def main():
create_file()
db = dapt.Delimited_file('test.csv')
ap = dapt.Param(db)
while True:
parameters = ap.next_parameters() #Get the next parameter
if parameters == None:
print("No more parameters to run!")
break
print("Request parameters: ")
print(parameters)
ap.successful(parameters["id"])
try:
ap.update_status(parameters['id'], 'Adding and inserting')
c = int(parameters['a']) + int(parameters['b'])
db.update_cell(db.get_row_index('id', parameters['id']), 'c', c)
# Update sheets to mark the test is finished
ap.successful(parameters["id"]
) #Test completed successfully so we mark it as such
# End tests
except ValueError:
# Test failed
print(ValueError)
print("Test failed")
ap.failed(parameters["id"], str(ValueError))
def test_Param_next_parameters():
create_simple_test_file()
db = dapt.Delimited_file('test.csv', ',')
param = dapt.Param(db)
actual = param.next_parameters()
expected = OrderedDict({'id':'t2', 'status':'in progress', 'a':'10', 'b':'10', 'c':''})
assert actual == expected, "Cannot get the next paramater set."
def test_Param_failed():
create_simple_test_file()
db = dapt.Delimited_file('test.csv', ',')
param = dapt.Param(db)
actual = param.next_parameters()
actual = param.failed(actual['id'], 'This is an error')
expected = OrderedDict({'id':'t2', 'status':'failed', 'a':'10', 'b':'10', 'c':''})
assert actual == expected, "Cannot update the status of the paramater set."
def test_Param_successful():
create_simple_test_file()
db = dapt.Delimited_file('test.csv', ',')
param = dapt.Param(db)
actual = param.next_parameters()
actual = param.successful(actual['id'])
expected = OrderedDict({'id':'t2', 'status':'successful', 'a':'10', 'b':'10', 'c':''})
assert actual == expected, "Cannot update the status of the paramater set."
def main(db_path, config_path):
# Set up DAPT objects: database (Delimited_file) and parameter manager (Param)
config = dapt.Config(path=config_path)
db = dapt.db.Delimited_file(db_path, delimiter=',')
ap = dapt.Param(db, config=config)
ap.number_of_runs = 1
print("Starting main script")
# Get the first parameter. Returns None if there are none
parameters = ap.next_parameters()
while parameters is not None:
print("Request parameters: %s" % parameters)
# Use a try/except to report errors if they occur during the pipeline
try:
# Reset PhysiCell from the previous run using PhysiCell's data-cleanup
print("Cleaning up folder")
ap.update_status(parameters['id'], 'clean')
os.system("make data-cleanup")
# Update the default settings with the given parameters
print("Creating parameters xml")
ap.update_status(parameters['id'], 'xml')
dapt.tools.create_XML(parameters, default_settings="config/PhysiCell_settings_default.xml", save_settings="config/PhysiCell_settings.xml")
# Run PhysiCell (execution method depends on OS)
print("Running test")
ap.update_status(parameters['id'], 'sim')
if platform.system() == 'Windows':
os.system("biorobots.exe")
else:
os.system("./biorobots")
# Moving final image to output folder
ap.update_status(parameters['id'], 'output')
shutil.copyfile('output/final.svg', '../outputs/%s_final.svg' % parameters["id"])
# Update sheets to mark the test is finished
ap.successful(parameters["id"])
except ValueError:
print("Test failed:")
print(ValueError)
ap.failed(parameters["id"], ValueError)
parameters = ap.next_parameters() #Get the next parameter
def test_Param_successful_fields():
create_complex_test_file()
db = dapt.Delimited_file('test.csv', ',')
param = dapt.Param(db)
actual = param.next_parameters()
expected = actual
actual = param.successful(actual['id'])
expected = OrderedDict({'id':'t2', 'start-time':'', 'end-time':'', 'status':'successful', 'comment':'','performed-by':'', 'a':'10', 'b':'10', 'c':''})
# Check to see if the time in the database are within 15 seconds of ours.
if (datetime.datetime.strptime(datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'), '%Y-%m-%d %H:%M:%S') - datetime.datetime.strptime(actual['start-time'], '%Y-%m-%d %H:%M:%S')).seconds < 15:
expected['start-time'] = actual['start-time']
if (datetime.datetime.strptime(datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'), '%Y-%m-%d %H:%M:%S') - datetime.datetime.strptime(actual['end-time'], '%Y-%m-%d %H:%M:%S')).seconds < 15:
expected['end-time'] = actual['end-time']
assert actual == expected, "Cannot update the status of the paramater set."
"""
Example of how to use DAPT with Google Sheets.
Before you can run this example, you need to create a new Google Sheet and add you Service Account Email as a collaborator with edit ability. If you are still confused you can follow the documentation guide.
"""
import dapt
import os, sys, csv
# You'll need to provide the sheet id
sheet_id = '1Nfm5oi0ovsETjk3gWATVbLaxI9XRSEwup64iHJoKdDE'
db = dapt.Sheet(spreedsheet_id=sheet_id, sheet_id=0, creds='../credentials.json')
ap = dapt.Param(db)
def init_sheet():
header = ['id', 'start-time', 'end-time', 'status', 'a', 'b', 'c']
for i in range(len(header)):
db.worksheet().update_cell(1, i+1, str(header[i]))
data = [{'id':'t1', 'start-time':'2019-09-06 17:23', 'end-time':'2019-09-06 17:36', 'status':'finished', 'a':'2', 'b':'4', 'c':'6'}, {'id':'t2', 'start-time':'', 'end-time':'', 'status':'', 'a':'10', 'b':'10', 'c':''}, {'id':'t3', 'start-time':'', 'end-time':'', 'status':'', 'a':'10', 'b':'-10', 'c':''}]
for i in range(3):
for j in range(len(header)):
db.worksheet().update_cell(i+2, j+1, data[i][header[j]])
#init_sheet()
input('If you go to the Google Sheet then you can see the sheet is now initialized.\nPress enter to run DAPT on the Google Sheet.')
"""
PhysiCell Example
=================
This file shows an example workflow with PhysiCell.
"""
import os, platform, datetime, time
import dapt
conf = dapt.Config('config.json')
sheet = dapt.Delimited_file('parameters.csv', delimiter=',')
ap = dapt.Param(sheet, conf)
box = dapt.Box(config=conf)
box.connect()
print("Starting main script")
parameters = ap.next_parameters() #Get the next parameter
while parameters is not None:
if parameters == None:
print("No more parameters to run!")
break
print("Request parameters: %s" % parameters)
try:
# Reset from the previous run
print("Cleaning up folder")
import os, platform
import dapt
config = dapt.Config(path='config.json')
db = dapt.db.Delimited_file('parameters.csv', delimiter=',')
params = dapt.Param(db, config=config)
p = params.next_parameters()
while p is not None:
dapt.tools.create_XML(p,
default_settings="PhysiCell_settings_default.xml",
save_settings="PhysiCell_settings.xml")
params.update_status(p["id"], 'running simulation')
if platform.system() == 'Windows':
os.system("biorobots.exe")
else:
os.system("./biorobots")
params.successful(p["id"])
p = params.next_parameters()
for key in parameters:
if key in off_limits:
next
node = root.find(key)
if node != None:
node.text = str(parameters[key])
tree.write(save_settings)
# Set up DAPT objects: database (Delimited_file) and parameter manager (Param)
db = dapt.db.Delimited_file('parameters.csv', delimiter=',')
params = dapt.Param(db)
# Get the first parameter. Returns None if there are none
p = params.next_parameters()
while p is not None:
print("Request parameters: %s" % p)
params.update_status(p["id"], 'updating PhysiCell settings')
# Update the default settings with the given parameters
create_XML(p, default_settings="PhysiCell_settings_default.xml", save_settings="PhysiCell_settings.xml")
params.update_status(p["id"], 'running simulation')