def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "%s/experiments" % (here)
self.experiments = glob("%s/*" % self.experiments_base)
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "/scif/data"
self.experiments = glob("%s/*md" % self.experiments_base)
class TestExperiment(TestCase):
def setUp(self):
self.ExpValidator = ExperimentValidator()
self.base = "/scif/apps"
self.experiments = glob("%s/*" % self.base)
self.contenders = [os.path.basename(x) for x in self.experiments]
def test_experiment(self):
"""test an experiment, including the markdown file, and repo itself
"""
print("...Test: Experiment Validation")
# First priority - the user gave an experiment folder
if "config.json" in self.contenders:
for experiment in self.experiments:
name = os.path.basename(experiment)
if name == "config.json":
valid = self.ExpValidator.validate(experiment,
validate_folder=False)
self.assertTrue(valid)
# Otherwise, the user gave a folder with subfolders
else:
for experiment in self.experiments:
name = os.path.basename(experiment)
if os.path.isdir(experiment):
print("Found experiment %s" % name)
valid = self.ExpValidator.validate(experiment)
self.assertTrue(valid)
class TestExperiment(TestCase):
def setUp(self):
self.ExpValidator = ExperimentValidator()
self.base = "/scif/apps"
self.experiments = glob("%s/*" %self.base)
self.contenders = [os.path.basename(x) for x in self.experiments]
def test_experiment(self):
'''test an experiment, including the markdown file, and repo itself
'''
print("...Test: Experiment Validation")
# First priority - the user gave an experiment folder
if "config.json" in self.contenders:
for experiment in self.experiments:
name = os.path.basename(experiment)
if name == "config.json":
valid = self.ExpValidator.validate(experiment, validate_folder=False)
self.assertTrue(valid)
# Otherwise, the user gave a folder with subfolders
else:
for experiment in self.experiments:
name = os.path.basename(experiment)
if os.path.isdir(experiment):
print('Found experiment %s' %name)
valid = self.ExpValidator.validate(experiment)
self.assertTrue(valid)
def validate(folder=None, cleanup=False):
'''validate
:param folder: full path to experiment folder with config.json. If path begins
with https, we assume to be starting from a repository.
'''
from expfactory.validator import ExperimentValidator
cli = ExperimentValidator()
return cli.validate(folder, cleanup=cleanup)
def validate(folder=None, cleanup=False):
'''validate
:param folder: full path to experiment folder with config.json. If path begins
with https, we assume to be starting from a repository.
'''
from expfactory.validator import ExperimentValidator
cli = ExperimentValidator()
return cli.validate(folder, cleanup=cleanup)
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "%s/docs/_library" % (here)
self.experiments = self.get_changed_files()
self.added = [x for x in self.experiments if '_library' in x]
print('Found %s changed or modified files.' % len(self.added))
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "/scif/data"
self.experiments = glob("%s/*md" %self.experiments_base)
class TestContribution(TestCase):
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "/scif/data"
self.experiments = glob("%s/*md" % self.experiments_base)
def test_contribution(self):
'''test an experiment, including the markdown file, and repo itself
'''
if len(self.experiments) == 0:
print(
'Please bind the directory with your markdown files for the library.'
)
sys.exit(1)
print("...Test: Global Library validation")
for ymlfile in self.experiments:
self.assertTrue(self.LibValidator.validate(ymlfile))
url = self.LibValidator.metadata['github']
self.assertTrue(self.ExpValidator.validate(url))
result = self.RuntimeValidator.validate(url)
print(result)
print(url)
self.assertTrue(result)
class TestContribution(TestCase):
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "/scif/data"
self.experiments = glob("%s/*md" %self.experiments_base)
def test_contribution(self):
'''test an experiment, including the markdown file, and repo itself
'''
if len(self.experiments) == 0:
print('Please bind the directory with your markdown files for the library.')
sys.exit(1)
print("...Test: Global Library validation")
for ymlfile in self.experiments:
self.assertTrue(self.LibValidator.validate(ymlfile))
url = self.LibValidator.metadata['github']
self.assertTrue(self.ExpValidator.validate(url))
result = self.RuntimeValidator.validate(url)
print(result)
print(url)
self.assertTrue(result)
class TestLibrary(TestCase):
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "%s/docs/_library" % (here)
self.experiments = self.get_changed_files()
self.added = [x for x in self.experiments if '_library' in x]
print('Found %s changed or modified files.' % len(self.added))
def get_changed_files(self):
'''use the Github compare url (provided by circle) to find
changed files between commits'''
# Fallback, return all files in experiment base
experiments = glob("%s/*" % self.experiments_base)
compare_url = os.environ.get("CIRCLE_COMPARE_URL")
# If the variable exists, we are running on Circle
if compare_url is not None:
print('Detected running in Circle CI')
# If defined, derive change list from compare url
if compare_url != '':
compare_url = "%s.patch" % compare_url
print("Compare URL: %s" % compare_url)
response = requests.get(compare_url)
if response.status_code == 200:
experiments = set(
re.findall(' docs/_library/.+[.]md', response.text))
experiments = [x.strip() for x in experiments]
# Otherwise, use all experiments
else:
print("No compare URL detected, using entire listing.")
experiments = glob('%s/*.md' % self.experiments_base)
else:
print("Not running in Circle Ci")
return experiments
def test_experiment(self):
'''test an experiment, including the markdown file, and repo itself
'''
print("...Test: Global Library validation")
for ymlfile in self.experiments:
if os.path.exists(ymlfile):
print("TESTING %s" % ymlfile)
self.assertTrue(self.LibValidator.validate(ymlfile))
url = self.LibValidator.metadata['github']
self.assertTrue(self.ExpValidator.validate(url))
result = self.RuntimeValidator.validate(url)
print(result)
print(url)
self.assertTrue(result)
def validate(self, folder):
'''validate is the first entrypoint function for running an experiment
or survey robot. It ensures that the content is valid,
and then calls _validate (should be defined in subclass)'''
validator = ExperimentValidator()
valid = validator.validate(folder)
if valid is True:
# IF missing favicon, add
self._check_favicon(folder)
valid = self._validate(folder)
bot.log("[done] stopping web server...")
self.httpd.server_close()
else:
bot.warning('%s is not valid, skipping robot testing.' %folder)
class TestLibrary(TestCase):
def setUp(self):
self.LibValidator = LibraryValidator()
self.ExpValidator = ExperimentValidator()
self.RuntimeValidator = RuntimeValidator()
self.experiments_base = "%s/experiments" % (here)
self.experiments = glob("%s/*" % self.experiments_base)
def test_library(self):
'''test_validate_library calls all subfunctions
'''
print("...Test: Global Library validation")
for jsonfile in self.experiments:
self.assertTrue(self.LibValidator.validate(jsonfile))
def test_single_experiments(self):
'''test_load_json ensures that all files load
'''
for jsonfile in self.experiments:
print("...%s" % os.path.basename(jsonfile))
config = read_json(jsonfile)
self.assertTrue('github' in config)
self.assertTrue(isinstance(config, dict))
url = config['github']
self.assertTrue(self.ExpValidator.validate(url))
def test_previews(self):
'''assert that each experiment is previewed at the Github page
where served
'''
bot.test('Testing experiment previews...')
for jsonfile in self.experiments:
experiment = os.path.basename(jsonfile)
print("...%s experiment preview?" % experiment)
config = read_json(jsonfile)
self.assertTrue('github' in config)
self.assertTrue(isinstance(config, dict))
url = config['github']
result = self.RuntimeValidator.validate(url)
print(result)
print(url)
self.assertTrue(result)
def main(args,parser,subparser):
folder = args.folder
if folder is None:
folder = os.getcwd()
source = args.src[0]
if source is None:
bot.error('Please provide a Github https address to install.')
sys.exit(1)
# Is the experiment valid?
cli = ExperimentValidator()
valid = cli.validate(source, cleanup=False)
exp_id = os.path.basename(source).replace('.git','')
if valid is True:
# Local Install
if os.path.exists(source):
config = load_experiment(source)
source = os.path.abspath(source)
else:
config = load_experiment("%s/%s" %(cli.tmpdir,exp_id))
source = "%s/%s" %(cli.tmpdir,exp_id)
exp_id = config['exp_id']
python_module = exp_id.replace('-','_').lower()
else:
bot.error('%s is not valid.' % exp_id)
sys.exit(1)
# Move static files to output folder
dest = "%s/%s" %(folder,exp_id)
bot.log("Installing %s to %s" %(exp_id, dest))
# Building container
in_container = False
if os.environ.get('SINGULARITY_IMAGE') is not None:
in_container = True
# Running, live container
elif os.environ.get('EXPFACTORY_CONTAINER') is not None:
in_container = True
if in_container is True:
# if in container, we always force
args.force = True
bot.log("Preparing experiment routes...")
template = get_template('experiments/template.py')
template = sub_template(template, '{{ exp_id }}', exp_id)
template = sub_template(template, '{{ exp_id_python }}', python_module)
# 1. Python blueprint
views = get_viewsdir(base=args.base)
view_output = "%s/%s.py" %(views, python_module)
save_template(view_output, template, base=views)
# 2. append to __init__
init = "%s/__init__.py" % views
with open(init,'a') as filey:
filey.writelines('from .%s import *\n' %python_module)
# 3. Instructions
if "instructions" in config:
instruct = "%s/%s.help" %(views, python_module)
with open(instruct,'w') as filey:
filey.writelines(config['instructions'])
if not os.path.exists(dest):
os.system('mkdir -p %s' %dest)
else:
if args.force is False:
bot.error('%s is not empty! Use --force to delete and re-create.' %folder)
sys.exit(1)
# We don't need to copy if experiment already there
if source != dest:
os.system('cp -R %s/* %s' %(source, dest))
def setUp(self):
self.ExpValidator = ExperimentValidator()
self.base = "/scif/apps"
self.experiments = glob("%s/*" % self.base)
self.contenders = [os.path.basename(x) for x in self.experiments]
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):
folder = args.folder
if folder is None:
folder = os.getcwd()
source = args.src[0]
if source is None:
bot.error('Please provide a Github https address to install.')
sys.exit(1)
# Is the experiment valid?
cli = ExperimentValidator()
valid = cli.validate(source, cleanup=False)
exp_id = os.path.basename(source).replace('.git', '')
if valid is True:
# Local Install
if os.path.exists(source):
config = load_experiment(source)
source = os.path.abspath(source)
else:
config = load_experiment("%s/%s" % (cli.tmpdir, exp_id))
source = "%s/%s" % (cli.tmpdir, exp_id)
exp_id = config['exp_id']
python_module = exp_id.replace('-', '_').lower()
else:
bot.error('%s is not valid.' % exp_id)
sys.exit(1)
# Move static files to output folder
dest = "%s/%s" % (folder, exp_id)
bot.log("Installing %s to %s" % (exp_id, dest))
# Building container
in_container = False
if os.environ.get('SINGULARITY_IMAGE') is not None:
in_container = True
# Running, live container
elif os.environ.get('EXPFACTORY_CONTAINER') is not None:
in_container = True
if in_container is True:
# if in container, we always force
args.force = True
bot.log("Preparing experiment routes...")
template = get_template('experiments/template.py')
template = sub_template(template, '{{ exp_id }}', exp_id)
template = sub_template(template, '{{ exp_id_python }}', python_module)
# 1. Python blueprint
views = get_viewsdir(base=args.base)
view_output = "%s/%s.py" % (views, python_module)
save_template(view_output, template, base=views)
# 2. append to __init__
init = "%s/__init__.py" % views
with open(init, 'a') as filey:
filey.writelines('from .%s import *\n' % python_module)
# 3. Instructions
if "instructions" in config:
instruct = "%s/%s.help" % (views, python_module)
with open(instruct, 'w') as filey:
filey.writelines(config['instructions'])
if not os.path.exists(dest):
os.system('mkdir -p %s' % dest)
else:
if args.force is False:
bot.error('%s is not empty! Use --force to delete and re-create.' %
folder)
sys.exit(1)
# We don't need to copy if experiment already there
if source != dest:
os.system('cp -R %s/* %s' % (source, dest))
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)
def setUp(self):
self.ExpValidator = ExperimentValidator()
self.base = "/scif/apps"
self.experiments = glob("%s/*" %self.base)
self.contenders = [os.path.basename(x) for x in self.experiments]
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)
