From 6f485e2f344a944cd9317896a9da976089384cc7 Mon Sep 17 00:00:00 2001
From: perezgonzalez-irene <iregon@noc.ac.uk>
Date: Wed, 12 Feb 2020 08:31:39 +0000
Subject: [PATCH] Added path validation
---
read.py | 26 ++++++++++++++++++--------
1 file changed, 18 insertions(+), 8 deletions(-)
diff --git a/read.py b/read.py
index d67a546..de13d03 100644
--- a/read.py
+++ b/read.py
@@ -9,8 +9,10 @@ a named model (included in the module) or as the path to a valid data model.
Data is validated against its data model after reading, producing a boolean mask.
-Calls the schemas, reader and valiate modules in the tool to access the data models,
-read the data and validate it.
+Uses submodules:
+- schemas
+- reader
+- valiate
@author: iregon
"""
@@ -83,13 +85,19 @@ def ERV(TextParser,read_sections_list, schema, code_tables_path):
return data, valid
def validate_arg(arg_name,arg_value,arg_type):
-
if arg_value and not isinstance(arg_value,arg_type):
logging.error('Argument {0} must be {1}, input type is {2}'.format(arg_name,arg_type,type(arg_value)))
return False
else:
return True
+def validate_path(arg_name,arg_value):
+ if arg_value and not os.path.isdir(arg_value):
+ logging.error('{0} could not find path {1}'.format(arg_name,arg_value))
+ return False
+ else:
+ return True
+
def read(source, data_model = None, data_model_path = None, sections = None,chunksize = None,
skiprows = None, out_path = None ):
@@ -114,9 +122,15 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
return
if not validate_arg('skiprows',skiprows,int):
return
+ if not validate_path('data_model_path',data_model_path):
+ return
+ if not validate_path('out_path',out_path):
+ return
# 1. Read data model
- # Schema reader will return None if schema does not validate
+ # Schema reader will return empty if cannot read schema or is not valid
+ # and will log the corresponding error
+ # multiple_reports_per_line error also while reading schema
logging.info("READING DATA MODEL SCHEMA FILE...")
schema = schemas.read_schema( schema_name = data_model, ext_schema_path = data_model_path)
if not schema:
@@ -127,10 +141,6 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
model_path = data_model_path
code_tables_path = os.path.join(model_path,'code_tables')
- # For future use: some work already done in schema reading
- if schema['header'].get('multiple_reports_per_line'):
- logging.error('File format not yet supported')
- sys.exit(1)
# 2. Read and validate data
imodel = data_model if data_model else data_model_path
--
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