}
branches = {'NeuroML2': 'development'}
all_repos.update(additional_repos)
projects = len(all_repos.keys())
if __name__ == "__main__":
start = datetime.datetime.now()
project_num = 1000
if len(sys.argv) == 2:
project_num = int(sys.argv[1])
for project in osb.get_projects(min_curation_level="Low",
limit=project_num):
print("\n%sPre checking OSB project: %s (%s)\n" %
("-" * 8, project.name, project.identifier))
if project.identifier not in ignores:
github_repo = project.github_repo
projects += 1
if github_repo is not None:
if github_repo.check_file_in_repository(".travis.yml"):
raw_url = github_repo.link_to_raw_file_in_repo(
'''
Script to check ModelDB references
'''
import osb
projects = 0
with_modeldb = 0
for project in osb.get_projects(min_curation_level="None"):
if project.is_standard_project():
print "\n-------- Project: %s\n" % project.name
projects+=1
if project.modeldb_reference:
print " OSB link:%shttp://opensourcebrain.org/projects/%s" % (" "*22, project.identifier)
print(" ModelDB link:%shttp://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=%s" % (' '*18, project.modeldb_reference))
with_modeldb +=1
else:
print " No ModelDB info for model"
print("\nThere were %i projects, %i of which had ModelDB information\n"%(projects, with_modeldb))
projects = len(all_repos.keys())
bad_projects_found = {}
if __name__ == "__main__":
start = datetime.datetime.now()
project_num = 1000
if len(sys.argv) == 2:
try:
project_num = int(sys.argv[1])
except:
print("ignoring...")
all_projs = osb.get_projects(min_curation_level="None", limit=project_num)
for project in all_projs:
print("\n%sPre checking OSB project: %s (%s)\n" %
("-" * 8, project.name, project.identifier))
if project.identifier not in ignores:
github_repo = project.github_repo
projects += 1
if github_repo is not None:
if github_repo.check_file_in_repository(".travis.yml"):
'''
Script to check ModelDB references
'''
# From https://github.com/OpenSourceBrain/OSB_API/tree/master/python
import osb
projects = 0
with_modeldb = 0
for project in osb.get_projects(min_curation_level="None"):
if project.is_standard_project():
print "\n-------- Project: %s\n" % project.name
projects += 1
if project.modeldb_reference:
print " OSB link:%shttp://opensourcebrain.org/projects/%s" % (
" " * 22, project.identifier)
print(
" ModelDB link:%shttp://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=%s"
% (' ' * 18, project.modeldb_reference))
with_modeldb += 1
else:
print " No ModelDB info for model"
print("\nThere were %i projects, %i of which had ModelDB information\n" %
(projects, with_modeldb))
'''
Script to check ModelDB references
'''
import osb
import operator
projects = 0
with_tags = 0
tags = {}
for project in osb.get_projects(min_curation_level="Low"):
if project.is_standard_project() or project.is_showcase():
print "\n-------- Project: %s\n" % project.name
projects+=1
if project.tags:
print " Project has tags: %s" % (project.tags)
with_tags +=1
for tag in project.tags:
if not tags.has_key(tag):
tags[tag] = 0
tags[tag] +=1
print("\nThere were %i projects, %i of which had tags\n"%(projects, with_tags))
sorted_tags = sorted(tags.iteritems(), key=operator.itemgetter(1), reverse=True)
for s in sorted_tags:
print("Only looking for NeuroML v1 files")
versionFolder = "NeuroML"
nml_schema_file = urlopen("http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd")
nml_suffix = ".xml"
nml2 = False
if len(sys.argv) == 2 and sys.argv[1]=='-local':
local = True
if local: print("Only checking local NeuroML files")
xmlschema_doc = etree.parse(nml_schema_file)
xmlschema = etree.XMLSchema(xmlschema_doc)
for project in osb.get_projects(min_curation_level="None", limit=project_num):
print("\n-------- Project: "+ project.name +" ("+ project.identifier +")"+ "\n")
ignores = ['blender-to-neuroml',
'olfactory-bulb-network-model-o-connor-angelo-and-jacob-2012',
'neurosciences-repository']
if project_num<30:
ignores += ['miglioreetal14_olfactorybulb3d', # Lots of NML2...
'alleninstituteneuroml', # Lots of NML2...
'blue-brain-project-showcase', # Lots of NML2...
'ca1-pv-fast-firing-cell-ferguson-et-al-2013']
if not ( project.is_standard_project() or project.is_showcase()):
print(" (Ignoring project as its category is: %s) "%project.category)
projects = len(all_repos.keys())
bad_projects_found = {}
if __name__ == "__main__":
start = datetime.datetime.now()
project_num = 1000
if len(sys.argv) == 2:
try:
project_num = int(sys.argv[1])
except:
print("ignoring...")
all_projs = osb.get_projects(min_curation_level="None",
limit=project_num)
for project in all_projs:
print("\n%sPre checking OSB project: %s (%s)\n" %
("-" * 8, project.name, project.identifier))
if project.identifier not in ignores:
github_repo = project.github_repo
projects += 1
if github_repo is not None:
if github_repo.check_file_in_repository(".travis.yml"):
if __name__ == "__main__":
project_num = 1000
if len(sys.argv) >= 2:
project_num = int(sys.argv[1])
url = 'http://www.opensourcebrain.org/projects.json'
if '-comodl' in sys.argv:
url = 'http://www.comodl.org/projects.json'
if '-local' in sys.argv:
url = 'http://localhost:3000/projects.json'
for project in osb.get_projects(min_curation_level="Low", limit=project_num, url=url, verbose=True):
print("\n%sProject: %s (%s)\n" % ("-"*8,project.name,project.identifier))
github_repo = project.github_repo
if project.is_standard_project() or project.is_showcase():
projects +=1
passed = 1
if project.status == None:
print(" No status!")
passed = 0
if project.is_standard_project():
if project.spine_classification == None:
# Installed packages.
import neuroml.loaders as loaders
import osb
import sciunit
from neuronunit import neuroelectro,tests,capabilities
from neuronunit.neuroconstruct import models
def qprint(string):
if not QUIET:
print(string)
ephys_property = "Resting Membrane Potential"
nml2_model_list = os.listdir(NEUROML2_PATH)
# Get projects with medium curation level.
osb_projects = osb.get_projects('Medium')
for model_name in nml2_model_list:
print(model_name)
path = os.path.join(NEUROML2_PATH,model_name)
nml_files = glob.glob(path+"/*.nml")
if not len(nml_files):
qprint("No .nml files found for model %s" % model_name)
for nml_file in nml_files:
nml = loaders.NeuroMLLoader.load(nml_file)
for cell in nml.cells:
nlex_id = cell.neuro_lex_id
if nlex_id is None:
project = osb.get_project_with_identifier(model_name,osb_projects)
if project:
nlex_id_list = project.NEUROLEX_IDS_CELLS
import osb
import sciunit
from neuronunit import neuroelectro, tests, capabilities
from neuronunit.neuroconstruct import models
def qprint(string):
if not QUIET:
print(string)
ephys_property = "Resting Membrane Potential"
nml2_model_list = os.listdir(NEUROML2_PATH)
# Get projects with medium curation level.
osb_projects = osb.get_projects('Medium')
for model_name in nml2_model_list:
print(model_name)
path = os.path.join(NEUROML2_PATH, model_name)
nml_files = glob.glob(path + "/*.nml")
if not len(nml_files):
qprint("No .nml files found for model %s" % model_name)
for nml_file in nml_files:
nml = loaders.NeuroMLLoader.load(nml_file)
for cell in nml.cells:
nlex_id = cell.neuro_lex_id
if nlex_id is None:
project = osb.get_project_with_identifier(
model_name, osb_projects)
if project:
NEUROML2_PATH = "/Users/rgerkin/NeuroML2" # Path to NeuroML2 compliant OSB models.
# Standard library.
import os
# Installed packages.
import sciunit
from neuronunit import neuroelectro,tests,capabilities
from neuronunit.neuroconstruct import models
import osb
osb_projects = osb.get_projects(1)
# Initialize the test with summary statistics from the reference data
# and arguments for the model (model).
from pythonnC.utils.putils import OSB_MODELS
brain_areas = os.listdir(OSB_MODELS)
models_tested = 0
nlex_ids = {}
for brain_area in brain_areas:
path = os.path.join(OSB_MODELS,brain_area)
if not os.path.isdir(path):
continue
neuron_types = os.listdir(path)
for neuron_type in neuron_types:
path = os.path.join(OSB_MODELS,brain_area,neuron_type)
if not os.path.isdir(path):
continue
model_names = os.listdir(path)
for model_name in model_names: