.0.0.1:5984/_utils/#login
• curl -f http://127.0.0.1:5984/
• curl -X POST -H "Content-Type: application/json; charset=utf-8" -d '{"name": "+", "password": "+"}' http://127.0.0.1:5984/_session

Notes on all systems

Run Pasta-ELN directly from commandline without installation

• python3 -m pasta_eln.gui
• python3 -m pasta_eln.installationTools
• python3 -m pasta_eln.Tests.3Projects
• pastaELN.py in home directory of repository

How to write code

How to write small python programs that do things

Backend

from pasta_eln.backend import Pasta
pasta = Pasta()
viewProj = pasta.db.getView('viewDocType/x0')
projID1  = [i['id'] for i in viewProj if 'PASTA' in i['value'][0]][0]
pasta.changeHierarchy(projID1)
print(pasta.outputHierarchy())

Frontend

For testing WIDGETS put this code into "pasta_eln/test.py":

from PySide6.QtWidgets import QApplication, QMainWindow
from .backend import Backend
from .communicate import Communicate
from .widgetDetails import Details

class MainWindow(QMainWindow):
  def __init__(self):
    super().__init__()
    self.backend = Backend()
    comm = Communicate(self.backend)
    widget = Details(comm)
    self.setCentralWidget(widget)
    comm.changeDetails.emit('m-a23019163b9c4fccb4edaab0feb2b5ee')

app = QApplication()
window = MainWindow()
window.show()
app.exec()

and execute "python -m pasta_eln.test"

For testing DIALOGS put this code into "pasta_eln/test.py":

import sys
from PySide6.QtWidgets import QApplication
from .GUI.form import Form
from .backend import Backend
from .guiCommunicate import Communicate

app = QApplication(sys.argv)
backend = Backend()
comm = Communicate(backend)
doc = backend.db.getDoc("m-3a43570c4fd84b1ab81a8863ae058fb0")
dialog = Form(comm, doc)
dialog.show()
sys.exit(app.exec())

and execute "python -m pasta_eln.test"

Profiling

Begin...

  from cProfile import Profile
  from pstats import SortKey, Stats
  with Profile() as profile:

End...

  (Stats(profile).strip_dirs().sort_stats(SortKey.CUMULATIVE).print_stats(100)) #end cProfile

For example: to profile the start of the program

  def startMain() -> None:
    """
    Main function to start GUI. Extra function is required to allow starting in module fashion
    """
    from cProfile import Profile
    from pstats import SortKey, Stats
    with Profile() as profile:
      app, window = mainGUI()
      window.show()
    (Stats(profile).strip_dirs().sort_stats(SortKey.CUMULATIVE).print_stats(100)) #end cProfile
    # if app:
    #   app.exec()

Debugging on a conventional install: linux

• 'sudo apt install python3-pudb' (not pip install)
• create small 'temp.py' into any folder, with this content from pasta_eln.gui import startMain startMain()
• start with 'pudb3 temp.py'

Running pytests (3.12)

• python3 -m tests.test_01_3Projects

General notes

• Find qt-awesome icons: qta-browser
• print works great in frontend and backend