submissions.forms.UniqueSubmissionMixin.check_submission_exists() - Code Metrics - Inspection of ":bug: test for submission attributes in UpdateSubm..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — devel ( 05b374...659f48 )

by Paolo

created 2020-01-31 14:44 UTC

UniqueSubmissionMixin.check_submission_exists() A

↳ Parent: submissions.forms

Complexity

Conditions

Size

Total Lines	23
Code Lines	9

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	9
dl	0
loc	23
rs	9.95
c	0
b	0
f	0
cc	2
nop	1

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 24 15:51:05 2018

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

import magic
import tempfile

from django import forms
from django.conf import settings

from common.constants import CRB_ANIM_TYPE, TEMPLATE_TYPE
from common.forms import RequestFormMixin
from common.helpers import get_admin_emails
from uid.models import Submission
from crbanim.helpers import CRBAnimReader
from excel.helpers import ExcelTemplateReader


class UniqueSubmissionMixin():
    def check_submission_exists(self):
        """Test if I already have a submission with the same data"""

        # get unique attributes
        unique_together = Submission._meta.unique_together[0]

        # get submitted attributes
        data = {key: self.cleaned_data.get(key) for key in unique_together
                if self.cleaned_data.get(key) is not None}

        # ovverride owner attribute
        data['owner'] = self.request.user

        # test for a submission object with the same attributes
        if Submission.objects.filter(**data).exists():
            msg = (
                "Error: There is already a submission with the same "
                "attributes. Please change one of the following: "
                "Gene bank name, Gene bank country, Data source type and "
                "Data source version")

            # raising an exception:
            raise forms.ValidationError(msg, code='invalid')


class SubmissionFormMixin(UniqueSubmissionMixin):
    def clean(self):
        # test if I have a submission with the provided data
        self.check_submission_exists()

        # I can call this method without providing a 'uploaded file'
        # (for instance, when omitting uploaded file)
        if "uploaded_file" in self.cleaned_data:
            # avoid file type for excel types (is not an text file)
            if ("datasource_type" in self.cleaned_data and
                    self.cleaned_data["datasource_type"] != TEMPLATE_TYPE):
                self.check_file_encoding()

            # check crbanim files only if provided
            if ("datasource_type" in self.cleaned_data and
                    self.cleaned_data["datasource_type"] == CRB_ANIM_TYPE):
                self.check_crbanim_columns()

            # check template files only if provided
            if ("datasource_type" in self.cleaned_data and
                    self.cleaned_data["datasource_type"] == TEMPLATE_TYPE):
                self.check_template_file()

    def check_file_encoding(self):
        uploaded_file = self.cleaned_data['uploaded_file']

        # read one chunk of such file
        chunk = next(uploaded_file.chunks())
        magic_line = magic.from_buffer(chunk)
        file_type = magic_line.split(",")[0]

        if "UTF-8" not in file_type and "ASCII" not in file_type:
            # create message and add error
            msg = (
                "Error: file not in UTF-8 nor ASCII format: "
                "format was %s" % file_type)

            # raising an exception:
            raise forms.ValidationError(msg, code='invalid')

    def check_crbanim_columns(self):
        """Check if a CRBanim file has mandatory columns"""

        uploaded_file = self.cleaned_data['uploaded_file']

        # read one chunk of such file
        chunk = next(uploaded_file.chunks())

        # now determine if CRBanim file is valid. chunk is in binary format
        # neet to convert to a string, fortunately I've already check that
        # file is in UTF-8
        check, not_found = CRBAnimReader.is_valid(chunk.decode("utf-8"))

        if check is False:
            msg = "Error: file lacks of CRBanim mandatory columns: %s" % (
                not_found)

            # raising an exception:
            raise forms.ValidationError(msg, code='invalid')

    def check_template_file(self):
        """Check if template file has columns and sheets"""

        uploaded_file = self.cleaned_data['uploaded_file']

        chunk = next(uploaded_file.chunks())
        magic_line = magic.from_buffer(chunk)

        if 'Microsoft' not in magic_line:
            msg = "The file you provided is not a Template file"
            raise forms.ValidationError(msg, code='invalid')

        # xlrd can manage only files. Write a temporary file
        with tempfile.NamedTemporaryFile(delete=True) as tmpfile:
            for chunk in uploaded_file.chunks():
                tmpfile.write(chunk)

            # open the file with proper model
            reader = ExcelTemplateReader()
            reader.read_file(tmpfile.name)

            # check that template has at least breed, animal, sample sheets
            check, not_found = reader.check_sheets()

            if check is False:
                msg = "Error: file lacks of Template mandatory sheets: %s" % (
                    not_found)

                # raising an exception:
                raise forms.ValidationError(msg, code='invalid')

            # check that template has at least breed, animal, sample sheets
            check, not_found = reader.check_columns()

            if check is False:
                msg = "Error: file lacks of Template mandatory columns: %s" % (
                    not_found)

                # raising an exception:
                raise forms.ValidationError(msg, code='invalid')


class SubmissionForm(SubmissionFormMixin, RequestFormMixin, forms.ModelForm):
    class Meta:
        model = Submission
        fields = (
            'title',
            'description',
            'gene_bank_name',
            'gene_bank_country',
            'organization',
            'datasource_type',
            'datasource_version',
            'uploaded_file'
        )

        help_texts = {
            'uploaded_file': 'Need to be in UTF-8 or ASCII format',
            'organization': (
                """Who owns the data. Not listed? please """
                """<a href="mailto:{0}?subject=please add my organization">"""
                """contact us</a>""".format(get_admin_emails()[0])
            ),
            'datasource_type': (
                """example: CryoWeb. Need an empty template file? """
                """download it from <a href="%s%s">here</a>""" % (
                    settings.MEDIA_URL,
                    "Image_sample_empty_template_20191002.xlsx")
            )
        }


# I use forms.Form since I need to pass primary key as a field,
# and I can't use it with a modelform
class ReloadForm(SubmissionFormMixin, RequestFormMixin, forms.ModelForm):
    # custom attributes
    agree_reload = forms.BooleanField(
        label="That's fine. Replace my submission data with this file",
        help_text="You have to check this box to reload your data")

    class Meta:
        model = Submission
        fields = (
            'datasource_type',
            'datasource_version',
            'uploaded_file',
        )

        help_texts = {
            'uploaded_file': 'Need to be in UTF-8 or ASCII format',
            'datasource_type': (
                """example: CryoWeb. Need an empty template file? """
                """download it from <a href="%s%s">here</a>""" % (
                    settings.MEDIA_URL,
                    "Image_sample_empty_template_20191002.xlsx")
            )
        }


class UpdateSubmissionForm(
        UniqueSubmissionMixin, RequestFormMixin, forms.ModelForm):
    class Meta:
        model = Submission
        fields = (
            'title',
            'description',
            'gene_bank_name',
            'gene_bank_country',
            'organization',
            "datasource_type",
            "datasource_version",
        )

        help_texts = {
            'organization': (
                """Who owns the data. Not listed? please """
                """<a href="mailto:{0}?subject=please add my organization">"""
                """contact us</a>""".format(get_admin_emails()[0])
            )
        }

    def clean(self):
        # test if I have a submission with the provided data
        self.check_submission_exists()


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Tue Jul 24 15:51:05 2018
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			import magic
10			import tempfile
11
12			from django import forms
13			from django.conf import settings
14
15			from common.constants import CRB_ANIM_TYPE, TEMPLATE_TYPE
16			from common.forms import RequestFormMixin
17			from common.helpers import get_admin_emails
18			from uid.models import Submission
19			from crbanim.helpers import CRBAnimReader
20			from excel.helpers import ExcelTemplateReader
21
22
23			class UniqueSubmissionMixin():
24			def check_submission_exists(self):
25			"""Test if I already have a submission with the same data"""
26
27			# get unique attributes
28			unique_together = Submission._meta.unique_together[0]
29
30			# get submitted attributes
31			data = {key: self.cleaned_data.get(key) for key in unique_together
32			if self.cleaned_data.get(key) is not None}
33
34			# ovverride owner attribute
35			data['owner'] = self.request.user
36
37			# test for a submission object with the same attributes
38			if Submission.objects.filter(**data).exists():
39			msg = (
40			"Error: There is already a submission with the same "
41			"attributes. Please change one of the following: "
42			"Gene bank name, Gene bank country, Data source type and "
43			"Data source version")
44
45			# raising an exception:
46			raise forms.ValidationError(msg, code='invalid')
47
48
49			class SubmissionFormMixin(UniqueSubmissionMixin):
50			def clean(self):
51			# test if I have a submission with the provided data
52			self.check_submission_exists()
53
54			# I can call this method without providing a 'uploaded file'
55			# (for instance, when omitting uploaded file)
56			if "uploaded_file" in self.cleaned_data:
57			# avoid file type for excel types (is not an text file)
58			if ("datasource_type" in self.cleaned_data and
59			self.cleaned_data["datasource_type"] != TEMPLATE_TYPE):
60			self.check_file_encoding()
61
62			# check crbanim files only if provided
63			if ("datasource_type" in self.cleaned_data and
64			self.cleaned_data["datasource_type"] == CRB_ANIM_TYPE):
65			self.check_crbanim_columns()
66
67			# check template files only if provided
68			if ("datasource_type" in self.cleaned_data and
69			self.cleaned_data["datasource_type"] == TEMPLATE_TYPE):
70			self.check_template_file()
71
72			def check_file_encoding(self):
73			uploaded_file = self.cleaned_data['uploaded_file']
74
75			# read one chunk of such file
76			chunk = next(uploaded_file.chunks())
77			magic_line = magic.from_buffer(chunk)
78			file_type = magic_line.split(",")[0]
79
80			if "UTF-8" not in file_type and "ASCII" not in file_type:
81			# create message and add error
82			msg = (
83			"Error: file not in UTF-8 nor ASCII format: "
84			"format was %s" % file_type)
85
86			# raising an exception:
87			raise forms.ValidationError(msg, code='invalid')
88
89			def check_crbanim_columns(self):
90			"""Check if a CRBanim file has mandatory columns"""
91
92			uploaded_file = self.cleaned_data['uploaded_file']
93
94			# read one chunk of such file
95			chunk = next(uploaded_file.chunks())
96
97			# now determine if CRBanim file is valid. chunk is in binary format
98			# neet to convert to a string, fortunately I've already check that
99			# file is in UTF-8
100			check, not_found = CRBAnimReader.is_valid(chunk.decode("utf-8"))
101
102			if check is False:
103			msg = "Error: file lacks of CRBanim mandatory columns: %s" % (
104			not_found)
105
106			# raising an exception:
107			raise forms.ValidationError(msg, code='invalid')
108
109			def check_template_file(self):
110			"""Check if template file has columns and sheets"""
111
112			uploaded_file = self.cleaned_data['uploaded_file']
113
114			chunk = next(uploaded_file.chunks())
115			magic_line = magic.from_buffer(chunk)
116
117			if 'Microsoft' not in magic_line:
118			msg = "The file you provided is not a Template file"
119			raise forms.ValidationError(msg, code='invalid')
120
121			# xlrd can manage only files. Write a temporary file
122			with tempfile.NamedTemporaryFile(delete=True) as tmpfile:
123			for chunk in uploaded_file.chunks():
124			tmpfile.write(chunk)
125
126			# open the file with proper model
127			reader = ExcelTemplateReader()
128			reader.read_file(tmpfile.name)
129
130			# check that template has at least breed, animal, sample sheets
131			check, not_found = reader.check_sheets()
132
133			if check is False:
134			msg = "Error: file lacks of Template mandatory sheets: %s" % (
135			not_found)
136
137			# raising an exception:
138			raise forms.ValidationError(msg, code='invalid')
139
140			# check that template has at least breed, animal, sample sheets
141			check, not_found = reader.check_columns()
142
143			if check is False:
144			msg = "Error: file lacks of Template mandatory columns: %s" % (
145			not_found)
146
147			# raising an exception:
148			raise forms.ValidationError(msg, code='invalid')
149
150
151			class SubmissionForm(SubmissionFormMixin, RequestFormMixin, forms.ModelForm):
152			class Meta:
153			model = Submission
154			fields = (
155			'title',
156			'description',
157			'gene_bank_name',
158			'gene_bank_country',
159			'organization',
160			'datasource_type',
161			'datasource_version',
162			'uploaded_file'
163			)
164
165			help_texts = {
166			'uploaded_file': 'Need to be in UTF-8 or ASCII format',
167			'organization': (
168			"""Who owns the data. Not listed? please """
169			"""<a href="mailto:{0}?subject=please add my organization">"""
170			"""contact us</a>""".format(get_admin_emails()[0])
171			),
172			'datasource_type': (
173			"""example: CryoWeb. Need an empty template file? """
174			"""download it from <a href="%s%s">here</a>""" % (
175			settings.MEDIA_URL,
176			"Image_sample_empty_template_20191002.xlsx")
177			)
178			}
179
180
181			# I use forms.Form since I need to pass primary key as a field,
182			# and I can't use it with a modelform
183			class ReloadForm(SubmissionFormMixin, RequestFormMixin, forms.ModelForm):
184			# custom attributes
185			agree_reload = forms.BooleanField(
186			label="That's fine. Replace my submission data with this file",
187			help_text="You have to check this box to reload your data")
188
189			class Meta:
190			model = Submission
191			fields = (
192			'datasource_type',
193			'datasource_version',
194			'uploaded_file',
195			)
196
197			help_texts = {
198			'uploaded_file': 'Need to be in UTF-8 or ASCII format',
199			'datasource_type': (
200			"""example: CryoWeb. Need an empty template file? """
201			"""download it from <a href="%s%s">here</a>""" % (
202			settings.MEDIA_URL,
203			"Image_sample_empty_template_20191002.xlsx")
204			)
205			}
206
207
208			class UpdateSubmissionForm(
209			UniqueSubmissionMixin, RequestFormMixin, forms.ModelForm):
210			class Meta:
211			model = Submission
212			fields = (
213			'title',
214			'description',
215			'gene_bank_name',
216			'gene_bank_country',
217			'organization',
218			"datasource_type",
219			"datasource_version",
220			)
221
222			help_texts = {
223			'organization': (
224			"""Who owns the data. Not listed? please """
225			"""<a href="mailto:{0}?subject=please add my organization">"""
226			"""contact us</a>""".format(get_admin_emails()[0])
227			)
228			}
229
230			def clean(self):
231			# test if I have a submission with the provided data
232			self.check_submission_exists()
233

cnr-ibba / IMAGE-InjectTool

Push — devel ( 05b374...659f48 )

UniqueSubmissionMixin.check_submission_exists() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like