How to use validate_attachments method in mailosaur-python

Best Python code snippet using mailosaur-python_python

test_integration.py

Source:test_integration.py

...91    if validator.same_columns_in_ref_and_test() and validator.all_test_columns_in_ref_and_test() and validator.check_samples_present() and validator.check_columns_match():92        return True93    else:94        return False95def validate_attachments(issue, file_to_find, validate_content=False):96    validation_status = 'Unknown'97    if len(issue.attachments) > 0:98        attachment_found = False99        for attachment in issue.attachments:100            if attachment.filename == file_to_find:101                attachment_found = True102                with tempfile.TemporaryDirectory() as tmpdir:103                    attachment.download(savepath=tmpdir, filename=file_to_find)104                    if os.path.getsize(os.path.join(tmpdir, file_to_find)) > 0:105                        if validate_content is True:106                            ref_csv = 'tests/ref_csvs/{}'.format(file_to_find)107                            content_ok = validate_csv_content(query_csv=os.path.join(tmpdir, file_to_find),108                                                              ref_csv='tests/ref_csvs/{}'.format(file_to_find))109                            if content_ok is True:110                                validation_status = 'Validated'111                            else:112                                validation_status = 'Reference content does not match query.'113                        else:114                                validation_status = 'Validated'115                    else:116                        validation_status = 'Uploaded file has zero size.'117        if attachment_found is False:118            validation_status = 'Could not find {}'.format(file_to_find)119    else:120        validation_status = 'No attachments, validation failed.'121    return validation_status122def md5(fname):123    """124    Gets MD5sum for a file - use for quick and dirty comparisons of files.125    Hooray for stackoverflow: https://stackoverflow.com/questions/3431825/generating-an-md5-checksum-of-a-file126    """127    hash_md5 = hashlib.md5()128    with open(fname, "rb") as f:129        for chunk in iter(lambda: f.read(4096), b""):130            hash_md5.update(chunk)131    return hash_md5.hexdigest()132def validate_csv_in_zip(issue, zip_file, report_file, ref_csv):133    """134    Crude validation that checks that CSV contents are the exact same between some folder in a zip135    file and a reference that we keep on hand.136    :param issue:137    :param zip_file:138    :param report_file:139    :param ref_csv:140    :return:141    """142    validation_status = 'Unknown'143    if len(issue.attachments) > 0:144        attachment_found = False145        for attachment in issue.attachments:146            if attachment.filename == zip_file:147                attachment_found = True148                with tempfile.TemporaryDirectory() as tmpdir:149                    downloaded_zip = os.path.join(tmpdir, zip_file)150                    attachment.download(savepath=tmpdir, filename=zip_file)151                    zipped_archive = zipfile.ZipFile(downloaded_zip)152                    zipped_archive.extractall(path=tmpdir)153                    if md5(ref_csv) == md5(os.path.join(tmpdir, report_file)):154                        validation_status = 'Validated'155                    else:156                        validation_status = 'Contents not identical. Check on what changed.'157        if attachment_found is False:158            validation_status = 'Could not find {}'.format(zip_file)159    else:160        validation_status = 'No attachments, validation failed.'161    return validation_status162def validate_ftp_upload(ftp_file, min_file_size=0):163    try:164        with tempfile.TemporaryDirectory() as tmpdir:165            urllib.request.urlretrieve(os.path.join(OUTGOING_FTP, ftp_file),166                                       os.path.join(tmpdir, ftp_file))167            if os.path.getsize(os.path.join(tmpdir, ftp_file)) > min_file_size:168                validation_status = 'Validated'169            else:170                validation_status = 'Uploaded file has zero size.'171    except:  # If file doesn't exist, something went wrong. Set validation status accordingly.172        validation_status = 'No uploaded file found on FTP'173    return validation_status174def monitor_issues(redmine, issue_dict, timeout):175    """176    Monitors issues for completion.177    :param redmine: Instantiated redmine instance.178    :param issue_dict: Dictionary created by create_test_issues (issue subjects as keys, issue IDs as values)179    :param timeout: Number of seconds to wait for all issues to finish running180    :return: Dictionary with issue subjects as keys, and some sort of status message for each as values181    """182    all_complete = False183    total_time_taken = 0184    increment = 30  # Check on issues every increment seconds185    # Create dictionary to track progress of each issue created.186    issues_validated = dict()187    for issue_subject in issue_dict:188        issues_validated[issue_subject] = 'Unknown'189    # Now loop through all the things!190    while all_complete is False and total_time_taken < timeout:191        logging.info('Checking tasks for completion')192        all_complete = True  # Set flag to true - if any of our issues are not finished, this gets set back to False193        # Check all issues for completion.194        for issue_subject in issue_dict:195            issue_id = issue_dict[issue_subject]196            issue = redmine.issue.get(issue_id, include=['attachments'])197            # AMR Summary #####198            if issue_subject == 'amrsummary' and issues_validated[issue_subject] == 'Unknown':199                if issue.status.id == 4:  # 4 corresponds to issue being complete.200                    issues_validated[issue_subject] = validate_attachments(issue, 'amr_summary.csv',201                                                                           validate_content=True)202                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))203                else:  # If hasn't finished yet, just wait!204                    all_complete = False205            # CLARK #####206            elif issue_subject == 'autoclark' and issues_validated[issue_subject] == 'Unknown':207                if issue.status.id == 4:208                    # TODO: Validate xlsx files?209                    issues_validated[issue_subject] = validate_attachments(issue, 'abundance.xlsx')210                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))211                else:212                    all_complete = False213            # ECGF #####214            elif issue_subject == 'ecgf' and issues_validated[issue_subject] == 'Unknown':215                if issue.status.id == 4:216                    issues_validated[issue_subject] = validate_csv_in_zip(issue=issue,217                                                                          zip_file='eCGF_output_{}.zip'.format(issue.id),218                                                                          report_file='{}_summary_report.csv'.format(issue.id),219                                                                          ref_csv='/mnt/nas2/redmine/applications/OLCRedmineAutomator/tests/ref_csvs/124_summary_report.csv')  # Hardcoded paths stink, fix me!220                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))221                else:222                    all_complete = False223            # EC TYPER #####224            elif issue_subject == 'ec_typer' and issues_validated[issue_subject] == 'Unknown':225                if issue.status.id == 4:226                    issues_validated[issue_subject] = validate_attachments(issue, 'ec_typer_report.tsv',227                                                                           validate_content=True)228                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))229                else:230                    all_complete = False231            # EXTERNAL RETRIEVE #####232            elif issue_subject == 'externalretrieve' and issues_validated[issue_subject] == 'Unknown':233                if issue.status.id == 4:234                    issues_validated[issue_subject] = validate_ftp_upload('{}.zip'.format(issue.id),235                                                                          min_file_size=1000)236                else:237                    all_complete = False238            # DIVERSITREE #####239            elif issue_subject == 'diversitree' and issues_validated[issue_subject] == 'Unknown':240                if issue.status.id == 4:241                    # TODO: HTML validation - should just be able to md5sum or something on file contents.242                    issues_validated[issue_subject] = validate_attachments(issue, 'diversitree_report.html')243                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))244                else:245                    all_complete = False246            # GENESEEKR #####247            elif issue_subject == 'geneseekr' and issues_validated[issue_subject] == 'Unknown':248                if issue.status.id == 4:249                    issues_validated[issue_subject] = validate_csv_in_zip(issue=issue,250                                                                          zip_file='geneseekr_output.zip',251                                                                          report_file='2014-SEQ-0276_blastn_sixteens_full.tsv',252                                                                          ref_csv='/mnt/nas2/redmine/applications/OLCRedmineAutomator/tests/ref_csvs/2014-SEQ-0276_blastn_sixteens_full.tsv')  # Hardcoded paths stink, fix me!253                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))254                else:255                    all_complete = False256            # POINTFINDER #####257            elif issue_subject == 'pointfinder' and issues_validated[issue_subject] == 'Unknown':258                if issue.status.id == 4:259                    issues_validated[issue_subject] = validate_csv_in_zip(issue=issue,260                                                                          zip_file='pointfinder_output.zip',261                                                                          report_file='PointFinder_results_summary.csv',262                                                                          ref_csv='/mnt/nas2/redmine/applications/OLCRedmineAutomator/tests/ref_csvs/PointFinder_results_summary.csv')  # Hardcoded paths stink, fix me!263                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))264                else:265                    all_complete = False266            # PROKKA #####267            elif issue_subject == 'prokka' and issues_validated[issue_subject] == 'Unknown':268                if issue.status.id == 4:269                    issues_validated[issue_subject] = validate_ftp_upload('prokka_output_{}.zip'.format(issue.id),270                                                                          min_file_size=1000)271                else:272                    all_complete = False273            # RESFINDER #####274            elif issue_subject == 'resfinder' and issues_validated[issue_subject] == 'Unknown':275                if issue.status.id == 4:276                    issues_validated[issue_subject] = validate_attachments(issue, 'resfinder_blastn.xlsx')277                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))278                else:279                    all_complete = False280            # SIPPRVERSE #####281            elif issue_subject == 'sipprverse' and issues_validated[issue_subject] == 'Unknown':282                if issue.status.id == 4:283                    issues_validated[issue_subject] = validate_csv_in_zip(issue=issue,284                                                                          zip_file='sipprverse_output.zip',285                                                                          report_file='mlst.csv',286                                                                          ref_csv='/mnt/nas2/redmine/applications/OLCRedmineAutomator/tests/ref_csvs/mlst.csv')  # Hardcoded paths stink, fix me!287                    logging.info('{} is complete, status is {}'.format(issue_subject, issues_validated[issue_subject]))288                else:289                    all_complete = False290            # STARAMR #####...

middleware.py

Source:middleware.py

...14from .tasks import run_judge15class OJSubmissionSerializer(serializers.Serializer):16    post = serializers.CharField()17    def validate_post(self, content):18        self.validate_attachments()19        starter = self.context['starter']20        thread = self.context['thread']21        uid = self.context['uid']22        ps = Problem.objects.filter(uid=UUID(uid))23        if ps.count() == 0:24            raise serializers.ValidationError(_('No such problem'))25        problem = ps[0]26        self.problem = problem27        sol = Solution.objects.filter(problem=problem, starter=starter)28        self.solution = None29        if sol.exists():30            solution = sol[0]31            if solution.thread != thread:32                raise serializers.ValidationError(_(33                    'Only one solution should be '34                    'submitted to the same problem'))35            self.solution = solution36    def validate_attachments(self):37        ids = self.context['attachments']38        attachments = Attachment.objects.filter(id__in=ids)39        if len(attachments) == 0:40            raise serializers.ValidationError(_('Must provide a attachment'))41        elif len(attachments) != 1:42            raise serializers.ValidationError(43                _('Only one attachment required'))44        upfile = attachments[0]45        if str(upfile.filetype) != 'ZIP':46            raise serializers.ValidationError(_('Only support ZIP file'))47        self.subject_path = osp.join(settings.MEDIA_ROOT, str(upfile.file))48    def post_save(self):49        problem = self.problem50        solution = self.solution51        starter = self.context['starter']52        thread = self.context['thread']53        if solution is None:54            solution = Solution.objects.create(problem=problem,55                                               starter=starter,56                                               thread=thread)57        solution.submit_counter = F('submit_counter') + 158        solution.save()59        problem_attachments = problem.thread.first_post.attachments60        target_id = None61        for a in problem_attachments:62            if a['filetype'] == 'SIEZIP':63                target_id = a['id']64                break65        target_path = Attachment.objects.get(id=target_id).file66        target_path = osp.join(settings.MEDIA_ROOT, str(target_path))67        run_judge.delay(thread.id, solution.id, self.subject_path,68                        problem.module_name, target_path, problem.judge_name,69                        problem.order_type)70class OJSubmissionMiddleware(PostingMiddleware):71    def get_serializer(self):72        return OJSubmissionSerializer(73            data=self.request.data,74            context={75                'mode': self.mode,76                'post': self.post,77                'thread': self.thread,78                'starter': self.user,79                'attachments': self.request.data['attachments'],80                'uid': get_problem_uid(self.request.data['post']),81            }82        )83    def use_this_middleware(self):84        if self.mode == PostingEndpoint.EDIT:85            is_sub_cate = str(self.post.category) == settings.OJ_SUB_CATE_NAME86        elif self.mode == PostingEndpoint.START:87            cate_id = self.request.data['category']88            is_sub_cate = Category.objects.filter(89                id=cate_id, name=settings.OJ_SUB_CATE_NAME).count() == 190        else:91            is_sub_cate = False92        uid = get_problem_uid(self.request.data['post'])93        if is_sub_cate and self.post.is_first_post and uid is not None:94            return True95        return False96    def post_save(self, serializer):97        serializer.post_save()98class OJReleaseSerializer(serializers.Serializer):99    post = serializers.CharField()100    def validate_attachments(self):101        ids = self.context['attachments']102        attachments = Attachment.objects.filter(id__in=ids)103        siezip_cnt = 0104        for upfile in attachments:105            if str(upfile.filetype) == 'SIEZIP':106                siezip_cnt += 1107        if siezip_cnt != 1:108            raise serializers.ValidationError(109                _('Requires one SIEZIP file'))110    def validate_post(self, content):111        self.validate_attachments()112        try:113            order_type, judge_name, module_name = extract_problem_kwargs(114                content)115        except Exception as e:116            raise serializers.ValidationError(_('Judge argument error'))117        self.order_type = order_type118        self.judge_name = judge_name119        self.module_name = module_name120    def save(self):121        thread = self.context['thread']122        starter = self.context['user']123        post = self.context['post']124        problem, created = Problem.objects.get_or_create(125            thread=thread, starter=starter)...

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