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How to use is_length method in assertpy
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vtfuncs.py
Source:vtfuncs.py 
1#!/bin/env python2# -*- coding: utf-8 -*-3"""4vtfuncs.py5Author: Francis Windram6Created: 27/03/197Docstr: This file contains many generic VecTraits functions with which to perform validation and other jobs8"""9import logging10from cStringIO import StringIO11from gluon.validators import *12from gluon import current13import datetime14from distutils.util import strtobool15import hashlib16from random import randint17from os.path import basename18import csv19# make it so this is only turned on when web2py is not the context20moduledebug = False21if moduledebug:22 import logzero23 logger = logzero.setup_logger(logfile="/tmp/vtfuncsdebug.log",24 formatter=logging.Formatter(25 '%(asctime)s - %(levelname)-7s - %(funcName)s - %(message)s')26 )27else:28 logger = logging.getLogger("web2py.app.vbdp")29def asciilogo():30 out = """31 32 /. 33 #@%/% ,%%*# 34 /@/ ,@@&. % 35 *%&@@&( %% #,&/ % 36 .&@@/ .#,#/ ,&@@@@@@@@@@@/ (/ ,&. &. .*%@&(/(&@&%%%(*.*/ 37 &%.(@#/* ,%* .&@@@@@@@@@@@@@&&@@&&%#(@@%*&%@@&/ .*#%%&@, # 38 %( %@* *@@@@@@@@@@@@@@%. (@@@%(((#%&@@/*.,@# ./ 39 ,# #( .@@/ .@@@@@@@@@@@@@@@@@@@@@@@*&@@@, .*%@@&/. %* 40 .&%% ,. ,@( .@@@@@@@@@@ %@@. (&. .(%@(. 41 ,@@, # /@(.@@@@@@@@@@ VECTORBYTE.ORG @@@@@&(, .&/ .( 42 ,#/. #@@/,% %@#/#@@@@@@@ @@@@@@@@@@@&(, #& %( 43 *%%.(@*,@@ /@@@&@@@@@@@@@@@(&@@@@@@@@@@@@@@@@@@@@@@@@@&(/,,,,,%@#*,*/(((/. 44 ,@@&@%.,/* .@@@@@@@@*.@@@&*. *&@@@@@@@@@@@@@@@@@@@@@@#. #@&,&, 45 (@,#. ,/#&@@@@@@@@@% (@* ,&@@@@@@@@@@@@@@@@@@@@@@# .&@@% 46 (@// #@@@@@@@@& (@@@@@@@@@@@@@@@@@@@@@@, #@@/ 47 %@&. *@@@@@& #, (@@@@@@@@@@@@@@@@@@@@@( ,@@* 48 .&@/ *&@@/ (, @(./%@@@@@@@@@@@@@@@@@@/ ,@@ 49 ,@&. .,,, (@/ #. &( *(%&@@@@@@@@@@@@@@/ ,@/ 50 *@( ,,# // %& ..,***,, .@%. 51 %& /@%. %@# ,%@@#, 52 ,@* %% ,&@&* ./&@&/. 53 .(@@/ .&, /&@#, ,#@@&(. 54 .(&@@%*. *&. /&@@#, ./&@, 55*#@@* #( ./&@@&%#(, .*#&@@&%#(/56 &, ... ...57 & 58 .( 59 *, 60 # 61 .% 62 *# 63 #* 64 #. 65 ,# 66 (, 67 #. 68 .( 69 */ 70 #, 71 ,&@@@@@, 72 ,@@@@@@@@@% 73 ,@@@@@@@@@@@, 74 *@@@@@@@@@@@/ 75 .&@@@@@@@@@@. 76 .&@@@@@@@@# 77 *#%#*.78 """79 return out80def list_to_dict(h, l):81 """82 Convert a set of two lists to a dictionary83 >>> list_to_dict(["test1", "test2"], [1, 2])84 {'test1': 1, 'test2': 2}85 >>> list_to_dict(["test1", "test2"], ["NA", "nan"])86 {'test1': '', 'test2': ''}87 """88 try:89 l = ["" if (x in {"", "NA", "na", "NaN", "nan"}) else x for x in l]90 return dict(zip(h, l))91 except TypeError:92 raise TypeError("Both headers and values must be in list format")93def data_to_dicts(h, d):94 """95 Convert a list of lists to a list of dicts given a header list96 >>> data_to_dicts(["test1", "test2"], [[1,2], [3,4]])97 [{'test1': 1, 'test2': 2}, {'test1': 3, 'test2': 4}]98 >>> data_to_dicts(["test1", "test2"], [[1,2], [3]])99 [{'test1': 1, 'test2': 2}, {'test1': 3}]100 """101 return [list_to_dict(h, x) for x in d]102def placeholder(x):103 def ph2(y):104 return [y, None]105 return ph2106class IS_BOOL():107 """108 Determines that the argument is (or can be represented as) an bool.109 True values are y, yes, t, true, on and 1.110 False values are "", n, no, f, false, off and 0.111 (Values are case-insensitive)112 Example:113 Used as::114 INPUT(_type='text', _name='name', requires=IS_BOOL())115 >>> IS_BOOL()(True)116 (True, None)117 >>> IS_BOOL()(False)118 (False, None)119 >>> IS_BOOL()("True")120 (True, None)121 >>> IS_BOOL()("False")122 (False, None)123 >>> IS_BOOL()("Yes")124 (True, None)125 >>> IS_BOOL()(100)126 (100, 'enter a boolean')127 """128 def __init__(129 self,130 error_message=None,131 ):132 if not error_message:133 self.error_message = "enter a boolean"134 else:135 self.error_message = error_message136 def __call__(self, value):137 # If value converts nicely to a bool138 try:139 v = bool(strtobool(str(value).lower()))140 return (v, None)141 except ValueError:142 pass143 return (value, self.error_message)144def validate_vectraits_rowdict(rowdict, buf):145 """146 :param rowdict:147 :param buf:148 :return:149 >>> validate_vectraits_rowdict({'originaltraitname': 'test'}, StringIO())150 (set([]), 0)151 >>> validate_vectraits_rowdict({'fail': 1}, StringIO())152 (set(['fail']), 1)153 >>> validate_vectraits_rowdict({'fail': 1, 'originaltraitname': 'test'}, StringIO())154 (set(['fail']), 1)155 >>> validate_vectraits_rowdict({'fail': 1, 'fail2': 2}, StringIO())156 (set(['fail', 'fail2']), 2)157 >>> validate_vectraits_rowdict({'originaltraitunit': "x"*256}, StringIO())158 (set(['originaltraitunit']), 1)159 >>> validate_vectraits_rowdict({'originaltraitvalue': "x"}, StringIO())160 (set(['originaltraitvalue']), 1)161 >>> validate_vectraits_rowdict({'originaltraitvalue': None}, StringIO())162 (set(['originaltraitvalue']), 2)163 >>> validate_vectraits_rowdict({'replicates': -1}, StringIO())164 (set(['replicates']), 1)165 >>> validate_vectraits_rowdict({'published': "1"}, StringIO())166 (set([]), 0)167 >>> validate_vectraits_rowdict({'published': "try again"}, StringIO())168 (set(['published']), 1)169 >>> validate_vectraits_rowdict({'contributoremail': ""}, StringIO())170 (set(['contributoremail']), 2)171 >>> validate_vectraits_rowdict({'contributoremail': "mrfrancis"}, StringIO())172 (set(['contributoremail']), 1)173 >>> validate_vectraits_rowdict({'locationdate': "04/08/1992"}, StringIO())174 (set([]), 0)175 >>> validate_vectraits_rowdict({'locationdate': "4 August 92"}, StringIO())176 (set(['locationdate']), 1)177 """178 validator_dict = {179 'originalid': [IS_NOT_EMPTY(), IS_LENGTH(20)],180 'originaltraitname': [IS_LENGTH(255)],181 'originaltraitdef': [],182 'standardisedtraitname': [IS_LENGTH(255)],183 'standardisedtraitdef': [],184 'originaltraitvalue': [IS_NOT_EMPTY(), IS_FLOAT_IN_RANGE(-1e100, 1e100)],185 'originaltraitunit': [IS_NOT_EMPTY(), IS_LENGTH(255)],186 'originalerrorpos': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],187 'originalerrorneg': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],188 'originalerrorunit': [IS_LENGTH(255)],189 'standardisedtraitvalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],190 'standardisedtraitunit': [IS_LENGTH(255)],191 'standardisederrorpos': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],192 'standardisederrorneg': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],193 'standardisederrorunit': [IS_LENGTH(255)],194 'replicates': [IS_INT_IN_RANGE(1, 2 ** 31)],195 'habitat': [IS_LENGTH(20)],196 'labfield': [IS_LENGTH(11)],197 'arenavalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],198 'arenaunit': [IS_LENGTH(255)],199 'arenavaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],200 'arenaunitsi': [IS_LENGTH(255)],201 'ambienttemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],202 'ambienttempmethod': [IS_LENGTH(255)],203 'ambienttempunit': [IS_LENGTH(255)],204 'ambientlight': [IS_LENGTH(255)],205 'ambientlightunit': [IS_LENGTH(255)],206 'secondstressor': [IS_LENGTH(255)],207 'secondstressordef': [IS_LENGTH(255)],208 'secondstressorvalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],209 'secondstressorunit': [IS_LENGTH(255)],210 'timestart': [IS_LENGTH(255)],211 'timeend': [IS_LENGTH(255)],212 'totalobstimevalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],213 'totalobstimeunit': [IS_LENGTH(255)],214 'totalobstimevaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],215 'totalobstimeunitsi': [IS_LENGTH(255)],216 'totalobstimenotes': [IS_LENGTH(255)],217 'resrepvalue': [IS_INT_IN_RANGE(-2 ** 31, 2 ** 31)],218 'resrepunit': [IS_LENGTH(255)],219 'resrepvaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],220 'resrepunitsi': [IS_LENGTH(255)],221 'location': [IS_NOT_EMPTY()],222 'locationtype': [IS_LENGTH(255)],223 'originallocationdate': [IS_LENGTH(255)],224 'locationdate': [IS_DATE(format='%d/%m/%Y', error_message='must be DD/MM/YYYY!')],225 'locationdateprecision': [IS_NOT_EMPTY(), IS_INT_IN_RANGE(0, 6)],226 'coordinatetype': [IS_LENGTH(255)],227 'latitude': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],228 'longitude': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],229 'interactor1': [IS_LENGTH(255)], # , Custom Validator, at least one filled:],230 'interactor1common': [IS_LENGTH(255)], # , Custom Validator, at least one filled:],231 'interactor1wholepart': [IS_LENGTH(255)],232 'interactor1wholeparttype': [IS_LENGTH(255)],233 'interactor1number': [IS_LENGTH(255)],234 'interactor1kingdom': [IS_LENGTH(50)],235 'interactor1phylum': [IS_LENGTH(50)],236 'interactor1class': [IS_LENGTH(50)],237 'interactor1order': [IS_LENGTH(50)],238 'interactor1family': [IS_LENGTH(50)],239 'interactor1genus': [IS_LENGTH(50)],240 'interactor1species': [IS_LENGTH(255)],241 'interactor1stage': [IS_LENGTH(255)],242 'interactor1temp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],243 'interactor1tempunit': [IS_LENGTH(255)],244 'interactor1tempmethod': [IS_LENGTH(255)],245 'interactor1growthtemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],246 'interactor1growthtempunit': [IS_LENGTH(255)],247 'interactor1growthdur': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],248 'interactor1growthdurunit': [IS_LENGTH(255)],249 'interactor1growthtype': [IS_LENGTH(255)],250 'interactor1acc': [IS_LENGTH(255)],251 'interactor1acctemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],252 'interactor1acctempnotes': [IS_LENGTH(255)],253 'interactor1acctime': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],254 'interactor1acctimenotes': [IS_LENGTH(255)],255 'interactor1acctimeunit': [IS_LENGTH(255)],256 'interactor1origtemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],257 'interactor1origtempnotes': [IS_LENGTH(255)],258 'interactor1origtime': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],259 'interactor1origtimenotes': [IS_LENGTH(255)],260 'interactor1origtimeunit': [IS_LENGTH(255)],261 'interactor1equilibtimevalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],262 'interactor1equilibtimeunit': [IS_LENGTH(255)],263 'interactor1size': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],264 'interactor1sizeunit': [IS_LENGTH(255)],265 'interactor1sizetype': [IS_LENGTH(255)],266 'interactor1sizesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],267 'interactor1sizeunitsi': [IS_LENGTH(255)],268 'interactor1denvalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],269 'interactor1denunit': [IS_LENGTH(255)],270 'interactor1dentypesi': [IS_LENGTH(255)],271 'interactor1denvaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],272 'interactor1denunitsi': [IS_LENGTH(255)],273 'interactor1massvaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],274 'interactor1massunitsi': [IS_LENGTH(255)],275 'interactor2': [IS_LENGTH(255)],276 'interactor2common': [IS_LENGTH(255)],277 'interactor2kingdom': [IS_LENGTH(50)],278 'interactor2phylum': [IS_LENGTH(50)],279 'interactor2class': [IS_LENGTH(50)],280 'interactor2order': [IS_LENGTH(50)],281 'interactor2family': [IS_LENGTH(50)],282 'interactor2genus': [IS_LENGTH(50)],283 'interactor2species': [IS_LENGTH(255)],284 'interactor2stage': [IS_LENGTH(255)],285 'interactor2temp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],286 'interactor2tempunit': [IS_LENGTH(255)],287 'interactor2tempmethod': [IS_LENGTH(255)],288 'interactor2growthtemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],289 'interactor2growthtempunit': [IS_LENGTH(255)],290 'interactor2growthdur': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],291 'interactor2growthdurunit': [IS_LENGTH(255)],292 'interactor2growthtype': [IS_LENGTH(255)],293 'interactor2acc': [IS_LENGTH(255)],294 'interactor2acctemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],295 'interactor2acctempnotes': [IS_LENGTH(255)],296 'interactor2acctime': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],297 'interactor2acctimenotes': [IS_LENGTH(255)],298 'interactor2acctimeunit': [IS_LENGTH(255)],299 'interactor2origtemp': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],300 'interactor2origtempnotes': [IS_LENGTH(255)],301 'interactor2origtime': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],302 'interactor2origtimenotes': [IS_LENGTH(255)],303 'interactor2origtimeunit': [IS_LENGTH(255)],304 'interactor2equilibtimevalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],305 'interactor2equilibtimeunit': [IS_LENGTH(255)],306 'interactor2size': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],307 'interactor2sizeunit': [IS_LENGTH(255)],308 'interactor2sizetype': [IS_LENGTH(255)],309 'interactor2sizesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],310 'interactor2sizeunitsi': [IS_LENGTH(255)],311 'interactor2denvalue': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],312 'interactor2denunit': [IS_LENGTH(255)],313 'interactor2dentypesi': [IS_LENGTH(255)],314 'interactor2denvaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],315 'interactor2denunitsi': [IS_LENGTH(255)],316 'interactor2massvaluesi': [IS_FLOAT_IN_RANGE(-1e100, 1e100)],317 'interactor2massunitsi': [IS_LENGTH(255)],318 'physicalprocess': [IS_LENGTH(255)],319 'physicalprocess_1': [IS_LENGTH(255)],320 'physicalprocess_2': [IS_LENGTH(255)],321 'citation': [IS_NOT_EMPTY(), IS_LENGTH(1500)],322 'doi': [IS_LENGTH(255)],323 'published': [IS_NOT_EMPTY(), IS_BOOL()],324 'embargorelease': [IS_NOT_EMPTY(), IS_DATE(format='%d/%m/%Y', error_message='must be DD/MM/YYYY!')],325 'figuretable': [IS_LENGTH(255)],326 'notes': [IS_LENGTH(2055)],327 'submittedby': [IS_NOT_EMPTY(), IS_LENGTH(255)],328 'contributoremail': [IS_NOT_EMPTY(), IS_EMAIL(), IS_LENGTH(255)],329 }330 notnull_cols = {331 "originalid",332 "originaltraitvalue",333 "originaltraitunit",334 "location",335 "locationdateprecision",336 "citation",337 "published",338 "embargorelease",339 "submittedby",340 "contributoremail",341 }342 notnull_trackerset = set()343 failcounter = 0344 failed_columns = set()345 for column in rowdict.keys():346 if column not in notnull_cols and rowdict[column] in {"", "NA", "na", "NaN", "nan"}:347 # Don't fail empty strings if they are not required columns348 continue349 if column in notnull_cols:350 notnull_trackerset.add(column)351 try:352 for v in validator_dict[column]: # Get validator from validator list353 if v(rowdict[column])[1]: # If it fails...354 failed_columns.add(column) # Append to failed column set355 failcounter += 1356 # Write to log and report357 logger.info('Column "{}" failed validator "{}, value:"{}"'.format(column, v.__class__.__name__,358 rowdict[column]))359 buf.write(' Column "{}" failed validator "{}, value:"{}"\n'.format(column, v.__class__.__name__,360 rowdict[column]))361 else:362 logger.debug('Column "{}" passed validator "{}"'.format(column, v.__class__.__name__))363 except KeyError:364 failed_columns.add(column) # If failed column does not exist, add to failed set365 failcounter += 1366 # Write to log and report367 logger.info('Invalid column name: "{}"'.format(column))368 buf.write(' Invalid column name: "{}"\n'.format(column))369 # Validate that either interactor1 or interactor1common is filled.370 missing_cols = notnull_cols.difference(notnull_trackerset)371 if missing_cols:372 failed_columns = failed_columns | missing_cols373 failcounter += len(missing_cols)374 logger.info('Missing essential columns: {}'.format(" ,".join(missing_cols)))375 buf.write(' Missing essential columns: {}\n'.format(", ".join(missing_cols)))376 return failed_columns, failcounter377def validate_vectraits(data, filename='test.csv'):378 """379 Validate a list of vectraits data and determine whether the form is correct for upload.380 :param data:381 :return: A dict of all columns which contain errors and on which line/s they occur382 >>> validate_vectraits([["test1", "originaltraitname"], [1,2], [3,4]])383 """384 # Print setup to log385 start = datetime.datetime.now()386 logger.info('{}'.format('-' * (38 + len(filename))))387 logger.info(' Validation of {} started at {}'.format(filename, start.strftime('%H:%M:%S')))388 logger.debug(' File length: {} rows'.format(len(data) - 1))389 logger.info('{}'.format('-' * (38 + len(filename))))390 # Print report setup to report buffer391 report = StringIO()392 report.write('\n{}\n'.format('-' * (17 + len(filename))))393 report.write(' VALIDATION REPORT\n\n')394 report.write(' File name: {}\n'.format(filename))395 report.write(' File length: {} rows\n'.format(len(data) - 1))396 report.write(' Started: {}\n'.format(start.strftime('%d-%m-%y %H:%M:%S')))397 report.write('{}\n\n'.format('-' * (17 + len(filename))))398 # Isolate header399 header = data.pop(0)400 errcounter = 0401 errlinecounter = 0402 failed = False403 # Validate header to make sure all columns are present, and reject if so.404 output = data_to_dicts(header, data)405 failed_dict = {}406 long_dataset = False407 log_triggers = {}408 if len(output) > 500:409 long_dataset = True410 trigger_list = [int(len(output) * (x / float(10))) - 1 for x in range(0, 11)]411 trigger_list[0] = 0412 percentile_list = [x * 10 for x in range(0, 11)]413 log_triggers = dict(zip(trigger_list, percentile_list))414 # Validate rows against validators using validate_vectraits_rows415 for i, item in enumerate(output):416 if long_dataset:417 if i in log_triggers.keys():418 logger.info('Validating row {}/{} ({}%)...'.format(i + 1, len(output), log_triggers[i]))419 else:420 logger.info('Validating row {}...'.format(i + 1))421 report.write('Validating row {}...\n'.format(i + 1))422 failed_items, errdelta = validate_vectraits_rowdict(item, report)423 if errdelta > 0:424 errcounter += errdelta425 errlinecounter += 1426 for entry in failed_items:427 try:428 failed_dict[entry].append(i + 1)429 except KeyError:430 failed_dict[entry] = [i + 1]431 # Return Validation dictionary432 # Finish up in log433 logger.info('{}'.format('-' * (38 + len(filename))))434 end = datetime.datetime.now()435 logger.info('Validation finished at {}'.format(end.strftime('%H:%M:%S')))436 logger.info(' Errors: {}'.format(errcounter))437 logger.info(' Failed lines: {}'.format(errlinecounter))438 time_elapsed = end - start439 logger.info('Validation time: {}'.format(time_elapsed))440 logger.info('{}'.format('-' * (38 + len(filename))))441 # Finish up in report442 report.write('\n{}\n'.format('-' * (17 + len(filename))))443 report.write(' VALIDATION COMPLETE\n\n')444 report.write(' Ended: {}\n'.format(end.strftime('%H:%M:%S')))445 report.write(' Errors: {}\n'.format(errcounter))446 report.write(' Failed lines: {}\n'.format(errlinecounter))447 report.write(' Time elapsed: {}\n'.format(time_elapsed))448 report.write('{}\n\n'.format('-' * (17 + len(filename))))449 report.write(' COLUMN REPORT \n\n')450 logger.info(failed_dict) # TODO: return this dict in the correct format.451 # TODO: convert this dict to a nice report and put into report buffer.452 for x, y in failed_dict.iteritems():453 if len(y) == 1:454 report.write('"{}" failed on row: {}\n'.format(x, y))455 else:456 report.write('"{}" failed on rows: {}\n'.format(x, y))457 if not randint(0, 19):458 report.write("\n\n\n")459 report.write(asciilogo())460 report_str = report.getvalue()461 if not long_dataset:462 logger.info(report_str)463 try:464 report.close() # TODO: Just for now465 except ValueError:466 pass467 if errcounter:468 failed = True469 return report_str, failed470class DataIntegrityError(Exception):471 pass472class VTUploadError(Exception):473 pass474def upload_vectraits_dataset(csvpath, templatepath="../static/templates/vectraits_template.csv", logger=False):475 """476 :param csvpath:477 :param templatepath:478 :return:479 >>> upload_vectraits_dataset("../uploads/tests/missingcols.csv", "path/to/nothing.csv")480 False481 >>> upload_vectraits_dataset("../uploads/tests/passing.csv")482 True483 >>> upload_vectraits_dataset("../uploads/tests/passing_long.csv")484 True485 >>> upload_vectraits_dataset("../uploads/tests/missingcols.csv")486 True487 >>> upload_vectraits_dataset("../uploads/tests/missingcols_long.csv")488 True489 """490 def md5sum(filename, blocksize=65536):491 """492 Generate md5 hash of a file in a memory-efficient manner493 :param filename: Path of file to be hashed494 :param blocksize: Size of block to read in each loop (default 64kB)495 :return: Hex representation of file hash (32B str)496 """497 hash = hashlib.md5()498 with open(filename, "rb") as f:499 for block in iter(lambda: f.read(blocksize), b""):500 hash.update(block)501 return hash.hexdigest()502 def noneadapter(x):503 """504 Return None rather than NaN to allow correct selection of null values in DAL.505 Seems hacky, but hopefully should be fast enough.506 """507 if pd.isna(x):508 return None509 return x510 import logzero511 if not logger:512 logger = logzero.setup_logger(logfile="logs/vtuploads.log",513 formatter=logging.Formatter(514 '%(asctime)s - %(levelname)-7s - %(funcName)s - %(message)s'),515 disableStderrLogger=True)516 logger.info("Turned on logger in upload_vectraits_dataset")517 # Load db connection518 db2 = current.db2519 # Simple check to make sure dataset hasn't been uploaded before.520 logger.info("Checking whether file is unique...")521 filemd5 = md5sum(csvpath)522 logger.debug("File hash = {}".format(filemd5))523 search = db2(524 (db2.dataset_hash.filehash == filemd5)525 ).select()526 if len(search) > 0:527 logger.error("File hash already in database!")528 raise VTUploadError("File hash {} for {} already in database".format(filemd5, csvpath))529 else:530 logger.info("New file! Processing...")531 logger.info("Starting data upload from {}".format(basename(csvpath)))532 import pandas as pd533 import numpy as np534 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #535 # â DATA PREP â #536 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #537 # Load csv538 logger.info("Opening data file...")539 try:540 datafile = pd.read_csv(csvpath)541 except IOError:542 logger.exception("Error opening data file {}".format(csvpath))543 raise VTUploadError("Error opening data file {}".format(csvpath))544 try:545 template = pd.read_csv(templatepath)546 except IOError:547 logger.exception("Error opening template file {}".format(templatepath))548 raise VTUploadError("Error opening template file {}".format(templatepath))549 # Check for missing columns, and if missing, insert with blank values550 logger.debug("datafile keys:{}".format(len(datafile.keys())))551 logger.debug("template keys:{}".format(len(template.keys())))552 difflist = list(set(template.keys()).difference(set(datafile.keys())))553 if difflist:554 logger.info("Creating missing columns: {}".format(difflist))555 missing_cols = pd.DataFrame(np.nan, index=range(0, len(datafile.index)), columns=difflist)556 logger.debug(missing_cols.dtypes)557 datafile = pd.concat([datafile, missing_cols], axis=1)558 # Create id fields in main table559 def idcat(*args):560 return " ".join([str(x) for x in args])561 datafile["locationidstr"] = np.vectorize(idcat)(datafile.location, datafile.locationtype,562 datafile.originallocationdate, datafile.locationdate,563 datafile.locationdateprecision, datafile.latitude,564 datafile.longitude)565 datafile["traitdescripidstr"] = np.vectorize(idcat)(datafile.physicalprocess, datafile.physicalprocess_1,566 datafile.physicalprocess_2)567 datafile["expcondidstr"] = np.vectorize(idcat)(datafile.replicates, datafile.habitat, datafile.labfield,568 datafile.arenavalue, datafile.arenaunit, datafile.arenavaluesi,569 datafile.arenaunitsi, datafile.resrepvalue, datafile.resrepunit,570 datafile.resrepvaluesi, datafile.resrepunitsi)571 datafile["interactor1idstr"] = np.vectorize(idcat)(datafile.interactor1kingdom,572 datafile.interactor1phylum,573 datafile.interactor1class,574 datafile.interactor1order,575 datafile.interactor1family,576 datafile.interactor1genus,577 datafile.interactor1species)578 datafile["interactor2idstr"] = np.vectorize(idcat)(datafile.interactor2kingdom,579 datafile.interactor2phylum,580 datafile.interactor2class,581 datafile.interactor2order,582 datafile.interactor2family,583 datafile.interactor2genus,584 datafile.interactor2species)585 datafile["sourceinfoidstr"] = np.vectorize(idcat)(datafile.originalid,586 datafile.figuretable,587 datafile.submittedby,588 datafile.contributoremail,589 datafile.citation,590 datafile.doi,591 datafile.published,592 datafile.embargorelease)593 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #594 # â LOCATIONS â #595 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #596 # Extract unique locations597 logger.info("Extracting unique locations...")598 locationnames = ["location", "locationtype", "originallocationdate", "locationdate", "locationdateprecision",599 "latitude", "longitude", "locationidstr"]600 locations = datafile[locationnames]601 locations_uni = locations.drop_duplicates().reset_index(drop=True)602 locations_uni["locationid"] = np.int(-1)603 # locations = locations.fillna(None) # Cannot replace with None as None is a different type to float64...604 # logger.debug(locations_uni)605 inscount = 0606 foundcoconut = 0607 errcount = 0608 for index, entry in locations_uni.iterrows():609 locationid = np.nan610 search = db2(611 (db2.studylocation.locationtext == noneadapter(entry.location)) &612 (db2.studylocation.locationtype == noneadapter(entry.locationtype)) &613 (db2.studylocation.originallocationdate == noneadapter(entry.originallocationdate)) &614 (db2.studylocation.locationdate == noneadapter(entry.locationdate)) &615 (db2.studylocation.locationdateprecision == noneadapter(entry.locationdateprecision)) &616 (db2.studylocation.latitude == noneadapter(entry.latitude)) &617 (db2.studylocation.longitude == noneadapter(entry.longitude))618 ).select(db2.studylocation.locationid)619 # logger.debug(len(search))620 if len(search) < 1:621 # insert into db622 inscount += 1623 locationid = db2.studylocation.insert(locationtext=noneadapter(entry.location),624 locationtype=noneadapter(entry.locationtype),625 originallocationdate=noneadapter(entry.originallocationdate),626 locationdate=noneadapter(entry.locationdate),627 locationdateprecision=noneadapter(entry.locationdateprecision),628 latitude=noneadapter(entry.latitude),629 longitude=noneadapter(entry.longitude))630 logger.debug("Inserted location id {}".format(locationid))631 elif len(search) == 1:632 # Use the found id633 foundcoconut += 1634 locationid = search[0].locationid635 else:636 errcount += 1637 logger.warning("Ambiguous location entry provided:\n\n{}\n\n{}".format(entry, search))638 locationid = search[0].locationid639 locations_uni.ix[index, "locationid"] = locationid640 logger.debug("--- TABLE: studylocation ---")641 logger.debug("Inserted: {}".format(inscount))642 logger.debug("Found: {}".format(foundcoconut))643 logger.debug("Errors: {}".format(errcount))644 logger.debug("----------------------------")645 # left join locations_uni to main df on locationidstr646 locations_uni = locations_uni[["locationidstr", "locationid"]]647 datafile = pd.merge(datafile, locations_uni, on="locationidstr", how="left")648 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #649 # â TAXONOMY â #650 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #651 # Extract unique Taxonomy entries652 logger.info("Extracting unique taxonomic groups...")653 interactor1_names = ["interactor1kingdom", "interactor1phylum", "interactor1class", "interactor1order",654 "interactor1family", "interactor1genus", "interactor1species", "interactor1idstr"]655 interactor2_names = ["interactor2kingdom", "interactor2phylum", "interactor2class", "interactor2order",656 "interactor2family", "interactor2genus", "interactor2species", "interactor2idstr"]657 interactor1_tax = datafile[interactor1_names]658 interactor2_tax = datafile[interactor2_names]659 # Rename columns in both dfs and merge together660 interactor1_tax.columns = ["taxkingdom", "taxphylum", "taxclass", "taxorder",661 "taxfamily", "taxgenus", "taxspecies", "interactoridstr"]662 interactor2_tax.columns = ["taxkingdom", "taxphylum", "taxclass", "taxorder",663 "taxfamily", "taxgenus", "taxspecies", "interactoridstr"]664 interactor_tax = pd.concat([interactor1_tax, interactor2_tax])665 interactor_tax_uni = interactor_tax.drop_duplicates().reset_index(drop=True)666 interactor_tax_uni["interactorxid"] = np.int(-1)667 inscount = 0668 foundcoconut = 0669 errcount = 0670 for index, entry in interactor_tax_uni.iterrows():671 interactorxid = np.nan672 search = db2(673 (db2.taxonomy.taxkingdom == noneadapter(entry.taxkingdom)) &674 (db2.taxonomy.taxphylum == noneadapter(entry.taxphylum)) &675 (db2.taxonomy.taxclass == noneadapter(entry.taxclass)) &676 (db2.taxonomy.taxorder == noneadapter(entry.taxorder)) &677 (db2.taxonomy.taxfamily == noneadapter(entry.taxfamily)) &678 (db2.taxonomy.taxgenus == noneadapter(entry.taxgenus)) &679 (db2.taxonomy.taxspecies == noneadapter(entry.taxspecies))680 ).select(db2.taxonomy.taxid)681 if len(search) < 1:682 # insert into db683 inscount += 1684 interactorxid = db2.taxonomy.insert(taxkingdom=noneadapter(entry.taxkingdom),685 taxphylum=noneadapter(entry.taxphylum),686 taxclass=noneadapter(entry.taxclass),687 taxorder=noneadapter(entry.taxorder),688 taxfamily=noneadapter(entry.taxfamily),689 taxgenus=noneadapter(entry.taxgenus),690 taxspecies=noneadapter(entry.taxspecies))691 logger.debug("Inserted taxonomy id {}".format(interactorxid))692 elif len(search) == 1:693 # Use the found id694 foundcoconut += 1695 interactorxid = search[0].taxid696 else:697 errcount += 1698 logger.warning("Ambiguous taxonomy entry provided:\n\n{}\n\n{}".format(entry, search))699 interactorxid = search[0].taxid700 interactor_tax_uni.ix[index, "interactorxid"] = interactorxid701 logger.debug("----- TABLE: taxonomy ------")702 logger.debug("Inserted: {}".format(inscount))703 logger.debug("Found: {}".format(foundcoconut))704 logger.debug("Errors: {}".format(errcount))705 logger.debug("----------------------------")706 # left join interactor_tax_uni to main df on interactoridstr707 interactor_tax_uni = interactor_tax_uni[["interactoridstr", "interactorxid"]]708 # We need to use a slightly different method here as this foreignid gets left-joined twice, once for each spp709 datafile = pd.merge(datafile, interactor_tax_uni, left_on="interactor1idstr", right_on="interactoridstr",710 how="left")711 datafile = datafile.rename(columns={"interactorxid": "interactor1id"})712 datafile = pd.merge(datafile, interactor_tax_uni, left_on="interactor2idstr", right_on="interactoridstr",713 how="left")714 datafile = datafile.rename(columns={"interactorxid": "interactor2id"})715 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #716 # â TRAITDESC â #717 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #718 # Extract unique trait descriptions719 logger.info("Extracting unique trait descriptions...")720 traitdescrip_names = ["physicalprocess", "physicalprocess_1", "physicalprocess_2", "traitdescripidstr"]721 traitdescrips = datafile[traitdescrip_names]722 traitdescrips_uni = traitdescrips.drop_duplicates().reset_index(drop=True)723 traitdescrips_uni["traitdescriptionid"] = np.int(-1)724 inscount = 0725 foundcoconut = 0726 errcount = 0727 for index, entry in traitdescrips_uni.iterrows():728 traitdescriptionid = np.nan729 search = db2(730 (db2.traitdescription.physicalprocess == noneadapter(entry.physicalprocess)) &731 (db2.traitdescription.physicalprocess_1 == noneadapter(entry.physicalprocess_1)) &732 (db2.traitdescription.physicalprocess_2 == noneadapter(entry.physicalprocess_2))733 ).select(db2.traitdescription.traitdesid)734 if len(search) < 1:735 # insert into db736 inscount += 1737 traitdescriptionid = db2.traitdescription.insert(physicalprocess=noneadapter(entry.physicalprocess),738 physicalprocess_1=noneadapter(entry.physicalprocess_1),739 physicalprocess_2=noneadapter(entry.physicalprocess_2))740 logger.debug("Inserted traitdescrip id {}".format(traitdescriptionid))741 elif len(search) == 1:742 # Use the found id743 foundcoconut += 1744 traitdescriptionid = search[0].traitdesid745 else:746 errcount += 1747 logger.warning("Ambiguous trait description entry provided:\n\n{}\n\n{}".format(entry, search))748 traitdescriptionid = search[0].traitdesid749 traitdescrips_uni.ix[index, "traitdescriptionid"] = traitdescriptionid750 logger.debug("--- TABLE: traitdescription ---")751 logger.debug("Inserted: {}".format(inscount))752 logger.debug("Found: {}".format(foundcoconut))753 logger.debug("Errors: {}".format(errcount))754 logger.debug("-------------------------------")755 # left join traitdescrips_uni to main df on traitdescripidstr756 traitdescrips_uni = traitdescrips_uni[["traitdescripidstr", "traitdescriptionid"]]757 datafile = pd.merge(datafile, traitdescrips_uni, on="traitdescripidstr", how="left")758 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #759 # â SOURCE INFO SETUP â #760 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #761 # Extract source info (incl. contrib & citation ids)762 logger.info("Extracting source information...")763 source_names = ["originalid", "figuretable", "submittedby", "contributoremail",764 "citation", "doi", "published", "embargorelease", "sourceinfoidstr"]765 source = datafile[source_names]766 source_uni = source.drop_duplicates().reset_index(drop=True)767 source_uni["sourceinfoid"] = np.int(-1)768 source_uni["contributoridstr"] = np.vectorize(idcat)(source_uni.submittedby, source_uni.contributoremail)769 source_uni["citationidstr"] = np.vectorize(idcat)(source_uni.citation, source_uni.doi,770 source_uni.published, source_uni.embargorelease)771 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #772 # â CONTRIBUTORS â #773 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #774 # Extract contributor775 logger.info("Extracting contributors...")776 contrib_names = ["submittedby", "contributoremail", "contributoridstr"]777 contrib = source_uni[contrib_names]778 contrib_uni = contrib.drop_duplicates().reset_index(drop=True)779 contrib_uni["contributorid"] = np.int(-1)780 inscount = 0781 foundcoconut = 0782 errcount = 0783 for index, entry in contrib_uni.iterrows():784 contributorid = np.nan785 search = db2(786 (db2.contributor.submittedby == noneadapter(entry.submittedby)) &787 (db2.contributor.contributoremail == noneadapter(entry.contributoremail))788 ).select(db2.contributor.contributorid)789 if len(search) < 1:790 # insert into db791 inscount += 1792 contributorid = db2.contributor.insert(submittedby=noneadapter(entry.submittedby),793 contributoremail=noneadapter(entry.contributoremail))794 logger.debug("Inserted contributor id {}".format(contributorid))795 elif len(search) == 1:796 # Use the found id797 foundcoconut += 1798 contributorid = search[0].contributorid799 else:800 errcount += 1801 logger.warning("Ambiguous contributor entry provided:\n\n{}\n\n{}".format(entry, search))802 contributorid = search[0].contributorid803 contrib_uni.ix[index, "contributorid"] = contributorid804 logger.debug("---- TABLE: contributor ----")805 logger.debug("Inserted: {}".format(inscount))806 logger.debug("Found: {}".format(foundcoconut))807 logger.debug("Errors: {}".format(errcount))808 logger.debug("----------------------------")809 # left join contrib_uni to source df on contributoridstr810 contrib_uni = contrib_uni[["contributoridstr", "contributorid"]]811 source_uni = pd.merge(source_uni, contrib_uni, on="contributoridstr", how="left")812 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #813 # â CITATIONS â #814 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #815 # Extract citation816 logger.info("Extracting citations...")817 citation_names = ["citation", "doi", "published", "embargorelease", "citationidstr"]818 citation = source_uni[citation_names]819 citation_uni = citation.drop_duplicates().reset_index(drop=True)820 citation_uni["citationid"] = np.int(-1)821 inscount = 0822 foundcoconut = 0823 errcount = 0824 for index, entry in citation_uni.iterrows():825 citationid = np.nan826 search = db2(827 (db2.citation.citation == noneadapter(entry.citation)) &828 (db2.citation.doi == noneadapter(entry.doi)) &829 (db2.citation.published == noneadapter(entry.published)) &830 (db2.citation.embargorelease == noneadapter(entry.embargorelease))831 ).select(db2.citation.citationid)832 if len(search) < 1:833 # insert into db834 inscount += 1835 citationid = db2.citation.insert(citation=noneadapter(entry.citation),836 doi=noneadapter(entry.doi),837 published=noneadapter(entry.published),838 embargorelease=noneadapter(entry.embargorelease))839 logger.debug("Inserted citation id {}".format(citationid))840 elif len(search) == 1:841 # Use the found id842 foundcoconut += 1843 citationid = search[0].citationid844 else:845 errcount += 1846 logger.warning("Ambiguous citation entry provided:\n\n{}\n\n{}".format(entry, search))847 citationid = search[0].citationid848 citation_uni.ix[index, "citationid"] = citationid849 logger.debug("----- TABLE: citation ------")850 logger.debug("Inserted: {}".format(inscount))851 logger.debug("Found: {}".format(foundcoconut))852 logger.debug("Errors: {}".format(errcount))853 logger.debug("----------------------------")854 # left join contrib_uni to source df on contributoridstr855 citation_uni = citation_uni[["citationidstr", "citationid"]]856 source_uni = pd.merge(source_uni, citation_uni, on="citationidstr", how="left")857 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #858 # â SOURCE INFO UPLOAD â #859 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #860 inscount = 0861 foundcoconut = 0862 errcount = 0863 for index, entry in source_uni.iterrows():864 sourceinfoid = np.nan865 search = db2(866 (db2.sourceinfo.originalid == noneadapter(entry.originalid)) &867 (db2.sourceinfo.contributorid == noneadapter(entry.contributorid)) &868 (db2.sourceinfo.citationid == noneadapter(entry.citationid)) &869 (db2.sourceinfo.figuretable == noneadapter(entry.figuretable))870 ).select(db2.sourceinfo.sourceid)871 if len(search) < 1:872 # insert into db873 inscount += 1874 sourceinfoid = db2.sourceinfo.insert(originalid=noneadapter(entry.originalid),875 contributorid=noneadapter(entry.contributorid),876 citationid=noneadapter(entry.citationid),877 figuretable=noneadapter(entry.figuretable))878 logger.debug("Inserted source info id {}".format(sourceinfoid))879 elif len(search) == 1:880 # Use the found id881 foundcoconut += 1882 sourceinfoid = search[0].sourceid883 else:884 errcount += 1885 logger.warning("Ambiguous source info entry provided:\n\n{}\n\n{}".format(entry, search))886 sourceinfoid = search[0].sourceid887 source_uni.ix[index, "sourceinfoid"] = sourceinfoid888 logger.debug("---- TABLE: sourceinfo -----")889 logger.debug("Inserted: {}".format(inscount))890 logger.debug("Found: {}".format(foundcoconut))891 logger.debug("Errors: {}".format(errcount))892 logger.debug("----------------------------")893 # left join source_uni to main df on sourceinfoidstr894 source_uni = source_uni[["sourceinfoidstr", "sourceinfoid"]]895 datafile = pd.merge(datafile, source_uni, on="sourceinfoidstr", how="left")896 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #897 # â EXP COND â #898 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #899 # Extract experimental conditions900 logger.info("Extracting experimental conditions...")901 expcond_names = ["replicates", "habitat", "labfield", "arenavalue", "arenaunit", "arenavaluesi", "arenaunitsi",902 "resrepvalue", "resrepunit", "resrepvaluesi", "resrepunitsi", "expcondidstr"]903 expcond = datafile[expcond_names]904 expcond_uni = expcond.drop_duplicates().reset_index(drop=True)905 expcond_uni["expcondid"] = np.int(-1)906 # logger.debug(locations_uni)907 inscount = 0908 foundcoconut = 0909 errcount = 0910 for index, entry in expcond_uni.iterrows():911 expcondid = np.nan912 search = db2(913 (db2.experimentalconditions.replicates == noneadapter(entry.replicates)) &914 (db2.experimentalconditions.habitat == noneadapter(entry.habitat)) &915 (db2.experimentalconditions.labfield == noneadapter(entry.labfield)) &916 (db2.experimentalconditions.arenavalue == noneadapter(entry.arenavalue)) &917 (db2.experimentalconditions.arenaunit == noneadapter(entry.arenaunit)) &918 (db2.experimentalconditions.arenavaluesi == noneadapter(entry.arenavaluesi)) &919 (db2.experimentalconditions.arenaunitsi == noneadapter(entry.arenaunitsi)) &920 (db2.experimentalconditions.resrepvalue == noneadapter(entry.resrepvalue)) &921 (db2.experimentalconditions.resrepunit == noneadapter(entry.resrepunit)) &922 (db2.experimentalconditions.resrepvaluesi == noneadapter(entry.resrepvaluesi)) &923 (db2.experimentalconditions.resrepunitsi == noneadapter(entry.resrepunitsi))924 ).select(db2.experimentalconditions.experimentid)925 if len(search) < 1:926 # insert into db927 inscount += 1928 expcondid = db2.experimentalconditions.insert(replicates=noneadapter(entry.replicates),929 habitat=noneadapter(entry.habitat),930 labfield=noneadapter(entry.labfield),931 arenavalue=noneadapter(entry.arenavalue),932 arenaunit=noneadapter(entry.arenaunit),933 arenavaluesi=noneadapter(entry.arenavaluesi),934 arenaunitsi=noneadapter(entry.arenaunitsi),935 resrepvalue=noneadapter(entry.resrepvalue),936 resrepunit=noneadapter(entry.resrepunit),937 resrepvaluesi=noneadapter(entry.resrepvaluesi),938 resrepunitsi=noneadapter(entry.resrepunitsi))939 logger.debug("Inserted experimentalconditions id {}".format(expcondid))940 elif len(search) == 1:941 # Use the found id942 foundcoconut += 1943 expcondid = search[0].experimentid944 else:945 errcount += 1946 # logger.warning("Ambiguous experimentalconditions entry provided:\n\n{}\n\n{}".format(entry, search))947 expcondid = search[0].experimentid948 expcond_uni.ix[index, "expcondid"] = expcondid949 logger.debug("--- TABLE: experimentalconditions ---")950 logger.debug("Inserted: {}".format(inscount))951 logger.debug("Found: {}".format(foundcoconut))952 logger.debug("Errors: {}".format(errcount))953 logger.debug("-------------------------------------")954 # left join expcond_uni to main df on expcondidstr955 expcond_uni = expcond_uni[["expcondidstr", "expcondid"]]956 datafile = pd.merge(datafile, expcond_uni, on="expcondidstr", how="left")957 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #958 # â MAIN TABLE â #959 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #960 # Make maintable (incl ids for all other tables)961 logger.info("Creating maintable data entries...")962 maintable_names = ['originalid', 'originaltraitname', 'originaltraitdef', 'standardisedtraitname',963 'standardisedtraitdef', 'originaltraitvalue', 'originaltraitunit', 'originalerrorpos',964 'originalerrorneg', 'originalerrorunit', 'standardisedtraitvalue', 'standardisedtraitunit',965 'standardisederrorpos', 'standardisederrorneg', 'standardisederrorunit', 'ambienttemp',966 'ambienttempmethod', 'ambienttempunit', 'ambientlight', 'ambientlightunit', 'secondstressor',967 'secondstressordef', 'secondstressorvalue', 'secondstressorunit', 'timestart', 'timeend',968 'totalobstimevalue', 'totalobstimeunit', 'totalobstimevaluesi', 'totalobstimeunitsi',969 'totalobstimenotes', 'interactor1', 'interactor1common', 'interactor1wholepart',970 'interactor1wholeparttype', 'interactor1number', 'interactor1stage', 'interactor1temp',971 'interactor1tempunit', 'interactor1tempmethod', 'interactor1growthtemp',972 'interactor1growthtempunit', 'interactor1growthdur', 'interactor1growthdurunit',973 'interactor1growthtype', 'interactor1acc', 'interactor1acctemp', 'interactor1acctempnotes',974 'interactor1acctime', 'interactor1acctimenotes', 'interactor1acctimeunit', 'interactor1origtemp',975 'interactor1origtempnotes', 'interactor1origtime', 'interactor1origtimenotes',976 'interactor1origtimeunit', 'interactor1equilibtimevalue', 'interactor1equilibtimeunit',977 'interactor1size', 'interactor1sizeunit', 'interactor1sizetype', 'interactor1sizesi',978 'interactor1sizeunitsi', 'interactor1denvalue', 'interactor1denunit', 'interactor1dentypesi',979 'interactor1denvaluesi', 'interactor1denunitsi', 'interactor1massvaluesi',980 'interactor1massunitsi', 'interactor2', 'interactor2common', 'interactor2stage',981 'interactor2temp', 'interactor2tempunit', 'interactor2tempmethod', 'interactor2growthtemp',982 'interactor2growthtempunit', 'interactor2growthdur', 'interactor2growthdurunit',983 'interactor2growthtype', 'interactor2acc', 'interactor2acctemp', 'interactor2acctempnotes',984 'interactor2acctime', 'interactor2acctimenotes', 'interactor2acctimeunit', 'interactor2origtemp',985 'interactor2origtempnotes', 'interactor2origtime', 'interactor2origtimenotes',986 'interactor2origtimeunit', 'interactor2equilibtimevalue', 'interactor2equilibtimeunit',987 'interactor2size', 'interactor2sizeunit', 'interactor2sizetype', 'interactor2sizesi',988 'interactor2sizeunitsi', 'interactor2denvalue', 'interactor2denunit', 'interactor2dentypesi',989 'interactor2denvaluesi', 'interactor2denunitsi', 'interactor2massvaluesi',990 'interactor2massunitsi', 'locationid', 'interactor1id', 'interactor2id', 'traitdescriptionid',991 'sourceinfoid', 'expcondid', 'notes']992 maintable = datafile[maintable_names]993 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #994 # â UPLOAD â #995 # âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ #996 # Upload to db997 logger.info("Uploading data to db...")998 inscount = 0999 log_triggers = {}1000 short_dataset = True1001 if len(maintable) > 100:1002 short_dataset = False1003 trigger_list = [int(len(maintable) * (x / float(10))) - 1 for x in range(0, 11)]1004 trigger_list[0] = 01005 percentile_list = [x * 10 for x in range(0, 11)]1006 log_triggers = dict(zip(trigger_list, percentile_list))1007 for index, entry in maintable.iterrows():1008 if not short_dataset:1009 if index in log_triggers.keys():1010 logger.info('Uploading row {}/{} ({}%)...'.format(index + 1, len(maintable), log_triggers[index]))1011 # insert into db1012 inscount += 11013 mainid = db2.maintable.insert(1014 originalid=noneadapter(entry.originalid),1015 originaltraitname=noneadapter(entry.originaltraitname),1016 originaltraitdef=noneadapter(entry.originaltraitdef),1017 standardisedtraitname=noneadapter(entry.standardisedtraitname),1018 standardisedtraitdef=noneadapter(entry.standardisedtraitdef),1019 originaltraitvalue=noneadapter(entry.originaltraitvalue),1020 originaltraitunit=noneadapter(entry.originaltraitunit),1021 originalerrorpos=noneadapter(entry.originalerrorpos),1022 originalerrorneg=noneadapter(entry.originalerrorneg),1023 originalerrorunit=noneadapter(entry.originalerrorunit),1024 standardisedtraitvalue=noneadapter(entry.standardisedtraitvalue),1025 standardisedtraitunit=noneadapter(entry.standardisedtraitunit),1026 standardisederrorpos=noneadapter(entry.standardisederrorpos),1027 standardisederrorneg=noneadapter(entry.standardisederrorneg),1028 standardisederrorunit=noneadapter(entry.standardisederrorunit),1029 ambienttemp=noneadapter(entry.ambienttemp),1030 ambienttempmethod=noneadapter(entry.ambienttempmethod),1031 ambienttempunit=noneadapter(entry.ambienttempunit),1032 ambientlight=noneadapter(entry.ambientlight),1033 ambientlightunit=noneadapter(entry.ambientlightunit),1034 secondstressor=noneadapter(entry.secondstressor),1035 secondstressordef=noneadapter(entry.secondstressordef),1036 secondstressorvalue=noneadapter(entry.secondstressorvalue),1037 secondstressorunit=noneadapter(entry.secondstressorunit),1038 timestart=noneadapter(entry.timestart),1039 timeend=noneadapter(entry.timeend),1040 totalobstimevalue=noneadapter(entry.totalobstimevalue),1041 totalobstimeunit=noneadapter(entry.totalobstimeunit),1042 totalobstimevaluesi=noneadapter(entry.totalobstimevaluesi),1043 totalobstimeunitsi=noneadapter(entry.totalobstimeunitsi),1044 totalobstimenotes=noneadapter(entry.totalobstimenotes),1045 interactor1=noneadapter(entry.interactor1),1046 interactor1common=noneadapter(entry.interactor1common),1047 interactor1wholepart=noneadapter(entry.interactor1wholepart),1048 interactor1wholeparttype=noneadapter(entry.interactor1wholeparttype),1049 interactor1number=noneadapter(entry.interactor1number),1050 interactor1stage=noneadapter(entry.interactor1stage),1051 interactor1temp=noneadapter(entry.interactor1temp),1052 interactor1tempunit=noneadapter(entry.interactor1tempunit),1053 interactor1tempmethod=noneadapter(entry.interactor1tempmethod),1054 interactor1growthtemp=noneadapter(entry.interactor1growthtemp),1055 interactor1growthtempunit=noneadapter(entry.interactor1growthtempunit),1056 interactor1growthdur=noneadapter(entry.interactor1growthdur),1057 interactor1growthdurunit=noneadapter(entry.interactor1growthdurunit),1058 interactor1growthtype=noneadapter(entry.interactor1growthtype),1059 interactor1acc=noneadapter(entry.interactor1acc),1060 interactor1acctemp=noneadapter(entry.interactor1acctemp),1061 interactor1acctempnotes=noneadapter(entry.interactor1acctempnotes),1062 interactor1acctime=noneadapter(entry.interactor1acctime),1063 interactor1acctimenotes=noneadapter(entry.interactor1acctimenotes),1064 interactor1acctimeunit=noneadapter(entry.interactor1acctimeunit),1065 interactor1origtemp=noneadapter(entry.interactor1origtemp),1066 interactor1origtempnotes=noneadapter(entry.interactor1origtempnotes),1067 interactor1origtime=noneadapter(entry.interactor1origtime),1068 interactor1origtimenotes=noneadapter(entry.interactor1origtimenotes),1069 interactor1origtimeunit=noneadapter(entry.interactor1origtimeunit),1070 interactor1equilibtimevalue=noneadapter(entry.interactor1equilibtimevalue),1071 interactor1equilibtimeunit=noneadapter(entry.interactor1equilibtimeunit),1072 interactor1size=noneadapter(entry.interactor1size),1073 interactor1sizeunit=noneadapter(entry.interactor1sizeunit),1074 interactor1sizetype=noneadapter(entry.interactor1sizetype),1075 interactor1sizesi=noneadapter(entry.interactor1sizesi),1076 interactor1sizeunitsi=noneadapter(entry.interactor1sizeunitsi),1077 interactor1denvalue=noneadapter(entry.interactor1denvalue),1078 interactor1denunit=noneadapter(entry.interactor1denunit),1079 interactor1dentypesi=noneadapter(entry.interactor1dentypesi),1080 interactor1denvaluesi=noneadapter(entry.interactor1denvaluesi),1081 interactor1denunitsi=noneadapter(entry.interactor1denunitsi),1082 interactor1massvaluesi=noneadapter(entry.interactor1massvaluesi),1083 interactor1massunitsi=noneadapter(entry.interactor1massunitsi),1084 interactor2=noneadapter(entry.interactor2),1085 interactor2common=noneadapter(entry.interactor2common),1086 interactor2stage=noneadapter(entry.interactor2stage),1087 interactor2temp=noneadapter(entry.interactor2temp),1088 interactor2tempunit=noneadapter(entry.interactor2tempunit),1089 interactor2tempmethod=noneadapter(entry.interactor2tempmethod),1090 interactor2growthtemp=noneadapter(entry.interactor2growthtemp),1091 interactor2growthtempunit=noneadapter(entry.interactor2growthtempunit),1092 interactor2growthdur=noneadapter(entry.interactor2growthdur),1093 interactor2growthdurunit=noneadapter(entry.interactor2growthdurunit),1094 interactor2growthtype=noneadapter(entry.interactor2growthtype),1095 interactor2acc=noneadapter(entry.interactor2acc),1096 interactor2acctemp=noneadapter(entry.interactor2acctemp),1097 interactor2acctempnotes=noneadapter(entry.interactor2acctempnotes),1098 interactor2acctime=noneadapter(entry.interactor2acctime),1099 interactor2acctimenotes=noneadapter(entry.interactor2acctimenotes),1100 interactor2acctimeunit=noneadapter(entry.interactor2acctimeunit),1101 interactor2origtemp=noneadapter(entry.interactor2origtemp),1102 interactor2origtempnotes=noneadapter(entry.interactor2origtempnotes),1103 interactor2origtime=noneadapter(entry.interactor2origtime),1104 interactor2origtimenotes=noneadapter(entry.interactor2origtimenotes),1105 interactor2origtimeunit=noneadapter(entry.interactor2origtimeunit),1106 interactor2equilibtimevalue=noneadapter(entry.interactor2equilibtimevalue),1107 interactor2equilibtimeunit=noneadapter(entry.interactor2equilibtimeunit),1108 interactor2size=noneadapter(entry.interactor2size),1109 interactor2sizeunit=noneadapter(entry.interactor2sizeunit),1110 interactor2sizetype=noneadapter(entry.interactor2sizetype),1111 interactor2sizesi=noneadapter(entry.interactor2sizesi),1112 interactor2sizeunitsi=noneadapter(entry.interactor2sizeunitsi),1113 interactor2denvalue=noneadapter(entry.interactor2denvalue),1114 interactor2denunit=noneadapter(entry.interactor2denunit),1115 interactor2dentypesi=noneadapter(entry.interactor2dentypesi),1116 interactor2denvaluesi=noneadapter(entry.interactor2denvaluesi),1117 interactor2denunitsi=noneadapter(entry.interactor2denunitsi),1118 interactor2massvaluesi=noneadapter(entry.interactor2massvaluesi),1119 interactor2massunitsi=noneadapter(entry.interactor2massunitsi),1120 locationid=noneadapter(entry.locationid),1121 interactor1id=noneadapter(entry.interactor1id),1122 interactor2id=noneadapter(entry.interactor2id),1123 traitdescriptionid=noneadapter(entry.traitdescriptionid),1124 sourceinfoid=noneadapter(entry.sourceinfoid),1125 expcondid=noneadapter(entry.expcondid),1126 notes=noneadapter(entry.notes),1127 )1128 logger.debug("----- TABLE: maintable -----")1129 logger.debug("Inserted: {}".format(inscount))1130 logger.debug("----------------------------")1131 logger.info("Data upload complete.")1132 logger.info("Adding successful hash to db")1133 hashid = db2.dataset_hash.insert(filehash=filemd5,1134 filename=basename(csvpath)[:128])1135 logger.info(asciilogo())1136 return True1137def eod_upload_run(logger=False):1138 """Upload all validated datafiles, then move to 'complete' when complete or 'errored' when errored."""1139 import os1140 import time1141 import shutil1142 import logzero1143 if not logger:1144 logger = logzero.setup_logger(logfile="logs/vtuploads.log",1145 formatter=logging.Formatter(1146 '%(asctime)s - %(levelname)-7s - %(funcName)s - %(message)s'),1147 disableStderrLogger=True)1148 logger.info("Turned on logger in eod_upload_run")1149 success = True1150 # Load db connection1151 db2 = current.db21152 logger.info("Starting upload run at {}".format(time.strftime("%H:%M:%S", time.gmtime())))1153 # Find all files in validated and set up paths1154 cwd = os.getcwd()1155 logger.info("CWD: {}".format(cwd)) # Just to check that the cwd is where we think it is when the scheduler is run...1156 uploadpath = os.path.join(cwd, "applications/VectorBiteDataPlatform/uploads")1157 validatedpath = os.path.join(uploadpath, "validated")1158 successpath = os.path.join(uploadpath, "completed")1159 failpath = os.path.join(uploadpath, "errored")1160 templatepath = os.path.join(cwd, "applications/VectorBiteDataPlatform/static/templates/vectraits_template.csv")1161 uploadfiles = [f for f in os.listdir(validatedpath) if os.path.isfile(os.path.join(validatedpath, f))]1162 logger.debug("Files to upload: {}".format(uploadfiles))1163 # Run upload_vectraits_dataset on each file1164 for candidatefile in uploadfiles:1165 candidatepath = os.path.join(validatedpath, candidatefile)1166 logger.info("Starting upload of {}".format(candidatepath))1167 uploadsuccess = False1168 try:1169 uploadsuccess = upload_vectraits_dataset(candidatepath, templatepath, logger)1170 db2.commit()1171 except VTUploadError:1172 logger.exception("Handled error encountered when processing {}".format(candidatefile))1173 success = False1174 db2.rollback()1175 except Exception:1176 logger.exception("Unhandled error encountered when processing {}".format(candidatefile))1177 success = False1178 db2.rollback()1179 try:1180 if uploadsuccess:1181 logger.info("Upload successful")1182 shutil.move(candidatepath, os.path.join(successpath, candidatefile))1183 else:1184 logger.info("Upload failed")1185 shutil.move(candidatepath, os.path.join(failpath, candidatefile))1186 except IOError:1187 logger.exception("File move failed, remains in validated folder.")1188 logger.info("Completed upload run at {}".format(time.strftime("%H:%M:%S", time.gmtime())))1189 return success1190if __name__ == "__main__":1191 # run testing code1192 import time1193 moduledebug = True1194 if moduledebug:1195 import logzero1196 logger = logzero.setup_logger(logfile="/tmp/vtfuncsdebug.log",1197 formatter=logging.Formatter(1198 '%(asctime)s - %(levelname)-7s - %(funcName)s - %(message)s'),1199 level=logging.DEBUG1200 )1201 else:1202 logger = logging.getLogger("web2py.app.vbdp")1203 logger.info("Test commencing at {}".format(time.strftime("%H:%M:%S", time.gmtime())))1204 # upload_vectraits_dataset("applications/VectorBiteDataPlatform/uploads/tests/passing_superlong.csv",1205 # "applications/VectorBiteDataPlatform/static/templates/vectraits_template.csv")1206 eod_upload_run(logger)...
db.py
Source:db.py
1# -*- coding: utf-8 -*-23#########################################################################4##Written by C. S. Schroeder, A Theory of Publishing5##Copyright (C) 2011 Equimind Financial LLC.6##7##Permission is hereby granted, free of charge, to any8##person obtaining a copy of this software and associated9##documentation files (the "Software"), to deal in the10##Software without restriction, including without limitation11##the rights to use, copy, modify, merge, publish,12##distribute, sublicense, and/or sell copies of the13##Software, and to permit persons to whom the Software is14##furnished to do so, subject to the following conditions:15##16##The above copyright notice and this permission notice17##shall be included in all copies or substantial portions of18##the Software.19##20##THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY21##KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE22##WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR23##PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS24##OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR25##OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR26##OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE27##SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.28##29## Powered by web2py, Thanks Massimo!30#########################################################################3132if not request.env.web2py_runtime_gae: 33 ## if NOT running on Google App Engine use SQLite or other DB34 db = DAL('sqlite://storage.sqlite') 35else:36 ## connect to Google BigTable (optional 'google:datastore://namespace')37 db = DAL('google:datastore') 38 ## store sessions and tickets there39 session.connect(request, response, db = db) 40 ## or store session in Memcache, Redis, etc.41 ## from gluon.contrib.memdb import MEMDB42 ## from google.appengine.api.memcache import Client43 ## session.connect(request, response, db = MEMDB(Client()))4445## by default give a view/generic.extension to all actions from localhost46## none otherwise. a pattern can be 'controller/function.extension'47response.generic_patterns = ['*'] if request.is_local else []48T.current_languages = ['en', 'en-en']49#T.force('es-es')50#########################################################################51## Here is sample code if you need for52## - email capabilities53## - authentication (registration, login, logout, ... )54## - authorization (role based authorization)55## - services (xml, csv, json, xmlrpc, jsonrpc, amf, rss)56## - old style crud actions57## (more options discussed in gluon/tools.py)58#########################################################################5960from gluon.tools import Auth, Crud, Service, PluginManager, prettydate61auth = Auth(db, hmac_key=Auth.get_or_create_key()) 62crud, service, plugins = Crud(db), Service(), PluginManager()6364## create all tables needed by auth if not custom tables65auth.define_tables() 6667if len(db(db.auth_group.role == 'admin').select())<1:68 db.auth_group.insert(role= 'admin', description="For administration of memebers")69if len(db(db.auth_group.role == 'reviewer').select())<1:70 db.auth_group.insert(role= 'reviewer', description="For submitting reviews")7172## user must be admin of application73## configure email74mail=auth.settings.mailer75## configure auth policy76auth.settings.registration_requires_verification = False77auth.settings.registration_requires_approval = False78auth.settings.reset_password_requires_verification = True7980## if you need to use OpenID, Facebook, MySpace, Twitter, Linkedin, etc.81## register with janrain.com, write your domain:api_key in private/janrain.key82##from gluon.contrib.login_methods.rpx_account import use_janrain83##use_janrain(auth,filename='private/janrain.key')8485#########################################################################86## Define your tables below (or better in another model file) for example87##88## >>> db.define_table('mytable',Field('myfield','string'))89##90## Fields can be 'string','text','password','integer','double','boolean'91## 'date','time','datetime','blob','upload', 'reference TABLENAME'92## There is an implicit 'id integer autoincrement' field93## Consult manual for more options, validators, etc.94##95## More API examples for controllers:96##97## >>> db.mytable.insert(myfield='value')98## >>> rows=db(db.mytable.myfield=='value').select(db.mytable.ALL)99## >>> for row in rows: print row.id, row.myfield100#########################################################################101102103db.define_table('reviewer', 104 Field('screenname', 'string', length=(30,2)),105 Field('userid', db.auth_user),106 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 107 Field('city', 'string', length=25, requires=IS_LENGTH(25,2)), 108 Field('state', 'string', length=25,requires=IS_LENGTH(25,2)), 109 Field('country', 'string', length=25,requires=IS_LENGTH(25,2)), 110 Field('loves', 'string', length=200,requires=IS_LENGTH(200,2)), 111 Field('likes', 'string', length=200,requires=IS_LENGTH(200,2)), 112 Field('dislikes', 'string', length=200,requires=IS_LENGTH(200,2)), 113 Field('about_me', 'text'))114115db.define_table('region', 116 Field('name', 'string', length=25,requires=IS_LENGTH(25,2)),117 Field('blurb', 'string', length=500,requires=IS_LENGTH(500,2)),118 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 119 Field('city', 'string', length=25, requires=IS_LENGTH(25,2)), 120 Field('state', 'string', length=25,requires=IS_LENGTH(25,2)), 121 Field('country', 'string', length=25,requires=IS_LENGTH(25,2)), 122 Field('product_categories', 'string', length=400,requires=IS_LENGTH(400,2)), 123 Field('product_lines', 'string', length=400,requires=IS_LENGTH(400,2)), 124 Field('famous_for', 'string', length=200,requires=IS_LENGTH(200,2)), 125 Field('about', 'text'))126127db.define_table('place', 128 Field('name', 'string', length=25,requires=IS_LENGTH(25,2)), 129 Field('blurb', 'string', length=500, requires=IS_LENGTH(500,2)),130 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 131 Field('region', db.region, required=True, requires=IS_IN_DB(db, 'region.id', '%(name)s')),132 Field('type', 'string', length=25, requires=IS_IN_SET([T('computing'), T('audio-visual'), T('mobile')])),133 Field('description', 'string', length=400,requires=IS_LENGTH(400,2)),134 Field('cost', 'string', length=200,requires=IS_LENGTH(200,2)), 135 Field('about', 'text'))136137db.define_table('event', 138 Field('name', 'string', length=25,requires=IS_LENGTH(25,2)), 139 Field('blurb', 'string', length=500,requires=IS_LENGTH(500,2)),140 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 141 Field('region', db.region, required=True, requires=IS_IN_DB(db, 'region.id', '%(name)s')),142 Field('place', db.place, requires=IS_NULL_OR(IS_IN_DB(db, 'place.id', '%(name)s'))),143 Field('description', 'string', length=200,requires=IS_LENGTH(200,2)),144 Field('cost', 'string', length=200,requires=IS_LENGTH(200,2)), 145 Field('about', 'text'))146147148class RatingWidget(SQLFORM.widgets.options):149 @staticmethod150 def widget(field, value, **attributes):151 attr = SQLFORM.widgets.options._attributes(field, {}, **attributes)152153 if isinstance(field.requires, IS_NULL_OR)\154 and hasattr(field.requires.other, 'options'):155 opts = [TD(INPUT(_type='radio', _name=field.name,156 _value='', value=value), '')]157 options = field.requires.other.options()158 elif hasattr(field.requires, 'options'):159 opts = []160 options = field.requires.options()161 else:162 raise SyntaxError, 'widget cannot determine options of %s' % field163 opts += [TD(INPUT(_type='radio', _name=field.name,164 _value=k, value=value), '') for (k, v) in options]165 return TABLE(TR(*(['low']+opts+['high'])), **attr) 166167168import datetime169170db.define_table('region_review', 171 Field('ref_id', db.region, required=True, requires=IS_IN_DB(db, 'region.id', '%(name)s')),172 Field('blurb', 'string', length=500,requires=IS_LENGTH(500,2)),173 Field('author', db.reviewer, requires=IS_IN_DB(db, 'reviewer.id', "%(screenname)s")),174 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 175 Field('photo1', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 176 Field('photo2', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 177 Field('title', 'string', length=100,requires=IS_LENGTH(100,2)), 178 Field('subject', 'string', length=25,requires=IS_LENGTH(25,2)), 179 Field('the_good', 'string', length=250,requires=IS_LENGTH(250,2)), 180 Field('the_bad', 'string', length=250,requires=IS_LENGTH(250,2)), 181 Field('date', 'datetime', default=datetime.datetime.now()), 182 Field('text', 'text'), 183 Field('rating', 'integer', default=1, requires=IS_IN_SET([1,2,3,4,5]), widget=RatingWidget.widget),184 Field('publish', 'boolean', default=True)185 )186187db.define_table('place_review', 188 Field('ref_id', db.place, required=True, requires=IS_IN_DB(db, 'place.id', '%(name)s')),189 Field('blurb', 'string', length=500,requires=IS_LENGTH(500,2)),190 Field('author', db.reviewer, requires=IS_IN_DB(db, 'reviewer.id', "%(screenname)s")),191 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 192 Field('photo1', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 193 Field('photo2', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 194 Field('title', 'string', length=100,requires=IS_LENGTH(100,2)), 195 Field('subject', 'string', length=25,requires=IS_LENGTH(25,2)), 196 Field('the_good', 'string', length=250,requires=IS_LENGTH(250,2)), 197 Field('the_bad', 'string', length=250,requires=IS_LENGTH(250,2)), 198 Field('date', 'datetime', default=datetime.datetime.now()), 199 Field('text', 'text'),200 Field('rating', 'integer', default=1, requires=IS_IN_SET([1,2,3,4,5]), widget=RatingWidget.widget),201 Field('publish', 'boolean', default=True)202 )203204db.define_table('event_review', 205 Field('ref_id', db.event, required=True, requires=IS_IN_DB(db, 'event.id', '%(name)s')),206 Field('blurb', 'string', length=500,requires=IS_LENGTH(500,2)),207 Field('author', db.reviewer, requires=IS_IN_DB(db, 'reviewer.id', "%(screenname)s")),208 Field('photo', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 209 Field('photo1', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 210 Field('photo2', 'upload', length=(130000, 1024), requires=[IS_IMAGE(), IS_LENGTH(130000, 1024)]), 211 Field('title', 'string', length=100,requires=IS_LENGTH(100,2)), 212 Field('subject', 'string', length=25,requires=IS_LENGTH(25,2)), 213 Field('the_good', 'string', length=250,requires=IS_LENGTH(250,2)), 214 Field('the_bad', 'string', length=250,requires=IS_LENGTH(250,2)), 215 Field('type', 'string', length=25,requires=IS_LENGTH(25,2)), 216 Field('date', 'datetime', default=datetime.datetime.now()), 217 Field('text', 'text'),218 Field('rating', 'integer', default=1, requires=IS_IN_SET([1,2,3,4,5]), widget=RatingWidget.widget),219 Field('publish', 'boolean', default=True)220 )221222223#############224##The following is Open source code modified for this application225##Taken from the "simple comments" web2py plugin.226##No licensing applicable227#############228import datetime229230db.define_table('plugin_simple_comments_comment',231 Field('tablename',232 writable=False,readable=False),233 Field('record_id','integer',234 writable=False,readable=False),235 Field('body','text', requires=[IS_NOT_EMPTY(), IS_LENGTH(1000, 1)],label=T('Your comment'), widget=SQLFORM.widgets.text.widget),236 Field('created_by',db.auth_user,default=auth.user_id,237 readable=False,writable=False),238 Field('created_on','datetime',default=datetime.datetime.now(),
...
test_predicates.py
Source:test_predicates.py
...3def test_unit_predicates():4 assert not is_(0)(1)5 assert (is_(0) | is_(1))(1)6 assert (is_none | is_(0))(0)7 assert is_length(1 * units.cm)8 assert is_length(30.0 * units.mm)...
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