Further Examples
Workspace Setup
To setup a Workspace on Labstep:
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import labstep
# Login
user = labstep.login('myaccount@labstep.com', 'mypassword')
# Create a new Workspace
workspace = user.newWorkspace(name='The Synthesis of Aspirin')
user.setWorkspace(workspace.id)
# Create an Experiment
my_experiment = user.newExperiment(name='Trial 1')
# Upload the reaction scheme
user.newFile('./aspirin_reaction_scheme.png')
# Create a Protocol
my_protocol = user.newProtocol('Aspirin Synthesis')
# Create Resource Category
chemicalCategory = user.newResourceCategory('Chemical')
chemicalCategory.addMetadata(fieldName='Molar mass')
chemicalCategory.addMetadata(fieldName='Density')
chemicalCategory.addMetadata(fieldName='Melting point')
# Add Resources
salicylic_acid = user.newResource('Salicylic Acid')
salicylic_acid.addComment('Here is the chemical structure',
'./salicylic_acid.png')
salicylic_acid.addMetadata(fieldName='Formula', value='C7H6O3')
salicylic_acid.addMetadata(fieldName='Hazards', value='Corrosive, irritant')
# etc...
Deleting Multiple Entities
You can use labstepPy to easily delete multiple different Entities on Labstep (a list of Experiments, Protocols, or Tags, etc.), either from within a specific Workspace or by performing a global delete.
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import labstep
# Login
user = labstep.login('myaccount@labstep.com', 'mypassword')
# Choose a Workspace
my_workspace = user.getWorkspaces(name='Structure of Protein A')[0]
user.setWorkspace(my_workspace.id)
# Delete a list of Tags for 'crystallisation'
# That are only in the Resource entity type
tags_to_delete = user.getTags(search_query='crystallisation', type='resource')
for i in range(len(tags_to_delete)):
print('TAGS TO DELETE =', tags_to_delete[i].name)
tags_to_delete[i].delete()
# Get the difference of two lists using set()
def diff(list1, list2):
return (list(set(list1) - set(list2)))
# Only keep experiments that investigate the protein structure by 'NMR'
# And store the IDs in a list
keep_experiments = user.getExperiments(search_query='NMR')
keep_exp_ids = []
for i in range(len(keep_experiments)):
print('EXPERIMENTS TO KEEP =', keep_experiments[i].name)
print('EXPERIMENT IDS TO KEEP =', keep_experiments[i].id)
keep_exp_ids.append(keep_experiments[i].id)
# Get all Experiment IDs
all_experiments = user.getExperiments()
all_exp_ids = []
for i in range(len(all_experiments)):
all_exp_ids.append(all_experiments[i].id)
# Find the IDs of Experiments to delete, and delete them
for i in diff(all_exp_ids, keep_exp_ids):
print('EXPERIMENT IDS TO DELETE =', i)
exp_to_delete = user.getExperiment(i)
exp_to_delete.delete()
Downloading Files
You can use labstepPy to download files uploaded directly to Labstep or attached to different Labstep entities
import labstep
user = labstep.login('myaccount@labstep.com', 'mypassword')
# A List of the authenticated user's files can be accessed
# via the getFiles method
my_files = user.getFiles()
my_file = my_files[0]
# Alternatively retrieve a list of files from a workspace
my_workspace = user.getWorkspaces()[0]
workspace_files = my_workspace.getFiles()
# Access the data via the getData method
rawData = my_file.getData()
# Or save directly as a new file
my_file.save()
# If you come across a file_id attached to another labstep entity
# you can retrieve the file using the User getFile method
my_file = user.getFile(123)
my_file.save()
A basic python GUI
In this basic example, a GUI is created that can be used to authenticate a user on Labstep and create new experiments.
import labstep
from tkinter import *
from tkinter import messagebox
from PIL import Image, ImageTk
class NewExperimentForm:
def __init__(self,root, user):
self.user = user
self.frame = Frame(root, width=100, height=50, pady=50,padx=50)
self.frame.place(relx=0.5, rely=0.5, anchor=CENTER)
Logo(self.frame)
self.name = LabelledInput(self.frame, 'Name')
self.submit_button = Button(self.frame, text="Create Experiment", command=self.action)
self.submit_button.pack()
def action(self):
name = self.name.get()
self.user.newExperiment(name)
class Logo:
def __init__(self,root):
load = Image.open("labstep_logo.png")
render = ImageTk.PhotoImage(load)
logo = Label(root, image=render)
logo.image = render
logo.pack()
class LabelledInput:
def __init__(self,root,name):
self.label = Label(root, text=name)
self.label.pack()
self.input = Entry(root,width=20)
self.input.pack()
def get(self):
return self.input.get()
class LoginForm:
def __init__(self,root,onSuccess):
self.onSuccess = onSuccess
# Define and place the frame for the login form
self.frame = Frame(root, width=100, height=50, pady=10,padx=10)
self.frame.place(relx=0.5, rely=0.5, anchor=CENTER)
# Place the labstep logo
Logo(self.frame)
# Username label and input
self.username = LabelledInput(self.frame,"Username")
# Api key label and input
self.apikey = LabelledInput(self.frame,"API key")
# Submit button
submit_button = Button(self.frame, text="Authenticate", command=self.onSubmit)
submit_button.pack()
# Function that runs when user hits enter
def onSubmit(self):
self.frame.place_forget() # hide login frame
username = self.username.get() # get user input
apikey = self.apikey.get() # get user input
user = labstep.authenticate(username,apikey) # Login via labstep API
messagebox.showinfo('Login Success', f'You have successfully authenticated as {user.first_name} {user.last_name}')
self.onSuccess(user)
class App:
def __init__(self):
self.window = Tk()
self.window.title("Labstep Python App")
self.window.geometry('600x400')
self.login()
def main(self,user):
NewExperimentForm(self.window,user)
def login(self):
LoginForm(self.window,self.main)
def start(self):
self.window.mainloop()
App().start()