first take on parsing available phenotypes from the input file

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():