def get_project(id):
client = pymongo.MongoClient(app.mongodb_uri)
project = client.nav.projects.find_one({'_id': ObjectId(id)})
if project:
meta = {
str(meta['_id']): meta
for meta in client.networks.meta.find({'status': 'success'})
}
try:
networks = project['networks']
networks = {id: True for id in meta.iterkeys() if networks.get(id)}
except KeyError:
# include all genemania networks except co-expression for new projects
networks = {
id: True
for id, it in meta.iteritems()
if it['collection'] == 'genemania'
and not it['type'] == 'co-expression'
}
project['networks'] = networks
client.nav.projects.save(project)
pre_return_value = serialize(project)
return_value = dumps(pre_return_value)
if (request.query.callback):
response.content_type = "application/javascript"
return "%s(%s);" % (request.query.callback, return_value)
return pre_return_value
#return serialize(project)
else:
return HTTPError(404)
def api_mongo_get(database, collection):
limit = get_value('limit', 0, int)
skip = get_value('skip', 0, int)
client = pymongo.MongoClient(app.mongodb_uri)
query = {k:v for k, v in request.query.iteritems() if not k == 'limit' and not k == 'skip'}
cursor = client[database][collection].find(query)
return {
'skip': skip,
'count': cursor.count(),
'records': [serialize(record) for record in cursor.limit(limit).skip(skip)]
}
def create_project():
client = pymongo.MongoClient(app.mongodb_uri)
project = {
'gene_list': [],
'include_neighbors': True,
'n_connected_neighbors': 20,
'n_hottest_neighbors': 20,
'do_heat_diffusion': False
}
set_status(project, 'created')
project['_id'] = str(client.nav.projects.insert(project))
return serialize(project)
def get_jobs(id):
client = pymongo.MongoClient(app.mongodb_uri)
jobs = list(client.nav.jobs.find({'project._id': ObjectId(id)}))
pre_return_value = {'records': serialize(jobs)}
return_value = dumps(pre_return_value)
if (request.query.callback):
response.content_type = "application/javascript"
return "%s(%s);" % (request.query.callback, return_value)
return pre_return_value
def get_networks():
client = pymongo.MongoClient(app.mongodb_uri)
pre_return_value = {
'networks':
serialize(list(client.networks.meta.find({'status': 'success'})))
}
return_value = dumps(pre_return_value)
if (request.query.callback):
response.content_type = "application/javascript"
return "%s(%s);" % (request.query.callback, return_value)
return pre_return_value
def api_mongo_get(database, collection):
limit = get_value('limit', 0, int)
skip = get_value('skip', 0, int)
client = pymongo.MongoClient(app.mongodb_uri)
query = {
k: v
for k, v in request.query.iteritems()
if not k == 'limit' and not k == 'skip'
}
cursor = client[database][collection].find(query)
return {
'skip': skip,
'count': cursor.count(),
'records':
[serialize(record) for record in cursor.limit(limit).skip(skip)]
}
def get_files(id):
client = pymongo.MongoClient(app.mongodb_uri)
project = client.nav.projects.find_one({'_id': ObjectId(id)})
try:
files = list(
client.files.meta.find(
{'_id': {
'$in': [f['_id'] for f in project.get('files', [])]
}}))
pre_return_value = {'records': serialize(files)}
return_value = dumps(pre_return_value)
if (request.query.callback):
response.content_type = "application/javascript"
return "%s(%s);" % (request.query.callback, return_value)
return pre_return_value
#return {'records': serialize(files)}
except:
return HTTPError(404)
def api_mongo_get_id(database, collection, id):
client = pymongo.MongoClient(app.mongodb_uri)
return serialize(client[database][collection].find_one({'_id': ObjectId(id)}))
def api_mongo_get_id(database, collection, id):
client = pymongo.MongoClient(app.mongodb_uri)
return serialize(client[database][collection].find_one(
{'_id': ObjectId(id)}))
