From c8808e3877f6bb03fc6bfd5d1ce8dcab6f34e342 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr> Date: Wed, 29 Mar 2017 22:47:39 +0200 Subject: [PATCH] first take on parsing available phenotypes from the input file --- .../controllers/default_controller.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/python-flask-server/swagger_server/controllers/default_controller.py b/python-flask-server/swagger_server/controllers/default_controller.py index 974f2c98..a11eb860 100644 --- a/python-flask-server/swagger_server/controllers/default_controller.py +++ b/python-flask-server/swagger_server/controllers/default_controller.py @@ -3,8 +3,16 @@ from swagger_server.models.phenotype import Phenotype from datetime import date, datetime from typing import List, Dict from six import iteritems +import pandas + from ..util import deserialize_date, deserialize_datetime +INIT_FILE_PATH = '/home/hmenager/jass/data/initTable.hdf5' #FIXME part of the config +PHENOLIST_DF = pandas.read_hdf(INIT_FILE_PATH,'PhenoList') +PHENOTYPES = [] +for index, row in PHENOLIST_DF.iterrows(): + phenotype = Phenotype(id=row['ID'], cohort=row['Cohort'], phenotype=row['Phenotype'], ref=row['Reference']) + PHENOTYPES.append(phenotype) def phenotypes_get(): """ @@ -13,10 +21,7 @@ def phenotypes_get(): :rtype: List[Phenotype] """ - phenotypes = [] - phenotypes.append(Phenotype(id="z_GIANT_BMI", cohort="GIANT", phenotype="BMI", ref="10.1038/ng.686")) - phenotypes.append(Phenotype(id="z_GIANT_HEIGHT", cohort="GIANT", phenotype="BMI", ref="10.1038/ng.3097")) - return phenotypes + return PHENOTYPES def projects_get(): -- GitLab