def process(self):
try:
p = get_project(self.job.inputs["project_id"])
vs = ViewSet(p.db, p.get_viewset_id())
create_thumbnails_from_ucsc(self.job.inputs["session_url"],
vs,
pixels=self.job.inputs["image_width"],
margins=self.job.inputs.get(
"margins", 0),
job=self.job)
p.set_data("has_images", True)
#send email
url = p.get_url(external=True)
user = db.session.query(User).filter_by(id=self.job.user_id).one()
send_email(user,
"Images Created",
"ucsc_image_job_finished",
url=url)
p.set_data("creating_images_job_status", "complete")
self.complete()
except Exception as e:
app.logger.exception("Error in ucsc upload # {}".format(
self.job.id))
p.set_data("creating_images_job_status", "failed")
self.failed(traceback.format_exc())
def create_from_avocato_output(self, output_dir=""):
self.set_data("remote_avacato_dir", output_dir)
remote_file = os.path.join(output_dir, "cell", "cell_all.csv")
tf = get_temporary_folder()
local_file = os.path.join(tf, "cell.csv")
remote_file = shlex.quote(remote_file)
os.system("wget {} -O {}".format(remote_file, local_file))
line_num = 0
headers = []
#work put headers
with open(local_file) as f:
for line in f:
arr = line.strip().split(",")
if line_num == 0:
for c, item in enumerate(arr, start=1):
headers.append({"name": item, "position": c})
line_num += 1
continue
if line_num == 1:
for c, item in enumerate(arr):
type = "text"
try:
int(item)
type = "integer"
except:
try:
float(item)
type = "double"
except:
pass
headers[c]["datatype"] = type
break
self.add_data_file(has_headers=True,
files={"upload_file": local_file},
fields=headers,
delimiter=",")
user = db.session.query(User).filter_by(id=self.owner).one()
send_email(user,
"Job Finished",
"job_finished",
url=self.get_url(external=True),
type="Avacato Visualisation")
def process(self):
try:
p = get_project(self.job.inputs["project_id"])
vs = ViewSet(p.db, p.get_viewset_id())
create_thumbnails_from_mlv(
self.job.inputs["tracks"],
vs,
image_width=self.job.inputs["image_width"],
margins=self.job.inputs.get("margins", 0),
job=self.job)
p.refresh_data()
p.set_data("has_images", True)
hid = self.get_input_parameter("history_id")
history = p.get_history(hid)
history["tracks"] = []
history["fields"] = []
history["graphs"] = []
history["status"] = "complete"
p.update()
#send email
url = p.get_url(external=True)
user = db.session.query(User).filter_by(id=self.job.user_id).one()
send_email(user,
"Images Created",
"ucsc_image_job_finished",
url=url)
self.complete()
except Exception as e:
p = get_project(self.job.inputs["project_id"])
hid = self.get_input_parameter("history_id")
history = p.get_history(hid)
history["status"] = "failed"
p.update()
app.logger.exception("Error in creating mlv images # {}".format(
self.job.id))
self.failed(traceback.format_exc())
def process(self, pword):
try:
p = get_project(self.job.inputs["project_id"])
p.set_data("zegami_upload_job", {
"job_id": self.job.id,
"job_status": "running"
})
vs = ViewSet(p.db, p.get_viewset_id())
credentials = {
"project": self.job.inputs["project"],
"username": self.job.inputs["username"],
"password": pword
}
url = vs.create_zegami_collection(name=p.name,
job=self.job,
credentials=credentials)
p.set_data("zegami_url", url)
vs.upload_images_to_zegami(job=self.job, credentials=credentials)
#send email
user = db.session.query(User).filter_by(id=self.job.user_id).one()
send_email(user,
"Zegami Collection Created",
"zegami_collection_created",
url=url)
self.complete()
except Exception as e:
app.logger.exception("Error in zegami upload # {}".format(
self.job.id))
p.set_data("zegami_upload_job", {
"job_id": self.job.id,
"job_status": "failed"
})
self.failed(traceback.format_exc())
def test_email():
from app.jobs.email import send_email
from app.databases.user_models import User
user = db.session.query(User).filter_by(id=2).one()
send_email(user, "test", "test_email", info="hello")