File size: 71,853 Bytes
06555b5 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 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 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 |
# metadata.py
"""Functionality to read and write metadata for CSV files.
This module implements (partially) the W3C recommendation
"Metadata Vocabulary for Tabular Data".
.. seealso:: https://www.w3.org/TR/tabular-metadata/
"""
import io
import re
import json
import shutil
import decimal
import pathlib
import typing
import zipfile
import operator
import warnings
import functools
import itertools
import contextlib
import collections
from urllib.parse import urljoin, urlparse, urlunparse
from language_tags import tags
import attr
import requests
import uritemplate
from . import utils
from .datatypes import DATATYPES
from .dsv import Dialect as BaseDialect, UnicodeReaderWithLineNumber, UnicodeWriter
from .frictionless import DataPackage
from . import jsonld
DEFAULT = object()
__all__ = [
'TableGroup',
'Table', 'Column', 'ForeignKey',
'Link', 'NaturalLanguage',
'Datatype',
'is_url',
'CSVW',
]
NAMESPACES = {
'csvw': 'http://www.w3.org/ns/csvw#',
'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
'xsd': 'http://www.w3.org/2001/XMLSchema#',
'dc': 'http://purl.org/dc/terms/',
'dcat': 'http://www.w3.org/ns/dcat#',
'prov': 'http://www.w3.org/ns/prov#',
'schema': 'http://schema.org/',
}
CSVW_TERMS = """Cell
Column
Datatype
Dialect
Direction
ForeignKey
JSON
NumericFormat
Row
Schema
Table
TableGroup
TableReference
Transformation
aboutUrl
base
columnReference
columns
commentPrefix
datatype
decimalChar
default
delimiter
describes
dialect
doubleQuote
encoding
foreignKeys
format
groupChar
header
headerRowCount
json
lang
length
lineTerminators
maxExclusive
maxInclusive
maxLength
maximum
minExclusive
minInclusive
minLength
minimum
name
notes
null
ordered
pattern
primaryKey
propertyUrl
quoteChar
reference
referencedRows
required
resource
row
rowTitles
rownum
schemaReference
scriptFormat
separator
skipBlankRows
skipColumns
skipInitialSpace
skipRows
source
suppressOutput
tableDirection
tableSchema
tables
targetFormat
textDirection
titles
transformations
trim
uriTemplate
url
valueUrl
virtual""".split()
is_url = utils.is_url
class Invalid:
pass
INVALID = Invalid()
@attr.s
class Dialect(BaseDialect):
"""
The spec is ambiguous regarding a default for the commentPrefix property:
> commentPrefix
> An atomic property that sets the comment prefix flag to the single provided value, which
> MUST be a string. The default is "#".
vs.
> comment prefix
> A string that, when it appears at the beginning of a row, indicates that the row is a
> comment that should be associated as a rdfs:comment annotation to the table. This is set
> by the commentPrefix property of a dialect description. The default is null, which means
> no rows are treated as comments. A value other than null may mean that the source numbers
> of rows are different from their numbers.
So, in order to pass the number formatting tests, with column names like `##.#`, we chose
the second reading - i.e. by default no rows are treated as comments.
"""
commentPrefix = attr.ib(
default=None,
converter=functools.partial(utils.converter, str, None, allow_none=True),
validator=attr.validators.optional(attr.validators.instance_of(str)))
def json_open(filename, mode='r', encoding='utf-8'):
assert encoding == 'utf-8'
return io.open(filename, mode, encoding=encoding)
def get_json(fname) -> typing.Union[list, dict]:
fname = str(fname)
if is_url(fname):
return requests.get(fname).json(object_pairs_hook=collections.OrderedDict)
with json_open(fname) as f:
return json.load(f, object_pairs_hook=collections.OrderedDict)
def log_or_raise(msg, log=None, level='warning', exception_cls=ValueError):
if log:
getattr(log, level)(msg)
else:
raise exception_cls(msg)
def nolog(level='warning'):
from types import MethodType
class Log(object):
pass
log = Log()
setattr(log, level, MethodType(lambda *args, **kw: None, log))
return log
class URITemplate(uritemplate.URITemplate):
def __eq__(self, other):
if isinstance(other, str):
return self.uri == other
if not hasattr(other, 'uri'):
return False
return super(URITemplate, self).__eq__(other)
def asdict(self, **kw):
return '{}'.format(self)
def uri_template_property():
"""
Note: We do not currently provide support for supplying the "_" variables like "_row"
when expanding a URI template.
.. seealso:: http://w3c.github.io/csvw/metadata/#uri-template-properties
"""
def converter_uriTemplate(v):
if v is None:
return None
if not isinstance(v, str):
warnings.warn('Invalid value for aboutUrl property')
return INVALID
return URITemplate(v)
return attr.ib(
default=None,
validator=attr.validators.optional(attr.validators.instance_of((URITemplate, Invalid))),
converter=converter_uriTemplate)
class Link:
"""
.. seealso:: http://w3c.github.io/csvw/metadata/#link-properties
"""
def __init__(self, string: typing.Union[str, pathlib.Path]):
if not isinstance(string, (str, pathlib.Path)):
raise ValueError('Invalid value for link property')
self.string = string
def __str__(self):
return self.string
def asdict(self, omit_defaults=True):
return self.string
def __eq__(self, other):
# FIXME: Only naive, un-resolved comparison is supported at the moment.
return self.string == other.string if isinstance(other, Link) else False
def resolve(self, base):
"""
Resolve a `Link` relative to `base`.
:param base:
:return: Either a string, representing a URL, or a `pathlib.Path` object, representing \
a local file.
"""
if hasattr(base, 'joinpath'):
if is_url(self.string):
return self.string
return (base if base.is_dir() else base.parent) / self.string
return urljoin(base, self.string)
def link_property(required=False):
return attr.ib(
default=None,
validator=attr.validators.optional(attr.validators.instance_of(Link)),
converter=lambda v: v if v is None else Link(v))
class NaturalLanguage(collections.OrderedDict):
"""
.. seealso:: http://w3c.github.io/csvw/metadata/#natural-language-properties
"""
def __init__(self, value):
super(NaturalLanguage, self).__init__()
self.value = value
if isinstance(self.value, str):
self[None] = [self.value]
elif isinstance(self.value, (list, tuple)):
if not all(isinstance(v, str) for v in self.value):
warnings.warn('titles with array values containing non-string values are ignored')
else:
self[None] = list(self.value)
elif isinstance(self.value, dict):
for k, v in self.value.items():
if not tags.check(k):
raise ValueError('Invalid language tag for NaturalLanguage')
if not isinstance(v, (list, tuple)):
v = [v]
titles = []
for vv in v:
if isinstance(vv, str):
titles.append(vv)
else:
warnings.warn('Title with value which is not a string is ignored')
self[k] = titles
else:
raise ValueError('invalid value type for NaturalLanguage')
def asdict(self, omit_defaults=True):
if list(self) == [None]:
if len(self[None]) == 1:
return self.getfirst()
return self[None]
return collections.OrderedDict(
('und' if k is None else k, v[0] if len(v) == 1 else v)
for k, v in self.items())
def add(self, string, lang=None):
if lang not in self:
self[lang] = []
self[lang].append(string)
def __str__(self):
return self.getfirst() or next(iter(self.values()))[0]
def getfirst(self, lang=None):
return self.get(lang, [None])[0]
def valid_id_property(v):
if not isinstance(v, str):
warnings.warn('Inconsistent link property')
return None
if v.startswith('_'):
raise ValueError('Invalid @id property: {}'.format(v))
return v
def valid_common_property(v):
if isinstance(v, dict):
if not {k[1:] for k in v if k.startswith('@')}.issubset(
{'id', 'language', 'type', 'value'}):
raise ValueError(
"Aside from @value, @type, @language, and @id, the properties used on an object "
"MUST NOT start with @.")
if '@value' in v:
if len(v) > 1:
if len(v) > 2 \
or set(v.keys()) not in [{'@value', '@language'}, {'@value', '@type'}] \
or not isinstance(v['@value'], (str, bool, int, decimal.Decimal)):
raise ValueError(
"If a @value property is used on an object, that object MUST NOT have "
"any other properties aside from either @type or @language, and MUST "
"NOT have both @type and @language as properties. The value of the "
"@value property MUST be a string, number, or boolean value.")
if '@language' in v and '@value' not in v:
raise ValueError(
"A @language property MUST NOT be used on an object unless it also has a "
"@value property.")
if '@id' in v:
v['@id'] = valid_id_property(v['@id'])
if '@language' in v:
if not (isinstance(v['@language'], str) and tags.check(v['@language'])):
warnings.warn('Invalid language tag')
del v['@language']
if '@type' in v:
vv = v['@type']
if isinstance(vv, str):
if vv.startswith('_:'):
raise ValueError(
'The value of any @id or @type contained within a metadata document '
'MUST NOT be a blank node.')
if not is_url(vv) and \
not any(vv == ns or vv.startswith(ns + ':') for ns in NAMESPACES) and \
vv not in CSVW_TERMS:
raise ValueError(
'The value of any member of @type MUST be either a term defined in '
'[csvw-context], a prefixed name where the prefix is a term defined in '
'[csvw-context], or an absolute URL.')
elif not isinstance(vv, (list, dict)):
raise ValueError('Invalid datatype for @type')
return {k: valid_common_property(vv) for k, vv in v.items()}
if isinstance(v, list):
return [valid_common_property(vv) for vv in v]
return v
@attr.s
class DescriptionBase:
"""Container for
- common properties (see http://w3c.github.io/csvw/metadata/#common-properties)
- @-properties.
"""
common_props = attr.ib(default=attr.Factory(dict))
at_props = attr.ib(default=attr.Factory(dict))
@classmethod
def partition_properties(cls,
d: typing.Union[dict, typing.Any],
type_name: typing.Optional[str] = None,
strict=True) -> typing.Union[dict, None]:
if d and not isinstance(d, dict):
return
fields = attr.fields_dict(cls)
type_name = type_name or cls.__name__
c, a, dd = {}, {}, {}
for k, v in (d or {}).items():
if k.startswith('@'):
if k == '@id':
v = valid_id_property(v)
if k == '@type' and v != type_name:
raise ValueError('Invalid @type property {} for {}'.format(v, type_name))
a[k[1:]] = v
elif ':' in k:
c[k] = valid_common_property(v)
else:
if strict and (k not in fields):
warnings.warn('Invalid property {} for {}'.format(k, type_name))
else:
dd[k] = v
return dict(common_props=c, at_props=a, **dd)
@classmethod
def fromvalue(cls, d: dict):
return cls(**cls.partition_properties(d))
def _iter_dict_items(self, omit_defaults):
def _asdict_single(v):
return v.asdict(omit_defaults=omit_defaults) if hasattr(v, 'asdict') else v
def _asdict_multiple(v):
if isinstance(v, (list, tuple)):
return [_asdict_single(vv) for vv in v]
return _asdict_single(v)
for k, v in sorted(self.at_props.items()):
yield '@' + k, _asdict_multiple(v)
for k, v in sorted(self.common_props.items()):
yield k, _asdict_multiple(v)
for k, v in utils.attr_asdict(self, omit_defaults=omit_defaults).items():
if k not in ('common_props', 'at_props'):
yield k, _asdict_multiple(v)
def asdict(self, omit_defaults=True) -> dict:
# Note: The `null` property is the only inherited, list-valued property where the default
# is not the empty list. Thus, to allow setting it to empty, we must treat `null` as
# special case here.
# See also https://www.w3.org/TR/tabular-metadata/#dfn-inherited-property
return collections.OrderedDict(
(k, v) for k, v in self._iter_dict_items(omit_defaults)
if (k == 'null' or (v not in ([], {}))))
def optional_int():
return attr.ib(
default=None,
validator=attr.validators.optional(attr.validators.instance_of(int)),
converter=lambda v: v if v is None else int(v))
@attr.s
class Datatype(DescriptionBase):
"""
A datatype description
Cells within tables may be annotated with a datatype which indicates the type of the values
obtained by parsing the string value of the cell.
.. seealso:: `<https://www.w3.org/TR/tabular-metadata/#datatypes>`_
"""
base = attr.ib(
default=None,
converter=functools.partial(
utils.converter,
str, 'string', allow_none=True, cond=lambda ss: ss is None or ss in DATATYPES),
validator=attr.validators.optional(attr.validators.in_(DATATYPES)))
format = attr.ib(default=None)
length = optional_int()
minLength = optional_int()
maxLength = optional_int()
minimum = attr.ib(default=None)
maximum = attr.ib(default=None)
minInclusive = attr.ib(default=None)
maxInclusive = attr.ib(default=None)
minExclusive = attr.ib(default=None)
maxExclusive = attr.ib(default=None)
@classmethod
def fromvalue(cls, v: typing.Union[str, dict, 'Datatype']) -> 'Datatype':
"""
:param v: Initialization data for `cls`; either a single string that is the main datatype \
of the values of the cell or a datatype description object, i.e. a `dict` or a `cls` \
instance.
:return: An instance of `cls`
"""
if isinstance(v, str):
return cls(base=v)
if isinstance(v, dict):
v.setdefault('base', 'string')
return cls(**cls.partition_properties(v))
if isinstance(v, cls):
return v
raise ValueError(v)
def __attrs_post_init__(self):
for attr_ in [
'minimum', 'maximum', 'minInclusive', 'maxInclusive', 'minExclusive', 'maxExclusive'
]:
if getattr(self, attr_) is not None:
setattr(self, attr_, self.parse(getattr(self, attr_)))
if self.length is not None:
if self.minLength is not None and self.length < self.minLength:
raise ValueError('minLength > length')
if self.maxLength is not None:
if self.length > self.maxLength:
raise ValueError('maxLength < length')
if self.minLength is not None and self.maxLength is not None \
and self.minLength > self.maxLength:
raise ValueError('minLength > maxLength')
if not isinstance(self.derived_description, dict):
raise ValueError() # pragma: no cover
if not isinstance(
self.basetype(),
tuple((DATATYPES[name] for name in ['decimal', 'float', 'datetime', 'duration']))):
if any([getattr(self, at) for at in
'minimum maximum minExclusive maxExclusive minInclusive maxInclusive'.split()]):
raise ValueError(
'Applications MUST raise an error if minimum, minInclusive, maximum, '
'maxInclusive, minExclusive, or maxExclusive are specified and the base '
'datatype is not a numeric, date/time, or duration type.')
if not isinstance(
self.basetype(),
(DATATYPES['string'], DATATYPES['base64Binary'], DATATYPES['hexBinary'])):
if self.length or self.minLength or self.maxLength:
raise ValueError(
'Applications MUST raise an error if length, maxLength, or minLength are '
'specified and the base datatype is not string or one of its subtypes, or a '
'binary type.')
if (self.minInclusive and self.minExclusive) or (self.maxInclusive and self.maxExclusive):
raise ValueError(
'Applications MUST raise an error if both minInclusive and minExclusive are '
'specified, or if both maxInclusive and maxExclusive are specified.')
if (self.minInclusive and self.maxExclusive and self.maxExclusive <= self.minInclusive) or \
(self.minInclusive and self.maxInclusive and self.maxInclusive < self.minInclusive):
raise ValueError('')
if (self.minExclusive and self.maxExclusive and self.maxExclusive <= self.minExclusive) or (
self.minExclusive and self.maxInclusive and self.maxInclusive <= self.minExclusive):
raise ValueError('')
if 'id' in self.at_props and any(
self.at_props['id'] == NAMESPACES['xsd'] + dt for dt in DATATYPES):
raise ValueError('datatype @id MUST NOT be the URL of a built-in datatype.')
if isinstance(self.basetype(), DATATYPES['decimal']) and \
'pattern' in self.derived_description:
if not set(self.derived_description['pattern']).issubset(set('#0.,;%‰E-+')):
self.format = None
warnings.warn('Invalid number pattern')
def asdict(self, omit_defaults=True):
res = DescriptionBase.asdict(self, omit_defaults=omit_defaults)
for attr_ in [
'minimum', 'maximum', 'minInclusive', 'maxInclusive', 'minExclusive', 'maxExclusive'
]:
if attr_ in res:
res[attr_] = self.formatted(res[attr_])
if len(res) == 1 and 'base' in res:
return res['base']
return res
@property
def basetype(self):
return DATATYPES[self.base]
@property
def derived_description(self):
return self.basetype.derived_description(self)
def formatted(self, v):
return self.basetype.to_string(v, **self.derived_description)
def parse(self, v):
if v is None:
return v
return self.basetype.to_python(v, **self.derived_description)
def validate(self, v):
if v is None:
return v
try:
l_ = len(v or '')
if self.length is not None and l_ != self.length:
raise ValueError('value must have length {}'.format(self.length))
if self.minLength is not None and l_ < self.minLength:
raise ValueError('value must have at least length {}'.format(self.minLength))
if self.maxLength is not None and l_ > self.maxLength:
raise ValueError('value must have at most length {}'.format(self.maxLength))
except TypeError:
pass
if self.basetype.minmax:
if self.minimum is not None and v < self.minimum:
raise ValueError('value must be >= {}'.format(self.minimum))
if self.minInclusive is not None and v < self.minInclusive:
raise ValueError('value must be >= {}'.format(self.minInclusive))
if self.minExclusive is not None and v <= self.minExclusive:
raise ValueError('value must be > {}'.format(self.minExclusive))
if self.maximum is not None and v > self.maximum:
raise ValueError('value must be <= {}'.format(self.maximum))
if self.maxInclusive is not None and v > self.maxInclusive:
raise ValueError('value must be <= {}'.format(self.maxInclusive))
if self.maxExclusive is not None and v >= self.maxExclusive:
raise ValueError('value must be < {}'.format(self.maxExclusive))
return v
def read(self, v):
return self.validate(self.parse(v))
def converter_null(v):
res = [] if v is None else (v if isinstance(v, list) else [v])
if not all(isinstance(vv, str) for vv in res):
warnings.warn('Invalid null property')
return [""]
return res
def converter_lang(v):
if not tags.check(v):
warnings.warn('Invalid language tag')
return 'und'
return v
@attr.s
class Description(DescriptionBase):
"""Adds support for inherited properties.
.. seealso:: http://w3c.github.io/csvw/metadata/#inherited-properties
"""
# To be able to resolve inheritance chains, we also provide a place to store a
# reference to the containing object. Note that this attribute is ignored when judging
# equality between objects. Thus, identically specified columns of different tables will be
# considered equal.
_parent = attr.ib(default=None, repr=False, eq=False)
aboutUrl = uri_template_property()
datatype = attr.ib(
default=None,
converter=lambda v: v if not v else Datatype.fromvalue(v))
default = attr.ib(
default="",
converter=functools.partial(utils.converter, str, "", allow_list=False),
)
lang = attr.ib(default="und", converter=converter_lang)
null = attr.ib(default=attr.Factory(lambda: [""]), converter=converter_null)
ordered = attr.ib(
default=None,
converter=functools.partial(utils.converter, bool, False, allow_none=True),
)
propertyUrl = uri_template_property()
required = attr.ib(default=None)
separator = attr.ib(
converter=functools.partial(utils.converter, str, None, allow_none=True),
default=None,
)
textDirection = attr.ib(
default=None,
converter=functools.partial(
utils.converter,
str, None, allow_none=True, cond=lambda v: v in [None, "ltr", "rtl", "auto", "inherit"])
)
valueUrl = uri_template_property()
def inherit(self, attr):
v = getattr(self, attr)
if v is None and self._parent:
return self._parent.inherit(attr) if hasattr(self._parent, 'inherit') \
else getattr(self._parent, attr)
return v
def inherit_null(self):
if self.null == [""]:
if self._parent and hasattr(self._parent, 'inherit_null'):
return self._parent.inherit_null()
return self.null
def converter_titles(v):
try:
return v if v is None else NaturalLanguage(v)
except ValueError:
warnings.warn('Invalid titles property')
return None
@attr.s
class Column(Description):
"""
A column description is an object that describes a single column.
The description provides additional human-readable documentation for a column, as well as
additional information that may be used to validate the cells within the column, create a
user interface for data entry, or inform conversion into other formats.
.. seealso:: `<https://www.w3.org/TR/tabular-metadata/#columns>`_
"""
name = attr.ib(
default=None,
converter=functools.partial(utils.converter, str, None, allow_none=True)
)
suppressOutput = attr.ib(
default=False,
converter=functools.partial(utils.converter, bool, False))
titles = attr.ib(
default=None,
validator=attr.validators.optional(attr.validators.instance_of(NaturalLanguage)),
converter=converter_titles)
virtual = attr.ib(default=False, converter=functools.partial(utils.converter, bool, False))
_number = attr.ib(default=None, repr=False)
def __str__(self):
return self.name or \
(self.titles and self.titles.getfirst()) or \
'_col.{}'.format(self._number)
def has_title(self, v):
if self.name and self.name == v:
return True
for tag, titles in (self.titles or {}).items():
if v in titles:
return tag or 'und'
return False
@property
def header(self):
return '{}'.format(self)
def read(self, v, strict=True):
required = self.inherit('required')
null = self.inherit_null()
default = self.inherit('default')
separator = self.inherit('separator')
datatype = self.inherit('datatype')
if not v:
v = default
if required and v in null:
if not strict:
warnings.warn('required column value is missing')
raise ValueError('required column value is missing')
if separator:
if not v:
v = []
elif v in null:
v = None
else:
v = (vv or default for vv in v.split(separator))
v = [None if vv in null else vv for vv in v]
elif v in null:
v = None
if datatype:
if isinstance(v, list):
try:
return [datatype.read(vv) for vv in v]
except ValueError:
if not strict:
warnings.warn('Invalid value for list element.')
return v
raise
return datatype.read(v)
return v
def write(self, v):
sep = self.inherit('separator')
null = self.inherit_null()
datatype = self.inherit('datatype')
def fmt(v):
if v is None:
return null[0]
if datatype:
return datatype.formatted(v)
return v
if sep:
return sep.join(fmt(vv) for vv in v or [])
return fmt(v)
def column_reference():
return attr.ib(
default=None,
validator=attr.validators.optional(attr.validators.instance_of(list)),
converter=lambda v: v if isinstance(v, list) or v is None else [v])
@attr.s
class Reference:
resource = link_property()
schemaReference = link_property()
columnReference = column_reference()
def __attrs_post_init__(self):
if self.resource is not None and self.schemaReference is not None:
raise ValueError(self)
@attr.s
class ForeignKey:
columnReference = column_reference()
reference = attr.ib(default=None)
@classmethod
def fromdict(cls, d):
if isinstance(d, dict):
try:
_ = Reference(**d['reference'])
except TypeError:
raise ValueError('Invalid reference property')
if not set(d.keys()).issubset({'columnReference', 'reference'}):
raise ValueError('Invalid foreignKey spec')
kw = dict(d, reference=Reference(**d['reference']))
return cls(**kw)
def asdict(self, **kw):
res = utils.attr_asdict(self, **kw)
res['reference'] = utils.attr_asdict(res['reference'], **kw)
return res
def converter_foreignKeys(v):
res = []
for d in functools.partial(utils.converter, dict, None)(v):
try:
res.append(ForeignKey.fromdict(d))
except TypeError:
warnings.warn('Invalid foreignKeys spec')
return res
@attr.s
class Schema(Description):
"""
A schema description is an object that encodes the information about a schema, which describes
the structure of a table.
:ivar columns: `list` of :class:`Column` descriptions.
:ivar foreignKeys: `list` of :class:`ForeignKey` descriptions.
.. seealso:: `<https://www.w3.org/TR/tabular-metadata/#schemas>`_
"""
columns = attr.ib(
default=attr.Factory(list),
converter=lambda v: [
Column.fromvalue(c) for c in functools.partial(utils.converter, dict, None)(
functools.partial(utils.converter, list, [])(v))])
foreignKeys = attr.ib(
default=attr.Factory(list),
converter=lambda v: [] if v is None else converter_foreignKeys(v))
primaryKey = column_reference()
rowTitles = attr.ib(
default=attr.Factory(list),
converter=lambda v: v if isinstance(v, list) else [v],
)
def __attrs_post_init__(self):
virtual, seen, names = False, set(), set()
for i, col in enumerate(self.columns):
if col.name and (col.name.startswith('_') or re.search(r'\s', col.name)):
warnings.warn('Invalid column name')
if col.virtual: # first virtual column sets the flag
virtual = True
elif virtual: # non-virtual column after virtual column!
raise ValueError('no non-virtual column allowed after virtual columns')
if not virtual:
if col.header in seen:
warnings.warn('Duplicate column name!')
if col.name:
if col.name in names:
raise ValueError('Duplicate column name {}'.format(col.name))
names.add(col.name)
seen.add(col.header)
col._parent = self
col._number = i + 1
for colref in self.primaryKey or []:
col = self.columndict.get(colref)
if col and not col.name:
warnings.warn('A primaryKey referenced column MUST have a `name` property')
self.primaryKey = None
@classmethod
def fromvalue(cls, v):
if isinstance(v, str):
try:
# The schema is referenced with a URL
v = requests.get(v).json()
except: # pragma: no cover # noqa: E722
return v
if not isinstance(v, dict):
if isinstance(v, int):
warnings.warn('Invalid value for tableSchema property')
v = {}
return cls(**cls.partition_properties(v))
@property
def columndict(self):
return {c.header: c for c in self.columns}
def get_column(self, name, strict=False):
col = self.columndict.get(name)
assert (not strict) or (col and col.name)
if not col:
for c in self.columns:
if c.titles and c.titles.getfirst() == name:
return c
if c.propertyUrl and c.propertyUrl.uri == name:
return c
return col
def dialect_props(d):
if not isinstance(d, dict):
warnings.warn('Invalid dialect spec')
return {}
partitioned = Description.partition_properties(d, type_name='Dialect', strict=False)
del partitioned['at_props']
del partitioned['common_props']
if partitioned.get('headerRowCount'):
partitioned['header'] = True
return partitioned
def valid_transformations(instance, attribute, value):
if not isinstance(value, list):
warnings.warn('Invalid transformations property')
for tr in value:
Description.partition_properties(tr, type_name='Template')
@attr.s
class TableLike(Description):
"""
A CSVW description object as encountered "in the wild", i.e. identified by URL on the web or
as file on disk.
Since `TableLike` objects may be instantiated from "externally referenced" objects
(via file paths or URLs), they have the necessary means to resolve
`link properties <https://www.w3.org/TR/tabular-metadata/#link-properties>`_
.. code-block:: python
>>> from csvw import Table, TableGroup, Link
>>> t = Table.from_file('tests/fixtures/csv.txt-table-metadata.json')
>>> Link('abc.txt').resolve(t.base)
PosixPath('tests/fixtures/abc.txt')
>>> tg = TableGroup.from_url(
... 'https://raw.githubusercontent.com/cldf/csvw/master/tests/fixtures/'
... 'csv.txt-metadata.json')
>>> str(tg.tables[0].url)
'csv.txt'
>>> tg.tables[0].url.resolve(tg.base)
'https://raw.githubusercontent.com/cldf/csvw/master/tests/fixtures/csv.txt'
and `URI template properties <https://www.w3.org/TR/tabular-metadata/#uri-template-properties>`_
(see :meth:`~TableLike.expand`).
"""
dialect = attr.ib(
default=None,
converter=lambda v: v if (v is None or isinstance(v, str))
else Dialect(**dialect_props(v)))
notes = attr.ib(default=attr.Factory(list))
tableDirection = attr.ib(
default='auto',
converter=functools.partial(
utils.converter, str, 'auto', cond=lambda s: s in ['rtl', 'ltr', 'auto']),
validator=attr.validators.in_(['rtl', 'ltr', 'auto']))
tableSchema = attr.ib(
default=None,
converter=lambda v: Schema.fromvalue(v))
transformations = attr.ib(
validator=valid_transformations,
default=attr.Factory(list),
)
url = link_property()
_fname = attr.ib(default=None) # The path of the metadata file.
def __attrs_post_init__(self):
if isinstance(self.dialect, str):
self.dialect = Dialect(**dialect_props(get_json(Link(self.dialect).resolve(self.base))))
if self.tableSchema and not (isinstance(self.tableSchema, str)):
self.tableSchema._parent = self
if 'id' in self.at_props and self.at_props['id'] is None:
self.at_props['id'] = self.base
ctx = self.at_props.get('context')
if isinstance(ctx, list):
for obj in ctx:
if (isinstance(obj, dict) and not set(obj.keys()).issubset({'@base', '@language'}))\
or (isinstance(obj, str) and obj != 'http://www.w3.org/ns/csvw'):
raise ValueError(
'The @context MUST have one of the following values: An array composed '
'of a string followed by an object, where the string is '
'http://www.w3.org/ns/csvw and the object represents a local context '
'definition, which is restricted to contain either or both of'
'@base and @language.')
if isinstance(obj, dict) and '@language' in obj:
if not tags.check(obj['@language']):
warnings.warn('Invalid value for @language property')
del obj['@language']
def get_column(self, spec):
return self.tableSchema.get_column(spec) if self.tableSchema else None
@classmethod
def from_file(cls, fname: typing.Union[str, pathlib.Path], data=None) -> 'TableLike':
"""
Instantiate a CSVW Table or TableGroup description from a metadata file.
"""
if is_url(str(fname)):
return cls.from_url(str(fname), data=data)
res = cls.fromvalue(data or get_json(fname))
res._fname = pathlib.Path(fname)
return res
@classmethod
def from_url(cls, url: str, data=None) -> 'TableLike':
"""
Instantiate a CSVW Table or TableGroup description from a metadata file specified by URL.
"""
data = data or get_json(url)
url = urlparse(url)
data.setdefault('@base', urlunparse((url.scheme, url.netloc, url.path, '', '', '')))
for table in data.get('tables', [data]):
if isinstance(table, dict) and isinstance(table.get('tableSchema'), str):
table['tableSchema'] = Link(table['tableSchema']).resolve(data['@base'])
res = cls.fromvalue(data)
return res
def to_file(self, fname: typing.Union[str, pathlib.Path], omit_defaults=True) -> pathlib.Path:
"""
Write a CSVW Table or TableGroup description as JSON object to a local file.
:param omit_defaults: The CSVW spec specifies defaults for most properties of most \
description objects. If `omit_defaults==True`, these properties will be pruned from \
the JSON object.
"""
fname = utils.ensure_path(fname)
data = self.asdict(omit_defaults=omit_defaults)
with json_open(str(fname), 'w') as f:
json.dump(data, f, indent=4, separators=(',', ': '))
return fname
@property
def base(self) -> typing.Union[str, pathlib.Path]:
"""
The "base" to resolve relative links against.
"""
at_props = self._parent.at_props if self._parent else self.at_props
ctxbase = None
for obj in self.at_props.get('context', []):
if isinstance(obj, dict) and '@base' in obj:
ctxbase = obj['@base']
if 'base' in at_props:
if ctxbase:
# If present, its value MUST be a string that is interpreted as a URL which is
# resolved against the location of the metadata document to provide the
# **base URL** for other URLs in the metadata document.
return Link(ctxbase).resolve(at_props['base'])
return at_props['base']
return self._parent._fname.parent if (self._parent and self._parent._fname) else \
(self._fname.parent if self._fname else None)
def expand(self, tmpl: URITemplate, row: dict, _row, _name=None, qname=False, uri=False) -> str:
"""
Expand a `URITemplate` using `row`, `_row` and `_name` as context and resolving the result
against `TableLike.url`.
.. code-block:: python
>>> from csvw import URITemplate, TableGroup
>>> tg = TableGroup.from_url(
... 'https://raw.githubusercontent.com/cldf/csvw/master/tests/fixtures/'
... 'csv.txt-metadata.json')
>>> tg.expand(URITemplate('/path?{a}{#b}'), dict(a='1', b='2'), None)
'https://raw.githubusercontent.com/path?1#2'
"""
assert not (qname and uri)
if tmpl is INVALID:
return self.url.resolve(self.base)
res = Link(
tmpl.expand(
_row=_row, _name=_name, **{_k: _v for _k, _v in row.items() if isinstance(_k, str)}
)).resolve(self.url.resolve(self.base) if self.url else self.base)
if not isinstance(res, pathlib.Path):
if qname:
for prefix, url in NAMESPACES.items():
if res.startswith(url):
res = res.replace(url, prefix + ':')
break
if uri:
if res != 'rdf:type':
for prefix, url in NAMESPACES.items():
if res.startswith(prefix + ':'):
res = res.replace(prefix + ':', url)
break
return res
@attr.s
class Table(TableLike):
"""
A table description is an object that describes a table within a CSV file.
`Table` objects provide access to schema manipulation either by manipulating the `tableSchema`
property directly or via higher-level methods like :meth:`~Table.add_foreign_key`
`Table` objects also mediate read/write access to the actual data through
- :meth:`~Table.write`
- :meth:`~Table.iterdicts`
.. seealso:: `<https://www.w3.org/TR/tabular-metadata/#tables>`_
"""
suppressOutput = attr.ib(default=False)
_comments = []
def add_foreign_key(self, colref, ref_resource, ref_colref):
"""
Add a foreign key constraint to `tableSchema.foreignKeys`.
:param colref: Column reference for the foreign key.
:param ref_resource: Referenced table.
:param ref_colref: Column reference of the key in the referenced table.
"""
colref = [colref] if not isinstance(colref, (tuple, list)) else colref
if not all(col in [c.name for c in self.tableSchema.columns] for col in colref):
raise ValueError('unknown column in foreignKey {0}'.format(colref))
self.tableSchema.foreignKeys.append(ForeignKey.fromdict({
'columnReference': colref,
'reference': {'resource': ref_resource, 'columnReference': ref_colref}
}))
def __attrs_post_init__(self):
TableLike.__attrs_post_init__(self)
if not self.url:
raise ValueError('url property is required for Tables')
@property
def local_name(self) -> typing.Union[str, None]:
return self.url.string if self.url else None
def _get_dialect(self) -> Dialect:
return self.dialect or (self._parent and self._parent.dialect) or Dialect()
def write(self,
items: typing.Iterable[typing.Union[dict, list, tuple]],
fname: typing.Optional[typing.Union[str, pathlib.Path]] = DEFAULT,
base: typing.Optional[typing.Union[str, pathlib.Path]] = None,
strict: typing.Optional[bool] = False,
_zipped: typing.Optional[bool] = False) -> typing.Union[str, int]:
"""
Write row items to a CSV file according to the table schema.
:param items: Iterator of `dict` storing the data per row.
:param fname: Name of the file to which to write the data.
:param base: Base directory relative to which to interpret table urls.
:param strict: Flag signaling to use strict mode when writing. This will raise `ValueError`\
if any row (dict) passed in `items` contains unspecified fieldnames.
:param _zipped: Flag signaling whether the resulting data file should be zipped.
:return: The CSV content if `fname==None` else the number of rows written.
"""
dialect = self._get_dialect()
non_virtual_cols = [c for c in self.tableSchema.columns if not c.virtual]
if fname is DEFAULT:
fname = self.url.resolve(pathlib.Path(base) if base else self.base)
rowcount = 0
with UnicodeWriter(fname, dialect=dialect) as writer:
if dialect.header:
writer.writerow([c.header for c in non_virtual_cols])
for item in items:
if isinstance(item, (list, tuple)):
row = [col.write(item[i]) for i, col in enumerate(non_virtual_cols)]
else:
if strict:
add = set(item.keys()) - {'{}'.format(col) for col in non_virtual_cols}
if add:
raise ValueError("dict contains fields not in fieldnames: {}".format(
', '.join("'{}'".format(field) for field in add)))
row = [
col.write(item.get(
col.header, item.get('{}'.format(col))))
for col in non_virtual_cols]
rowcount += 1
writer.writerow(row)
if fname is None:
return writer.read()
if fname and _zipped:
fpath = pathlib.Path(fname)
with zipfile.ZipFile(
str(fpath.parent.joinpath(fpath.name + '.zip')),
'w',
compression=zipfile.ZIP_DEFLATED
) as zipf:
zipf.write(str(fpath), arcname=fpath.name)
fpath.unlink()
return rowcount
def check_primary_key(self, log=None, items=None) -> bool:
success = True
if items is not None:
warnings.warn('the items argument of check_primary_key '
'is deprecated (its content will be ignored)') # pragma: no cover
if self.tableSchema.primaryKey:
get_pk = operator.itemgetter(*self.tableSchema.primaryKey)
seen = set()
# Read all rows in the table, ignoring errors:
for fname, lineno, row in self.iterdicts(log=nolog(), with_metadata=True):
pk = get_pk(row)
if pk in seen:
log_or_raise(
'{0}:{1} duplicate primary key: {2}'.format(fname, lineno, pk),
log=log)
success = False
else:
seen.add(pk)
return success
def __iter__(self):
return self.iterdicts()
def iterdicts(
self,
log=None,
with_metadata=False,
fname=None,
_Row=collections.OrderedDict,
strict=True,
) -> typing.Generator[dict, None, None]:
"""Iterate over the rows of the table
Create an iterator that maps the information in each row to a `dict` whose keys are
the column names of the table and whose values are the values in the corresponding
table cells, or for virtual columns (which have no values) the valueUrl for that
column. This includes columns not specified in the table specification.
Note: If the resolved data filename does not exist - but there is a zip file of the form
`fname+'.zip'`, we try to read the data from this file after unzipping.
:param log: Logger object (default None) The object that reports parsing errors.\
If none is given, parsing errors raise ValueError instead.
:param bool with_metadata: (default False) Also yield fname and lineno
:param fname: file-like, pathlib.Path, or str (default None)\
The file to be read. Defaults to inheriting from a parent object, if one exists.
:param strict: Flag signaling whether data is read strictly - i.e. raising `ValueError` \
when invalid data is encountered - or not - i.e. only issueing a warning and returning \
invalid data as `str` as provided by the undelying DSV reader.
:return: A generator of dicts or triples (fname, lineno, dict) if with_metadata
"""
dialect = self._get_dialect()
fname = fname or self.url.resolve(self.base)
colnames, virtualcols, requiredcols = [], [], set()
for col in self.tableSchema.columns:
if col.virtual:
if col.valueUrl:
virtualcols.append((col.header, col.valueUrl))
else:
colnames.append(col.header)
if col.required:
requiredcols.add(col.header)
with contextlib.ExitStack() as stack:
if is_url(fname):
handle = io.TextIOWrapper(
io.BytesIO(requests.get(str(fname)).content), encoding=dialect.encoding)
else:
handle = fname
fpath = pathlib.Path(fname)
if not fpath.exists():
zipfname = fpath.parent.joinpath(fpath.name + '.zip')
if zipfname.exists():
zipf = stack.enter_context(zipfile.ZipFile(str(zipfname)))
handle = io.TextIOWrapper(
zipf.open([n for n in zipf.namelist() if n.endswith(fpath.name)][0]),
encoding=dialect.encoding)
reader = stack.enter_context(UnicodeReaderWithLineNumber(handle, dialect=dialect))
reader = iter(reader)
# If the data file has a header row, this row overrides the header as
# specified in the metadata.
if dialect.header:
try:
_, header = next(reader)
if not strict:
if self.tableSchema.columns and len(self.tableSchema.columns) < len(header):
warnings.warn('Column number mismatch')
for name, col in zip(header, self.tableSchema.columns):
res = col.has_title(name)
if (not col.name) and not res:
warnings.warn('Incompatible table models')
if isinstance(res, str) and res.split('-')[0] not in [
'und', (self.lang or 'und').split('-')[0]]:
warnings.warn('Incompatible column titles')
except StopIteration: # pragma: no cover
return
else:
header = colnames
# If columns in the data are ordered as in the spec, we can match values to
# columns by index, rather than looking up columns by name.
if (header == colnames) or \
(len(self.tableSchema.columns) >= len(header) and not strict):
# Note that virtual columns are only allowed to come **after** regular ones,
# so we can simply zip the whole columns list, and silently ignore surplus
# virtual columns.
header_cols = list(zip(header, self.tableSchema.columns))
elif not strict and self.tableSchema.columns and \
(len(self.tableSchema.columns) < len(header)):
header_cols = []
for i, cname in enumerate(header):
try:
header_cols.append((cname, self.tableSchema.columns[i]))
except IndexError:
header_cols.append((
'_col.{}'.format(i + 1),
Column.fromvalue({'name': '_col.{}'.format(i + 1)})))
else:
header_cols = [(h, self.tableSchema.get_column(h)) for h in header]
header_cols = [(j, h, c) for j, (h, c) in enumerate(header_cols)]
missing = requiredcols - set(c.header for j, h, c in header_cols if c)
if missing:
raise ValueError('{0} is missing required columns {1}'.format(fname, missing))
for lineno, row in reader:
required = {h: j for j, h, c in header_cols if c and c.required}
res = _Row()
error = False
if (not header_cols) and row:
header_cols = [
(i,
'_col.{}'.format(i + 1),
Column.fromvalue({'name': '_col.{}'.format(i + 1)}))
for i, _ in enumerate(row)]
for (j, k, col), v in zip(header_cols, row):
# see http://w3c.github.io/csvw/syntax/#parsing-cells
if col:
try:
res[col.header] = col.read(v, strict=strict)
except ValueError as e:
if not strict:
warnings.warn(
'Invalid column value: {} {}; {}'.format(v, col.datatype, e))
res[col.header] = v
else:
log_or_raise(
'{0}:{1}:{2} {3}: {4}'.format(fname, lineno, j + 1, k, e),
log=log)
error = True
if k in required:
del required[k]
else:
if strict:
warnings.warn(
'Unspecified column "{0}" in table {1}'.format(k, self.local_name))
res[k] = v
for k, j in required.items():
if k not in res:
log_or_raise(
'{0}:{1}:{2} {3}: {4}'.format(
fname, lineno, j + 1, k, 'required column value is missing'),
log=log)
error = True
# Augment result with regular columns not provided in the data:
for key in colnames:
res.setdefault(key, None)
# Augment result with virtual columns:
for key, valueUrl in virtualcols:
res[key] = valueUrl.expand(**res)
if not error:
if with_metadata:
yield fname, lineno, res
else:
yield res
self._comments = reader.comments
def converter_tables(v):
res = []
for vv in v:
if not isinstance(vv, (dict, Table)):
warnings.warn('Invalid value for Table spec')
else:
res.append(Table.fromvalue(vv) if isinstance(vv, dict) else vv)
return res
@attr.s
class TableGroup(TableLike):
"""
A table group description is an object that describes a group of tables.
A `TableGroup` delegates most of its responsibilities to the `Table` objects listed in its
`tables` property. For convenience, `TableGroup` provides methods to
- read data from all tables: :meth:`TableGroup.read`
- write data for all tables: :meth:`TableGroup.write`
It also provides a method to check the referential integrity of data in related tables via
:meth:`TableGroup.check_referential_integrity`
.. seealso:: `<https://www.w3.org/TR/tabular-metadata/#table-groups>`_
"""
tables = attr.ib(repr=False, default=attr.Factory(list), converter=converter_tables)
def __attrs_post_init__(self):
TableLike.__attrs_post_init__(self)
for table in self.tables:
table._parent = self
@classmethod
def from_frictionless_datapackage(cls, dp):
return DataPackage(dp).to_tablegroup(cls)
def read(self):
"""
Read all data of a TableGroup
"""
return {tname: list(t.iterdicts()) for tname, t in self.tabledict.items()}
def write(self,
fname: typing.Union[str, pathlib.Path],
strict: typing.Optional[bool] = False,
_zipped: typing.Optional[bool] = False,
**items: typing.Iterable[typing.Union[list, tuple, dict]]):
"""
Write a TableGroup's data and metadata to files.
:param fname: Filename for the metadata file.
:param items: Keyword arguments are used to pass iterables of rows per table, where the \
table URL is specified as keyword.
"""
fname = pathlib.Path(fname)
for tname, rows in items.items():
self.tabledict[tname].write(rows, base=fname.parent, strict=strict, _zipped=_zipped)
self.to_file(fname)
def copy(self, dest: typing.Union[pathlib.Path, str]):
"""
Write a TableGroup's data and metadata to files relative to `dest`, adapting the `base`
attribute.
:param dest:
:return:
"""
dest = pathlib.Path(dest)
for table in self.tables:
shutil.copy(str(table.url.resolve(self.base)), str(table.url.resolve(dest)))
self._fname = dest / self._fname.name
self.to_file(self._fname)
@property
def tabledict(self) -> typing.Dict[str, Table]:
return {t.local_name: t for t in self.tables}
def foreign_keys(self) -> typing.List[typing.Tuple[Table, list, Table, list]]:
return [
(
self.tabledict[fk.reference.resource.string],
fk.reference.columnReference,
t,
fk.columnReference)
for t in self.tables for fk in t.tableSchema.foreignKeys
if not fk.reference.schemaReference]
def validate_schema(self, strict=False):
try:
for st, sc, tt, tc in self.foreign_keys():
if len(sc) != len(tc):
raise ValueError(
'Foreign key error: non-matching number of columns in source and target')
for scol, tcol in zip(sc, tc):
scolumn = st.tableSchema.get_column(scol, strict=strict)
tcolumn = tt.tableSchema.get_column(tcol, strict=strict)
if not (scolumn and tcolumn):
raise ValueError(
'Foregin key error: missing column "{}" or "{}"'.format(scol, tcol))
if scolumn.datatype and tcolumn.datatype and \
scolumn.datatype.base != tcolumn.datatype.base:
raise ValueError(
'Foregin key error: non-matching datatype "{}:{}" or "{}:{}"'.format(
scol, scolumn.datatype.base, tcol, tcolumn.datatype.base))
except (KeyError, AssertionError) as e:
raise ValueError('Foreign key error: missing table "{}" referenced'.format(e))
def check_referential_integrity(self, data=None, log=None, strict=False):
"""
Strict validation does not allow for nullable foreign key columns.
"""
if data is not None:
warnings.warn('the data argument of check_referential_integrity '
'is deprecated (its content will be ignored)') # pragma: no cover
if strict:
for t in self.tables:
for fk in t.tableSchema.foreignKeys:
for row in t:
if any(row.get(col) is None for col in fk.columnReference):
raise ValueError('Foreign key column is null: {} {}'.format(
[row.get(col) for col in fk.columnReference], fk.columnReference))
try:
self.validate_schema()
success = True
except ValueError as e:
success = False
log_or_raise(str(e), log=log, level='error')
fkeys = self.foreign_keys()
# FIXME: We only support Foreign Key references between tables!
fkeys = sorted(fkeys, key=lambda x: (x[0].local_name, x[1], x[2].local_name))
# Grouping by local_name of tables - even though we'd like to have the table objects
# around, too. This it to prevent going down the rabbit hole of comparing table objects
# for equality, when comparison of the string names is enough.
for _, grp in itertools.groupby(fkeys, lambda x: x[0].local_name):
grp = list(grp)
table = grp[0][0]
t_fkeys = [(key, [(child, ref) for _, _, child, ref in kgrp])
for key, kgrp in itertools.groupby(grp, lambda x: x[1])]
get_seen = [(operator.itemgetter(*key), set()) for key, _ in t_fkeys]
for row in table.iterdicts(log=log):
for get, seen in get_seen:
if get(row) in seen:
# column references for a foreign key are not unique!
if strict:
success = False
seen.add(get(row))
for (key, children), (_, seen) in zip(t_fkeys, get_seen):
single_column = (len(key) == 1)
for child, ref in children:
get_ref = operator.itemgetter(*ref)
for fname, lineno, item in child.iterdicts(log=log, with_metadata=True):
colref = get_ref(item)
if colref is None:
continue
elif single_column and isinstance(colref, list):
# We allow list-valued columns as foreign key columns in case
# it's not a composite key. If a foreign key is list-valued, we
# check for a matching row for each of the values in the list.
colrefs = colref
else:
colrefs = [colref]
for colref in colrefs:
if not single_column and None in colref: # pragma: no cover
# TODO: raise if any(c is not None for c in colref)?
continue
elif colref not in seen:
log_or_raise(
'{0}:{1} Key `{2}` not found in table {3}'.format(
fname,
lineno,
colref,
table.url.string),
log=log)
success = False
return success
class CSVW:
"""
Python API to read CSVW described data and convert it to JSON.
"""
def __init__(self, url: str, md_url: typing.Optional[str] = None, validate: bool = False):
self.warnings = []
w = None
with contextlib.ExitStack() as stack:
if validate:
w = stack.enter_context(warnings.catch_warnings(record=True))
no_header = False
try:
md = get_json(md_url or url)
# The URL could be read as JSON document, thus, the user supplied us with overriding
# metadata as per https://w3c.github.io/csvw/syntax/#overriding-metadata
except json.decoder.JSONDecodeError:
# So we got a CSV file, no JSON. Let's locate metadata using the other methods.
md, no_header = self.locate_metadata(url)
self.no_metadata = set(md.keys()) == {'@context', 'url'}
if "http://www.w3.org/ns/csvw" not in md.get('@context', ''):
raise ValueError('Invalid or no @context')
if 'tables' in md:
if not md['tables'] or not isinstance(md['tables'], list):
raise ValueError('Invalid TableGroup with empty tables property')
if is_url(url):
self.t = TableGroup.from_url(url, data=md)
self.t.validate_schema(strict=True)
else:
self.t = TableGroup.from_file(url, data=md)
else:
if is_url(url):
self.t = Table.from_url(url, data=md)
if no_header:
if self.t.dialect:
self.t.dialect.header = False # pragma: no cover
else:
self.t.dialect = Dialect(header=False)
else:
self.t = Table.from_file(url, data=md)
self.tables = self.t.tables if isinstance(self.t, TableGroup) else [self.t]
for table in self.tables:
for col in table.tableSchema.columns:
if col.name and (re.search(r'\s', col.name) or col.name.startswith('_')):
col.name = None
self.common_props = self.t.common_props
if w:
self.warnings.extend(w)
@property
def is_valid(self) -> bool:
"""
Performs CSVW validation.
.. note::
For this to also catch problems during metadata location, the
`CSVW` instance must be initialized with `validate=True`.
"""
if self.warnings:
return False
with warnings.catch_warnings(record=True) as w:
for table in self.tables:
for _ in table.iterdicts(strict=False):
pass
if not table.check_primary_key(): # pragma: no cover
warnings.warn('Duplicate primary key')
if not self.tablegroup.check_referential_integrity(strict=True):
warnings.warn('Referential integrity check failed')
if w:
self.warnings.extend(w)
return not bool(self.warnings)
@property
def tablegroup(self):
return self.t if isinstance(self.t, TableGroup) else \
TableGroup(at_props={'base': self.t.base}, tables=self.tables)
@staticmethod
def locate_metadata(url=None) -> typing.Tuple[dict, bool]:
"""
Implements metadata discovery as specified in
`§5. Locating Metadata <https://w3c.github.io/csvw/syntax/#locating-metadata>`_
"""
def describes(md, url):
for table in md.get('tables', [md]):
# FIXME: We check whether the metadata describes a CSV file just superficially,
# by comparing the last path components of the respective URLs.
if url.split('/')[-1] == table['url'].split('/')[-1]:
return True
return False
no_header = False
if url and is_url(url):
# §5.2 Link Header
# https://w3c.github.io/csvw/syntax/#link-header
res = requests.head(url)
no_header = bool(re.search(r'header\s*=\s*absent', res.headers.get('content-type', '')))
desc = res.links.get('describedby')
if desc and desc['type'] in [
"application/csvm+json", "application/ld+json", "application/json"]:
md = get_json(Link(desc['url']).resolve(url))
if describes(md, url):
return md, no_header
else:
warnings.warn('Ignoring linked metadata because it does not reference the data')
# §5.3 Default Locations and Site-wide Location Configuration
# https://w3c.github.io/csvw/syntax/
# #default-locations-and-site-wide-location-configuration
res = requests.get(Link('/.well-known/csvm').resolve(url))
locs = res.text if res.status_code == 200 else '{+url}-metadata.json\ncsv-metadata.json'
for line in locs.split('\n'):
res = requests.get(Link(URITemplate(line).expand(url=url)).resolve(url))
if res.status_code == 200:
try:
md = res.json()
if describes(md, url):
return md, no_header
warnings.warn('Ignoring metadata because it does not reference the data')
except json.JSONDecodeError:
pass
# §5.4 Embedded Metadata
# https://w3c.github.io/csvw/syntax/#embedded-metadata
# We only recognize column names read from the first row of a CSV file.
elif url:
# Default Locations for local files:
if pathlib.Path(str(url) + '-metadata.json').exists():
return get_json(pathlib.Path(str(url) + '-metadata.json')), no_header
res = {
'@context': "http://www.w3.org/ns/csvw",
'url': url,
}
if not is_url(url or ''):
# No metadata detected for a local CSV file. To make table reading work, we set the
# directory as @base and the filename as url property of the description.
p = pathlib.Path(url)
res['@base'] = str(p)
res['url'] = p.name
return res, no_header
def to_json(self, minimal=False):
"""
Implements algorithm described in `<https://w3c.github.io/csvw/csv2json/#standard-mode>`_
"""
res = collections.OrderedDict()
# Insert any notes and non-core annotations specified for the group of tables into object
# G according to the rules provided in § 5. JSON-LD to JSON.
if self.t.common_props and not isinstance(self.t, Table):
res.update(jsonld.to_json(self.t.common_props, flatten_list=True))
res['tables'] = [
self._table_to_json(table) for table in self.tables if not table.suppressOutput]
if minimal:
return list(
itertools.chain(*[[r['describes'][0] for r in t['row']] for t in res['tables']]))
return res
def _table_to_json(self, table):
res = collections.OrderedDict()
# FIXME: id
res['url'] = str(table.url.resolve(table.base))
if 'id' in table.at_props:
res['@id'] = table.at_props['id']
if table.notes:
res['notes'] = jsonld.to_json(table.notes)
# Insert any notes and non-core annotations specified for the group of tables into object
# G according to the rules provided in § 5. JSON-LD to JSON.
res.update(jsonld.to_json(table.common_props))
cols = collections.OrderedDict([(col.header, col) for col in table.tableSchema.columns])
for col in cols.values():
col.propertyUrl = col.inherit('propertyUrl')
col.valueUrl = col.inherit('valueUrl')
row = [
self._row_to_json(table, cols, row, rownum, rowsourcenum)
for rownum, (_, rowsourcenum, row) in enumerate(
table.iterdicts(with_metadata=True, strict=False), start=1)
]
if table._comments:
res['rdfs:comment'] = [c[1] for c in table._comments]
res['row'] = row
return res
def _row_to_json(self, table, cols, row, rownum, rowsourcenum):
res = collections.OrderedDict()
res['url'] = '{}#row={}'.format(table.url.resolve(table.base), rowsourcenum)
res['rownum'] = rownum
if table.tableSchema.rowTitles:
res['titles'] = [
t for t in [row.get(name) for name in table.tableSchema.rowTitles] if t]
if len(res['titles']) == 1:
res['titles'] = res['titles'][0]
# Insert any notes and non-core annotations specified for the group of tables into object
# G according to the rules provided in § 5. JSON-LD to JSON.
res['describes'] = self._describes(table, cols, row, rownum)
return res
def _describes(self, table, cols, row, rownum):
triples = []
aboutUrl = table.tableSchema.inherit('aboutUrl')
if aboutUrl:
triples.append(jsonld.Triple(
about=None, property='@id', value=table.expand(aboutUrl, row, _row=rownum)))
for i, (k, v) in enumerate(row.items(), start=1):
col = cols.get(k)
if col and (col.suppressOutput or col.virtual):
continue
# Skip null values:
null = col.inherit_null() if col else table.inherit_null()
if (null and v in null) or v == "" or (v is None) or \
(col and col.separator and v == []):
continue
triples.append(jsonld.Triple.from_col(
table,
col,
row,
'_col.{}'.format(i)
if (not table.tableSchema.columns and not self.no_metadata) else k,
v,
rownum))
for col in table.tableSchema.columns:
if col.virtual:
triples.append(jsonld.Triple.from_col(table, col, row, col.header, None, rownum))
return jsonld.group_triples(triples)
|