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Commit e1ce3f1b authored by Jochem Bijlard's avatar Jochem Bijlard
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DRY transmart ETL based on stringified constraint descriptor

parent 111b4401
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fractalis/data/etl.py
View file @ e1ce3f1b
......@@ -34,7 +34,7 @@ class ETL(Task, metaclass=abc.ABCMeta):
@abc.abstractmethod
def produces(self) -> str:
"""This specifies the fractalis internal format that this ETL
produces. Can be one of: ['categorical', 'numerical']
produces. Can be one of: ['categorical', 'numerical', 'numerical_array']
"""
pass
......
fractalis/data/etls/transmart/etl_categorical.py
View file @ e1ce3f1b
"""Provides categorical concept ETL for tranSMART."""
import logging
from fractalis.data.etls.transmart.shared import create_etl_type, CATEGORICAL_FIELD
from pandas import DataFrame
from fractalis.data.etl import ETL
from fractalis.data.etls.transmart.shared import extract_data
logger = logging.getLogger(__name__)
class CategoricalETL(ETL):
"""CategoricalETL implements support for tranSMARTs 'categorical' type."""
name = 'transmart_categorical_etl'
produces = 'categorical'
@staticmethod
def can_handle(handler: str, descriptor: dict) -> bool:
return handler == 'transmart' and \
descriptor['data_type'] == 'categorical'
def extract(self, server: str, token: str, descriptor: dict) -> dict:
return extract_data(server=server, descriptor=descriptor, token=token)
def transform(self, raw_data: dict, descriptor: dict) -> DataFrame:
rows = []
for entry in raw_data['cells']:
idx = entry['dimensionIndexes'][2]
id = raw_data['dimensionElements']['patient'][idx]['inTrialId']
value = entry['numericValue']
rows.append([id, value])
df = DataFrame(rows, columns=['id', 'value'])
return df
CategoricalETL = create_etl_type(
name_='transmart_categorical_etl',
produces_='categorical',
field_name=CATEGORICAL_FIELD
)
fractalis/data/etls/transmart/etl_highdim.py
View file @ e1ce3f1b
"""Provides highdim concept ETL for tranSMART."""
import logging
from fractalis.data.etls.transmart.shared import create_etl_type, NUMERICAL_FIELD
import requests
from pandas import DataFrame
from fractalis.data.etl import ETL
logger = logging.getLogger(__name__)
class HighdimETL(ETL):
"""HighdimETL implements support for tranSMARTs 'highdim' type."""
name = 'transmart_highdim_etl'
produces = 'highdim'
@staticmethod
def can_handle(handler: str, descriptor: dict) -> bool:
return handler == 'transmart' and descriptor['data_type'] == 'highdim'
def extract(self, server: str, token: str, descriptor: dict) -> dict:
r = requests.get(url='{}/v2/observations'.format(server),
params={
'constraint': '{{"type": "concept","path": "{}"}}'
''.format(descriptor["path"]),
'projection': 'log_intensity',
'type': 'autodetect'
},
headers={
'Accept': 'application/x-protobuf',
'Authorization': 'Bearer {}'.format(token)
},
timeout=2000)
if r.status_code != 200:
error = "Target server responded with " \
"status code {}.".format(r.status_code)
logger.error(error)
raise ValueError(error)
try:
pass # TODO
except Exception as e:
logger.exception(e)
raise ValueError("Got unexpected data format.")
def transform(self, raw_data: dict, descriptor: dict) -> DataFrame:
rows = []
for entry in raw_data['cells']:
idx = entry['dimensionIndexes'][2]
id = raw_data['dimensionElements']['patient'][idx]['inTrialId']
value = entry['numericValue']
rows.append([id, value])
df = DataFrame(rows, columns=['id', 'value'])
return df
HighdimETL = create_etl_type(
name_='transmart_highdim_etl',
produces_='numerical_array',
field_name=NUMERICAL_FIELD
)
fractalis/data/etls/transmart/etl_numerical.py
View file @ e1ce3f1b
"""Provides numerical concept ETL for tranSMART."""
import logging
from fractalis.data.etls.transmart.shared import create_etl_type, NUMERICAL_FIELD
from pandas import DataFrame
from fractalis.data.etl import ETL
from fractalis.data.etls.transmart.shared import extract_data
logger = logging.getLogger(__name__)
class NumericalETL(ETL):
"""NumericalETL implements support for tranSMARTs 'numerical' type."""
name = 'transmart_numerical_etl'
produces = 'numerical'
@staticmethod
def can_handle(handler: str, descriptor: dict) -> bool:
return (handler == 'transmart' and
descriptor['data_type'] == 'numerical')
def extract(self, server: str, token: str, descriptor: dict) -> dict:
return extract_data(server=server, descriptor=descriptor, token=token)
def transform(self, raw_data: dict, descriptor: dict) -> DataFrame:
rows = []
for entry in raw_data['cells']:
idx = entry['dimensionIndexes'][2]
id = raw_data['dimensionElements']['patient'][idx]['inTrialId']
value = entry['numericValue']
rows.append([id, value])
df = DataFrame(rows, columns=['id', 'value'])
return df
NumericalETL = create_etl_type(
name_='transmart_numerical_etl',
produces_='numerical',
field_name=NUMERICAL_FIELD
)
fractalis/data/etls/transmart/handler_transmart.py
View file @ e1ce3f1b
......@@ -26,7 +26,7 @@ class TransmartHandler(ETLHandler):
@staticmethod
def make_label(descriptor: dict) -> str:
return descriptor['path']
return descriptor['label']
def _get_token_for_credentials(self, server: str, auth: dict) -> str:
try:
......
fractalis/data/etls/transmart/shared.py
View file @ e1ce3f1b
"""This module provides shared functionality to the transmart ETLs."""
import logging
import pandas as pd
from urllib.parse import unquote_plus
import requests
from fractalis.data.etl import ETL
logger = logging.getLogger(__name__)
NUMERICAL_FIELD = 'numericValue'
CATEGORICAL_FIELD = 'stringValue'
def extract_data(server: str, descriptor: dict, token: str) -> dict:
"""Extract data from transmart.
......@@ -14,24 +20,115 @@ def extract_data(server: str, descriptor: dict, token: str) -> dict:
:param descriptor: Dict describing the data to download.
:param token: The token used for authentication.
"""
params = dict(
constraint=descriptor['constraint'],
type='clinical'
)
if descriptor['data_type'] == 'numerical_array':
params['type'] = 'autodetect'
params['projection'] = 'log_intensity'
if 'biomarker_constraint' in descriptor:
params['biomarker_constraint'] = descriptor['biomarker_constraint']
r = requests.get(url='{}/v2/observations'.format(server),
params={
'constraint': '{{"type": "concept","path": "{}"}}'
''.format(descriptor["path"]),
'type': 'autodetect'
},
params=params,
headers={
'Accept': 'application/json',
'Authorization': 'Bearer {}'.format(token)
},
timeout=2000)
logger.info('URL called: {}'.format(
unquote_plus(r.url))
)
if r.status_code != 200:
error = "Target server responded with " \
"status code {}.".format(r.status_code)
error = "Target server responded with status code {}. Message: {}.".\
format(r.status_code, r.json())
logger.error(error)
raise ValueError(error)
try:
return r.json()
except Exception as e:
logger.exception(e)
raise ValueError("Got unexpected data format.")
def get_dimension_index(obs, dimension):
return list(obs['dimensionElements'].keys()).index(dimension)
def get_dimension_element(obs, dimension, index):
return obs['dimensionElements'][dimension][index]
def transform_clinical(raw_data: dict, value_field: str) -> pd.DataFrame:
patient_idx = get_dimension_index(raw_data, 'patient')
rows = []
for entry in raw_data['cells']:
patient_element = entry['dimensionIndexes'][patient_idx]
patient = get_dimension_element(raw_data, 'patient', patient_element)
rows.append([
patient['inTrialId'],
entry[value_field]
])
df = pd.DataFrame(rows, columns=['id', 'value'])
feature = df.columns[1]
df.insert(1, 'feature', feature)
return df
def transform_highdim(raw_data: dict):
sample_idx = get_dimension_index(raw_data, 'assay')
feature_idx = get_dimension_index(raw_data, 'biomarker')
rows = []
for entry in raw_data['cells']:
sample_element = entry['dimensionIndexes'][sample_idx]
sample = get_dimension_element(raw_data, 'assay', sample_element)
feature_element = entry['dimensionIndexes'][feature_idx]
feature = get_dimension_element(raw_data, 'biomarker', feature_element)
rows.append([
sample['sampleCode'],
entry[NUMERICAL_FIELD],
feature['label']
])
df = pd.DataFrame(rows, columns=['id', 'value', 'feature'])
return df
def create_etl_type(name_, produces_, field_name):
"""
Create a ETL task class based on a specific input type.
:param name_: task name for registry.
:param produces_: output type.
:param field_name: name of cell in observation (numericValue, stringValue)
:return: ETL task class
"""
class TransmartETL(ETL):
name = name_
produces = produces_
@staticmethod
def can_handle(handler: str, descriptor: dict) -> bool:
return handler == 'transmart' and descriptor['data_type'] == produces_
def extract(self, server: str, token: str, descriptor: dict) -> dict:
return extract_data(server=server, descriptor=descriptor, token=token)
def transform(self, raw_data: dict, descriptor: dict) -> pd.DataFrame:
if self.produces in ('numerical', 'categorical'):
return transform_clinical(raw_data, field_name)
if self.produces == 'numerical_array':
return transform_highdim(raw_data)
return TransmartETL
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