Source code for mdf_reader.reader.get_sections

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#"""
#Created on Tue Apr 30 09:38:17 2019
#
#Splits string reports in sections using a data model layout.
#
#Input and output are simple pandas dataframes, with the output dataframe
#column names being the section names
#
#To work with a pandas TextParser, loop through this module.
#
#Internally works assuming highest complexity in the input data model:
#multiple non sequential sections
#
#DEV NOTES:
#    
#1) make sure we use Series when working with Series, DataFrames otherwise...
#like now:
#  threads[thread_id]['data'] = pd.Series(threads[thread_id]['parent_data'][0].str[0:section_len])
#instead of:
#  threads[thread_id]['data'] = pd.DataFrame(threads[thread_id]['parent_data'][0].str[0:section_len])
#
#on data import in import_data.py, we use pd.read_fwf because is more general
#use, also support to chunking would make converting to series a bit dirty...
#
#2) Can we extend (do we need to?) this to reading sequential sections with
#    no sentinals? apparently (see td11) we are already able to do that:
#        provided the section is in a sequential parsing_order group
#
#@author: iregon
#
#Have to documents the threads approach!!!!
#
#"""

import pandas as pd
from copy import deepcopy
import logging

#   ---------------------------------------------------------------------------
#   FUNCTIONS TO PERFORM INITIAL SEPARATION OF SECTIONS: MAIN IS GET_SECTIONS()
#   ---------------------------------------------------------------------------
[docs]def extract_data():
    section_len = section_lens.get(threads[thread_id]['section'])
    if section_len:
        threads[thread_id]['data'] = pd.Series(threads[thread_id]['parent_data'][0].str[0:section_len]) # object consistency needed here
        threads[thread_id]['modulo'] = pd.DataFrame(threads[thread_id]['parent_data'][0].str[section_len:]) # object consistency needed here
    else:
        threads[thread_id]['data'] = pd.Series(threads[thread_id]['parent_data'][0].str[0:]) #threads[thread_id]['parent_data'].copy()
        # Could even be like with section_len (None in section_len will read to the end)
        threads[thread_id]['modulo'] = pd.DataFrame(columns = [0]) # Just for consistency
    del threads[thread_id]['parent_data']

[docs]def add_next_children():
    global children_parsing_order, branch_parsing_order, children_group_type, children_group_number
    children_parsing_order = deepcopy(threads[thread_id]['parsing_order'])
    branch_parsing_order = deepcopy(threads[thread_id]['parsing_order'])
    children_group_type = list(children_parsing_order[0])[0]
    children_group_number = threads[thread_id]['children_group_number']
    threads[thread_id]['children_no'] = 0
    threads[thread_id]['children'] = []
    add_children()

[docs]def add_higher_group_children():
    global children_parsing_order, branch_parsing_order, children_group_type, children_group_number
    children_parsing_order = deepcopy(threads[thread_id]['parsing_order'])
    children_parsing_order.pop(0) # Move to next group of sections
    if len(children_parsing_order) > 0:
        branch_parsing_order = deepcopy(threads[thread_id]['parsing_order'])
        branch_parsing_order.pop(0)
        children_group_type = list(children_parsing_order[0])[0]
        children_group_number = threads[thread_id]['children_group_number'] + 1
        add_children()

[docs]def add_children():
    if children_group_type == 's':
        add_static_children()
    else:
        add_dynamic_children()

[docs]def add_static_children():
    threads[thread_id]['children_no'] += 1
    children_thread_id = str(children_group_number) + str(0) + thread_id
    threads[thread_id]['children'].append(children_thread_id)
    # Now build children's thread
    children_section = children_parsing_order[0][children_group_type].pop(0)
    grandchildren_group_number = children_group_number
    if len(children_parsing_order[0][children_group_type]) == 0:
        children_parsing_order.pop(0)
        if len(children_parsing_order) > 0:
            grandchildren_group_number += 1
        else:
            grandchildren_group_number = None
    threads[children_thread_id] = {'parsing_order':children_parsing_order}
    threads[children_thread_id]['group_number'] = children_group_number
    threads[children_thread_id]['group_type'] = children_group_type
    threads[children_thread_id]['section'] = children_section
    threads[children_thread_id]['parent_data'] = threads[thread_id]['modulo']
    threads[thread_id]['modulo'].iloc[0:0] # Remove reports from modulo
    threads[children_thread_id]['children_group_number'] = grandchildren_group_number

[docs]def add_dynamic_children():
    for i in range(0,len(children_parsing_order[0][children_group_type])):
        branch_i_parsing_order = deepcopy(branch_parsing_order)
        children_thread_id = str(children_group_number) + str(i+1) + thread_id
        # Now build children's thread
        children_section = children_parsing_order[0][children_group_type].pop(0)
        children_idx = threads[thread_id]['modulo'].loc[threads[thread_id]['modulo'][0].str[0:sentinals_lens.get(children_section)] == sentinals.get(children_section)].index
        if len(children_idx) == 0:
            continue
        threads[thread_id]['children'].append(children_thread_id)
        threads[thread_id]['children_no'] += 1
        branch_i_parsing_order[0][children_group_type].remove(children_section)
        grandchildren_group_number = children_group_number
        if len(branch_i_parsing_order[0][children_group_type]) == 0 or children_group_type == 'e':
            branch_i_parsing_order.pop(0)
            if len(children_parsing_order) > 0:
                grandchildren_group_number += 1
            else:
                grandchildren_group_number = None
        threads[children_thread_id] = {'parsing_order':branch_i_parsing_order}
        threads[children_thread_id]['group_number'] = children_group_number
        threads[children_thread_id]['group_type'] = children_group_type
        threads[children_thread_id]['section'] = children_section
        threads[children_thread_id]['parent_data'] = threads[thread_id]['modulo'].loc[children_idx]
        threads[thread_id]['modulo'].drop(children_idx,inplace = True)
        threads[children_thread_id]['children_group_number'] = grandchildren_group_number
    if (len(threads[thread_id]['modulo'])) > 0:
        add_higher_group_children()

[docs]def extract_sections(string_df):
    # threads elements:
    #    'parsing_order'            What needs to be applied to current parent data
    #    'group_number'             Order in the global parsing order
    #    'group_type'               Is it sequential, exclusive or optional
    #    'section'                  Section name to be extracted from parent_data to data
    #    'parent_data'              Inital data from which section must be extracted
    #    'data'                     Section data extracted from parent_data
    #    'modulo'                   Reminder of parent_data after extracting section (data)
    #    'children_no'              Number of children threads to build, based on next parsing order list element. Resets to number of active children
    #    'children'                 Thread id for every child
    #    'children_group_number'    Group number (in the global parsing order, of the children)
    global sentinals, section_lens, sentinal_lens, parsing_order
    global children_group_type
    global threads
    global thread_id
    global group_type

    # Initial "node': input data
    threads = dict()
    thread_id = '00'
    threads_queue = [thread_id]
    threads[thread_id] = {'parsing_order':parsing_order}
    threads[thread_id]['group_number'] = 0
    threads[thread_id]['group_type'] = None
    threads[thread_id]['section'] = None
    threads[thread_id]['parent_data'] = string_df
    threads[thread_id]['data'] = None
    threads[thread_id]['modulo'] = threads[thread_id]['parent_data']
    del threads[thread_id]['parent_data']
    threads[thread_id]['children_group_number'] = 1
    add_next_children()
    threads_queue.extend(threads[thread_id]['children'])
    threads_queue.remove(thread_id)
    # And now, once initialized, let it grow:
    logging.info('Processing section partitioning threads')
    while threads_queue:
        thread_id = threads_queue[0]
        logging.info('{} ...'.format(thread_id))
        group_type = threads[thread_id]['group_type']
        # get section data
        extract_data()
        # kill thread if nothing there
        if len(threads[thread_id]['data']) == 0:
            del threads[thread_id]
            logging.info('{} deleted: no data'.format(thread_id))
            threads_queue.pop(0)
            continue
        # build children threads
        if len(threads[thread_id]['parsing_order']) > 0  and len(threads[thread_id]['modulo']) > 0:
            add_next_children()
            threads_queue.extend(threads[thread_id]['children'])
            #del threads[thread_id]['modulo'] # not until we control what to do whit leftovers....
        threads_queue.pop(0)
        logging.info('done')
    section_dict = dict()
    section_groups = [ d[x] for d in parsing_order for x in d.keys() ]
    sections = [item for sublist in section_groups for item in sublist]
    
    for section in sections:
        section_dict[section] = pd.Series()
        thread_ids = [ x for x in threads.keys() if threads[x]['section'] == section ]
        for thread_id in thread_ids:
            section_dict[section] = section_dict[section].append(threads[thread_id]['data'],ignore_index=False)
        section_dict[section].sort_index(inplace=True)
    return section_dict

#   ---------------------------------------------------------------------------
#   MAIN
#   ---------------------------------------------------------------------------
[docs]def main(string_df, schema, read_sections):
    """

    Returns a pandas dataframe with a report per row
    and the report sections split along the columns.
    Each section is a block string and only the sections
    listed in read_sections parameter are output.
    
    Parameters
    ----------
    string_df : pandas.DataFrame
        Pandas dataframe with a unique column with
        the reports as a block string
        
    schema : dict 
        Data source data model schema 
    
    read_sections : list 
        Sections to output from the complete report
        

    Returns
    -------
    pandas.DataFrame 
        Dataframe with the report sections split 
        along the columns.
    

    """
    global sentinals, section_lens, sentinals_lens
    global parsing_order
    # Proceed to split sections if more than one
    # else return section in a named column
    if len(schema['sections'].keys())> 1:
        section_lens = { section: schema['sections'][section]['header'].get('length') for section in schema['sections'].keys()}
        sentinals = { section: schema['sections'][section]['header'].get('sentinal') for section in schema['sections'].keys()}
        sentinals_lens = { section: len(sentinals.get(section)) if sentinals.get(section) else 0 for section in sentinals.keys()}
        parsing_order = schema['header']['parsing_order']
        # Get sections separated: section dict has a key:value pair for each
        # section in the data model. If the section does not exist in the data,
        # the value is an empty pd.Series
        section_dict = extract_sections(string_df)
        # Paste in order (as read_sections) in a single dataframe with columns
        # named as sections:
        # - Drop unwanted sections
        # - Keep requested but non-existent sections
        df_out = pd.DataFrame()
        for section in read_sections:
            df_out = pd.concat([df_out,section_dict[section].rename(section)],sort = False,axis=1)
    else:
        df_out = string_df
        df_out.columns = read_sections

    return df_out