First commit

.gitignore

+/**/.DS_Store
+/**/*.py[cod]
+/**/__pycache__
+Tool_validation.py

README.md

+A. Get code from GitHub
+
+Download zip from https://github.com/perezgonzalez-irene/mdf_reader.git
+
+Clone repo: git clone https://github.com/perezgonzalez-irene/mdf_reader.git
+
+B. Create \____init____.py in code parent directory so python treats it as containing a package
+  touch \____init____.py
+
+C. Create python3 virtual environment in code directory
+
+(1) cd mdf_reader
+
+(2) Create environment
+
+    local:
+	     python3 -m virtualenv --system-site-packages myenv
+
+    jasmin: (python3 still not default/operative, but following works)
+
+      1. Set path and activate conda environment
+      export PATH=/apps/contrib/jaspy/miniconda_envs/jaspy3.7/m3-4.5.11/bin:$PATH
+      source activate jaspy3.7-m3-4.5.11-r20181219
+
+      2. Create your own virtualenv - you only do this once!
+      virtualenv --system-site-packages myenv
+
+(3) Activate environment:
+
+    source ./myenv/bin/activate
+
+(4) Install specific package versions:
+
+    pip install -r requirements.txt
+
+To deactivate environment:
+
+	deactivate
+
+
+D. Add module parent directory to python path (PYTHONPATH env variable)
+  - from terminal:
+  export PYTHONPATH=$toolParentDirectory:${PYTHONPATH}
+  - In python:
+  import sys
+  sys.path.append(toolParentDirectory)
+
+E. Run a test:
+
+import mdf_reader
+
+import matplotlib.pyplot as plt
+
+data = mdf_reader.tests.imma1_buoys_nosupp()
+
+data = mdf_reader.tests.imma1_buoys_supp()
+
+data = td11_deck187_nosupp()
+
+ax = data[section_name][field_name].plot(label='x')
+
+data[section_name][field_name].plot(ax = ax ,label='y')
+
+....
+
+plt.show()

__init__.py

+ # Following to access the subpackages main modules (or/and functions) directly wihout loops through the full subpackage path
+from .schemas import schemas as schemas
+from .schemas import code_tables as code_tables
+from .tests import tests as tests
+from .read import read as read

common/converters.py

+from __future__ import division
+from __future__ import print_function
+from __future__ import absolute_import
+
+from mdf_reader import properties
+import numpy as np
+import pandas as pd
+
+# 1. dtype must be defined in dtype_properties.data_types
+#>>> if not np.dtype('int8'):
+#...     print('No data type')
+#...
+#>>> if not np.dtype('int786'):
+#...     print('No data type')
+#...
+#Traceback (most recent call last):
+#  File "<stdin>", line 1, in <module>
+#TypeError: data type "int786" not understood
+#
+#   Watch this, for my objects I want to catch both empty and blank strings as missing
+#   empty_string = ''
+#   blank_string = '     '
+#   len(empty_string) == 0
+#   len(blank_string) != 0
+#   len(empty_string) == len(blank_string.lstrip()) == 0
+#   So, we'll eval: len(value.lstrip())
+#
+# return data.astype(self.dtype, casting = 'safe')
+# safe casting specifies, otherwise converts np.nan to some real number depending on dtype.
+
+    
+
+class df_converters():
+    def __init__(self, dtype):
+        self.dtype = dtype
+        self.numeric_scale = 1. if self.dtype in properties.numpy_floats else 1
+        self.numeric_offset = 0. if self.dtype in properties.numpy_floats else 0
+    def object_to_numeric(self, data, scale = None, offset = None):
+        scale = scale if scale else self.numeric_scale
+        offset = offset if offset else self.numeric_offset
+        #  Convert to numeric, then scale (?!) and give it's actual int type
+        data = pd.to_numeric(data,errors = 'coerce') # astype fails on strings, to_numeric manages errors....!
+        data = offset + data * scale
+        try:
+            return data.astype(self.dtype, casting = 'safe')
+        except:
+            return data
+
+    def object_to_object(self,data,missing_value = None,disable_white_strip = False):
+        # With strip() an empty element after stripping, is just an empty element, no NaN...
+        if not disable_white_strip:
+            return data.str.strip()
+        else:
+            if disable_white_strip == 'l':
+                return data.str.rstrip()
+            elif disable_white_strip == 'r':
+                return data.str.lstrip()
+            else:
+                return data
+
+    def object_to_datetime(self,data, datetime_format = "%Y%m%d"):
+        data = pd.to_datetime(data, format = datetime_format, errors = 'coerce')
+        return data
+
+converters = dict()
+for dtype in properties.numeric_types:
+    converters[dtype] = df_converters(dtype).object_to_numeric
+converters['datetime'] = df_converters('datetime').object_to_datetime
+converters['str'] = df_converters('str').object_to_object
+converters['object'] = df_converters('object').object_to_object
+converters['key'] = df_converters('key').object_to_object
\ No newline at end of file

common/decoders.py

+from __future__ import division
+from __future__ import print_function
+from __future__ import absolute_import
+
+import numpy as np
+import pandas as pd
+import string
+import logging
+from mdf_reader import properties
+
+
+#for importer, modname, ispkg in pkgutil.walk_packages(path=package.__path__,prefix=package.__name__+'.',onerror=lambda x: None):
+#    print(modname.split(".")[-1])
+# TO DECODE FROM OBJECT TO INTEGER
+#
+# Decodes input object type pd.series to a specified data type
+#
+# On missing data, the resulting DATA type in numerics will be as integer promotion to accomodate np.nan:
+# Promotion dtype for storing NAs: integer	cast to float64
+# (https://pandas.pydata.org/pandas-docs/version/0.22/gotchas.html#nan-integer-na-values-and-na-type-promotions)
+#
+# return base10.astype(self.dtype, casting = 'safe')
+# safe casting specified, otherwise converts np.nan to some number depending on dtype.
+
+def signed_overpunch_i(x):
+        # Blanks and np.nan as missing data
+        # In TDF-11, mix of overpunch and no overpunch: include integers in dictionary
+        # Define decoding dictionary: should do this smart-like: None where non-existing keys!!!!
+        overpunch_number =  { string.digits[i]:str(i) for i in range(0,10)}
+        overpunch_number.update({ string.ascii_uppercase[i]:str(i+1) for i in range(0,9)})
+        overpunch_number.update({ string.ascii_uppercase[i]:str(i-8) for i in range(9,18)})
+        overpunch_number.update({'{':str(0)})
+        overpunch_number.update({'<':str(0)})
+        overpunch_number.update({'}':str(0)})
+        overpunch_number.update({'!':str(0)})
+        overpunch_factor =  { string.digits[i]:1 for i in range(0,10)}
+        overpunch_factor.update({ string.ascii_uppercase[i]:1 for i in range(0,9)})
+        overpunch_factor.update({ string.ascii_uppercase[i]:-1 for i in range(9,18)})
+        overpunch_factor.update({'}':-1})
+        overpunch_factor.update({'!':-1})
+        overpunch_factor.update({'{':1})
+        overpunch_factor.update({'<':1})
+        try:
+            n = "".join(list(map(lambda x: overpunch_number.get(x,np.nan), list(x) ))) if x==x else np.nan
+            f = np.prod(list(map(lambda x: overpunch_factor.get(x,np.nan), list(x) ))) if x==x else np.nan
+            converted = f*int(n) if f and n and n == n and f == f else np.nan
+            return converted 
+        except Exception as e:
+            print('ERROR decoding element: {}'.format(x))
+            print(e)
+            print('Conversion sequence:')
+            try:
+                print('number base conversion: {}'.format(n))
+            except:
+                pass
+            try:
+                print('factor conversion: {}'.format(f))
+            except:
+                pass            
+            return np.nan
+
+class df_decoders():
+    def __init__(self, dtype):
+        self.dtype = dtype if dtype in properties.numeric_types else 'object'
+    def signed_overpunch(self, data ):
+        decoded_numeric = np.vectorize(signed_overpunch_i,otypes=[float])(data)
+        try:
+            return decoded_numeric.astype(self.dtype, casting = 'safe')
+        except:
+            return decoded_numeric
+    def base36(self, data):
+        # int(str(np.nan),36) ==> 30191
+        # Had to do the following because the astype() below did not seem to convert
+        # to object element-wise, but the full thing. As a result, str methods
+        # in converters from objects originating here were failing: the column
+        # was dtype = 'object', but the elements inside where 'int'....
+        # Checked that manually a seemed to be happening that way....   
+        if self.dtype == 'object' : 
+            base10 = np.array([str(int(str(i), 36)) if i == i and i else np.nan for i in data ])
+        else:
+            base10 = np.array([int(str(i), 36) if i == i and i else np.nan for i in data ])
+            
+        try:
+            return base10.astype(self.dtype, casting = 'safe')
+        except:
+            return base10
+
+
+
+decoders = dict()
+
+decoders['signed_overpunch'] = dict()
+for dtype in properties.numeric_types:
+    decoders['signed_overpunch'][dtype] = df_decoders(dtype).signed_overpunch
+decoders['signed_overpunch']['key'] = df_decoders('key').signed_overpunch
+
+decoders['base36'] = dict()
+for dtype in properties.numeric_types:
+    decoders['base36'][dtype] = df_decoders(dtype).base36
+decoders['base36']['key'] = df_decoders('key').base36
+
+
+## Now add the file format specific decoders
+#import pkgutil
+#import importlib
+#from mdf_reader import fs_decoders
+#package=fs_decoders
+#for importer, modname, ispkg in pkgutil.walk_packages(path=package.__path__,prefix=package.__name__+'.',onerror=lambda x: None):
+#    file_format = modname.split(".")[-1]
+#    try:
+#        file_format_decoders = importlib.import_module(modname, package=None).decoders
+#        for decoder in file_format_decoders.keys():
+#            decoders[".".join([file_format,decoder])] = file_format_decoders.get(decoder)
+#    except Exception as e:
+#        logging.error("Error loading {0} decoders: {1}".format(modname,e))
+#

common/functions.py

+from __future__ import division
+from __future__ import print_function
+from __future__ import absolute_import
+
+import pandas as pd
+
+def df_prepend_datetime(df,date_columns,date_format,date_name = "_datetime"):
+    to_convert = df[date_columns].astype(str).apply("-".join, axis=1)
+    return pd.concat([pd.DataFrame(pd.to_datetime(to_convert, format = "-".join(date_format), errors = 'coerce'),columns = [date_name]),df],sort = False,axis=1)
\ No newline at end of file

common/logging_hdlr.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr  3 08:45:03 2019
+
+@author: iregon
+"""
+
+import logging
+
+def init_logger(module, level = 'INFO', fn=None):
+    # !!! here overriide potential previous config of logging
+    from imp import reload # python 2.x don't need to import reload, use it directly
+    reload(logging)
+    level = logging.getLevelName(level)
+    logging_params = {
+        'level': level,
+        'format': '%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    }
+    if fn is not None:
+        logging_params['filename'] = fn
+    logging.basicConfig(**logging_params)
+    logging.info('init basic configure of logging success')
+    return logging.getLogger(module)
\ No newline at end of file

common/pandas_TextParser_hdlr.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr  2 10:34:56 2019
+
+Assumes we are never writing a header!
+
+@author: iregon
+"""
+
+import pandas as pd
+import mdf_reader.common.logging_hdlr as logging_hdlr
+
+logger = logging_hdlr.init_logger(__name__,level = 'DEBUG')
+
+def restore(TextParser_ref,TextParser_options):
+    try:
+        TextParser_ref.seek(0)
+        TextParser = pd.read_csv( TextParser_ref, names = TextParser_options['names'],chunksize = TextParser_options['chunksize'], dtype = TextParser_options['dtype']) #, skiprows = options['skiprows'])
+        return TextParser
+    except Exception as e:
+        logger.error('Failed to restore TextParser', exc_info=True)
+        return TextParser
+
+def is_not_empty(TextParser):
+    try:
+        TextParser_ref = TextParser.f
+        TextParser_options = TextParser.orig_options
+    except Exception as e:
+        logger.error('Failed to process input. Input type is {}'.format(type(TextParser)), exc_info=True)
+        return
+    try:
+        first_chunk = TextParser.get_chunk()
+        TextParser = restore(TextParser_ref,TextParser_options)
+        if len(first_chunk) > 0:
+            logger.debug('Is not empty')
+            return True, TextParser
+        else:
+            return False, TextParser
+    except Exception:
+         return False, TextParser

common/plots.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Apr 11 13:45:38 2019
+
+Look into validation results
+
+Need to type:
+    
+    %matplotlib auto
+
+if ipython and want to get the interactive plots!
+
+
+@author: iregon
+"""
+import mdf_reader
+import pandas as pd
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+#------------------------------------------------------------------------------
+def plot_numeric_validation(data,mask,element,valid_max,valid_min, units):
+    bbox_props = dict(boxstyle="round", fc="w", ec="0.5", alpha=0.9)
+    plt.figure()
+    ax = data.plot(label = 'data')
+    # Carefull, something may not be working here in the no data tag!!!
+    no_data = True if len(data.loc[data.notna()]) == 0 else False
+    data.where(~mask).plot(marker = 'o',color = 'r',ax=ax,label='not valid')
+    true_value = data.where(mask).median()
+    if not true_value or np.isnan(true_value):
+        if valid_max != None and valid_min != None:
+            true_value = valid_min + (valid_max - valid_min)/2.
+        else:
+            true_value = 1
+    falses = pd.Series(index = data.index, data = true_value)
+    falses.where(~mask & data.isna()).plot(marker = 'o',color = 'r',ax=ax,label='_nolegend_')
+    trues = pd.Series(index = data.index,data = true_value )
+    trues.where(mask).plot(color = 'YellowGreen',ax=ax,label='valid')
+    if valid_max != None and valid_min != None:
+        ax.fill_between(data.index, valid_min,valid_max,
+                            facecolor='DarkSlateGrey', alpha=0.25, interpolate=False, label='valid range',zorder=5)
+    ax.grid(linestyle=':',which='major',color='grey')
+    if units:
+        ax.set_ylabel(units, fontsize=10)
+    ax.set_xlabel('idx')
+    if no_data:
+        ax.text((ax.get_xlim()[1] - ax.get_xlim()[0])/2,ax.get_ylim()[0] + (ax.get_ylim()[1] - ax.get_ylim()[0])/2, "no data", ha="center", va="center", size=20,bbox=bbox_props)
+    plt.legend()
+    plt.title(element + ' validation')
+    plt.show()
+    
+def plot_categorical_validation(data,mask,element,codetable):
+    merged = pd.concat([data,mask],axis = 1)
+    merged.columns = ['data','mask']
+    counts = pd.DataFrame(index =merged['data'].value_counts(dropna = False).sort_index().index )
+    counts['Data'] = merged['data'].value_counts(dropna = False).sort_index()
+    # Watch here, need to convert to str so that NaNs are not removed from the grouping!
+    # Could be dangerous if we are not just counting, but then, we would not need the NaNs...
+    counts.index = counts.index.fillna(str(np.nan))
+    counts['Not valid'] = merged.astype(str).query('mask == "False"').groupby('data').count()
+    counts['Valid'] = merged.astype(str).query('mask == "True"').groupby('data').count()
+    fig = plt.figure() # Create matplotlib figure
+    ax = fig.add_subplot(111) # Create matplotlib axes
+    ax2 = ax.twinx() # Create another axes that shares the same x-axis as ax.
+    width = 0.4
+    counts['Data'].plot(kind='bar', ax=ax, width=width, position=1, color = 'DarkCyan', label = 'data counts')    
+    counts[['Not valid','Valid']].plot(kind='bar', stacked=True, ax=ax2, width=width, position=0,legend = False, color = ['DarkRed','YellowGreen'])
+    ax.set_yscale("log")
+    ax.set_ylabel('data counts', fontsize=10)
+    ax2.set_yscale("log")
+    ax2.set_ylabel('validation counts', fontsize=10)
+    ax.legend(loc = 2)
+    ax2.legend()
+    ax.grid(linestyle=':',which='major',color='grey')
+    plt.title(element + " validation \n Codetable: " + codetable)
+    ax.set_xlim(-1,len(counts))
+    ax.set_xlabel('code')
+    ax2.set_xlim(-1,len(counts))
+    ax.set_ylim(0.5,ax.get_ylim()[1])
+    ax2.set_ylim(0.5,ax2.get_ylim()[1])
+    plt.show()
+#------------------------------------------------------------------------------
+
+def plot_model_validation(imodel):
+    for element in imodel['atts'].keys():
+        title_element = element if not isinstance(element,tuple) else element[1] + " (" + element[0] + ")"
+        dtype = imodel['atts'].get(element).get('column_type')
+        if dtype in mdf_reader.properties.numeric_types: 
+            valid_max = imodel['atts'].get(element).get('valid_max')
+            valid_min = imodel['atts'].get(element).get('valid_min')
+            units = imodel['atts'].get(element).get('units')
+            plot_numeric_validation(imodel['data'][element],imodel['valid_mask'][element],title_element, valid_max, valid_min, units)  
+        elif dtype == 'key':
+            # ...mmm should account for multi-keyed combinations
+            codetable = imodel['atts'].get(element).get('codetable')
+            if not codetable:
+                codetable = 'undefined'
+            plot_categorical_validation(imodel['data'][element],imodel['valid_mask'][element],title_element,codetable)
+
+

docs/.gitignore

+*
+*/
+!.gitignore
+!User_manual.docx

properties.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+
+
+"""
+import glob
+import os
+import io
+import pandas as pd
+
+
+# Supported formats, sources and internal data models -------------------------
+supported_meta_file_formats = ['fixed_width','delimited']
+schema_path = os.path.join(os.path.dirname(__file__),'schemas','lib')
+supported_file_formats = [ os.path.basename(x).split(".")[0] for x in glob.glob(schema_path + '/*/*.json') if os.path.basename(x).split(".")[0] == os.path.dirname(x).split("/")[-1]]
+supported_sources = [pd.DataFrame, pd.io.parsers.TextFileReader, io.StringIO]
+
+# Data types ------------------------------------------------------------------
+numpy_integers = ['int8','int16','int32','int64','uint8','uint16','uint32','uint64']
+numpy_floats = ['float16','float32','float64']
+numeric_types = numpy_integers.copy()
+numeric_types.extend(numpy_floats)
+
+object_types = ['str','object','key','datetime']
+
+data_types = object_types.copy()
+data_types.extend(numpy_integers)
+data_types.extend(numpy_floats)
+
+pandas_dtypes = {}
+for dtype in object_types:
+    pandas_dtypes[dtype] = 'object'
+pandas_dtypes.update({ x:x for x in numeric_types })
+
+# ....and how they are managed
+data_type_conversion_args = {}
+for dtype in numeric_types:
+    data_type_conversion_args[dtype] = ['scale','offset']
+data_type_conversion_args['str'] = ['disable_white_strip']
+data_type_conversion_args['object'] = ['disable_white_strip'] 
+data_type_conversion_args['key'] = ['disable_white_strip']
+data_type_conversion_args['datetime'] = ['datetime_format'] 
+
+# Misc ------------------------------------------------------------------------
+tol = 1E-10
+dummy_level = '_section'
\ No newline at end of file

read.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 30 09:38:17 2019
+
+Reads source data (file, pandas DataFrame or pd.io.parsers.TextFileReader) to 
+a pandas DataFrame. The source data model needs to be input to the module as 
+a named model (included in the module) or as the path to a 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.
+
+@author: iregon
+"""
+import os
+import sys
+import pandas as pd
+from mdf_reader.reader import reader as reader
+from mdf_reader.validate import validate as validate
+import mdf_reader.schemas as schemas
+import mdf_reader.properties as properties
+import mdf_reader.common.pandas_TextParser_hdlr as pandas_TextParser_hdlr
+import logging
+import json
+
+def read(source, data_model = None, data_model_path = None, sections = None,chunksize = None,
+         supp_section = None, supp_model = None, supp_model_path = None,
+         skiprows = None, out_path = None ):
+
+    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. Make sure min info is available
+    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
+    if not isinstance(source,tuple(properties.supported_sources)):
+        if not source:
+            logging.error('Data source is empty (first argument to read()) ')
+            return
+        elif not os.path.isfile(source):
+            logging.error('Can\'t reach data source {} as a file'.format(source))
+            logging.info('Supported in-memory data sources are {}'.format(",".join(properties.supported_sources)))
+            return
+
+    # 1. Read schema(s) and get file format
+    logging.info("READING DATA MODEL SCHEMA FILE...")
+    schema = schemas.read_schema( schema_name = data_model, ext_schema_path = data_model_path)
+    if not schema:
+        return
+    if supp_section:
+        logging.info("READING SUPPLEMENTAL DATA MODEL SCHEMA FILE...")
+        supp_schema = schemas.read_schema( schema_name = supp_model, ext_schema_path = supp_model_path)
+        if not supp_schema:
+            return
+    else:
+        supp_schema = None
+    # 2. Read data
+    imodel = data_model if data_model else data_model_path
+    logging.info("EXTRACTING DATA FROM MODEL: {}".format(imodel))
+    data, valid = reader.read_model(source,schema, sections = sections, chunksize = chunksize, skiprows = skiprows)
+    # 3. Read additional format: on error, return what's been read so far...
+    # Mmmmm, make sure we can mix meta_file_formats: eg. core('FIXED_WIDTH')-supp("DELIMITED")           
+    if supp_section:
+        i_suppmodel = supp_model if supp_model else supp_model_path
+        logging.info("EXTRACTING SUPPLEMENTAL DATA FROM MODEL: {}".format(i_suppmodel))
+        data, valid = reader.add_supplemental(data, supp_section, supp_schema, valid)
+        if isinstance(data,pd.io.parsers.TextFileReader):
+            logging.info('...RESTORING DATA PARSER')
+            data = pandas_TextParser_hdlr.restore(data.f,data.orig_options)
+
+    # 4. Create out data attributes
+    logging.info("CREATING OUTPUT DATA ATTRIBUTES FROM DATA MODEL(S)")
+    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, data_model, supp_section = supp_section, supp_schema = supp_schema, supp_model = supp_model )
+
+    # 5. Complete data validation
+    logging.info("VALIDATING DATA")
+    valid = validate.validate(data, out_atts, valid, data_model = data_model, data_model_path = data_model_path, supp_section = supp_section, supp_model = supp_model, supp_model_path = supp_model_path) 
+    if isinstance(data,pd.io.parsers.TextFileReader):
+            logging.info('...RESTORING DATA PARSER')
+            data = pandas_TextParser_hdlr.restore(data.f,data.orig_options)
+            
+    if out_path:
+        logging.info('WRITING DATA TO FILES IN: {}'.format(out_path))
+        cols = [ x for x in data ]
+        if isinstance(cols[0],tuple):
+            header = [":".join(x) for x in cols]
+            out_atts_json = { ":".join(x):out_atts.get(x) for x in out_atts.keys() }
+        else:
+            header = cols
+            out_atts_json = out_atts
+        data.to_csv(os.path.join(out_path,'data.csv'), header = header, encoding = 'utf-8',index = True, index_label='index')
+        valid.to_csv(os.path.join(out_path,'valid_mask.csv'), header = header, encoding = 'utf-8',index = True, index_label='index')
+        with open(os.path.join(out_path,'atts.json'),'w') as fileObj:
+            json.dump(out_atts_json,fileObj,indent=4)
+            
+    return {'data':data,'atts':out_atts,'valid_mask':valid}
+
+if __name__=='__main__':
+    kwargs = dict(arg.split('=') for arg in sys.argv[2:])
+    if 'sections' in kwargs.keys():
+        kwargs.update({ 'sections': [ x.strip() for x in kwargs.get('sections').split(",")] })
+    read(sys.argv[1], 
+         **kwargs) # kwargs
\ No newline at end of file

reader/__init__.py

+

reader/meta_formats/__init__.py

+from . import fixed_width
+from . import delimited

reader/meta_formats/delimited.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 30 09:38:17 2019
+
+Reads source data from a data model with delimited fields to a pandas
+DataFrame.
+
+Assumes source data as data model layout and all sections and elements in data.
+Reads in full data content, then decodes and converts the elements.
+ 
+Internally works assuming highest complexity in the input data model: 
+multiple sequential sections
+
+@author: iregon
+"""
+
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+# CAREFULL HERE:
+# Note that in Python 3, the io.open function is an alias for the built-in open function.
+# The built-in open function only supports the encoding argument in Python 3, not Python 2.
+# https://docs.python.org/3.4/library/io.html?highlight=io
+import io
+from io import open # To allow for encoding definition
+from io import StringIO as StringIO
+
+import sys
+import pandas as pd
+import numpy as np
+from copy import deepcopy
+import logging
+import csv # To disable quoting
+import mdf_reader.common.functions as functions
+from mdf_reader.common.converters import converters
+from mdf_reader.common.decoders import decoders
+import mdf_reader.properties as properties
+
+if sys.version_info[0] >= 3:
+    py3 = True
+else:
+    py3 = False
+    from io import BytesIO as BytesIO
+
+#   ---------------------------------------------------------------------------
+#   FUNCTION TO PREPARE SOURCE DATA TO WHAT GET_SECTIONS() EXPECTS, AN ITERABLE:
+#   EITHER A PD.IO.PARSERS.TEXTFILEREADER OR A LIST, DEPENDING ON 
+#   SOURCE TYPE AND CHUNKSIZE ARGUMENT
+#   BASICALLY 1 RECORD (ONE OR MULTIPLE REPORTS) IN ONE LINE
+#   ---------------------------------------------------------------------------
+def source_11(source, schema, chunksize = None, skiprows = None, delimiter = ',' ):
+    # 11: 1 REPORT PER RECORD IN ONE LINE
+    if isinstance(source,pd.DataFrame):
+        TextParser = source
+        TextParser = [TextParser]
+    elif isinstance(source,pd.io.parsers.TextFileReader):
+        TextParser = source
+    else:
+        names = [ (x,y) for x in schema['sections'].keys() for y in schema['sections'][x]['elements'].keys()]
+        missing = { x:schema['sections'][x[0]]['elements'][x[1]].get('missing_value') for x in names }
+        TextParser = pd.read_csv(source,header = None, delimiter = delimiter, encoding = 'utf-8',
+                                 dtype = 'object', skip_blank_lines = False, chunksize = chunksize,
+                                 skiprows = skiprows, names = names, na_values = missing)
+        if not chunksize:
+            TextParser = [TextParser]
+    return TextParser
+
+def source_1x(source,schema, chunksize = None, skiprows = None, delimiter = ',' ):
+    # 1X: MULTIPLE REPORTS PER RECORD IN ONE LINE
+    return source_11(source,schema, chunksize = chunksize, skiprows = skiprows, delimiter = ',' )
+#   ---------------------------------------------------------------------------
+#   MAIN FUNCTIONS
+#   ---------------------------------------------------------------------------
+def source_to_df(source, schema, read_sections, idx_offset = 0):
+    
+    column_names = []
+    for section in schema['sections']:
+        column_names.extend([ (section,i) for i in schema['sections'][section]['elements'] ])
+    multiindex = True if len(read_sections) > 1 or read_sections[0] != properties.dummy_level else False
+    out_dtypes = dict()
+    out_dtypes.update({ (section,i):properties.pandas_dtypes.get(schema['sections'][section]['elements'][i].get('column_type')) for i in schema['sections'][section]['elements'].keys() } )
+
+    I_CHUNK = 0
+    output_buffer = StringIO() if py3 else BytesIO()
+    valid_buffer = StringIO() if py3 else BytesIO()
+    for df in source: # Indices here are kept are those according to the full record
+        logging.info('Processing chunk {}'.format(I_CHUNK))
+        # 0. Name columns
+        df.columns = pd.MultiIndex.from_tuples(column_names)
+        # 1. Remove sections not requested
+        drop_sections = [ x for x in schema['sections'] if x not in read_sections ]
+        df.drop(drop_sections, axis = 1, level = 0, inplace = True)
+        # 2. Decode, scale|offset and convert to dtype (ints will be floats if NaNs)
+        dtypes = dict()
+        encodings = dict()
+        valid = pd.DataFrame(index = df.index, columns = df.columns)
+        for section in read_sections:
+            dtypes.update({ (section,i):schema['sections'][section]['elements'][i]['column_type'] for i in schema['sections'][section]['elements'] })
+            encoded = [ (x) for x in schema['sections'][section]['elements'] if 'encoding' in schema['sections'][section]['elements'][x]]
+            encodings.update({ (section,i):schema['sections'][section]['elements'][i]['encoding'] for i in encoded })
+        for element in dtypes.keys():
+                missing = df[element].isna()
+                if element in encoded:
+                    df[element] = decoders.get(encodings.get(element)).get(dtypes.get(element))(df[element]) 
+                          
+                kwargs = { converter_arg:schema['sections'][element[0]]['elements'][element[1]].get(converter_arg) for converter_arg in properties.data_type_conversion_args.get(dtypes.get(element))  }
+                df[element] = converters.get(dtypes.get(element))(df[element], **kwargs) 
+                
+                valid[element] = missing | df[element].notna()
+        # Add _datetime section: watch this if we mean to do multiple reports in record!!!
+        # for this to be valid, would have to assume that same day reports and that date in common report section....
+        # If datetime is derived from within the actual report, then we would have add _datetime after expansion on dataframe posprocessing
+        if schema['header'].get('date_parser'):
+            date_parser = schema['header'].get('date_parser')
+            date_name = ('_datetime','_datetime') if multiindex else '_datetime'
+            date_elements = [(date_parser['section'],x) for x in date_parser['elements'] ] if date_parser.get('section') else date_parser.get('elements')
+            out_dtypes.update({ date_name: 'object' })
+            df = functions.df_prepend_datetime(df, date_elements, date_parser['format'], date_name = date_name )
+            valid = pd.concat([pd.DataFrame(index = valid.index, data = True,columns = [date_name]),valid],sort = False,axis=1)
+            
+        out_dtypes.update({ i:df[i].dtype.name for i in df if df[i].dtype.name in properties.numpy_floats})   
+        if idx_offset > 0:  
+            df.index = df.index + idx_offset
+        # If I get into the section: is it really only removing that named element from that section???? have to check 
+        #element[section].drop([element],axis=1,level=1,inplace = True)
+        # Drop level 0 in multilevel if len(read_sections)==1 or section is dummy
+        # 3. Add chunk data to output
+        header = False if I_CHUNK == 0 else False
+        df.to_csv(output_buffer,header = header, mode = 'a', encoding = 'utf-8',index = False)
+        valid.to_csv(valid_buffer,header=header, mode = 'a', encoding = 'utf-8',index = False)
+        I_CHUNK += 1
+ 
+    return output_buffer, valid_buffer, out_dtypes
\ No newline at end of file

reader/reader.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 30 09:38:17 2019
+
+Reads source data from a data model to a pandas DataFrame.
+
+Optionally, it reads supplemental data from the same source (from a different
+ data model) and pastes that to the output DataFrame
+
+Uses the meta_formats generic submodules ('delimited' and 'fixed_width') to
+pre-format data source and read either generic type of data model.
+
+@author: iregon
+"""
+
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+# CAREFULL HERE:
+# Note that in Python 3, the io.open function is an alias for the built-in open function.
+# The built-in open function only supports the encoding argument in Python 3, not Python 2.
+# https://docs.python.org/3.4/library/io.html?highlight=io
+from io import StringIO as StringIO
+import sys
+import pandas as pd
+import numpy as np
+import logging
+from . import meta_formats
+from .. import properties
+
+if sys.version_info[0] >= 3:
+    py3 = True
+else:
+    py3 = False
+    from io import BytesIO as BytesIO
+
+# Get pandas dtype for time_stamps
+pandas_timestamp_dtype = pd.to_datetime(pd.DataFrame(['20000101'])[0],format='%Y%m%d').dtypes
+
+def add_supplemental(data, supp_section, supp_schema, valid):
+    # Supplemental data needs to have no sectioning: cannot merge dfs with different level depths in the columns...
+    try:
+
+        supp_format = supp_schema['header'].get('format')
+
+        if supp_format in properties.supported_meta_file_formats:
+            TextParser = data if isinstance(data, pd.io.parsers.TextFileReader) else [data]
+            TextParser_valid = valid if isinstance(valid, pd.io.parsers.TextFileReader) else [valid]
+            chunksize = data.orig_options['chunksize'] if isinstance(TextParser,pd.io.parsers.TextFileReader) else None
+            iidx_offset = chunksize if chunksize else 0
+            output_buffer = StringIO() if py3 else BytesIO()
+            output_buffer_valid = StringIO() if py3 else BytesIO()
+            I_CHUNK = 0
+            for idata,ivalid in zip(TextParser,TextParser_valid):
+                date_columns = list(np.where(idata.dtypes == pandas_timestamp_dtype)[0])
+                dtypes = idata.dtypes.to_dict()
+                supp, supp_valid = read_model(idata[supp_section],supp_schema, idx_offset = I_CHUNK*iidx_offset )
+                supp_date_columns = list(np.where(supp.dtypes == pandas_timestamp_dtype)[0] + len(idata.columns) - 1 )
+                date_columns.extend(supp_date_columns)
+                date_columns = [ int(x) for x in date_columns ] # reader date parser won't take numpy.int64 from np.where as col index
+                if I_CHUNK == 0:
+                    o_supp_dtypes = supp.dtypes.to_dict()
+                else:
+                    o_supp_dtypes.update({ i:supp[i].dtype for i in supp if supp[i].dtype in properties.numpy_floats})
+                supp_elements = supp.columns.to_list()
+                supp_dtypes = {}
+                for element in supp_elements:
+                    supp_dtypes[(supp_section,element)] =  o_supp_dtypes.get(element)
+                dtypes.pop((supp_section,idata[supp_section].columns.to_list()[0]), None)
+                idata.drop(supp_section, axis = 1, inplace = True, level = 0)# OMG: apparently, with multiindex, this does not drop the columns from idata.columns
+                ivalid.drop(supp_section, axis = 1, inplace = True, level = 0)
+                supp.columns = [ (supp_section,x) for x in supp.columns ]
+                supp_valid.columns = [ (supp_section,x) for x in supp_valid.columns ]
+                dtypes.update(supp_dtypes)
+                supp.index = idata.index
+                supp_valid.index = ivalid.index
+                column_names = [ x for x in idata if x[0] != supp_section ]
+                column_names.extend([ x for x in supp ])
+                new_dtypes = { x:dtypes.get(x) for x in column_names }
+                idata = pd.concat([idata,supp],sort = False,axis=1)
+                ivalid = pd.concat([ivalid,supp_valid],sort = False,axis=1)
+                idata.to_csv(output_buffer,header=False, mode = 'a', encoding = 'utf-8',index = False)
+                ivalid.to_csv(output_buffer_valid,header=False, mode = 'a', encoding = 'utf-8',index = False)
+                I_CHUNK += 1
+            
+            output_buffer.seek(0)
+            output_buffer_valid.seek(0)
+            for element in list(dtypes):
+                if new_dtypes.get(element) == pandas_timestamp_dtype:
+                    new_dtypes[element] = 'object' # Only on output (on reading) will be then converted to datetime64[ns] type, cannot specify 'datetime' here: have to go through parser
+            data = pd.read_csv(output_buffer,names = idata.columns, dtype = new_dtypes, chunksize = chunksize, parse_dates = date_columns )
+            valid = pd.read_csv(output_buffer_valid,names = ivalid.columns, chunksize = chunksize)
+            return data, valid
+        else:
+            logging.error('Supplemental file format not supported: {}'.format(supp_format))
+            logging.warning('Supplemental data not extracted from supplemental section')
+            return data, valid
+    except Exception as e:
+        logging.warning('Supplemental data not extracted from supplemental section', exc_info=True)
+        return data, valid
+
+
+def read_model(source,schema, sections = None, chunksize = None, skiprows = None, idx_offset = 0):
+
+    meta_format = schema['header'].get('format')
+    if meta_format not in properties.supported_meta_file_formats:
+        logging.error('File format read from input schema not supported: {}'.format(meta_format))
+        return
+    meta_reader = ".".join(['meta_formats',meta_format])
+
+    # 0. GET META FORMAT SUBCLASS ---------------------------------------------
+    if schema['header'].get('multiple_reports_per_line'): # needs to eval to True if set and True and to false if not set or false, without breaking
+        format_subclass = '1x'
+    else:
+        format_subclass = '11'
+
+    # 1. PARSE SCHEMA ---------------------------------------------------------
+
+    delimiter = schema['header'].get('delimiter')
+    parsing_order = schema['header'].get('parsing_order')
+
+    # 2. DEFINE OUTPUT --------------------------------------------------------
+    # 2.1 Sections to read
+    if not sections:
+        sections = [ x.get(y) for x in parsing_order for y in x ]
+        read_sections = [y for x in sections for y in x]
+    else:
+        read_sections = sections
+    multiindex = True if len(read_sections) > 1 or read_sections[0] != properties.dummy_level else False
+    
+    if format_subclass == '1x':
+        return schema
+    # 2.1 Elements names: same order as declared in schema, which is the order in which the readers read them...
+    names = []
+    if schema['header'].get('date_parser'):
+        if multiindex:
+            names.extend([('_datetime','_datetime')])
+        else:
+            names.extend(['_datetime'])
+
+    for section in read_sections:
+        if multiindex:
+            names.extend([ (section,x) for x in schema['sections'][section]['elements'].keys() if not schema['sections'][section]['elements'][x].get('ignore') ])
+        else:
+            names.extend([ x for x in schema['sections'][section]['elements'].keys() if not schema['sections'][section]['elements'][x].get('ignore') ])
+
+    # 3. GET DATA FROM SOURCE (DF, FILE OR TEXTREADER):------------------------
+    #    SIMPLE STRING PER REPORT/LINE
+    logging.info("Getting input data from source...")
+    source_function = eval(meta_reader + "." + "_".join(['source',format_subclass]))
+    TextParser = source_function(source,schema, chunksize = chunksize, skiprows = skiprows, delimiter = delimiter)
+    # 4. DO THE ACTUAL READING
+    reader_function = eval(meta_reader + "." + 'source_to_df')
+    logging.info("Reading data...")
+    [output_buffer,valid_buffer,dtypes] = reader_function(TextParser, schema, read_sections = read_sections, idx_offset = idx_offset )
+    # 5. OUTPUT DATA:----------------------------------------------------------
+    # WE'LL NEED TO POSPROCESS THIS WHEN READING MULTIPLE REPORTS PER LINE
+    output_buffer.seek(0)
+    valid_buffer.seek(0)
+    logging.info("Wrapping output....")
+    chunksize = TextParser.orig_options['chunksize'] if isinstance(TextParser,pd.io.parsers.TextFileReader) else None
+    logging.info('Data')
+    # '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: will fail
+    date_columns = [] # Needs to be the numeric index of the column, as seems not to be able to work with tupples....
+    for i,element in enumerate(list(dtypes)):
+        if dtypes.get(element) == 'datetime':
+            date_columns.append(i)
+    df_reader = pd.read_csv(output_buffer,names = names, chunksize = chunksize, dtype = dtypes, parse_dates = date_columns)
+    logging.info('Mask')
+    valid_reader = pd.read_csv(valid_buffer,names = names, chunksize = chunksize)
+
+    return df_reader, valid_reader

requirements.txt

+#Python 3.7.3
+matplotlib==3.0.3
+numpy==1.16.2
+pandas==0.24.2