From 7e68e768ba2a31131139d32042daf952223ec1c2 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Fri, 7 May 2021 11:27:45 +0200
Subject: [PATCH] Convert root organisms.yml to list instead of dict
---
speciesData.py | 2 +-
templates/organisms.yml.j2 | 2 +-
utilities.py | 8 +++-----
3 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/speciesData.py b/speciesData.py
index 3684522..2d0ce21 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -23,7 +23,7 @@ class SpeciesData:
return string
def __init__(self, parameters_dictionary):
- # self.config_dictionary = None
+ self.name = parameters_dictionary["name"]
self.parameters_dictionary = parameters_dictionary
parameters_dictionary_description=parameters_dictionary["description"]
self.species = self.clean_string(parameters_dictionary_description["species"])
diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2
index 83ab58f..e196a2d 100644
--- a/templates/organisms.yml.j2
+++ b/templates/organisms.yml.j2
@@ -1,4 +1,4 @@
-{{ name }}:
+- name: {{ name }}
description:
genus: {{ genus }}
species: {{ species }}
diff --git a/utilities.py b/utilities.py
index 2bb532d..30387d5 100755
--- a/utilities.py
+++ b/utilities.py
@@ -44,14 +44,12 @@ def parse_input(input_file):
:return:
"""
- parsed_sp_dict_list = []
+ sp_dict_list = []
try:
with open(input_file, 'r') as stream:
try:
- yaml_dict = yaml.safe_load(stream)
- for k, v in yaml_dict.items():
- parsed_sp_dict_list.append(v)
+ sp_dict_list = yaml.safe_load(stream)
except yaml.YAMLError as err:
logging.critical("Input file is not in YAML format")
sys.exit(err)
@@ -62,7 +60,7 @@ def parse_input(input_file):
logging.critical("The specified input file cannot be read (%s)" % input_file)
sys.exit()
- return parsed_sp_dict_list
+ return sp_dict_list
def filter_empty_not_empty_items(li):
--
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