def make_email_subject(job_id):
"""
Creates a subject line specific to a job.
Args:
job_id (str): a unique identifier for a job
Returns:
str: the subject line containing the job ID, description, and
job type
Raises:
Exception: raises any exception resulting from the database
fetch and formatting
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
if tfvars.environment in ['dev', 'qa']:
return "Nephele Job: {id} ({type} - {desc}) -- {env}"\
.format(env=tfvars.environment,
id=job_id,
type=job.job_type.name,
desc=job.description)
return "Nephele Job: {id} ({type} - {desc})"\
.format(id=job_id,
type=job.job_type.name,
desc=job.description)
except sqlalchemy.orm.exc.NoResultFound:
raise RuntimeError(
'Unable to find job, failed to make_email_subject', job_id)
def get_job_type_details(job_id):
"""
Gets details about the job type from the job ID.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a valid job ID
Returns:
dict: a dict containing the job name and data type::
{
'name': pipe_name,
'data_type': data_type,
'ami_id': ami_id,
'default_instance_type': default_instance_type
}
Raises:
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
job_details = {}
job_details['name'] = job.job_type.name
job_details['data_type'] = job.job_type.data_type
job_details['ami_id'] = job.job_type.ami_id
job_details['default_instance_type'] = \
job.job_type.default_instance_type
return job_details
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_user_and_email_by_email(email_addr):
with nephele2.db_read() as db:
try:
user = db.query(User).filter_by(email_address=email_addr).one()
user_email = user.user_address
return (user, user_email)
except sqlalchemy.orm.exc.NoResultFound:
return (None, None)
def get_job(job_id):
"""
Gets a job by it's primary key.
"""
with nephele2.db_read() as db:
try:
return db.query(Job).filter_by(job_id=job_id).one()
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_old_unsubmitted_jobs():
"""Looks up jobs that were created > a day ago and have not
been submitted.
Args:
db (SQLClient): a SQLAlchemy database read connection
Returns:
list(str): a list of old job IDs.
"""
yesterday = datetime.now() - timedelta(hours=24)
with nephele2.db_read() as db:
jobs = db.query(Job).filter(Job.status == "Initializing",
Job.created < yesterday)
return [j.job_id for j in jobs.all()]
def get_user_by_email(email_addr):
"""
Retrieves the user by email address.
Args:
db (SQLClient): a SQLAlchemy database read connection
email_addr (str): a validly formatted email address
Returns:
:obj:`User`: a User object
"""
with nephele2.db_read() as db:
try:
return db.query(User).filter_by(email_address=email_addr).one()
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_old_unconfirmed_users():
"""Looks up users who registered > a day ago and have not confirmed.
Args:
db (SQLClient): a SQLAlchemy database read connection
Returns:
list(str): list of bad emails.
Raises:
Exception: any exception thrown
"""
yesterday = datetime.now() - timedelta(hours=24)
with nephele2.db_read() as db:
users = db.query(UserEmail).filter(
UserEmail.is_confirmed.is_(False),
UserEmail.subscr_date < yesterday)
return [u.address for u in users.all()]
def get_job_type_by_name(name):
"""
Gets a JobType object by name.
Args:
db (SQLClient): a SQLAlchemy database read connection
name (str): name of the job to run, from job_type.name
Returns:
:obj:`JobType`: a JobType object
Raises:
"""
with nephele2.db_read() as db:
try:
return db.query(JobType).filter(JobType.name == name).one()
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_user_by_job_id(job_id):
"""
Returns a User object associated with the job_id.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a valid job ID
Returns:
:obj:`User`: a User object
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.user
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_job_status(job_id):
"""
Gets the status for the job with the requested ID.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a valid job ID
Returns:
str: the status of the requested job, one of
['Pending','Pre-Processing', 'Running','Failed','Succeeded']
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.status
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_machine_info(machine_id):
"""
Returns a MachineInfo object.
Args:
db (SQLClient): a SQLAlchemy database read connection
machine_id (str): an AWS machine ID
Returns:
:obj:`MachineInfo`: a MachineInfo object
Raises:
"""
with nephele2.db_read() as db:
try:
return db.query(MachineInfo).filter_by(
instance_id=machine_id).one()
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_machine_info_by_job_id(job_id):
"""
Returns the MachineInfo object associated with the specified job, if
one exists.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a valid job ID (required)
Returns:
:obj:`MachinInfo`: a MachineInfo object
Raises:
"""
with nephele2.db_read() as db:
try:
return db.query(MachineInfo).filter_by(job_id=job_id).one()
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_job_description(job_id):
"""
Returns the job description, may be NULL.
Args:
job_id (str): a job id
Returns:
str: a string describing the job or NULL
Raises:
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.description
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_error_msg(job_id):
"""
Returns the error message for the job. Value may be NULL.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a unique identifier for a job
Returns:
str: the error message string for the job
Raises:
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.error_msg
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_job_id(instance_id):
"""
Retrieves the job ID mapped to the given machine_id.
Args:
instance_id (str): an AWS machine identifier
Returns:
str: a job id
Raises:
"""
with nephele2.db_read() as db:
try:
machine = db.query(MachineInfo).filter_by(
instance_id=instance_id).one()
return machine.job_id
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_job_arguments(job_id):
"""
Gets the arguments for the requested job.
These are the arguments that will actually be used for running the job.
Args:
job_id (str): a unique identifier for a job
Returns:
str: the arguments for the job as a JSON string
Raises:
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.args
except sqlalchemy.orm.exc.NoResultFound:
return None
def get_subscribed_user_email():
"""
Gets a list of all confirmed email address, that aren't flagged as bad,
that are subscribed to the newsletter.
Args:
db (SQLClient): a SQLAlchemy database read connection
Returns:
list(str): a list of email addresses
Raises:
"""
with nephele2.db_read() as db:
users = db.query(UserEmail).filter(
UserEmail.subscribed.is_(True),
UserEmail.is_confirmed.is_(True),
UserEmail.is_bad.isnot(True)).all()
addresses = []
for user in users:
addresses.append(user.address)
return addresses
def get_data_transferred(job_id):
"""
Gets the data transfer status for the job with the requested ID.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a valid job ID
Returns:
bool: transfer status of the requested job
Raises:
RuntimeError: if job can't be found
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.transferred
except sqlalchemy.orm.exc.NoResultFound:
raise RuntimeError(
'Cannot find job, unable to get transferred status',
job_id)
def get_script_name(job_id):
"""
Gets the script location for the type of job associated with the
job_id.
Args:
db (SQLClient): a SQLAlchemy database read connection
job_id (str): a valid job ID
Returns:
str: script name
Examples:
>>> with nephele2.db_write() as db:
a = get_script_name(db,"1")
print(a)
"QIIME/qiime.py"
"""
with nephele2.db_read() as db:
try:
job = db.query(Job).filter_by(job_id=job_id).one()
return job.job_type.package + '/' + job.job_type.script_name
except sqlalchemy.orm.exc.NoResultFound:
return None