From a956de603b54d8551afb9fe7558a82df957f340f Mon Sep 17 00:00:00 2001
From: perezgonzalez-irene <iregon@noc.ac.uk>
Date: Fri, 21 Feb 2020 14:16:05 +0000
Subject: [PATCH] Comments edited
---
read.py | 39 +++++++++++++++++++++++----------------
1 file changed, 23 insertions(+), 16 deletions(-)
diff --git a/read.py b/read.py
index cc4b4d9..f5938a1 100644
--- a/read.py
+++ b/read.py
@@ -42,16 +42,18 @@ def ERV(TextParser,read_sections_list, schema, code_tables_path):
valid_buffer = StringIO()
for i_chunk, string_df in enumerate(TextParser):
- # a. Get a DF with sections separated in columns:
- # - one section per column
+
+ # 1. Get a DF with 1 column per sections:
# - only sections requested, ignore rest
# - requested NA sections as NaN columns
- # - columns order as in read_sections_list
+ # - columns(sections) order as in read_sections_list
+
sections_df = get_sections.get_sections(string_df, schema, read_sections_list)
- # b. Read elements from sections: along data chunks, resulting data types
- # may vary if gaps, keep track of data types!
- # Sections as parsed in the same order as sections_df.columns
+ # 2. Read elements from sections: along data chunks, resulting data types
+ # may vary if gaps, keep track of data types: add Intxx pandas classes rather than intxx to avoid this!
+ # Sections are parsed in the same order as sections_df.columns
+
[data_df, valid_df, out_dtypesi ] = read_sections.read_sections(sections_df, schema)
if i_chunk == 0:
out_dtypes = copy.deepcopy(out_dtypesi)
@@ -59,13 +61,17 @@ def ERV(TextParser,read_sections_list, schema, code_tables_path):
for k in out_dtypesi:
if out_dtypesi in properties.numpy_floats:
out_dtypes.update({ k:out_dtypesi.get(k) })
-
+
+ # 3. Validate data elements
+
valid_df = validate.validate(data_df, valid_df, schema, code_tables_path)
- # Save to buffer
+
+ # 4. Save to buffer
data_df.to_csv(data_buffer,header = False, mode = 'a', encoding = 'utf-8',index = False)
valid_df.to_csv(valid_buffer,header = False, mode = 'a', encoding = 'utf-8',index = False)
+
# Create the output
- # WE'LL NEED TO POSPROCESS THIS WHEN READING MULTIPLE REPORTS PER LINE
+ # WE'LL NEED TO POSPROCESS THIS WHEN READING MULTIPLE REPORTS PER LINE, IF EVER...
data_buffer.seek(0)
valid_buffer.seek(0)
logging.info("Wrapping output....")
@@ -73,6 +79,7 @@ def ERV(TextParser,read_sections_list, schema, code_tables_path):
# (source is either pd.io.parsers.TextFileReader or a file with chunksize specified on input):
# This way it supports direct chunksize property inheritance if the input source was a pd.io.parsers.TextFileReader
chunksize = TextParser.orig_options['chunksize'] if isinstance(TextParser,pd.io.parsers.TextFileReader) else None
+
# 'datetime' is not a valid pandas dtype: Only on output (on reading) will be then converted (via parse_dates) to datetime64[ns] type,
# cannot specify 'datetime' (of any kind) here: would fail, need to change to 'object' and tell the date parser where it is
date_columns = [] # Needs to be the numeric index of the column, as seems not to be able to work with tupples....
@@ -109,7 +116,7 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
logging.basicConfig(format='%(levelname)s\t[%(asctime)s](%(filename)s)\t%(message)s',
level=logging.INFO,datefmt='%Y%m%d %H:%M:%S',filename=None)
- # 0. Validate input
+ # 0. VALIDATE INPUT
if not data_model and not data_model_path:
logging.error('A valid data model name or path to data model must be provided')
return
@@ -127,7 +134,7 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
if not validate_path('out_path',out_path):
return
- # 1. Read data model
+ # 1. GET DATA MODEL
# 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
@@ -142,7 +149,7 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
code_tables_path = os.path.join(model_path,'code_tables')
- # 2. Read and validate data
+ # 2. READ AND VALIDATE DATA
imodel = data_model if data_model else data_model_path
logging.info("EXTRACTING DATA FROM MODEL: {}".format(imodel))
@@ -163,12 +170,12 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
logging.info("Extracting and reading sections")
data,valid = ERV(TextParser,read_sections_list, schema, code_tables_path)
- # 3. Create out data attributes
+ # 3. CREATE OUTPUT DATA ATTRIBUTES
logging.info("CREATING OUTPUT DATA ATTRIBUTES FROM DATA MODEL")
data_columns = [ x for x in data ] if isinstance(data,pd.DataFrame) else data.orig_options['names']
out_atts = schemas.df_schema(data_columns, schema)
- # 4. Output to files if requested
+ # 4. OUTPUT TO FILES IF REQUESTED
if out_path:
enlisted = False
if not isinstance(data,pd.io.parsers.TextFileReader):
@@ -190,7 +197,7 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
header = cols
out_atts_json = out_atts
data_df.to_csv(os.path.join(out_path,'data.csv'), header = header, mode = mode, encoding = 'utf-8',index = True, index_label='index')
- valid_df.to_csv(os.path.join(out_path,'valid_mask.csv'), header = header, mode = mode, encoding = 'utf-8',index = True, index_label='index')
+ valid_df.to_csv(os.path.join(out_path,'mask.csv'), header = header, mode = mode, encoding = 'utf-8',index = True, index_label='index')
if enlisted:
data = data[0]
valid = valid[0]
@@ -200,7 +207,7 @@ def read(source, data_model = None, data_model_path = None, sections = None,chun
with open(os.path.join(out_path,'atts.json'),'w') as fileObj:
json.dump(out_atts_json,fileObj,indent=4)
- # 5. Return data
+ # 5. RETURN DATA
class output():
def __init__(self):
self.data = data
--
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