class Task(Document):
schema_version = StringField(validate=validate.Length(max=10), default='1')
test = ReferenceField('Test')
test_suite = StringField(
validate=validate.Length(max=100)) # embedded document from Test
testcases = ListField(StringField())
schedule_date = DateTimeField(default=datetime.datetime.utcnow)
run_date = DateTimeField()
status = StringField(validate=validate.Length(max=50), default='waiting')
comment = StringField(validate=validate.Length(max=1000))
kickedoff = IntField(validate=validate.Range(min=0), default=0)
endpoint_list = ListField(UUIDField())
parallelization = BooleanField(default=False)
endpoint_run = ReferenceField('Endpoint')
priority = IntField(validate=validate.Range(min=QUEUE_PRIORITY_MIN,
max=QUEUE_PRIORITY_MAX),
default=QUEUE_PRIORITY_DEFAULT)
variables = DictField()
tester = ReferenceField('User')
upload_dir = StringField(validate=validate.Length(max=100))
test_results = ListField(ReferenceField('TestResult'))
organization = ReferenceField(
'Organization') # embedded document from Test
team = ReferenceField('Team') # embedded document from Test
class Meta:
collection_name = 'tasks'
class Predicted(Document):
predicted = fields.StringField(required=True) # dataset name
department = fields.StringField(required=True) # assign the dataset to department
team = fields.StringField(required=True) # assign the dateset to team
createDate = fields.DateTimeField(validate=validate.Range(min=pd.Timestamp(1990, 1, 1)), required=True)
updateDate = fields.DateTimeField(validate=validate.Range(min=pd.Timestamp(1990, 1, 1)), required=True)
class Meta():
collection = db.predicted
class MySchema(Schema):
dict = fields.DictField(attribute='in_mongo_dict', allow_none=True)
kdict = fields.DictField(keys=fields.StringField(
validate=validate.Length(0, 1)))
vdict = fields.DictField(values=fields.IntField(
validate=validate.Range(max=5)))
kvdict = fields.DictField(
keys=fields.StringField(validate=validate.Length(0, 1)),
values=fields.IntField(validate=validate.Range(max=5)))
dtdict = fields.DictField(values=fields.DateTimeField)
class Account(Document):
#
username = fields.StringField(required=True)
password = fields.StringField(required=True)
createDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1990, 1, 1)), required=True)
updateDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1990, 1, 1)), required=True)
class Meta():
collection = db.account
class User(Document):
#
name = fields.StringField(required=True)
department = fields.StringField(required=True)
team = fields.StringField(required=True)
createDate = fields.DateTimeField(
validate=validate.Range(min=pd.Timestamp(1990, 1, 1)), required=True)
updateDate = fields.DateTimeField(
validate=validate.Range(min=pd.Timestamp(1990, 1, 1)), required=True)
accountRef = fields.StringField(required=True)
class Meta():
collection = db.user
class MLmodel(Document):
#
description = fields.StringField(required=True) # to remember the functionality of the pkl file
filename = fields.StringField(required=True) # plk file name
path = fields.StringField(required=True) # path of the plk file
version = fields.StringField(required=True) # plk file version
department = fields.StringField(required=True) # assign the model to department
team = fields.StringField(required=True) # assign the model to team
features = fields.StringField(required=True) # features have to be assigned
name = fields.StringField(required=True) # model name
isDeployed = fields.BooleanField(required=True,default=False)
createDate = fields.DateTimeField(validate=validate.Range(min=pd.Timestamp(1990,1,1)),required=True)
updateDate = fields.DateTimeField(validate=validate.Range(min=pd.Timestamp(1990,1,1)),required=True)
class Meta():
collection = db.mlmodel
class FormField(EmbeddedDocument): # pylint: disable=abstract-method
"""
A field in a form to fill out.
Taken from fenetre/db.py.
"""
# This should be a substring of the nearest label text to the control we're filling in.
# Optional _not automatically set_
expected_label_segment = fields.StrField(required=False, default=None)
# Index on page (includes headings)
index_on_page = fields.IntField(required=True,
validate=validate.Range(min=0))
# Value to fill in.
# The grammar for this field is in fieldexpr.py in lockbox.
target_value = fields.StrField(required=True)
# Type of field
kind = fields.StrField(required=True,
validate=validate.OneOf(
[x.value for x in FormFieldType]))
# Is this field critical? as in; if we don't fill it in do we still submit the form?
critical = fields.BoolField(default=True)
class Rate(Document):
from_user = fields.ReferenceField('User', required=True)
to_user = fields.ReferenceField('User', required=True)
rate = fields.IntField(required=True,
validate=validate.Range(min=1, max=5))
description = fields.StrField()
date = fields.DateTimeField()
class ClinicalSample(Document):
clinicalSampleCode = fields.StringField(required=True)
sampleCounter = fields.IntegerField(required=True)
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=True)
workflowTag = fields.StrField(required=False)
quality = fields.StrField(required=False)
description = fields.StrField()
processingPerson = fields.StrField()
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "clinicalSample"
class User(Document):
username = fields.StrField(required=True, unique=True)
email = fields.EmailField(required=True, unique=True)
firstname = fields.StrField()
lastname = fields.StrField()
# birthday = fields.DateTimeField()
birthday = fields.DateTimeField(validate=validate.Range(min=datetime.datetime(1900, 1, 1)))
password = fields.StrField(required=True) # Don't store it in clear in real life !
date_created = fields.DateTimeField(default=datetime.datetime.now())
date_modified = fields.DateTimeField(default=datetime.datetime.now())
# authored_docs = fields.ListField(fields.ReferenceField("Paper"))
def update(self, *args, **kwargs):
if not self.date_created:
self.date_created = datetime.datetime.now()
self.date_modified = datetime.datetime.now()
return super(User, self).update(*args, **kwargs)
class Meta:
# collection = db.users
collection_name = 'users'
def get_thread_karma(self):
"""
fetch the number of votes this user has had on his/her threads
1.) Get id's of all threads by this user
2.) See how many of those threads also were upvoted but not by
the person him/her self.
"""
# thread_ids = [t.id for t in self.threads]
# select = thread_upvotes.select(db.and_(
# thread_upvotes.c.thread_id.in_(thread_ids),
# thread_upvotes.c.user_id != self.id
# )
# )
# rs = db.engine.execute(select)
# return rs.rowcount
# TODO
return Thread.find({"user_id":self.id}).count()
def get_comment_karma(self):
"""
fetch the number of votes this user has had on his/her comments
"""
# TODO
return Comment.find({'user_id': self.id}).count()
def threads(self):
app.logger.debug(Thread.find({"user_id":self.id})[:])
return list(Thread.find({"user_id":self.id}))
def comments(self):
app.logger.debug(list(Comment.find({"user_id":self.id})))
return list(Comment.find({"user_id":self.id}))
class IntermediateSample(Document):
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=True)
clinicalSamples = fields.ListField(fields.ObjectIdField, required=False)
parentSamples = fields.ListField(fields.ObjectIdField, required=False)
protocolName = fields.StrField(required=True)
workflowTag = fields.StrField(required=False)
sopFileName = fields.StrField(required=False)
description = fields.StrField()
processingPerson = fields.StrField()
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "intermediateSample"
class User(Document):
email = fields.EmailField(required=True, unique=True)
birthday = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
friends = fields.ListField(fields.ReferenceField("User"))
class Meta:
collection = db.user
class Artefact(Document):
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=False)
# SOP
sopFileName = fields.StrField(required=False)
encodedFileId = fields.ObjectIdField(required=False)
artefactClass = fields.StrField(required=False)
description = fields.StrField(required=False)
owner = fields.StrField(required=False)
revision = fields.StrField(required=False)
processingPerson = fields.StrField()
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "Artefacts"
class InviteGroup(Document):
code = fields.StrField(unique=True,
required=True,
validate=validate.Length(equal=INVITE_CODE_LENGTH))
limit = fields.IntField(required=True, validate=validate.Range(min=1))
available_uses = fields.IntField(required=True,
validate=validate.Range(min=0))
# expiration_date = fields.DateTimeField()
async def create_new_code(self, limit, code=None):
from models.utils import create_new_invite_code
self.code = code if code is not None else await create_new_invite_code(
)
self.limit = limit
self.available_uses = limit
await self.commit()
return self
class MyDoc(Document):
dk = fields.IntField(marshmallow_data_key='dkdk')
at = fields.IntField(marshmallow_attribute='atat')
re = fields.IntField(marshmallow_required=True)
an = fields.IntField(marshmallow_allow_none=True)
lo = fields.IntField(marshmallow_load_only=True)
do = fields.IntField(marshmallow_dump_only=True)
va = fields.IntField(marshmallow_validate=validate.Range(min=0))
em = fields.IntField(
marshmallow_error_messages={'invalid': 'Wrong'})
class MSReadySample(Document):
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=True)
clinicalSamples = fields.ListField(fields.ObjectIdField, required=False)
intermediateSampleId = fields.ObjectIdField(required=True)
msReadySampleName = fields.StrField(required=False)
workflowTag = fields.StrField(required=False)
quality = fields.StrField(required=False)
peptideNo = fields.FloatField(required=False)
description = fields.StrField(required=False)
concentration = fields.StrField(required=False)
processingPerson = fields.StrField(required=False)
currentLocation = fields.StrField(required=False)
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "msReadySample"
class SWATHAnalysis(Document):
swathId = fields.IntegerField(required=False)
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=True)
clinicalSamples = fields.ListField(fields.ObjectIdField, required=False)
msRunIds = fields.ListField(fields.ObjectIdField, required=False)
protocolId = fields.StrField(required=True)
protocolName = fields.StrField(required=False)
sopFileName = fields.StrField(required=False)
proteinMatrixFileName = fields.StrField(required=False)
description = fields.StrField(required=False)
workflowTag = fields.StrField(required=False)
spectralLibraryId = fields.ObjectIdField(required=True)
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "SWATHAnalysis"
class SpectralLibrary(Document):
libId = fields.IntegerField(required=False)
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=True)
clinicalSamples = fields.ListField(fields.ObjectIdField, required=False)
msRunIds = fields.ListField(fields.ObjectIdField, required=False)
protocolId = fields.StrField(required=True)
protocolName = fields.StrField(required=False)
sopFileName = fields.StrField(required=False)
specLibFilename = fields.StrField(required=False)
description = fields.StrField(required=False)
proteinDatabaseOrganism = fields.StrField(required=True)
proteinDatabaseVersion = fields.StrField(required=True)
workflowTag = fields.StrField(required=False)
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "SpectralLibrary"
class MSRun(Document):
runId = fields.IntegerField(required=False)
name = fields.StrField(required=True)
projectId = fields.ObjectIdField(required=True)
clinicalSamples = fields.ListField(fields.ObjectIdField, required=False)
msReadySampleId = fields.ObjectIdField(required=True)
msReadySampleName = fields.StrField(required=False)
protocolId = fields.StrField(required=True)
protocolName = fields.StrField(required=False)
sopFileName = fields.StrField(required=False)
description = fields.StrField(required=False)
instrumentId = fields.StrField(required=True)
instrumentMethod = fields.StrField(required=False)
runCode = fields.StrField(required=False)
status = fields.StrField(required=False)
processingPerson = fields.StrField(required=False)
workflowTag = fields.StrField(required=False)
createdDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
updatedDate = fields.DateTimeField(
validate=validate.Range(min=datetime(1900, 1, 1)))
class Meta:
collection_name = "MSRun"
class MySchema(BaseSchema):
with_max = fields.IntField(validate=validate.Range(max=99))
class TaskQueue(Document):
'''
Per endpoint per priority queue
'''
schema_version = StringField(validate=validate.Length(max=10), default='1')
priority = IntField(validate=validate.Range(min=QUEUE_PRIORITY_MIN,
max=QUEUE_PRIORITY_MAX),
default=QUEUE_PRIORITY_DEFAULT)
tasks = ListField(ReferenceField('Task'), default=[])
endpoint = ReferenceField('Endpoint')
running_task = ReferenceField('Task', allow_none=True, default=missing)
rw_lock = BooleanField(default=False)
organization = ReferenceField('Organization')
team = ReferenceField('Team')
to_delete = BooleanField(default=False)
class Meta:
collection_name = 'task_queues'
async def acquire_lock(self):
for i in range(LOCK_TIMEOUT):
if await self.collection.find_one_and_update(
{
'_id': self.pk,
'rw_lock': False
}, {'$set': {
'rw_lock': True
}}):
return True
await asyncio.sleep(0.1)
else:
return False
async def release_lock(self):
await self.collection.find_one_and_update({'_id': self.pk},
{'$set': {
'rw_lock': False
}})
async def pop(self):
if not await self.acquire_lock():
return None
await self.reload()
if len(self.tasks) == 0:
await self.release_lock()
return None
task = self.tasks.pop(0)
task = await task.fetch()
self.running_task = task
await self.commit()
await self.release_lock()
return task
async def push(self, task):
if not await self.acquire_lock():
raise RuntimeError('failed to acquire queue lock')
self.tasks.append(task)
await self.commit()
await self.release_lock()
async def flush(self, cancelled=False):
if not await self.acquire_lock():
raise RuntimeError('failed to acquire queue lock')
if cancelled:
for task in self.tasks:
task.status = 'cancelled'
await task.commit()
self.tasks = []
await self.commit()
await self.release_lock()
return True
class Industry(EmbeddedDocument):
industry = fields.ReferenceField('Tag', required=True)
experience = fields.IntField(required=True,
validate=validate.Range(min=0, max=100))
class Punishment(umongo.EmbeddedDocument):
type = fields.IntegerField(required=True, allow_none=True)
mute_for = fields.IntegerField()
captcha_type = fields.IntegerField(validate=validate.Range(0, 2))
class MySchema(EmbeddedSchema):
with_max = fields.IntField(validate=validate.Range(max=99))
class Game(BaseDocument):
"""
This is how we are going to store the game
"""
STATUS_CREATED = 'created'
STATUS_IN_PROGRESS = 'in_progress'
STATUS_TIE = 'tie'
STATUS_FINISHED = 'finished'
STATUS = [
STATUS_CREATED,
STATUS_IN_PROGRESS,
STATUS_TIE,
STATUS_FINISHED,
]
players = fields.ListField(
fields.ReferenceField("User"),
)
multiplayer = fields.BoolField(
default=False,
)
board = fields.ListField(
fields.ListField(
fields.StrField()
)
)
status = fields.StrField(
validate=validate.OneOf(STATUS),
default=STATUS_CREATED
)
created_at = fields.DateTimeField(
default=datetime.datetime.now(),
)
winner = fields.ReferenceField("User")
size = fields.IntegerField(
validate=[validate.Range(3, 10)],
default=3,
)
def pre_insert(self):
"""
Fill the board and do multiplayer validations
"""
if not self.players:
raise ValidationError(
"There should be at least one player",
)
if len(self.players) > 2:
raise ValidationError(
"Maximum two players"
)
if len(self.players) == 2:
self.multiplayer = True
else:
self.multiplayer = False
self.board = [["" for i in range(self.size)] for y in range(self.size)]
pass
class Meta:
"""
ODM Metadata
"""
collection = db.games
class MySchema(EmbeddedSchema):
a = fields.IntField()
b = fields.IntField(attribute='in_mongo_b')
c = fields.IntField(allow_none=True,
validate=validate.Range(min=1, max=5))
class UserTempl(Document):
email = fields.EmailField(required=True, unique=True)
birthday = fields.DateTimeField(validate=validate.Range(
min=datetime(1900, 1, 1)))
friend = fields.ReferenceField("UserTempl")
