def create_new_project_and_upload_fastq(project_name, sample_data_list,
experiment_name):
'''
A function for uploading afstq files to basespace after creating a new project
:param project_name: A project name
:param sample_data_list: Sample data list containing following information
sample_name (str)
read_count (str)
read_length (str)
fastq_path (list)
:param experiment_name: Experiment name
:retruns: None
'''
try:
myAPI = BaseSpaceAPI()
project = myAPI.createProject(project_name) # create new project
appResults = project.\
createAppResult(\
myAPI,
"FastqUpload",
"uploading project data",
appSessionId='') # create new app results for project
myAppSession = appResults.AppSession # get app session
__create_sample_and_upload_data(\
api=myAPI,
appSessionId=myAppSession.Id,
appSession=myAppSession,
project_id=project.Id,
sample_data_list=sample_data_list,
exp_name=experiment_name
) # upload fastq
myAppSession.setStatus(
myAPI, 'complete',
"finished file upload") # mark app session a complete
except:
if myAppSession and \
len(project.getAppResults(myAPI,statuses=['Running']))>0:
myAppSession.setStatus(
myAPI, 'complete',
"failed file upload") # comment for failed jobs
raise
help="Target upload directory (default: %(default)s)")
parser.add_argument("--sdir",
"-s",
type=str,
default="",
help="Target subdirectory (default: %(default)s)")
parser.add_argument("--name", "-n", type=str, help="Target file name")
args = parser.parse_args()
print "Connecting to BaseSpace API server..."
myAPI = BaseSpaceAPI()
user = myAPI.getUserById('current')
print "Connected to server, username: %s" % user
p = myAPI.createProject(args.project)
appResults = p.createAppResult(myAPI, args.dir, "", appSessionId="")
myAppSession = appResults.AppSession
myAppSession.setStatus(myAPI, "running", "uploading data")
if not args.name or len(args.file):
args.name = os.path.basename(args.file)
print "Uploading file %(file)s to %(project)s:%(dir)s/%(sdir)s/%(name)s" % args.__dict__
appResults.uploadFile(myAPI, args.file, args.name, args.sdir, "text/plain")
myAppSession.setStatus(myAPI, "complete", "data uploaded")
print "File successfully uploaded"
"""
import os
import sys
# Add relative path libraries
SCRIPT_DIR = os.path.abspath(os.path.dirname(__file__))
sys.path.append(os.path.abspath(os.path.sep.join([SCRIPT_DIR, "..", "lib"])))
sys.path.append(os.path.abspath(os.path.sep.join([SCRIPT_DIR, "..", "..", "basespace-python-sdk", "src"])))
from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
import Repository
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Create a project')
parser.add_argument('-n', '--name', type=str, required=True, dest="name", help='name of project')
parser.add_argument('-p', '--path', type=str, required=True, dest="path", help='path where project should write')
args = parser.parse_args()
baseSpaceAPI = BaseSpaceAPI()
if not os.path.exists(args.path):
print "must specify an output directory that already exists!"
sys.exit(1)
print "attempting to create/retrieve BaseSpace project"
project = baseSpaceAPI.createProject(args.name)
print "got Id: %s" % project.Id
Repository.AddProject(args.name, args.path, project.Id)