excel.helpers.exceltemplate.ExcelTemplateReader.check_species() - Code Metrics - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

ExcelTemplateReader.check_species() A
last analyzed 2023-06-12 09:55 UTC

↳ Parent: excel.helpers.exceltemplate

Complexity

Conditions

Size

Total Lines	9
Code Lines	4

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	4
dl	0
loc	9
rs	10
c	0
b	0
f	0
cc	1
nop	2

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jul  5 16:31:45 2019

@author: Paolo Cozzi <[email protected]>
"""

import xlrd
import logging
import datetime

from collections import defaultdict, namedtuple

from common.constants import ACCURACIES
from uid.helpers import FileDataSourceMixin
from uid.models import DictSex, DictCountry

from .exceptions import ExcelImportError

# Get an instance of a logger
logger = logging.getLogger(__name__)

# defining the template columns in need for data import
TEMPLATE_COLUMNS = {
    'breed': [
        'Supplied breed',
        # 'Mapped breed',
        # 'Mapped breed ontology library',
        # 'Mapped breed ontology accession',
        'EFABIS Breed country',
        'Species',
        # 'Species ontology library',
        # 'Species ontology accession'
    ],
    'animal': [
        'Animal id in data source',
        'Animal description',
        'Alternative animal ID',
        'Father id in data source',
        'Mother id in data source',
        'Breed',
        'Species',
        'Sex',
        'Birth date',
        'Birth location',
        'Birth location longitude',
        'Birth location latitude',
        'Birth location accuracy'
    ],
    'sample': [
        'Sample id in data source',
        'Alternative sample ID',
        'Sample description',
        'Animal id in data source',
        'Specimen collection protocol',
        'availability',
        'Collection date',
        'Collection place latitude',
        'Collection place longitude',
        'Collection place',
        'Collection place accuracy',
        'Organism part',
        'Developmental stage',
        'Physiological stage',
        'Animal age at collection',
        'Sample storage',
        'Sample storage processing',
        'Sampling to preparation interval'
    ]
}


class ExcelTemplateReader(FileDataSourceMixin):
    """A class to read template excel files"""

    def __init__(self):
        # read xls file and track it
        self.book = None
        self.sheet_names = []

    def read_file(self, filename):
        # read xls file and track it
        self.book = xlrd.open_workbook(filename)
        self.sheet_names = self.book.sheet_names()

    def check_sheets(self):
        """Test for the minimal sheets required to upload data"""

        not_found = []

        for sheet_name in TEMPLATE_COLUMNS.keys():
            if sheet_name not in self.sheet_names:
                not_found.append(sheet_name)
                logger.error(
                    "required sheet {name} not found in template".format(
                        name=sheet_name)
                )

        if len(not_found) > 0:
            return False, not_found

        else:
            logger.debug("This seems to be a valid Template file")
            return True, not_found

    def check_columns(self):
        """Test for minimal column required for template load"""

        not_found = defaultdict(list)

        for sheet_name in TEMPLATE_COLUMNS.keys():
            # get a sheet from xls workbook
            sheet = self.book.sheet_by_name(sheet_name)

            # get header from sheet
            header = sheet.row_values(0)

            for column in TEMPLATE_COLUMNS[sheet_name]:
                if column not in header:
                    not_found[sheet_name].append(column)
                    logger.error(
                        "required column {column} not found in sheet "
                        "{sheet_name}".format(
                            sheet_name=sheet_name,
                            column=column)
                    )

        if len(not_found) > 0:
            return False, not_found

        else:
            logger.debug("This seems to be a valid Template file")
            return True, not_found

    def get_sheet_records(self, sheet_name):
        """Generic functions to iterate on excel records"""

        # this is the sheet I need
        sheet = self.book.sheet_by_name(sheet_name)

        # now get columns to create a collection objects
        header = sheet.row_values(0)

        column_idxs = {}

        # get the column index I need
        for column in TEMPLATE_COLUMNS[sheet_name]:
            try:
                idx = header.index(column)

            except ValueError as e:
                logger.error(e)
                raise ExcelImportError(
                    "Column '%s' not found in '%s' sheet" % (
                        column, sheet_name))

            column_idxs[column.lower().replace(" ", "_")] = idx

        # get new column names
        columns = column_idxs.keys()

        # create a namedtuple object
        Record = namedtuple(sheet_name.capitalize(), columns)

        # iterate over record, mind the header column
        for i in range(1, sheet.nrows):
            # get a row from excel file
            row = sheet.row_values(i)

            # get the data I need
            data = [row[column_idxs[column]] for column in columns]

            # replace all empty  occurences in a list
            data = [None if col in [""]
                    else col for col in data]

            # stripping columns
            data = [col.strip() if type(col) is str
                    else col for col in data]

            # treat integers as integers
            data = [int(col) if type(col) is float and col.is_integer()
                    else col for col in data]

            # fix date fields. Search for 'date' in column names
            date_idxs = [column_idxs[column] for column in columns if
                         'date' in column]

            # fix date objects using datetime, as described here:
            # https://stackoverflow.com/a/13962976/4385116
            for idx in date_idxs:
                if not data[idx]:
                    continue

                # forcing a date object
                data[idx] = datetime.datetime(
                    *xlrd.xldate_as_tuple(
                        data[idx],
                        self.book.datemode
                    )
                ).date()

            # get a new object
            record = Record._make(data)

            yield record

    def get_breed_records(self):
        """Iterate among breeds record"""

        # this is the sheet I need
        sheet_name = "breed"
        return self.get_sheet_records(sheet_name)

    def get_animal_records(self):
        """Iterate among animal records"""

        # this is the sheet I need
        sheet_name = "animal"
        return self.get_sheet_records(sheet_name)

    def get_sample_records(self):
        """Iterate among sample records"""

        # this is the sheet I need
        sheet_name = "sample"
        return self.get_sheet_records(sheet_name)

    def get_animal_from_sample(self, sample):
        """get an animal record from a sample record"""

        animals = [
            animal for animal in self.get_animal_records() if
            animal.animal_id_in_data_source == sample.animal_id_in_data_source
        ]

        # animal is supposed to be unique
        if len(animals) != 1:
            raise ExcelImportError(
                "Can't determine a unique animal from '{sample}' "
                "record data. Animal objects found: {animals}".format(
                    sample=sample, animals=animals))

        return animals[0]

    def get_breed_from_animal(self, record):
        """Get a breed record from an animal record"""

        breeds = [
            breed for breed in self.get_breed_records()
            if breed.supplied_breed == record.breed and
            breed.species == record.species]

        # breed is supposed to be unique, from UID constraints. However
        # I could place the same breed name for two countries. In that case,
        # I cant derive a unique breed from users data
        if len(breeds) != 1:
            raise ExcelImportError(
                "Can't determine a unique breed for '%s:%s' from user data" %
                (record.breed, record.species))

        return breeds[0]

    def check_species(self, country):
        """Check if all species are defined in UID DictSpecies. If not,
        create dictionary term"""

        column = 'species'
        item_set = set([breed.species for breed in self.get_breed_records()])

        # call FileDataSourceMixin.check_species
        return super().check_species(column, item_set, country, create=True)

    def check_species_in_animal_sheet(self):
        """Check if all animal species are defined in breed sheet"""

        check = True
        not_found = []

        reference_set = set(
            [breed.species for breed in self.get_breed_records()])

        test_set = set(
            [animal.species for animal in self.get_animal_records()])

        for specie in test_set:
            if specie not in reference_set:
                check = False
                not_found.append(specie)

        return check, not_found

    def check_sex(self):
        """Check that all sex records are present in database"""

        column = 'sex'
        item_set = set([animal.sex for animal in self.get_animal_records()])

        # call FileDataSourceMixin.check_items
        return self.check_items(item_set, DictSex, column)

    def check_countries(self):
        """Check that all efabis countries are present in database"""

        column = "efabis_breed_country"
        item_set = set([breed.efabis_breed_country for
                        breed in self.get_breed_records()])

        # call FileDataSourceMixin.check_items
        return self.check_items(item_set, DictCountry, column)

    def __check_accuracy(self, item_set):
        """A generic method to test for accuracies"""

        # a list of not found terms and a status to see if something is missing
        # or not
        not_found = []
        result = True

        for item in item_set:
            try:
                ACCURACIES.get_value_by_desc(item)

            except KeyError:
                logger.warning("accuracy level '%s' not found" % (item))
                not_found.append(item)

        if len(not_found) != 0:
            result = False

        return result, not_found

    def check_accuracies(self):
        """Check accuracy specified in table"""

        item_set = set([animal.birth_location_accuracy
                        for animal in self.get_animal_records()])

        # test for accuracy in animal table
        result_animal, not_found_animal = self.__check_accuracy(item_set)

        item_set = set([sample.collection_place_accuracy
                        for sample in self.get_sample_records()])

        # test for accuracy in sample table
        result_sample, not_found_sample = self.__check_accuracy(item_set)

        # merge two results
        check = result_animal and result_sample
        not_found = set(not_found_animal + not_found_sample)

        if check is False:
            logger.error(
                    "Couldnt' find those accuracies in constants:")
            logger.error(not_found)

        return check, not_found


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Fri Jul 5 16:31:45 2019
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			import xlrd
10			import logging
11			import datetime
12
13			from collections import defaultdict, namedtuple
14
15			from common.constants import ACCURACIES
16			from uid.helpers import FileDataSourceMixin
17			from uid.models import DictSex, DictCountry
18
19			from .exceptions import ExcelImportError
20
21			# Get an instance of a logger
22			logger = logging.getLogger(__name__)
23
24			# defining the template columns in need for data import
25			TEMPLATE_COLUMNS = {
26			'breed': [
27			'Supplied breed',
28			# 'Mapped breed',
29			# 'Mapped breed ontology library',
30			# 'Mapped breed ontology accession',
31			'EFABIS Breed country',
32			'Species',
33			# 'Species ontology library',
34			# 'Species ontology accession'
35			],
36			'animal': [
37			'Animal id in data source',
38			'Animal description',
39			'Alternative animal ID',
40			'Father id in data source',
41			'Mother id in data source',
42			'Breed',
43			'Species',
44			'Sex',
45			'Birth date',
46			'Birth location',
47			'Birth location longitude',
48			'Birth location latitude',
49			'Birth location accuracy'
50			],
51			'sample': [
52			'Sample id in data source',
53			'Alternative sample ID',
54			'Sample description',
55			'Animal id in data source',
56			'Specimen collection protocol',
57			'availability',
58			'Collection date',
59			'Collection place latitude',
60			'Collection place longitude',
61			'Collection place',
62			'Collection place accuracy',
63			'Organism part',
64			'Developmental stage',
65			'Physiological stage',
66			'Animal age at collection',
67			'Sample storage',
68			'Sample storage processing',
69			'Sampling to preparation interval'
70			]
71			}
72
73
74			class ExcelTemplateReader(FileDataSourceMixin):
75			"""A class to read template excel files"""
76
77			def __init__(self):
78			# read xls file and track it
79			self.book = None
80			self.sheet_names = []
81
82			def read_file(self, filename):
83			# read xls file and track it
84			self.book = xlrd.open_workbook(filename)
85			self.sheet_names = self.book.sheet_names()
86
87			def check_sheets(self):
88			"""Test for the minimal sheets required to upload data"""
89
90			not_found = []
91
92			for sheet_name in TEMPLATE_COLUMNS.keys():
93			if sheet_name not in self.sheet_names:
94			not_found.append(sheet_name)
95			logger.error(
96			"required sheet {name} not found in template".format(
97			name=sheet_name)
98			)
99
100			if len(not_found) > 0:
101			return False, not_found
102
103			else:
104			logger.debug("This seems to be a valid Template file")
105			return True, not_found
106
107			def check_columns(self):
108			"""Test for minimal column required for template load"""
109
110			not_found = defaultdict(list)
111
112			for sheet_name in TEMPLATE_COLUMNS.keys():
113			# get a sheet from xls workbook
114			sheet = self.book.sheet_by_name(sheet_name)
115
116			# get header from sheet
117			header = sheet.row_values(0)
118
119			for column in TEMPLATE_COLUMNS[sheet_name]:
120			if column not in header:
121			not_found[sheet_name].append(column)
122			logger.error(
123			"required column {column} not found in sheet "
124			"{sheet_name}".format(
125			sheet_name=sheet_name,
126			column=column)
127			)
128
129			if len(not_found) > 0:
130			return False, not_found
131
132			else:
133			logger.debug("This seems to be a valid Template file")
134			return True, not_found
135
136			def get_sheet_records(self, sheet_name):
137			"""Generic functions to iterate on excel records"""
138
139			# this is the sheet I need
140			sheet = self.book.sheet_by_name(sheet_name)
141
142			# now get columns to create a collection objects
143			header = sheet.row_values(0)
144
145			column_idxs = {}
146
147			# get the column index I need
148			for column in TEMPLATE_COLUMNS[sheet_name]:
149			try:
150			idx = header.index(column)
151
152			except ValueError as e:
153			logger.error(e)
154			raise ExcelImportError(
155			"Column '%s' not found in '%s' sheet" % (
156			column, sheet_name))
157
158			column_idxs[column.lower().replace(" ", "_")] = idx
159
160			# get new column names
161			columns = column_idxs.keys()
162
163			# create a namedtuple object
164			Record = namedtuple(sheet_name.capitalize(), columns)
165
166			# iterate over record, mind the header column
167			for i in range(1, sheet.nrows):
168			# get a row from excel file
169			row = sheet.row_values(i)
170
171			# get the data I need
172			data = [row[column_idxs[column]] for column in columns]
173
174			# replace all empty occurences in a list
175			data = [None if col in [""]
176			else col for col in data]
177
178			# stripping columns
179			data = [col.strip() if type(col) is str
180			else col for col in data]
181
182			# treat integers as integers
183			data = [int(col) if type(col) is float and col.is_integer()
184			else col for col in data]
185
186			# fix date fields. Search for 'date' in column names
187			date_idxs = [column_idxs[column] for column in columns if
188			'date' in column]
189
190			# fix date objects using datetime, as described here:
191			# https://stackoverflow.com/a/13962976/4385116
192			for idx in date_idxs:
193			if not data[idx]:
194			continue
195
196			# forcing a date object
197			data[idx] = datetime.datetime(
198			*xlrd.xldate_as_tuple(
199			data[idx],
200			self.book.datemode
201			)
202			).date()
203
204			# get a new object
205			record = Record._make(data)
206
207			yield record
208
209			def get_breed_records(self):
210			"""Iterate among breeds record"""
211
212			# this is the sheet I need
213			sheet_name = "breed"
214			return self.get_sheet_records(sheet_name)
215
216			def get_animal_records(self):
217			"""Iterate among animal records"""
218
219			# this is the sheet I need
220			sheet_name = "animal"
221			return self.get_sheet_records(sheet_name)
222
223			def get_sample_records(self):
224			"""Iterate among sample records"""
225
226			# this is the sheet I need
227			sheet_name = "sample"
228			return self.get_sheet_records(sheet_name)
229
230			def get_animal_from_sample(self, sample):
231			"""get an animal record from a sample record"""
232
233			animals = [
234			animal for animal in self.get_animal_records() if
235			animal.animal_id_in_data_source == sample.animal_id_in_data_source
236			]
237
238			# animal is supposed to be unique
239			if len(animals) != 1:
240			raise ExcelImportError(
241			"Can't determine a unique animal from '{sample}' "
242			"record data. Animal objects found: {animals}".format(
243			sample=sample, animals=animals))
244
245			return animals[0]
246
247			def get_breed_from_animal(self, record):
248			"""Get a breed record from an animal record"""
249
250			breeds = [
251			breed for breed in self.get_breed_records()
252			if breed.supplied_breed == record.breed and
253			breed.species == record.species]
254
255			# breed is supposed to be unique, from UID constraints. However
256			# I could place the same breed name for two countries. In that case,
257			# I cant derive a unique breed from users data
258			if len(breeds) != 1:
259			raise ExcelImportError(
260			"Can't determine a unique breed for '%s:%s' from user data" %
261			(record.breed, record.species))
262
263			return breeds[0]
264
265			def check_species(self, country):
266			"""Check if all species are defined in UID DictSpecies. If not,
267			create dictionary term"""
268
269			column = 'species'
270			item_set = set([breed.species for breed in self.get_breed_records()])
271
272			# call FileDataSourceMixin.check_species
273			return super().check_species(column, item_set, country, create=True)
274
275			def check_species_in_animal_sheet(self):
276			"""Check if all animal species are defined in breed sheet"""
277
278			check = True
279			not_found = []
280
281			reference_set = set(
282			[breed.species for breed in self.get_breed_records()])
283
284			test_set = set(
285			[animal.species for animal in self.get_animal_records()])
286
287			for specie in test_set:
288			if specie not in reference_set:
289			check = False
290			not_found.append(specie)
291
292			return check, not_found
293
294			def check_sex(self):
295			"""Check that all sex records are present in database"""
296
297			column = 'sex'
298			item_set = set([animal.sex for animal in self.get_animal_records()])
299
300			# call FileDataSourceMixin.check_items
301			return self.check_items(item_set, DictSex, column)
302
303			def check_countries(self):
304			"""Check that all efabis countries are present in database"""
305
306			column = "efabis_breed_country"
307			item_set = set([breed.efabis_breed_country for
308			breed in self.get_breed_records()])
309
310			# call FileDataSourceMixin.check_items
311			return self.check_items(item_set, DictCountry, column)
312
313			def __check_accuracy(self, item_set):
314			"""A generic method to test for accuracies"""
315
316			# a list of not found terms and a status to see if something is missing
317			# or not
318			not_found = []
319			result = True
320
321			for item in item_set:
322			try:
323			ACCURACIES.get_value_by_desc(item)
324
325			except KeyError:
326			logger.warning("accuracy level '%s' not found" % (item))
327			not_found.append(item)
328
329			if len(not_found) != 0:
330			result = False
331
332			return result, not_found
333
334			def check_accuracies(self):
335			"""Check accuracy specified in table"""
336
337			item_set = set([animal.birth_location_accuracy
338			for animal in self.get_animal_records()])
339
340			# test for accuracy in animal table
341			result_animal, not_found_animal = self.__check_accuracy(item_set)
342
343			item_set = set([sample.collection_place_accuracy
344			for sample in self.get_sample_records()])
345
346			# test for accuracy in sample table
347			result_sample, not_found_sample = self.__check_accuracy(item_set)
348
349			# merge two results
350			check = result_animal and result_sample
351			not_found = set(not_found_animal + not_found_sample)
352
353			if check is False:
354			logger.error(
355			"Couldnt' find those accuracies in constants:")
356			logger.error(not_found)
357
358			return check, not_found
359

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ExcelTemplateReader.check_species() A last analyzed 2023-06-12 09:55 UTC

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ExcelTemplateReader.check_species() A
last analyzed 2023-06-12 09:55 UTC