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How to use report_file method in Robotframework
Best Python code snippet using robotframework
verify_network_via_no_proxy.py
Source:verify_network_via_no_proxy.py 
1import os2import subprocess3import time4import requests5from Common import common_function6from Common.log import log7from Test_Suite.verify_network_via_http_proxy import ProxyTest8910class NoProxyTest(ProxyTest):11 def __init__(self, protocol_name='noproxy', bypass_setting=False):12 super().__init__(protocol_name, bypass_setting)1314 def set_no_proxy(self, fill_all_protocol, bypass_text, case_name, report_file):15 log.info('set bypass: {}'.format(bypass_text))16 steps = {17 'step_name': 'set {} {}'.format(self.protocol, bypass_text),18 'result': 'Fail',19 'expect': 'icon can be recognised',20 'actual': '',21 'note': ''}22 proxy_list = ['http', 'ftp', 'https']23 t = self.dns.open_dns()24 if not t:25 log.info('Failed to recognise DNS icon')26 steps['actual'] = 'Failed to recognise DNS icon'27 common_function.update_cases_result(report_file, case_name, steps)28 self.dns.close_dns()29 return30 if fill_all_protocol:31 for i in proxy_list:32 proxy_text = self.get_proxy_server('proxy3').replace(self.protocol, 'http')33 t2 = self.dns.set_value(i, proxy_text)34 if not t2:35 log.info('Failed to recognise {} icon'.format(i))36 steps['actual'] = 'Failed to recognise {} icon'.format(i)37 common_function.update_cases_result(report_file, case_name, steps)38 self.dns.close_dns()39 return40 t3 = self.dns.set_value(self.protocol, bypass_text)41 time.sleep(5)42 if not t3:43 log.info('Failed to recognise noproxy icon')44 steps['actual'] = 'Failed to recognise noproxy icon'45 common_function.update_cases_result(report_file, case_name, steps)46 self.dns.close_dns()47 return48 t4 = self.dns.close_dns()49 if not t4:50 log.info('Failed to recognise apply icon')51 steps['actual'] = 'Failed to recognise apply icon'52 common_function.update_cases_result(report_file, case_name, steps)53 return54 log.info('proxy set successfully')55 steps['actual'] = 'proxy set successfully'56 steps['result'] = 'Pass'57 common_function.update_cases_result(report_file, case_name, steps)58 return True5960 def website_test(self, url, flag, case_name, report_file):61 if flag:62 expect = 20063 msg = "verify {} can be accessed".format(url)64 else:65 expect = 'Error'66 msg = "verify {} can not be accessed".format(url)67 steps = {68 'step_name': "test {}".format(url),69 'result': '',70 'expect': 'status code should be {}'.format(expect),71 'actual': '',72 'note': ''}73 log.info(msg)74 log.info('current ip: {}'.format(common_function.get_ip()))75 log.info('get status code from {}'.format(url))76 data = self.get_website_response()77 actual = 'status code is {}'.format(data)78 log.info(actual)79 if data == expect:80 s = 'Pass'81 rs = True82 else:83 s = 'Fail'84 rs = False85 log.info('test {}'.format(s))86 steps['result'] = s87 steps['actual'] = actual88 common_function.update_cases_result(report_file, case_name, steps)89 return rs9091 @staticmethod92 def website_test222(bypass_text, accessed_list, not_accessed_list, case_name, report_file):93 log.info('wait 10s')94 time.sleep(10)95 rs = False96 steps = {97 'step_name': "test no proxy: ".format(bypass_text),98 'result': '',99 'expect': 'status code should be 200',100 'actual': '',101 'note': ''}102 for j in accessed_list:103 log.info("verify {} can be accessed".format(j))104 log.info('get data from {}'.format(j))105 try:106 data = requests.get(j, timeout=5).status_code107 except Exception:108 data = 'Error'109 log.info('status code is: {}'.format(data))110111 if data == 200:112 s = 'Pass'113 rs = True114 else:115 s = 'Fail'116 rs = False117 log.info('test {}'.format(s))118 steps['result'] = s119 common_function.update_cases_result(report_file, case_name, steps)120 for i in not_accessed_list:121 log.info("verify {} can not be accessed".format(i))122 log.info('get data from {}'.format(i))123 try:124 data = requests.get(i, timeout=5).status_code125 except Exception:126 data = 'Error'127 log.info('status code is: {}'.format(data))128 steps = {129 'step_name': "verify {} can not be accessed".format(i),130 'result': '',131 'expect': 'status code should be Error',132 'actual': data,133 'note': ''}134 if data == 'Error':135 s = 'Pass'136 rs = True137 else:138 s = 'Fail'139 rs = False140 log.info('test {}'.format(s))141 steps['result'] = s142 common_function.update_cases_result(report_file, case_name, steps)143 return rs144145 def set_proxy_bypass(self, proxy_text, case_name, report_file):146 steps = {147 'step_name': "set {}: {}".format(self.protocol, proxy_text),148 'result': 'Fail',149 'expect': 'icon can be recognised',150 'actual': '',151 'note': ''}152 t = self.dns.open_dns()153 if not t:154 steps['actual'] = 'Failed to recognise DNS icon'155 common_function.update_cases_result(report_file, case_name, steps)156 return157 t2 = self.dns.set_value(self.protocol, proxy_text)158 if not t2:159 steps['actual'] = 'Failed to recognise {} icon'.format(self.protocol)160 common_function.update_cases_result(report_file, case_name, steps)161 return162 t4 = self.dns.close_dns()163 if not t4:164 steps['actual'] = 'Failed to recognise apply icon'165 common_function.update_cases_result(report_file, case_name, steps)166 return167 self.reboot()168169 def reset_env_last(self):170 log.info('restore env default after the last step')171 # common_function.import_profile()172 self.dns.open_dns()173 for i in ['http', 'ftp', 'https']:174 self.dns.clear_text(i)175 self.dns.clear_text(self.protocol)176 self.dns.close_dns()177 subprocess.run('reboot')178 time.sleep(10)179180181def set_bypass_baidu(**kwargs):182 case_name = kwargs.get("case_name")183 report_file = kwargs.get("report_file")184 no_proxy_test = kwargs.get('obj')185 bypass_text = 'http://www.baidu.com'186 if no_proxy_test.set_no_proxy(True, bypass_text, case_name, report_file):187 no_proxy_test.reboot()188 else:189 no_proxy_test.reset_env_halfway()190 return False191192193def test_bypass_baidu(**kwargs):194 case_name = kwargs.get("case_name")195 report_file = kwargs.get("report_file")196 no_proxy_test = kwargs.get('obj')197 a = ['http://www.google.com']198 n = ['http://www.baidu.com']199 for url in a:200 if not no_proxy_test.website_test(url, True, case_name, report_file):201 no_proxy_test.reset_env_halfway()202 return False203 for url in n:204 if not no_proxy_test.website_test(url, False, case_name, report_file):205 no_proxy_test.reset_env_halfway()206 return False207 return True208209210def set_bypass_baidu_google(**kwargs):211 case_name = kwargs.get("case_name")212 report_file = kwargs.get("report_file")213 no_proxy_test = kwargs.get('obj')214 bypass_text = 'http://www.baidu.com,http://www.google.com'215 if no_proxy_test.set_no_proxy(False, bypass_text, case_name, report_file):216 no_proxy_test.reboot()217 else:218 no_proxy_test.reset_env_halfway()219 return False220221222def test_bypass_baidu_google(**kwargs):223 case_name = kwargs.get("case_name")224 report_file = kwargs.get("report_file")225 no_proxy_test = kwargs.get('obj')226 a = ['http://www.youtube.com']227 n = ['http://www.baidu.com', 'http://www.google.com']228 for url in a:229 if not no_proxy_test.website_test(url, True, case_name, report_file):230 no_proxy_test.reset_env_halfway()231 return False232 for url in n:233 if not no_proxy_test.website_test(url, False, case_name, report_file):234 no_proxy_test.reset_env_halfway()235 return False236 return True237238239def set_bypass_contain_baidu(**kwargs):240 case_name = kwargs.get("case_name")241 report_file = kwargs.get("report_file")242 no_proxy_test = kwargs.get('obj')243 bypass_text = '.baidu.com'244 if no_proxy_test.set_no_proxy(False, bypass_text, case_name, report_file):245 no_proxy_test.reboot()246 else:247 no_proxy_test.reset_env_halfway()248 return False249250251def test_bypass_contain_baidu(**kwargs):252 case_name = kwargs.get("case_name")253 report_file = kwargs.get("report_file")254 no_proxy_test = kwargs.get('obj')255 a = ['http://www.youtube.com']256 n = ['http://www.baidu.com', 'http://map.baidu.com']257 for url in a:258 if not no_proxy_test.website_test(url, True, case_name, report_file):259 no_proxy_test.reset_env_halfway()260 return False261 for url in n:262 if not no_proxy_test.website_test(url, False, case_name, report_file):263 no_proxy_test.reset_env_halfway()264 return False265 no_proxy_test.reset_env_last()266 return True267268269def finish(**kwargs):270 log.info('pave the way for the finish')271272273def start(case_name, kwargs):274 steps_list = (275 "set_bypass_baidu",276 "test_bypass_baidu",277 "set_bypass_baidu_google",278 "test_bypass_baidu_google",279 "set_bypass_contain_baidu",280 "test_bypass_contain_baidu",281 "finish"282 )283 no_proxy_test = NoProxyTest()284 result_file = common_function.get_current_dir(r'Test_Report', '{}.yaml'.format(common_function.check_ip_yaml()))285 common_function.new_cases_result(result_file, case_name)286 # no_proxy_test.tp.switch_mode()287 common_function.case_steps_run_control(steps_list, __name__, case_name=case_name, log=log,
...
oonireport.py
Source:oonireport.py
1from __future__ import print_function2import os3import sys4import json5import yaml6from twisted.python import usage7from twisted.internet import defer, task, reactor8from ooni.constants import CANONICAL_BOUNCER_ONION9from ooni.reporter import OONIBReporter, OONIBReportLog10from ooni.utils import log11from ooni.settings import config12from ooni.backend_client import BouncerClient, CollectorClient13from ooni import __version__14@defer.inlineCallbacks15def lookup_collector_client(report_header, bouncer):16 oonib_client = BouncerClient(bouncer)17 net_tests = [{18 'test-helpers': [],19 'input-hashes': [],20 'name': report_header['test_name'],21 'version': report_header['test_version'],22 }]23 result = yield oonib_client.lookupTestCollector(24 net_tests25 )26 collector_client = CollectorClient(27 address=result['net-tests'][0]['collector']28 )29 defer.returnValue(collector_client)30class NoIDFound(Exception):31 pass32def report_path_to_id(report_file):33 measurement_dir = os.path.dirname(report_file)34 measurement_id = os.path.basename(measurement_dir)35 if os.path.dirname(measurement_dir) != config.measurements_directory:36 raise NoIDFound37 return measurement_id38@defer.inlineCallbacks39def upload(report_file, collector=None, bouncer=None, measurement_id=None):40 oonib_report_log = OONIBReportLog()41 collector_client = None42 if collector:43 collector_client = CollectorClient(address=collector)44 try:45 # Try to guess the measurement_id from the file path46 measurement_id = report_path_to_id(report_file)47 except NoIDFound:48 pass49 log.msg("Attempting to upload %s" % report_file)50 if report_file.endswith(".njson"):51 report = NJSONReportLoader(report_file)52 else:53 log.warn("Uploading of YAML formatted reports will be dropped in "54 "future versions")55 report = YAMLReportLoader(report_file)56 if bouncer and collector_client is None:57 collector_client = yield lookup_collector_client(report.header,58 bouncer)59 if collector_client is None:60 if measurement_id:61 report_log = yield oonib_report_log.get_report_log(measurement_id)62 collector_settings = report_log['collector']63 print(collector_settings)64 if collector_settings is None or len(collector_settings) == 0:65 log.warn("Skipping uploading of %s since this measurement "66 "was run by specifying no collector." %67 report_file)68 defer.returnValue(None)69 elif isinstance(collector_settings, dict):70 collector_client = CollectorClient(settings=collector_settings)71 elif isinstance(collector_settings, str):72 collector_client = CollectorClient(address=collector_settings)73 else:74 log.msg("Looking up collector with canonical bouncer." % report_file)75 collector_client = yield lookup_collector_client(report.header,76 CANONICAL_BOUNCER_ONION)77 oonib_reporter = OONIBReporter(report.header, collector_client)78 log.msg("Creating report for %s with %s" % (report_file,79 collector_client.settings))80 report_id = yield oonib_reporter.createReport()81 report.header['report_id'] = report_id82 if measurement_id:83 log.debug("Marking it as created")84 yield oonib_report_log.created(measurement_id,85 collector_client.settings)86 log.msg("Writing report entries")87 for entry in report:88 yield oonib_reporter.writeReportEntry(entry)89 log.msg("Written entry")90 log.msg("Closing report")91 yield oonib_reporter.finish()92 if measurement_id:93 log.debug("Closing log")94 yield oonib_report_log.closed(measurement_id)95@defer.inlineCallbacks96def upload_all(collector=None, bouncer=None, upload_incomplete=False):97 oonib_report_log = OONIBReportLog()98 reports_to_upload = yield oonib_report_log.get_to_upload()99 for report_file, value in reports_to_upload:100 try:101 yield upload(report_file, collector, bouncer,102 value['measurement_id'])103 except Exception as exc:104 log.exception(exc)105 if upload_incomplete:106 reports_to_upload = yield oonib_report_log.get_incomplete()107 for report_file, value in reports_to_upload:108 try:109 yield upload(report_file, collector, bouncer,110 value['measurement_id'])111 except Exception as exc:112 log.exception(exc)113def print_report(report_file, value):114 print("* %s" % report_file)115 print(" %s" % value['last_update'])116@defer.inlineCallbacks117def status():118 oonib_report_log = OONIBReportLog()119 reports_to_upload = yield oonib_report_log.get_to_upload()120 print("Reports to be uploaded")121 print("----------------------")122 for report_file, value in reports_to_upload:123 print_report(report_file, value)124 reports_in_progress = yield oonib_report_log.get_in_progress()125 print("Reports in progress")126 print("-------------------")127 for report_file, value in reports_in_progress:128 print_report(report_file, value)129 reports_incomplete = yield oonib_report_log.get_incomplete()130 print("Incomplete reports")131 print("------------------")132 for report_file, value in reports_incomplete:133 print_report(report_file, value)134class ReportLoader(object):135 _header_keys = (136 'probe_asn',137 'probe_cc',138 'probe_ip',139 'probe_city',140 'test_start_time',141 'test_name',142 'test_version',143 'options',144 'input_hashes',145 'software_name',146 'software_version',147 'data_format_version',148 'report_id',149 'test_helpers',150 'annotations',151 'id'152 )153 def __iter__(self):154 return self155 def close(self):156 self._fp.close()157class YAMLReportLoader(ReportLoader):158 def __init__(self, report_filename):159 self._fp = open(report_filename)160 self._yfp = yaml.safe_load_all(self._fp)161 self.header = self._yfp.next()162 def next(self):163 try:164 return self._yfp.next()165 except StopIteration:166 self.close()167 raise StopIteration168class NJSONReportLoader(ReportLoader):169 def __init__(self, report_filename):170 self._fp = open(report_filename)171 self.header = self._peek_header()172 def _peek_header(self):173 header = {}174 first_entry = json.loads(next(self._fp))175 for key in self._header_keys:176 header[key] = first_entry.get(key, None)177 self._fp.seek(0)178 return header179 def next(self):180 try:181 entry = json.loads(next(self._fp))182 for key in self._header_keys:183 entry.pop(key, None)184 test_keys = entry.pop('test_keys')185 entry.update(test_keys)186 return entry187 except StopIteration:188 self.close()189 raise StopIteration190class Options(usage.Options):191 synopsis = """%s [options] upload | status192""" % (os.path.basename(sys.argv[0]),)193 optFlags = [194 ["default-collector", "d", "Upload the reports to the default "195 "collector that is looked up with the "196 "canonical bouncer."]197 ]198 optParameters = [199 ["configfile", "f", None,200 "Specify the configuration file to use."],201 ["collector", "c", None,202 "Specify the collector to upload the result to."],203 ["bouncer", "b", None,204 "Specify the bouncer to query for a collector."]205 ]206 def opt_version(self):207 print("oonireport version: %s" % __version__)208 sys.exit(0)209 def parseArgs(self, *args):210 if len(args) == 0:211 raise usage.UsageError(212 "Must specify at least one command"213 )214 return215 self['command'] = args[0]216 if self['command'] not in ("upload", "status"):217 raise usage.UsageError(218 "Must specify either command upload or status"219 )220 if self['command'] == "upload":221 try:222 self['report_file'] = args[1]223 except IndexError:224 self['report_file'] = None225def tor_check():226 if not config.tor.socks_port:227 log.err("Currently oonireport requires that you start Tor yourself "228 "and set the socks_port inside of ooniprobe.conf")229 sys.exit(1)230def oonireport(_reactor=reactor, _args=sys.argv[1:]):231 options = Options()232 try:233 options.parseOptions(_args)234 except Exception as exc:235 print("Error: %s" % exc)236 print(options)237 sys.exit(2)238 config.global_options = dict(options)239 config.set_paths()240 config.read_config_file()241 if options['default-collector']:242 options['bouncer'] = CANONICAL_BOUNCER_ONION243 if options['command'] == "upload" and options['report_file']:244 log.start()245 tor_check()246 return upload(options['report_file'],247 options['collector'],248 options['bouncer'])249 elif options['command'] == "upload":250 log.start()251 tor_check()252 return upload_all(options['collector'],253 options['bouncer'])254 elif options['command'] == "status":255 return status()256 else:257 print(options)258def run():259 task.react(oonireport)260if __name__ == "__main__":...
acm_analysis.py
Source:acm_analysis.py
1#2# This script perform a mca on clinical data3# except medication variable and control patients (for now)4# use the acm_clinical.R script.5# Create .tex reports6#7### REFORMAT INPUT FILES ###8"""9-> Convert stupid tsv files into clean csv files10-> Create a file with only the "Clinical" variables 11 (and no medication variable)12"""13index_to_keep = []14medication_index = []15data = open("data/clinical_i2b2trans_1.txt", "r")16output = open("data/clinical_i2b2trans_1.csv", "w")17output_clinical = open("data/clinical_data_phase_1.csv", "w")18cmpt = 019for line in data:20 line = line.split("\n")21 line = line[0]22 line_in_array = line.split("\t")23 if(cmpt == 0):24 index = 025 header_in_string = ""26 clinical_header_in_string = ""27 for element in line_in_array:28 header_in_string += str(element)+","29 element_in_array = element.split("\\")30 if("Clinical" in element_in_array or "Autoantibody" in element_in_array):31 index_to_keep.append(index)32 clinical_header_in_string += str(element)+","33 index += 134 header_in_string = header_in_string[:-1]35 header_in_string = header_in_string.replace(" ", "")36 output.write(header_in_string+"\n")37 clinical_header_in_string = clinical_header_in_string[:-1]38 clinical_header_in_string = clinical_header_in_string.replace(" ", "")39 output_clinical.write(clinical_header_in_string+"\n")40 else:41 index = 042 line_in_string = ""43 clinical_line_in_string = ""44 for element in line_in_array:45 line_in_string += str(element)+","46 if(index in index_to_keep):47 clinical_line_in_string += str(element)+","48 index += 149 line_in_string = line_in_string[:-1]50 line_in_string = line_in_string.replace(" ", "")51 output.write(line_in_string+"\n")52 clinical_line_in_string = clinical_line_in_string[:-1]53 clinical_line_in_string = clinical_line_in_string.replace(" ", "")54 output_clinical.write(clinical_line_in_string+"\n")55 cmpt += 156output_clinical.close()57output.close()58data.close()59### RUN R SCRIPT ###60"""61-> load reformated data62-> perform mca63-> create figures64"""65import os66os.system("Rscript acm_clinical.R")67### CREATE TEX FILES ###68"""69-> create a tex file for each subset of data70"""71sub_data_list = ["lung", "kidney", "nerveSystem", "skin", "muscleAndSkeletal", "comorbidity", "vascular", "gastro", "heart", "diagnosis", "autoantibody", "symptom"]72for data in sub_data_list:73 data_file_name = "latex\\"+str(data)+"_report.tex"74 report_file = open(data_file_name, "w")75 report_file.write("\\documentclass[a4paper,9pt]{extarticle}\n")76 report_file.write("\\usepackage[utf8]{inputenc}\n")77 report_file.write("\\usepackage[T1]{fontenc}\n")78 report_file.write("\\usepackage{graphicx}\n")79 report_file.write("\\usepackage{xcolor}\n")80 report_file.write("\\usepackage{tikz}\n")81 report_file.write("\\usepackage{pgfplots}\n")82 report_file.write("\\usepackage{amsmath,amssymb,textcomp}\n")83 report_file.write("\\everymath{\displaystyle}\n\n")84 report_file.write("\\usepackage{times}\n")85 report_file.write("\\renewcommand\\familydefault{\\sfdefault}\n")86 report_file.write("\\usepackage{tgheros}\n")87 report_file.write("\\usepackage[defaultmono,scale=0.85]{droidmono}\n\n")88 report_file.write("\\usepackage{multicol}\n")89 report_file.write("\\setlength{\\columnseprule}{0pt}\n")90 report_file.write("\\setlength{\\columnsep}{20.0pt}\n\n")91 report_file.write("\\usepackage{geometry}\n")92 report_file.write("\\geometry{\n")93 report_file.write("a4paper,\n")94 report_file.write("total={210mm,297mm},\n")95 report_file.write("left=10mm,right=10mm,top=10mm,bottom=15mm}\n\n")96 report_file.write("\\linespread{1.30}\n\n")97 report_file.write("\\makeatletter\n")98 report_file.write("\\renewcommand*{\\maketitle}{%\n")99 report_file.write("\\noindent\n")100 report_file.write("\\begin{minipage}{0.4\\textwidth}\n")101 report_file.write("\\begin{tikzpicture}\n")102 report_file.write("\\node[rectangle,rounded corners=6pt,inner sep=10pt,fill=blue!50!black,text width= 0.75\\textwidth] {\\color{white}\\Huge \\@title};\n")103 report_file.write("\\end{tikzpicture}\n")104 report_file.write("\\end{minipage}\n")105 report_file.write("\\hfill\n")106 report_file.write("\\begin{minipage}{0.55\\textwidth}\n")107 report_file.write("\\begin{tikzpicture}\n")108 report_file.write("\\node[rectangle,rounded corners=3pt,inner sep=10pt,draw=blue!50!black,text width= 0.95\\textwidth] {\\LARGE \\@author};\n")109 report_file.write("\\end{tikzpicture}\n")110 report_file.write("\\end{minipage}\n")111 report_file.write("\\bigskip\\bigskip\n")112 report_file.write("}%\n")113 report_file.write("\\makeatother\n\n")114 report_file.write("\\usepackage[explicit]{titlesec}\n")115 report_file.write("\\newcommand*\\sectionlabel{}\n")116 report_file.write("\\titleformat{\\section}\n")117 report_file.write("\t{\\gdef\\sectionlabel{}\n")118 report_file.write("\t\\normalfont\\sffamily\\Large\\bfseries\\scshape}\n")119 report_file.write("\t{\\gdef\\sectionlabel{\\thesection\\ }}{0pt}\n")120 report_file.write("\t{\n")121 report_file.write("\\noindent\n")122 report_file.write("\\begin{tikzpicture}\n")123 report_file.write("\\node[rectangle,rounded corners=3pt,inner sep=4pt,fill=blue!50!black,text width= 0.95\\columnwidth] {\\color{white}\\sectionlabel#1};\n")124 report_file.write("\\end{tikzpicture}\n")125 report_file.write("\t}\n")126 report_file.write("\\titlespacing*{\\section}{0pt}{15pt}{10pt}\n\n")127 report_file.write("\\usepackage{fancyhdr}\n")128 report_file.write("\\makeatletter\n")129 report_file.write("\\pagestyle{fancy}\n")130 report_file.write("\\fancyhead{}\n")131 report_file.write("\\fancyfoot[C]{\\footnotesize \\textcopyright\\ \\@date\\ \\ \\@author}\n")132 report_file.write("\\renewcommand{\\headrulewidth}{0pt}\n")133 report_file.write("\\renewcommand{\\footrulewidth}{0pt}\n")134 report_file.write("\\makeatother\\title{"+str(data)+" dataset}\n")135 report_file.write("\\author{ACM exploration}\n")136 report_file.write("\\date{2017}\n")137 report_file.write("\\begin{document}\n")138 report_file.write("\\maketitle\n\n\n")139 report_file.write("\\section{Overview - Dimmensions}\n\n")140 report_file.write("\\begin{center}\n")141 report_file.write("\\begin{tabular}{c c}\n")142 report_file.write("\t\\includegraphics[scale=0.35]{\"IMAGES/explain_variance_"+str(data)+"\"} & \\includegraphics[scale=0.35]{\"IMAGES/variable_contribution_"+str(data)+"\"} \\\\ \n")143 report_file.write("\tExplained variability & Variables conributions \\\\ \n")144 report_file.write("\\end{tabular}{}\n")145 report_file.write("\\end{center}\n\n")146 report_file.write("\\section{Overview - individuals}\n\n")147 report_file.write("\\begin{center}\n")148 report_file.write("\\begin{tabular}{c c}\n")149 report_file.write("\t\\includegraphics[scale=0.35]{\"IMAGES/individuals_disease_"+str(data)+"\"} & \\includegraphics[scale=0.35]{\"IMAGES/individuals_sex_"+str(data)+"\"} \\\\ \n")150 report_file.write("\tGrouped by disease & Grouped by sex \\\\ \n")151 report_file.write("\\end{tabular}{}\n\n")152 report_file.write("\\begin{tabular}{c}\n")153 report_file.write("\t\\includegraphics[scale=0.35]{\"IMAGES/individuals_center_"+str(data)+"\"} \\\\ \n")154 report_file.write("Grouped by center \\\\ \n")155 report_file.write("\\end{tabular}{} \n\n")156 report_file.write("\\end{center}\n")157 report_file.write("\\end{document}\n")...
artifact_report.py
Source:artifact_report.py
1import html2import os3from scripts.html_parts import *4from scripts.version_info import macCocktail_version5class ArtifactHtmlReport:6 def __init__(self, artifact_name, artifact_category=''):7 self.report_file = None8 self.report_file_path = ''9 self.script_code = ''10 self.artifact_name = artifact_name11 self.artifact_category = artifact_category # unused12 def __del__(self):13 if self.report_file:14 self.end_artifact_report()15 def start_artifact_report(self, report_folder, artifact_file_name, artifact_description=''):16 '''Creates the report HTML file and writes the artifact name as a heading'''17 self.report_file = open(os.path.join(report_folder, f'{artifact_file_name}.temphtml'), 'w', encoding='utf8')18 self.report_file.write(page_header.format(f'macCocktail - {self.artifact_name} report'))19 self.report_file.write(body_start.format(f'macCocktail {macCocktail_version}'))20 self.report_file.write(body_sidebar_setup)21 self.report_file.write(body_sidebar_dynamic_data_placeholder) # placeholder for sidebar data22 self.report_file.write(body_sidebar_trailer)23 self.report_file.write(body_main_header)24 self.report_file.write(body_main_data_title.format(f'{self.artifact_name} report', artifact_description))25 self.report_file.write(body_spinner) # Spinner till data finishes loading26 #self.report_file.write(body_infinite_loading_bar) # Not working!27 def add_script(self, script=''):28 '''Adds a default script or the script supplied'''29 if script:30 self.script_code += script31 else:32 self.script_code += default_responsive_table_script33 def write_artifact_data_table(self, data_headers, data_list, source_path, 34 write_total=True, write_location=True, html_escape=True, cols_repeated_at_bottom=True,35 table_responsive=True, table_style='', table_id='dtBasicExample'):36 ''' Writes info about data, then writes the table to html file37 Parameters38 ----------39 data_headers : List/Tuple of table column names40 data_list : List/Tuple of lists/tuples which contain rows of data41 source_path : Source path of data42 write_total : Toggles whether to write out a line of total rows written43 write_location : Toggles whether to write the location of data source44 html_escape : If True (default), then html special characters are encoded45 cols_repeated_at_bottom : If True (default), then col names are also at the bottom of the table46 table_responsive : If True (default), div class is table_responsive47 table_style : Specify table style like "width: 100%;"48 table_id : Specify an identifier string, which will be referenced in javascript49 '''50 if (not self.report_file):51 raise ValueError('Output report file is closed/unavailable!')52 num_entries = len(data_list)53 if write_total:54 self.write_minor_header(f'Total number of entries: {num_entries}', 'h6')55 if write_location:56 self.write_lead_text(f'{self.artifact_name} parsed from: {source_path}')57 self.report_file.write('<br />')58 if table_responsive:59 self.report_file.write("<div class='table-responsive'>")60 61 table_head = '<table id="{}" class="table table-striped table-bordered table-xsm" cellspacing="0" {}>'\62 '<thead>'.format(table_id, (f'style="{table_style}"') if table_style else '')63 self.report_file.write(table_head)64 self.report_file.write('<tr>' + ''.join( ('<th class="th-sm">{}</th>'.format(html.escape(str(x))) for x in data_headers) ) + '</tr>')65 self.report_file.write('</thead><tbody>')66 if html_escape:67 for row in data_list:68 self.report_file.write('<tr>' + ''.join( ('<td>{}</td>'.format(html.escape(str(x) if x != None else '')) for x in row) ) + '</tr>')69 else:70 for row in data_list:71 self.report_file.write('<tr>' + ''.join( ('<td>{}</td>'.format(str(x) if x != None else '') for x in row) ) + '</tr>')72 73 self.report_file.write('</tbody>')74 if cols_repeated_at_bottom:75 self.report_file.write('<tfoot><tr>' + ''.join( ('<th>{}</th>'.format(html.escape(str(x))) for x in data_headers) ) + '</tr></tfoot>')76 self.report_file.write('</table>')77 if table_responsive:78 self.report_file.write("</div>")79 def add_section_heading(self, heading, size='h2'):80 heading = html.escape(heading)81 data = '<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center pt-3 pb-2 mb-3 border-bottom">'\82 ' <{0} class="{0}">{1}</{0}>'\83 '</div>'84 self.report_file.write(data.format(size, heading))85 def write_minor_header(self, heading, heading_tag=''):86 heading = html.escape(heading)87 if heading_tag:88 self.report_file.write(f'<{heading_tag}>{heading}</{heading_tag}>')89 else:90 self.report_file.write(f'<h3 class="h3">{heading}</h3>')91 92 def write_lead_text(self, text):93 self.report_file.write(f'<p class="lead">{text}</p>')94 def write_raw_html(self, code):95 self.report_file.write(code)96 def end_artifact_report(self):97 if self.report_file:98 self.report_file.write(body_main_trailer + body_end + self.script_code + page_footer)99 self.report_file.close()100 self.report_file = None...
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