def test_validate(self):
validation = validate(self.experiment)
self.assertTrue(validation)
# Create temporary directory and test invalid config.json
broken_experiment = "%s/broken_experiment" % self.tmpdir
copy_directory(self.experiment, broken_experiment)
# Missing file specified
shutil.copyfile("%s/experiment.js" % broken_experiment,
"%s/pizza.js" % broken_experiment)
os.remove("%s/experiment.js" % broken_experiment)
self.assertFalse(validate(broken_experiment))
shutil.copyfile("%s/pizza.js" % broken_experiment,
"%s/experiment.js" % broken_experiment)
# Invalid field for template
broken_config = self.config[:]
broken_config[0]["template"] = "invalid_framework"
self.save_config(broken_config, broken_experiment)
self.assertFalse(validate(broken_experiment))
# Missing required field
broken_config = self.config[:]
del broken_config[0]["exp_id"]
self.save_config(broken_config, broken_experiment)
self.assertFalse(validate(broken_experiment))
def test_validate(self):
validation = validate(self.experiment)
self.assertTrue(validation)
# Create temporary directory and test invalid config.json
broken_experiment = "%s/broken_experiment" %self.tmpdir
copy_directory(self.experiment,broken_experiment)
# Missing file specified
shutil.copyfile("%s/experiment.js" %broken_experiment,"%s/pizza.js" %broken_experiment)
os.remove("%s/experiment.js" %broken_experiment)
self.assertFalse(validate(broken_experiment))
shutil.copyfile("%s/pizza.js" %broken_experiment,"%s/experiment.js" %broken_experiment)
# Invalid field for template
broken_config = self.config[:]
broken_config[0]["template"] = "invalid_framework"
self.save_config(broken_config,broken_experiment)
self.assertFalse(validate(broken_experiment))
# Missing required field
broken_config = self.config[:]
del broken_config[0]["exp_id"]
self.save_config(broken_config,broken_experiment)
self.assertFalse(validate(broken_experiment))
def install_experiments(experiment_tags=None, repo_type="experiments"):
# We will return list of experiments that did not install successfully
errored_experiments = []
tmpdir = custom_battery_download(repos=[repo_type, "battery"])
# The git commit is saved with the experiment as the "version"
repo = Repo("%s/%s" % (tmpdir, repo_type))
commit = repo.commit("master").__str__()
experiments = get_experiments("%s/%s" % (tmpdir, repo_type), load=True, warning=False)
if experiment_tags != None:
experiments = [e for e in experiments if e[0]["exp_id"] in experiment_tags]
for experiment in experiments:
try:
performance_variable = None
rejection_variable = None
if "experiment_variables" in experiment[0]:
if isinstance(experiment[0]["experiment_variables"], list):
for var in experiment[0]["experiment_variables"]:
if var["type"].lower().strip() == "bonus":
performance_variable = parse_experiment_variable(var)
elif var["type"].lower().strip() == "credit":
rejection_variable = parse_experiment_variable(var)
else:
parse_experiment_variable(var) # adds to database
if isinstance(experiment[0]["reference"], list):
reference = experiment[0]["reference"][0]
else:
reference = experiment[0]["reference"]
cognitive_atlas_task = get_cognitiveatlas_task(experiment[0]["cognitive_atlas_task_id"])
new_experiment, _ = ExperimentTemplate.objects.update_or_create(
exp_id=experiment[0]["exp_id"],
defaults={
"name": experiment[0]["name"],
"cognitive_atlas_task": cognitive_atlas_task,
"publish": bool(experiment[0]["publish"]),
"time": experiment[0]["time"],
"reference": reference,
"version": commit,
"template": experiment[0]["template"],
"performance_variable": performance_variable,
"rejection_variable": rejection_variable,
},
)
new_experiment.save()
experiment_folder = "%s/%s/%s" % (tmpdir, repo_type, experiment[0]["exp_id"])
output_folder = "%s/%s/%s" % (media_dir, repo_type, experiment[0]["exp_id"])
if os.path.exists(output_folder):
shutil.rmtree(output_folder)
copy_directory(experiment_folder, output_folder)
except:
errored_experiments.append(experiment[0]["exp_id"])
shutil.rmtree(tmpdir)
return errored_experiments
def install_experiments(experiment_tags=None,repo_type="experiments"):
# We will return list of experiments that did not install successfully
errored_experiments = []
tmpdir = custom_battery_download(repos=[repo_type,"battery"])
# The git commit is saved with the experiment as the "version"
repo = Repo("%s/%s" %(tmpdir,repo_type))
commit = repo.commit('master').__str__()
experiments = get_experiments("%s/%s" %(tmpdir,repo_type),load=True,warning=False)
if experiment_tags != None:
experiments = [e for e in experiments if e[0]["exp_id"] in experiment_tags]
for experiment in experiments:
try:
performance_variable = None
rejection_variable = None
if "experiment_variables" in experiment[0]:
if isinstance(experiment[0]["experiment_variables"],list):
for var in experiment[0]["experiment_variables"]:
if var["type"].lower().strip() == "bonus":
performance_variable = parse_experiment_variable(var)
elif var["type"].lower().strip() == "credit":
rejection_variable = parse_experiment_variable(var)
else:
parse_experiment_variable(var) # adds to database
if isinstance(experiment[0]["reference"],list):
reference = experiment[0]["reference"][0]
else:
reference = experiment[0]["reference"]
cognitive_atlas_task = get_cognitiveatlas_task(experiment[0]["cognitive_atlas_task_id"])
new_experiment,_ = ExperimentTemplate.objects.update_or_create(exp_id=experiment[0]["exp_id"],
defaults={"name":experiment[0]["name"],
"cognitive_atlas_task":cognitive_atlas_task,
"publish":bool(experiment[0]["publish"]),
"time":experiment[0]["time"],
"reference":reference,
"version":commit,
"template":experiment[0]["template"],
"performance_variable":performance_variable,
"rejection_variable":rejection_variable})
new_experiment.save()
experiment_folder = "%s/%s/%s" %(tmpdir,repo_type,experiment[0]["exp_id"])
output_folder = "%s/%s/%s" %(media_dir,repo_type,experiment[0]["exp_id"])
if os.path.exists(output_folder):
shutil.rmtree(output_folder)
copy_directory(experiment_folder,output_folder)
except:
errored_experiments.append(experiment[0]["exp_id"])
shutil.rmtree(tmpdir)
return errored_experiments
def generate_base(battery_dest,tasks=None,experiment_repo=None,survey_repo=None,game_repo=None,
add_experiments=True,add_surveys=True,add_games=True,battery_repo=None,warning=True):
'''generate_base returns a folder with downloaded experiments, surveys, and battery, either specified by the user or a temporary directory, to be used by generate_local and generate (for psiturk)
:param battery_dest: [required] is the output folder for your battery. This folder MUST NOT EXIST.
:param battery_repo: location of psiturk-battery repo to use as a template. If not specified, will be downloaded to a temporary directory
:param experiment_repo: location of a expfactory-experiments repo to check for valid experiments. If not specified, will be downloaded to a temporary directory
:param survey_repo: location of a expfactory-surveys repo to check for valid surveys. If not specified, will be downloaded to a temporary directory
:param tasks: a list of experiments and surveys, meaning the "exp_id" variable in the config.json, to include. This variable also conincides with the tasks folder name.
:param warning: show warnings when validating experiments (default True)
'''
if experiment_repo == None or battery_repo == None or survey_repo == None or game_repo == None:
tmpdir = custom_battery_download()
if experiment_repo == None:
experiment_repo = "%s/experiments" %(tmpdir)
if battery_repo == None:
battery_repo = "%s/battery" %(tmpdir)
if survey_repo == None:
survey_repo = "%s/surveys" %(tmpdir)
if game_repo == None:
game_repo = "%s/games" %(tmpdir)
# Copy battery skeleton to destination
copy_directory(battery_repo,battery_dest)
valid_experiments = []
valid_surveys = []
valid_games = []
if add_experiments == True:
valid_experiments = get_experiments(experiment_repo,warning=warning)
if add_surveys == True:
valid_surveys = get_experiments(survey_repo,warning=warning,repo_type="surveys")
if add_games == True:
valid_games = get_experiments(game_repo,warning=warning,repo_type="games")
# If the user wants to select a subset
if tasks != None:
valid_experiments = [x for x in valid_experiments if os.path.basename(x) in [os.path.basename(e) for e in tasks]]
valid_surveys = [x for x in valid_surveys if os.path.basename(x) in [os.path.basename(e) for e in tasks]]
valid_games = [x for x in valid_games if os.path.basename(x) in [os.path.basename(e) for e in tasks]]
base = {"battery_repo":battery_repo,
"experiment_repo":experiment_repo,
"survey_repo":survey_repo,
"game_repo":game_repo,
"experiments":valid_experiments,
"surveys":valid_surveys,
"games":valid_games}
return base
def move_experiments(valid_experiments,battery_dest,repo_type="experiments"):
'''move_experiments
Moves valid experiments into the experiments folder in battery repo
:param valid_experiments: a list of full paths to valid experiments
:param battery_dest: full path to battery destination folder
:param repo_type: the kind of task to move (default is experiments)
'''
moved_experiments = []
for valid_experiment in valid_experiments:
try:
experiment_folder = os.path.basename(valid_experiment)
copy_directory(valid_experiment,"%s/static/%s/%s" %(battery_dest,repo_type,experiment_folder))
moved_experiments.append(valid_experiment)
except:
print "Cannot move %s, will not be added." %(valid_experiment)
return moved_experiments
def move_experiments(valid_experiments, battery_dest, repo_type="experiments"):
'''move_experiments
Moves valid experiments into the experiments folder in battery repo
:param valid_experiments: a list of full paths to valid experiments
:param battery_dest: full path to battery destination folder
:param repo_type: the kind of task to move (default is experiments)
'''
moved_experiments = []
for valid_experiment in valid_experiments:
try:
experiment_folder = os.path.basename(valid_experiment)
copy_directory(
valid_experiment, "%s/static/%s/%s" %
(battery_dest, repo_type, experiment_folder))
moved_experiments.append(valid_experiment)
except:
print("Cannot move %s, will not be added." % (valid_experiment))
return moved_experiments
def install_experiment_static(experiment,
to_dir,
from_dir,
update=True,
version=None):
'''install_experiment_static will install an experiment object static files to
the battery static folder. In the case of a special expfactory template (survey, experiment,
or game) the template is rendered and then saved. If successful, returns True, otherwise False.
:param experiment: the expdj.apps.experiments.models.Experiment
:param to_dir: the directory to install to, typically in a battery folder
:param from_dir: the temporary directory
:param update: if the experiment files exist, remove them and install again (an update)
:param version: if specified, will write a version id to the folder in file VERSION
'''
if os.path.exists(to_dir):
if update == True:
shutil.rmtree(to_dir)
else:
# Experiment static install fail, found files and update is not True
return False
# Copy all experiment files into the folder
copy_directory(from_dir, to_dir)
battery = experiment.battery
router_url = (
"%s%s" %
(DOMAIN_NAME, battery.get_router_url(experiment.id))).encode('utf-8')
if experiment.template in ['survey', 'jspsych']:
index_html = install_experiment_template(experiment=experiment,
battery=battery,
router_url=router_url,
to_dir=to_dir)
else:
try:
index_html = install_experiment_custom(experiment=experiment,
battery=battery,
router_url=router_url,
to_dir=to_dir)
except Exception, message:
return message
def tmp_experiment(folder=None, battery_folder=None):
'''generate temporary directory with experiment
:param folder: full path to experiment folder to preview (experiment, survey, or game). If none specified, PWD is used
:param battery_folder: full path to battery folder to use as a template. If none specified, the expfactory-battery repo will be used.
'''
if folder == None:
folder = os.path.abspath(os.getcwd())
if battery_folder == None:
tmpdir = custom_battery_download(repos=["battery"])
# If user has supplied a local battery folder, copy to tempdir
else:
tmpdir = tempfile.mkdtemp()
copy_directory(battery_folder, "%s/battery" % tmpdir)
experiment = load_experiment("%s" % folder)
tag = experiment[0]["exp_id"]
# Determine experiment template
experiment_type = "experiments"
if experiment[0]["template"] == "survey":
experiment_type = "surveys"
elif experiment[0]["template"] == "phaser":
experiment_type = "games"
# We will copy the entire experiment into the battery folder
battery_folder = "%s/battery" % (tmpdir)
experiment_folder = "%s/static/%s/%s" % (battery_folder, experiment_type,
tag)
if os.path.exists(experiment_folder):
shutil.rmtree(experiment_folder)
copy_directory(folder, experiment_folder)
index_file = "%s/index.html" % (battery_folder)
# Generate code for js and css
exp_template = get_experiment_html(experiment, experiment_folder)
filey = open(index_file, "w")
filey.writelines(exp_template)
filey.close()
os.chdir(battery_folder)
return tmpdir
def tmp_experiment(folder=None,battery_folder=None):
'''generate temporary directory with experiment
:param folder: full path to experiment folder to preview (experiment, survey, or game). If none specified, PWD is used
:param battery_folder: full path to battery folder to use as a template. If none specified, the expfactory-battery repo will be used.
'''
if folder==None:
folder=os.path.abspath(os.getcwd())
if battery_folder == None:
tmpdir = custom_battery_download(repos=["battery"])
# If user has supplied a local battery folder, copy to tempdir
else:
tmpdir = tempfile.mkdtemp()
copy_directory(battery_folder,"%s/battery" %tmpdir)
experiment = load_experiment("%s" %folder)
tag = experiment[0]["exp_id"]
# Determine experiment template
experiment_type = "experiments"
if experiment[0]["template"] == "survey":
experiment_type = "surveys"
elif experiment[0]["template"] == "phaser":
experiment_type = "games"
# We will copy the entire experiment into the battery folder
battery_folder = "%s/battery" %(tmpdir)
experiment_folder = "%s/static/%s/%s" %(battery_folder,experiment_type,tag)
if os.path.exists(experiment_folder):
shutil.rmtree(experiment_folder)
copy_directory(folder,experiment_folder)
index_file = "%s/index.html" %(battery_folder)
# Generate code for js and css
exp_template = get_experiment_html(experiment,experiment_folder)
filey = open(index_file,"w")
filey.writelines(exp_template)
filey.close()
os.chdir(battery_folder)
return tmpdir
def main(args,parser,subparser):
template = 'build/docker/Dockerfile.template'
# Full path to template is required if provided via input
if args.input is not None:
template = args.input
template = get_template(template)
# For now, only one database provided
database = args.database
studyid = args.studyid
experiments = args.experiments
branch = "-b %s" %os.environ.get('EXPFACTORY_BRANCH','master')
headless = "false"
if args.headless is True:
headless = "true"
template = sub_template(template,"{{studyid}}",studyid)
template = sub_template(template,"{{database}}",database)
template = sub_template(template,"{{headless}}",headless)
template = sub_template(template,"{{branch}}",branch)
if args.headless is True:
bot.info("Headless build detected, you will need to generate tokens for application entry with expfactory users --new")
library = get_library(key='name')
apps = "\n"
# Add local experiments to library, first preference
local_installs = 0
for experiment in experiments:
if os.path.exists(experiment):
bot.info('local experiment %s found, validating...' %experiment)
# Is the experiment valid?
cli = ExperimentValidator()
valid = cli.validate(experiment, cleanup=False)
if valid is True:
local_installs +=1
config = load_experiment(experiment)
exp_id = config['exp_id']
# If we aren't building in the experiment directory, we need to copy there
output_dir = "%s/%s" %(os.path.abspath(os.path.dirname(args.output)), exp_id)
experiment_dir = os.path.abspath(experiment)
if output_dir != experiment_dir:
copy_directory(experiment_dir, output_dir)
config['local'] = os.path.abspath(experiment)
library[exp_id] = config
# Warn the user that local installs are not reproducible (from recipe)
if local_installs > 0:
bot.warning("%s local installs detected: build is not reproducible without experiment folders" %local_installs)
# Build Image with Experiments
for experiment in experiments:
exp_id = os.path.basename(experiment)
if exp_id in library:
config = library[exp_id]
app = "LABEL EXPERIMENT_%s /scif/apps/%s\n" %(exp_id, exp_id)
# Here add custom build routine, should be list of lines
if "install" in config:
commands = "\n".join(["RUN %s "%s for x in config['install']]).strip('\n')
app = "%s%s\n" %(app, commands)
# The final installation step, either from Github (url) or local folder
if "local" in config:
app = "%sADD %s /scif/apps/%s\n" %(app, exp_id, exp_id)
app = "%sWORKDIR /scif/apps\nRUN expfactory install %s\n" %(app, exp_id)
else:
app = "%sWORKDIR /scif/apps\nRUN expfactory install %s\n" %(app, config['github'])
apps = "%s%s\n" %(apps,app)
else:
bot.warning('%s not in library, check spelling & punctuation.' %exp_id)
if apps == "\n":
bot.error('No valid experiments found, cancelling recipe build.')
sys.exit(1)
template = sub_template(template,"{{experiments}}",apps)
outfile = write_file(args.output,template)
bot.log("Recipe written to %s" %outfile)
from expfactory.experiment import get_experiments, get_validation_fields
from expfactory.utils import copy_directory, sub_template
from expfactory.vm import custom_battery_download
from glob import glob
import shutil
import json
import os
# Download experiments to temporary directory
tmpdir = custom_battery_download()
static_content = glob("%s/battery/static/*" %tmpdir)
# Update entire static directory
copy_to = os.path.abspath("static/")
for content in static_content:
basename = os.path.basename(content)
if os.path.isfile(content):
shutil.copyfile(content,"%s/%s" %(copy_to,basename))
else:
if os.path.exists("%s/%s" %(copy_to,basename)):
shutil.rmtree("%s/%s" %(copy_to,basename))
copy_directory(content,"%s/%s" %(copy_to,basename))
shutil.rmtree(tmpdir)
def generate_new_survey(battery, exp_id, questions, lookup=None, update=True):
'''generate_new_survey will use the survey template to generate a new survey (with config.json) in
the install_dir. If the folder already exists, the files will be replaced given that update=True (default)
:param battery: the battery to install the experiment to.
:param exp_id: the exp_id, the unique id for the survey
:param questions: the file handle for the questions
:param update: Replace or update the files, if the survey already exists (default is True)
:param lookup: (not required) a dictionary of values to look up for the config.json
'''
# First install to temporary directory
tmpdir = tempfile.mkdtemp()
# What is the battery install_dir?
install_dir = battery.get_install_dir()
# Copy the survey template to the folder (all required files)
needs_validation = "%s/%s" % (tmpdir, exp_id)
copy_directory(survey_template, needs_validation)
# Write the questions there
with open('%s/survey.tsv' % (needs_validation), 'wb+') as destination:
for chunk in questions.chunks():
destination.write(chunk)
# Names must have quotes
if "contributors" in lookup:
if len(lookup['contributors']) > 0:
lookup['contributors'] = ",".join(
['"%s"' % (n) for n in lookup["contributors"].split(',')])
# Remove weird /M carriage returns
if "notes" in lookup:
if len(lookup["notes"]) > 0:
lookup['notes'] = ''.join(lookup['notes'].replace('\r\n', ''))
# Read in the template files for config.json
template = get_template("surveys/new_survey/config.json.template")
lookup["exp_id"] = exp_id
del lookup['questions']
config = template.render(context=lookup)
write_template(config.encode('utf-8'),
"%s/config.json" % (needs_validation))
os.remove("%s/config.json.template" % (needs_validation))
# Finally, validate the survey. If valid, add to database.
valid = validate_surveys([exp_id],
tmpdir,
survey_file="survey.tsv",
delim="\t")
if valid == True:
install_folder = '%s/%s' % (install_dir, exp_id)
# The version will be the datetime string
version = datetime.now().strftime("%s")
# Install the folder as a new experiment!
new_experiment, _ = Experiment.objects.update_or_create(
exp_id=exp_id,
battery=battery,
defaults={
"name": lookup["name"],
"time": lookup["time"],
"reference": lookup["reference"],
"version": version,
"template": "survey"
})
new_experiment.save()
success = install_experiment_static(experiment=new_experiment,
to_dir=install_folder,
from_dir=needs_validation,
version=version,
update=update)
if success != True:
# If success returns as not true, is a mesage to indicate error
valid = "%s: %s" (exp_id, success)
shutil.rmtree(tmpdir)
return valid
def generate_base(battery_dest,
tasks=None,
experiment_repo=None,
survey_repo=None,
game_repo=None,
battery_repo=None,
warning=True):
'''generate_base returns a folder with downloaded experiments, surveys, and battery, either specified by the user or a temporary directory, to be used by generate_local and generate (for psiturk)
:param battery_dest: [required] is the output folder for your battery. This folder MUST NOT EXIST.
:param battery_repo: location of psiturk-battery repo to use as a template. If not specified, will be downloaded to a temporary directory
:param experiment_repo: location of a expfactory-experiments repo to check for valid experiments. If not specified, will be downloaded to a temporary directory
:param survey_repo: location of a expfactory-surveys repo to check for valid surveys. If not specified, will be downloaded to a temporary directory
:param tasks: a list of experiments and surveys, meaning the "exp_id" variable in the config.json, to include. This variable also conincides with the tasks folder name.
:param warning: show warnings when validating experiments (default True)
'''
repos = []
tmpdir = None
if battery_repo == None:
tmpdir = custom_battery_download(repos=['battery'])
battery_repo = "%s/battery" % (tmpdir)
if experiment_repo == None and survey_repo == None and game_repo == None:
tmpdir = custom_battery_download(tmpdir,
['experiments', 'surveys', 'games'])
experiment_repo = "%s/experiments" % (tmpdir)
survey_repo = "%s/surveys" % (tmpdir)
game_repo = "%s/games" % (tmpdir)
# Copy battery skeleton to destination
copy_directory(battery_repo, battery_dest)
valid_experiments = []
valid_surveys = []
valid_games = []
if experiment_repo is not None:
valid_experiments = get_experiments(experiment_repo, warning=warning)
if survey_repo is not None:
valid_surveys = get_experiments(survey_repo,
warning=warning,
repo_type="surveys")
if game_repo is not None:
valid_games = get_experiments(game_repo,
warning=warning,
repo_type="games")
# If the user wants to select a subset
if tasks != None:
valid_experiments = [
x for x in valid_experiments
if os.path.basename(x) in [os.path.basename(e) for e in tasks]
]
valid_surveys = [
x for x in valid_surveys
if os.path.basename(x) in [os.path.basename(e) for e in tasks]
]
valid_games = [
x for x in valid_games
if os.path.basename(x) in [os.path.basename(e) for e in tasks]
]
base = {
"battery_repo": battery_repo,
"experiment_repo": experiment_repo,
"survey_repo": survey_repo,
"game_repo": game_repo,
"experiments": valid_experiments,
"surveys": valid_surveys,
"games": valid_games
}
return base
def generate_experiment_web(output_dir,experiment_folder=None,survey_folder=None,games_folder=None,
make_table=True,make_index=True,make_experiments=True,make_data=True,
make_surveys=True,make_games=True):
'''get_experiment_table
Generate a table with links to preview all experiments
:param experiment_folder: folder with experiments inside
:param survey_folder: folder with surveys inside
:param games_folder: folder with games inside
:param output_dir: output folder for experiment and table html, and battery files
:param make_table: generate table.html
:param make_index: generate d3 visualization index
:param make_experiments: generate experiment preview files (linked from table and index)
:param make_data: generate json/tsv data to download
:param make_surveys: generate static files for surveys repos
:param make_games: generate static files for games repos
'''
repos=["experiments","battery"]
if make_surveys == True:
repos.append("surveys")
if make_games == True:
repos.append("games")
tmpdir = custom_battery_download(repos=repos)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
if experiment_folder == None:
experiment_folder = "%s/experiments" %tmpdir
experiments = get_experiments(experiment_folder,load=True, warning=False)
experiment_tags = [x[0]["exp_id"] for x in experiments]
battery_repo = "%s/battery" %(tmpdir)
if survey_folder == None:
survey_folder = "%s/surveys" %tmpdir
if games_folder == None:
games_folder = "%s/games" %tmpdir
# If the user wants surveys and/or games, add them on to tasks
tasks = experiments
if make_surveys == True:
surveys = get_experiments(survey_folder,load=True,warning=False,repo_type="surveys")
survey_tags = [x[0]["exp_id"] for x in surveys]
tasks = experiments + surveys
if make_games == True:
games = get_experiments(games_folder,load=True,warning=False,repo_type="games")
games_tags = [x[0]["exp_id"] for x in games]
tasks = tasks + games
# Fields to keep for the table
fields = ['preview','exp_id','template',
'contributors','time',
'cognitive_atlas_task_id']
valid = pandas.DataFrame(columns=fields)
# Make a table of experiment information
for experiment in tasks:
for field in experiment[0].keys():
if field in fields:
values = experiment[0][field]
# Join lists with a comma
if field == "reference":
if values != '':
values = '<a href="%s" target="_blank">%s</a>' %(values,values)
if isinstance(values,list):
values = ",".join(values)
valid.loc[experiment[0]["exp_id"],field] = values
# Add a preview link
valid.loc[experiment[0]["exp_id"],"preview"] = '<a href="%s.html" target="_blank">DEMO</a>' %(experiment[0]["exp_id"])
# If the user wants to create the index page
if make_index == True:
output_index = os.path.abspath("%s/index.html" %output_dir)
# For each experiment, we will prepare an interactive node for the site
nodes = []
for experiment in tasks:
nodes.append('{"cluster": 1, "radius": "10", "color": colors[%s], "exp_id": "%s" }' %(choice([0,1,2]),experiment[0]["exp_id"]))
# Generate index page
index_template = get_template("%s/templates/expfactory_index.html" %get_installdir())
index_template = index_template.replace("[SUB_NODES_SUB]",",".join(nodes))
index_template = index_template.replace("[SUB_TOTAL_SUB]",str(len(nodes)))
filey = open(output_index,"wb")
filey.writelines(index_template)
filey.close()
# Update entire static directory
old_dirs = ["templates","static"]
for folder in old_dirs:
copy_to = os.path.abspath("%s/%s" %(output_dir,folder))
copy_from = "%s/battery/%s" %(tmpdir,folder)
if os.path.exists(copy_to):
shutil.rmtree(copy_to)
copy_directory(copy_from,copy_to)
# Copy the favicon to web base
shutil.copyfile("%s/battery/static/favicon.ico" %tmpdir,"%s/favicon.ico" %output_dir)
# Clear old experiments
experiment_dir = os.path.abspath("%s/static/experiments/" %output_dir)
if os.path.exists(experiment_dir):
shutil.rmtree(experiment_dir)
# Clear old surveys, copy updated valid surveys into survey directory
if make_surveys == True:
survey_dir = os.path.abspath("%s/static/surveys/" %output_dir)
if os.path.exists(survey_dir):
shutil.rmtree(survey_dir)
valid_surveys = ["%s/%s" %(survey_folder,x[0]["exp_id"]) for x in surveys]
move_experiments(valid_surveys,battery_dest=output_dir,repo_type="surveys")
# Clear old surveys, copy updated valid surveys into survey directory
if make_games == True:
games_dir = os.path.abspath("%s/static/games/" %output_dir)
if os.path.exists(games_dir):
shutil.rmtree(games_dir)
valid_games = ["%s/%s" %(games_folder,x[0]["exp_id"]) for x in games]
move_experiments(valid_games,battery_dest=output_dir,repo_type="games")
# Copy updated valid experiments into our experiment directory
valid_experiments = ["%s/%s" %(experiment_folder,x[0]["exp_id"]) for x in experiments]
move_experiments(valid_experiments,battery_dest=output_dir)
# If the user wants to make a table
if make_table == True:
table_template = get_template("%s/templates/table.html" %get_installdir())
output_table = os.path.abspath("%s/table.html" %output_dir)
# First prepare rendered table
table = '<table id="fresh-table" class="table">\n<thead>\n'
for field in fields:
table = '%s<th data-field="%s" data-sortable="true">%s</th>' %(table,field,field)
table = '%s\n</thead>\n<tbody>\n' %(table)
for row in valid.iterrows():
table = "%s<tr>\n" %(table)
for field in row[1]:
table = "%s<td>%s</td>\n" %(table,field)
table = "%s</tr>\n" %(table)
table = "%s</tbody></table>\n" %(table)
# Write the new table
table_template = table_template.replace("[[SUB_TABLE_SUB]]",table)
filey = open("%s/table.html" %output_dir,"wb")
filey.writelines(table_template)
filey.close()
if make_experiments == True:
experiments_template = get_template("%s/templates/experiments_categories.html" %get_installdir())
output_exp = os.path.abspath("%s/experiments.html" %output_dir)
if "CIRCLE_BRANCH" in os.environ.keys():
experiment_page = table_template
else:
experiment_page = get_cognitiveatlas_hierarchy(experiment_tags=experiment_tags,get_html=True)
# Write the new table
filey = open(output_exp,"wb")
filey.writelines(experiment_page)
filey.close()
# For each experiment, we will generate a demo page
for experiment in experiments:
demo_page = os.path.abspath("%s/%s.html" %(output_dir,experiment[0]["exp_id"]))
exp_template = get_experiment_html(experiment,"%s/%s" %(experiment_folder,experiment[0]["exp_id"]))
filey = open(demo_page,"wb")
filey.writelines(exp_template)
filey.close()
# if the user wants to make surveys
if make_surveys == True:
for experiment in surveys:
demo_page = os.path.abspath("%s/%s.html" %(output_dir,experiment[0]["exp_id"]))
exp_template = get_experiment_html(experiment,"%s/%s" %(survey_folder,experiment[0]["exp_id"]))
filey = open(demo_page,"wb")
filey.writelines(exp_template)
filey.close()
# if the user wants to make surveys
if make_games == True:
for experiment in games:
demo_page = os.path.abspath("%s/%s.html" %(output_dir,experiment[0]["exp_id"]))
exp_template = get_experiment_html(experiment,"%s/%s" %(games_folder,experiment[0]["exp_id"]))
filey = open(demo_page,"wb")
filey.writelines(exp_template)
filey.close()
# If the user wants to make data
if make_data == True:
data_folder = os.path.abspath("%s/data" %output_dir)
if not os.path.exists(data_folder):
os.mkdir(data_folder)
save_pretty_json("%s/expfactory-experiments.json" %(data_folder),json.loads(valid.to_json(orient="records")))
valid.to_csv("%s/expfactory-experiments.tsv" %(data_folder),sep="\t",index=None)
valid.to_pickle("%s/expfactory-experiments.pkl" %(data_folder))
def main(args, parser, subparser):
# List of experiments is required
template = get_template('build/docker/Dockerfile.template')
# For now, only one database provided
database = args.database
studyid = args.studyid
experiments = args.experiments
template = sub_template(template, "{{studyid}}", studyid)
template = sub_template(template, "{{database}}", database)
library = get_library(key='name')
apps = "\n"
# Add local experiments to library, first preference
local_installs = 0
for experiment in experiments:
if os.path.exists(experiment):
bot.info('local experiment %s found, validating...' % experiment)
# Is the experiment valid?
cli = ExperimentValidator()
valid = cli.validate(experiment, cleanup=False)
if valid is True:
local_installs += 1
config = load_experiment(experiment)
exp_id = config['exp_id']
# If we aren't building in the experiment directory, we need to copy there
output_dir = "%s/%s" % (os.path.abspath(
os.path.dirname(args.output)), exp_id)
experiment_dir = os.path.abspath(experiment)
if output_dir != experiment_dir:
copy_directory(experiment_dir, output_dir)
config['local'] = os.path.abspath(experiment)
library[exp_id] = config
# Warn the user that local installs are not reproducible (from recipe)
if local_installs > 0:
bot.warning(
"%s local installs detected: build is not reproducible without experiment folders"
% local_installs)
# Build Image with Experiments
for experiment in experiments:
exp_id = os.path.basename(experiment)
if exp_id in library:
config = library[exp_id]
app = "LABEL EXPERIMENT_%s /scif/apps/%s\n" % (exp_id, exp_id)
# Here add custom build routine, should be list of lines
if "install" in config:
commands = "\n".join(
["RUN %s " % s for x in config['install']]).strip('\n')
app = "%s%s\n" % (app, commands)
# The final installation step, either from Github (url) or local folder
if "local" in config:
app = "%sADD %s /scif/apps/%s\n" % (app, exp_id, exp_id)
app = "%sWORKDIR /scif/apps\nRUN expfactory install %s\n" % (
app, exp_id)
else:
app = "%sWORKDIR /scif/apps\nRUN expfactory install %s\n" % (
app, config['github'])
apps = "%s%s\n" % (apps, app)
else:
bot.warning('%s not in library, check spelling & punctuation.' %
exp_id)
if apps == "\n":
bot.error('No valid experiments found, cancelling recipe build.')
sys.exit(1)
template = sub_template(template, "{{experiments}}", apps)
outfile = write_file(args.output, template)
bot.log("Recipe written to %s" % outfile)
def main(args, parser, subparser):
template = "build/docker/Dockerfile.template"
# Full path to template is required if provided via input
if args.input is not None:
template = args.input
template = get_template(template)
# For now, only one database provided
database = args.database
studyid = args.studyid
experiments = args.experiments
branch = "-b %s" % os.environ.get("EXPFACTORY_BRANCH", "master")
headless = "false"
if args.headless is True:
headless = "true"
template = sub_template(template, "{{studyid}}", studyid)
template = sub_template(template, "{{database}}", database)
template = sub_template(template, "{{headless}}", headless)
template = sub_template(template, "{{branch}}", branch)
if args.headless is True:
bot.info(
"Headless build detected, you will need to generate tokens for application entry with expfactory users --new"
)
library = get_library(key="name")
apps = "\n"
# Add local experiments to library, first preference
local_installs = 0
for experiment in experiments:
if os.path.exists(experiment):
bot.info("local experiment %s found, validating..." % experiment)
# Is the experiment valid?
cli = ExperimentValidator()
valid = cli.validate(experiment, cleanup=False)
if valid is True:
local_installs += 1
config = load_experiment(experiment)
exp_id = config["exp_id"]
# If we aren't building in the experiment directory, we need to copy there
output_dir = "%s/%s" % (
os.path.abspath(os.path.dirname(args.output)),
exp_id,
)
experiment_dir = os.path.abspath(experiment)
if output_dir != experiment_dir:
copy_directory(experiment_dir, output_dir)
config["local"] = os.path.abspath(experiment)
library[exp_id] = config
# Warn the user that local installs are not reproducible (from recipe)
if local_installs > 0:
bot.warning(
"%s local installs detected: build is not reproducible without experiment folders"
% local_installs
)
# Build Image with Experiments
for experiment in experiments:
exp_id = os.path.basename(experiment)
if exp_id in library:
config = library[exp_id]
app = "LABEL EXPERIMENT_%s /scif/apps/%s\n" % (exp_id, exp_id)
# Here add custom build routine, should be list of lines
if "install" in config:
commands = "\n".join(["RUN %s " % s for x in config["install"]]).strip(
"\n"
)
app = "%s%s\n" % (app, commands)
# The final installation step, either from Github (url) or local folder
if "local" in config:
app = "%sADD %s /scif/apps/%s\n" % (app, exp_id, exp_id)
app = "%sWORKDIR /scif/apps\nRUN expfactory install %s\n" % (
app,
exp_id,
)
else:
app = "%sWORKDIR /scif/apps\nRUN expfactory install %s\n" % (
app,
config["github"],
)
apps = "%s%s\n" % (apps, app)
else:
bot.warning("%s not in library, check spelling & punctuation." % exp_id)
if apps == "\n":
bot.error("No valid experiments found, cancelling recipe build.")
sys.exit(1)
template = sub_template(template, "{{experiments}}", apps)
outfile = write_file(args.output, template)
bot.log("Recipe written to %s" % outfile)