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 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845
|
# attempt to model requires_value...
# conditional can descend...
from abc import abstractmethod
from typing import (
Any,
Callable,
cast,
Dict,
Iterable,
List,
Mapping,
NamedTuple,
Optional,
Sequence,
Type,
TypeVar,
Union,
)
from pydantic import (
AfterValidator,
AliasChoices,
AnyUrl,
BaseModel,
ConfigDict,
create_model,
Discriminator,
Field,
field_validator,
HttpUrl,
model_validator,
RootModel,
StrictBool,
StrictFloat,
StrictInt,
StrictStr,
Tag,
TypeAdapter,
)
from pydantic.json_schema import SkipJsonSchema
from typing_extensions import (
Annotated,
Literal,
Protocol,
)
from ._base import ToolSourceBaseModel
from ._types import (
cast_as_type,
expand_annotation,
is_optional,
list_type,
optional,
optional_if_needed,
union_type,
)
from .parameter_validators import (
EmptyFieldParameterValidatorModel,
ExpressionParameterValidatorModel,
InRangeParameterValidatorModel,
LengthParameterValidatorModel,
NoOptionsParameterValidatorModel,
RegexParameterValidatorModel,
StaticValidatorModel,
)
from .tool_source import (
DrillDownOptionsDict,
JsonTestCollectionDefDict,
JsonTestDatasetDefDict,
)
# TODO:
# - implement data_ref on rules and implement some cross model validation
# + request: Return info needed to build request pydantic model at runtime.
# + request_internal: This is a pydantic model to validate what Galaxy expects to find in the database,
# in particular dataset and collection references should be decoded integers.
StateRepresentationT = Literal[
"request",
"request_internal",
"request_internal_dereferenced",
"landing_request",
"landing_request_internal",
"job_runtime",
"job_internal",
"test_case_xml",
"workflow_step",
"workflow_step_linked",
]
DEFAULT_MODEL_NAME = "DynamicModelForTool"
RawStateDict = Dict[str, Any]
# could be made more specific - validators need to be classmethod
ValidatorDictT = Dict[str, Callable]
class DynamicModelInformation(NamedTuple):
name: str
definition: tuple
validators: ValidatorDictT
class StrictModel(BaseModel):
model_config = ConfigDict(extra="forbid")
class ConnectedValue(BaseModel):
discriminator: Literal["ConnectedValue"] = Field(alias="__class__")
def allow_connected_value(type: Type):
return union_type([type, ConnectedValue])
def allow_batching(job_template: DynamicModelInformation, batch_type: Optional[Type] = None) -> DynamicModelInformation:
job_py_type: Type = job_template.definition[0]
default_value = job_template.definition[1]
batch_type = batch_type or job_py_type
class BatchRequest(StrictModel):
meta_class: Literal["Batch"] = Field(..., alias="__class__")
values: List[batch_type] # type: ignore[valid-type]
request_type = union_type([job_py_type, BatchRequest])
return DynamicModelInformation(
job_template.name,
(request_type, default_value),
{}, # should we modify these somehow?
)
class Validators:
def validate_not_none(cls, v):
assert v is not None, "null is an invalid value for attribute"
return v
class ParamModel(Protocol):
@property
def name(self) -> str: ...
@property
def request_requires_value(self) -> bool:
# if this is a non-optional type and no default is defined - an
# input value MUST be specified.
...
def safe_field_name(name: str) -> str:
if name.startswith("_"):
return f"X{name}"
return name
def dynamic_model_information_from_py_type(
param_model: ParamModel, py_type: Type, requires_value: Optional[bool] = None, validators=None
):
name = safe_field_name(param_model.name)
if requires_value is None:
requires_value = param_model.request_requires_value
initialize = ... if requires_value else None
py_type_is_optional = is_optional(py_type)
validators = validators or {}
if not py_type_is_optional and not requires_value:
validators["not_null"] = field_validator(name)(Validators.validate_not_none)
return DynamicModelInformation(
name,
(py_type, Field(initialize, alias=param_model.name if param_model.name != name else None)),
validators,
)
# We probably need incoming (parameter def) and outgoing (parameter value as transmitted) models,
# where value in the incoming model means "default value" and value in the outgoing model is the actual
# value a user has set. (incoming/outgoing from the client perspective).
class BaseToolParameterModelDefinition(ToolSourceBaseModel):
name: Annotated[
str,
Field(description="Parameter name. Used when referencing parameter in workflows or inside command templating."),
]
parameter_type: str
@abstractmethod
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
"""Return info needed to build Pydantic model at runtime for validation."""
class BaseGalaxyToolParameterModelDefinition(BaseToolParameterModelDefinition):
hidden: bool = False
label: Annotated[
Optional[str], Field(description="Will be displayed on the tool page as the label of the parameter.")
] = None
help: Annotated[
Optional[str],
Field(
description="Short bit of text, rendered on the tool form just below the associated field to provide information about the field."
),
] = None
argument: Annotated[
Optional[str],
Field(
description="""If the parameter reflects just one command line argument of a certain tool, this tag should be set to that particular argument. It is rendered in parenthesis after the help section, and it will create the name attribute (if not given explicitly) from the argument attribute by stripping leading dashes and replacing all remaining dashes by underscores (e.g. if argument="--long-parameter" then name="long_parameter" is implicit)."""
),
] = None
is_dynamic: bool = False
optional: Annotated[bool, Field(description="If `false`, parameter must have a value.")] = False
class LabelValue(BaseModel):
label: str
value: str
selected: bool
TextCompatiableValidators = Union[
LengthParameterValidatorModel,
RegexParameterValidatorModel,
ExpressionParameterValidatorModel,
EmptyFieldParameterValidatorModel,
]
def pydantic_to_galaxy_type(value: Any) -> Any:
"""We use advanced Pydantic types like URL but the Galaxy validators only expect strings for these."""
if isinstance(value, AnyUrl):
return str(value)
return value
VT = TypeVar("VT", bound=StaticValidatorModel)
def decorate_type_with_validators_if_needed(py_type: Type, static_validator_models: Sequence[VT]) -> Type:
pydantic_validator = pydantic_validator_for(static_validator_models)
if pydantic_validator:
return expand_annotation(py_type, [pydantic_validator])
else:
return py_type
# Looks like Annotated only work with one PlainValidator so condensing all static validators
# into a single PlainValidator for pydantic.
def pydantic_validator_for(static_validator_models: Sequence[VT]) -> Optional[AfterValidator]:
if static_validator_models:
def validator(v: Any) -> Any:
gx_val = pydantic_to_galaxy_type(v)
for static_validator_model in static_validator_models:
static_validator_model.statically_validate(gx_val)
return v
return AfterValidator(validator)
else:
return None
class TextParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_text"] = "gx_text"
type: Literal["text"]
area: bool = False
default_value: Optional[str] = Field(default=None, alias="value")
default_options: List[LabelValue] = []
validators: List[TextCompatiableValidators] = []
@property
def py_type(self) -> Type:
return optional_if_needed(StrictStr, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = decorate_type_with_validators_if_needed(self.py_type, self.validators)
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return False
NumberCompatiableValidators = Union[InRangeParameterValidatorModel,]
class IntegerParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_integer"] = "gx_integer"
type: Literal["integer"]
optional: bool = False
value: Optional[int] = None
min: Optional[int] = None
max: Optional[int] = None
validators: List[NumberCompatiableValidators] = []
@property
def py_type(self) -> Type:
return optional_if_needed(StrictInt, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type
validators = self.validators[:]
if self.min is not None or self.max is not None:
validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
py_type = decorate_type_with_validators_if_needed(py_type, validators)
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
elif _is_landing_request(state_representation):
requires_value = False
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return not self.optional and self.value is None
class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_float"] = "gx_float"
type: Literal["float"]
value: Optional[float] = None
min: Optional[float] = None
max: Optional[float] = None
validators: List[NumberCompatiableValidators] = []
@property
def py_type(self) -> Type:
return optional_if_needed(union_type([StrictInt, StrictFloat]), self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
elif _is_landing_request(state_representation):
requires_value = False
validators = self.validators[:]
if self.min is not None or self.max is not None:
validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
py_type = decorate_type_with_validators_if_needed(py_type, validators)
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return False
DataSrcT = Literal["hda", "ldda"]
MultiDataSrcT = Literal["hda", "ldda", "hdca"]
# @jmchilton you meant CollectionSrcT - fix that at some point please.
CollectionStrT = Literal["hdca"]
TestCaseDataSrcT = Literal["File"]
class LegacyRequestModelAttributes(StrictModel):
# Here for bioblend's sake, should be stripped
map_over_type: SkipJsonSchema[Optional[str]] = Field(None, exclude=True)
hid: SkipJsonSchema[Optional[int]] = Field(None, exclude=True)
workflow_step_id: SkipJsonSchema[Optional[str]] = Field(None, exclude=True)
label: SkipJsonSchema[Optional[str]] = Field(None, exclude=True)
class DataRequestHda(LegacyRequestModelAttributes):
src: Literal["hda"] = "hda"
id: StrictStr
class DataRequestLdda(LegacyRequestModelAttributes):
src: Literal["ldda"] = "ldda"
id: StrictStr
class DataRequestLd(LegacyRequestModelAttributes):
src: Literal["ld"] = Field(deprecated=True)
id: StrictStr
class DataRequestHdca(LegacyRequestModelAttributes):
src: Literal["hdca"] = "hdca"
id: StrictStr
class DatasetHash(StrictModel):
hash_function: Literal["MD5", "SHA-1", "SHA-256", "SHA-512"]
hash_value: StrictStr
class BaseDataRequest(StrictModel):
url: StrictStr = Field(..., alias="location")
name: Optional[StrictStr] = None
ext: StrictStr
dbkey: StrictStr = "?"
deferred: StrictBool = False
created_from_basename: Optional[StrictStr] = None
info: Optional[StrictStr] = None
tags: Optional[List[str]] = None
hashes: Optional[List[DatasetHash]] = None
space_to_tab: bool = False
to_posix_lines: bool = False
# to implement:
# tags
model_config = ConfigDict(extra="forbid", populate_by_name=True)
@model_validator(mode="before")
@classmethod
def allow_filetype_and_extension(cls, data: Any):
if isinstance(data, dict):
extension = data.get("filetype")
if extension:
data = data.copy()
data.pop("filetype")
data["ext"] = extension
extension = data.get("extension")
if extension:
data = data.copy()
data.pop("extension")
data["ext"] = extension
return data
class DataRequestUri(BaseDataRequest):
# calling it url instead of uri to match data fetch schema...
src: Literal["url"] = "url"
class FileRequestUri(BaseDataRequest):
class_: Literal["File"] = Field(..., alias="class")
src: None = Field(None, exclude=True)
class CollectionElementDataRequestUri(FileRequestUri):
class_: Literal["File"] = Field(..., alias="class")
identifier: StrictStr = Field(
...,
description="A unique identifier for this element within the collection.",
validation_alias=AliasChoices("identifier", "name"),
)
class CollectionElementCollectionRequestUri(StrictModel):
class_: Literal["Collection"] = Field(..., alias="class")
identifier: StrictStr = Field(
...,
description="A unique identifier for this element within the collection.",
validation_alias=AliasChoices("identifier", "name"),
)
collection_type: StrictStr
elements: List[
Annotated[
Union["CollectionElementCollectionRequestUri", CollectionElementDataRequestUri],
Field(discriminator="class_"),
]
]
@model_validator(mode="before")
@classmethod
def allow_collection_type_by_type(cls, data: Any):
if isinstance(data, dict):
collection_type = data.get("type")
if collection_type:
data = data.copy()
data.pop("type")
data["collection_type"] = collection_type
return data
class DataRequestCollectionUri(StrictModel):
class_: Literal["Collection"] = Field(..., alias="class")
collection_type: str
elements: List[
Annotated[
Union[CollectionElementCollectionRequestUri, CollectionElementDataRequestUri], Field(discriminator="class_")
]
]
deferred: StrictBool = False
name: Optional[StrictStr] = None
src: None = Field(None, exclude=True)
_DataRequest = Annotated[
Union[DataRequestHda, DataRequestLdda, DataRequestLd, DataRequestUri], Field(discriminator="src")
]
DataRequest: Type = cast(Type, _DataRequest)
DataOrCollectionRequest = Union[_DataRequest, FileRequestUri, DataRequestCollectionUri, DataRequestHdca]
FileOrCollectionRequest = Annotated[Union[FileRequestUri, DataRequestCollectionUri], Field(discriminator="class_")]
DataRequestHda.model_rebuild()
DataRequestLd.model_rebuild()
DataRequestLdda.model_rebuild()
DataRequestUri.model_rebuild()
DataRequestHdca.model_rebuild()
DataRequestCollectionUri.model_rebuild()
DataOrCollectionRequestAdapter: TypeAdapter[DataOrCollectionRequest] = TypeAdapter(DataOrCollectionRequest)
class BatchDataInstance(StrictModel):
src: MultiDataSrcT
id: StrictStr
MultiDataInstance: Type = cast(
Type,
Annotated[
union_type([DataRequestHda, DataRequestLdda, DataRequestHdca, DataRequestUri]), Field(discriminator="src")
],
)
MultiDataRequest: Type = union_type([MultiDataInstance, list_type(MultiDataInstance)])
class DataRequestInternalHda(StrictModel):
src: Literal["hda"]
id: StrictInt
class DataRequestInternalLdda(StrictModel):
src: Literal["ldda"]
id: StrictInt
class DataRequestInternalHdca(StrictModel):
src: Literal["hdca"]
id: StrictInt
class DataInternalJson(StrictModel):
class_: Annotated[Literal["File"], Field(alias="class")]
basename: Annotated[
str,
Field(
description="The base name of the file, that is, the name of the file without any leading directory path"
),
]
location: str
path: Annotated[str, Field(description="The absolute path to the file on disk.")]
listing: Optional[List[str]] # Should be recursive
nameroot: Annotated[Optional[str], Field(description="The basename root such that nameroot + nameext == basename")]
nameext: Annotated[
Optional[str], Field(description="The basename extension such that nameroot + nameext == basename")
]
format: Annotated[str, Field(description="The datatype extension of the file, e.g. 'txt', 'bam', 'fastq.gz'.")]
# "secondaryFiles": List[Any],
checksum: Optional[str]
size: int
class DataCollectionInternalJson(RootModel):
root: Dict[str, DataInternalJson]
class RecursiveDataCollectionInternalJson(RootModel):
root: Dict[str, Union[DataInternalJson, "RecursiveDataCollectionInternalJson"]]
RecursiveDataCollectionInternalJson.model_rebuild()
class DataCollectionPaired(StrictModel):
forward: DataInternalJson
reverse: DataInternalJson
DataRequestInternal: Type = cast(
Type, Annotated[Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestUri], Field(discriminator="src")]
)
DataRequestInternalDereferenced: Type = cast(
Type,
Annotated[Union[DataRequestInternalHda, DataRequestInternalLdda], Field(discriminator="src")],
)
DataJobInternal = DataRequestInternalDereferenced
class BatchDataInstanceInternal(StrictModel):
src: MultiDataSrcT
id: StrictInt
MultiDataInstanceInternal: Type = cast(
Type,
Annotated[
Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestInternalHdca, DataRequestUri],
Field(discriminator="src"),
],
)
MultiDataInstanceInternalDereferenced: Type = cast(
Type,
Annotated[
Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestInternalHdca], Field(discriminator="src")
],
)
MultiDataRequestInternal: Type = union_type([MultiDataInstanceInternal, list_type(MultiDataInstanceInternal)])
MultiDataRequestInternalDereferenced: Type = union_type(
[MultiDataInstanceInternalDereferenced, list_type(MultiDataInstanceInternalDereferenced)]
)
class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_data"] = "gx_data"
type: Literal["data"]
extensions: Annotated[
List[str],
Field(
description="Limit inputs to datasets with these extensions. Use 'data' to allow all input datasets.",
examples=["txt", "tabular", "tiff"],
),
] = ["data"]
multiple: Annotated[bool, Field(description="Allow multiple values to be selected.")] = False
min: Optional[int] = None
max: Optional[int] = None
@property
def py_type(self) -> Type:
base_model: Type
if self.multiple:
base_model = MultiDataRequest
else:
base_model = DataRequest
return optional_if_needed(base_model, self.optional)
@property
def py_type_internal_json(self) -> Type:
base_model: Type
if self.multiple:
base_model = list_type(DataInternalJson)
else:
base_model = DataInternalJson
return optional_if_needed(base_model, self.optional)
@property
def py_type_internal(self) -> Type:
base_model: Type
if self.multiple:
base_model = MultiDataRequestInternal
else:
base_model = DataRequestInternal
return optional_if_needed(base_model, self.optional)
@property
def py_type_internal_dereferenced(self) -> Type:
base_model: Type
if self.multiple:
base_model = MultiDataRequestInternalDereferenced
else:
base_model = DataRequestInternalDereferenced
return optional_if_needed(base_model, self.optional)
@property
def py_type_test_case(self) -> Type:
base_model: Type
if self.multiple:
base_model = list_type(JsonTestDatasetDefDict)
else:
base_model = JsonTestDatasetDefDict
return optional_if_needed(base_model, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
if state_representation == "request":
return allow_batching(dynamic_model_information_from_py_type(self, self.py_type), BatchDataInstance)
if state_representation == "landing_request":
return allow_batching(
dynamic_model_information_from_py_type(self, self.py_type, requires_value=False), BatchDataInstance
)
elif state_representation == "request_internal":
return allow_batching(
dynamic_model_information_from_py_type(self, self.py_type_internal), BatchDataInstanceInternal
)
elif state_representation == "landing_request_internal":
return allow_batching(
dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=False),
BatchDataInstanceInternal,
)
elif state_representation == "request_internal_dereferenced":
return allow_batching(
dynamic_model_information_from_py_type(self, self.py_type_internal_dereferenced),
BatchDataInstanceInternal,
)
elif state_representation == "job_internal":
return dynamic_model_information_from_py_type(self, self.py_type_internal_dereferenced, requires_value=True)
elif state_representation == "job_runtime":
return dynamic_model_information_from_py_type(self, self.py_type_internal_json, requires_value=True)
elif state_representation == "test_case_xml":
return dynamic_model_information_from_py_type(self, self.py_type_test_case)
elif state_representation == "workflow_step":
return dynamic_model_information_from_py_type(self, type(None), requires_value=False)
elif state_representation == "workflow_step_linked":
return dynamic_model_information_from_py_type(self, ConnectedValue)
@property
def request_requires_value(self) -> bool:
return not self.optional
class DataCollectionRequest(StrictModel):
src: CollectionStrT
id: StrictStr
class DataCollectionRequestInternal(StrictModel):
src: CollectionStrT
id: StrictInt
CollectionAdapterSrcT = Literal["CollectionAdapter"]
class AdaptedDataCollectionRequestBase(StrictModel):
src: CollectionAdapterSrcT
class AdaptedDataCollectionPromoteDatasetToCollectionRequest(AdaptedDataCollectionRequestBase):
adapter_type: Literal["PromoteDatasetToCollection"]
collection_type: Literal["list", "paired_or_unpaired"]
adapting: DataRequestHda
# calling this name and element_identifier to align with fetch API, etc...
class AdapterElementRequest(DataRequestHda):
name: str # element_identifier
class AdaptedDataCollectionPromoteDatasetsToCollectionRequest(AdaptedDataCollectionRequestBase):
adapter_type: Literal["PromoteDatasetsToCollection"]
# could allow list in here without changing much else I think but I'm trying to keep these tight in scope
collection_type: Literal["paired", "paired_or_unpaired"]
adapting: List[AdapterElementRequest]
AdaptedDataCollectionRequest = Annotated[
Union[
AdaptedDataCollectionPromoteDatasetToCollectionRequest, AdaptedDataCollectionPromoteDatasetsToCollectionRequest
],
Field(discriminator="adapter_type"),
]
AdaptedDataCollectionRequestTypeAdapter = TypeAdapter(AdaptedDataCollectionRequest) # type:ignore[var-annotated]
class DatasetCollectionElementReference(StrictModel):
src: Literal["dce"]
id: StrictInt
class AdaptedDataCollectionPromoteCollectionElementToCollectionRequestInternal(AdaptedDataCollectionRequestBase):
adapter_type: Literal["PromoteCollectionElementToCollection"]
adapting: DatasetCollectionElementReference
class AdaptedDataCollectionPromoteDatasetToCollectionRequestInternal(AdaptedDataCollectionRequestBase):
adapter_type: Literal["PromoteDatasetToCollection"]
collection_type: Literal["list", "paired_or_unpaired"]
adapting: DataRequestInternalHda
class AdapterElementRequestInternal(DataRequestInternalHda):
name: str # element_identifier
class AdaptedDataCollectionPromoteDatasetsToCollectionRequestInternal(AdaptedDataCollectionRequestBase):
adapter_type: Literal["PromoteDatasetsToCollection"]
# could allow list in here without changing much else I think but I'm trying to keep these tight in scope
collection_type: Literal["paired", "paired_or_unpaired"]
adapting: List[AdapterElementRequestInternal]
AdaptedDataCollectionRequestInternal = Annotated[
Union[
AdaptedDataCollectionPromoteCollectionElementToCollectionRequestInternal,
AdaptedDataCollectionPromoteDatasetToCollectionRequestInternal,
AdaptedDataCollectionPromoteDatasetsToCollectionRequestInternal,
],
Field(discriminator="adapter_type"),
]
AdaptedDataCollectionRequestInternalTypeAdapter = TypeAdapter(
AdaptedDataCollectionRequestInternal
) # type:ignore[var-annotated]
class DataCollectionParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_data_collection"] = "gx_data_collection"
type: Literal["data_collection"]
collection_type: Optional[str] = None
extensions: List[str] = ["data"]
value: Optional[Dict[str, Any]]
@property
def py_type(self) -> Type:
return optional_if_needed(DataCollectionRequest, self.optional)
@property
def py_type_internal(self) -> Type:
return optional_if_needed(DataCollectionRequestInternal, self.optional)
@property
def py_type_internal_json(self) -> Type:
if self.collection_type == "list":
return optional_if_needed(list_type(DataInternalJson), self.optional)
elif self.collection_type:
base_type: Optional[Type] = None
for subtype in reversed(self.collection_type.split(":")):
if subtype == "paired":
base_type = DataCollectionPaired
elif subtype == "list":
if base_type is None:
base_type = Dict[str, DataInternalJson]
else:
base_type = Dict[str, base_type] # type: ignore[valid-type] # we use this at runtime to build pydantic model
else:
raise Exception(f"unkown subtype '{subtype}' in collection_type '{self.collection_type}'")
else:
base_type = union_type(
[list_type(DataInternalJson), DataCollectionPaired, RecursiveDataCollectionInternalJson]
)
assert base_type
return optional_if_needed(base_type, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
if state_representation == "request":
return allow_batching(dynamic_model_information_from_py_type(self, self.py_type))
elif state_representation == "landing_request":
return allow_batching(dynamic_model_information_from_py_type(self, self.py_type, requires_value=False))
elif state_representation == "landing_request_internal":
return allow_batching(
dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=False)
)
elif state_representation in ["request_internal", "request_internal_dereferenced"]:
return allow_batching(dynamic_model_information_from_py_type(self, self.py_type_internal))
elif state_representation == "job_internal":
return dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=True)
elif state_representation == "job_runtime":
return dynamic_model_information_from_py_type(self, self.py_type_internal_json, requires_value=True)
elif state_representation == "workflow_step":
return dynamic_model_information_from_py_type(self, type(None), requires_value=False)
elif state_representation == "workflow_step_linked":
return dynamic_model_information_from_py_type(self, ConnectedValue)
elif state_representation == "test_case_xml":
return dynamic_model_information_from_py_type(self, JsonTestCollectionDefDict)
else:
raise NotImplementedError(
f"Have not implemented data collection parameter models for state representation {state_representation}"
)
@property
def request_requires_value(self) -> bool:
return not self.optional and self.value is None
class HiddenParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_hidden"] = "gx_hidden"
type: Literal["hidden"]
value: Optional[str]
validators: List[TextCompatiableValidators] = []
@property
def py_type(self) -> Type:
return optional_if_needed(StrictStr, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type
requires_value = not self.optional and self.value is None
py_type = decorate_type_with_validators_if_needed(py_type, self.validators)
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
elif state_representation == "workflow_step" and not self.optional:
# allow it to be linked in so force allow optional...
py_type = optional(py_type)
requires_value = False
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return not self.optional and self.value is None
def ensure_color_valid(value: Optional[Any]):
if value is None:
return
if not isinstance(value, str):
raise ValueError(f"Invalid color value type {value.__class__} encountered.")
value_str: str = value
message = f"Invalid color value string format {value_str} encountered."
if len(value_str) != 7:
raise ValueError(message + "0")
if value_str[0] != "#":
raise ValueError(message + "1")
for byte_str in value_str[1:]:
if byte_str not in "0123456789abcdef":
raise ValueError(message + "2")
class ColorParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_color"] = "gx_color"
type: Literal["color"]
value: Optional[str] = None
@property
def py_type(self) -> Type:
return optional_if_needed(StrictStr, self.optional)
@staticmethod
def validate_color_str(value) -> str:
ensure_color_valid(value)
return value
@staticmethod
def validate_color_str_if_value(value) -> str:
if value:
ensure_color_valid(value)
return value
@staticmethod
def validate_color_str_or_connected_value(value) -> str:
if not isinstance(value, ConnectedValue):
ensure_color_valid(value)
return value
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type
requires_value = self.request_requires_value
initialize = ... if requires_value else None
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
validators = {
"color_format": field_validator(self.name)(ColorParameterModel.validate_color_str_or_connected_value)
}
elif state_representation == "workflow_step":
validators = {"color_format": field_validator(self.name)(ColorParameterModel.validate_color_str_if_value)}
else:
validators = {"color_format": field_validator(self.name)(ColorParameterModel.validate_color_str)}
return DynamicModelInformation(
self.name,
(py_type, initialize),
validators,
)
@property
def request_requires_value(self) -> bool:
return False
class BooleanParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_boolean"] = "gx_boolean"
type: Literal["boolean"]
value: Optional[bool] = False
truevalue: Optional[str] = None
falsevalue: Optional[str] = None
@property
def py_type(self) -> Type:
return optional_if_needed(StrictBool, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
# these parameters always have an implicit default - either None if
# if it is optional or 'checked' if not (itself defaulting to False).
return False
class DirectoryUriParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_directory_uri"] = "gx_directory_uri"
type: Literal["directory"]
validators: List[TextCompatiableValidators] = []
@property
def py_type(self) -> Type:
return AnyUrl
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type
py_type = decorate_type_with_validators_if_needed(py_type, self.validators)
if state_representation == "workflow_step_linked":
py_type = allow_connected_value(py_type)
requires_value = self.request_requires_value
if _is_landing_request(state_representation):
requires_value = False
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return True
class RulesMapping(StrictModel):
type: str
columns: List[StrictInt]
class RulesModel(StrictModel):
rules: List[Dict[str, Any]]
mappings: List[RulesMapping]
class RulesParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_rules"] = "gx_rules"
type: Literal["rules"]
@property
def py_type(self) -> Type:
return RulesModel
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return dynamic_model_information_from_py_type(self, self.py_type)
@property
def request_requires_value(self) -> bool:
return True
SelectCompatiableValidators = Union[NoOptionsParameterValidatorModel,]
class SelectParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_select"] = "gx_select"
type: Literal["select"]
options: Optional[List[LabelValue]] = None
multiple: bool = False
validators: List[SelectCompatiableValidators] = []
@staticmethod
def split_str(cls, data: Any) -> Any:
if isinstance(data, str):
return [x.strip() for x in data.split(",")]
return data
def py_type_if_required(self, allow_connections: bool = False) -> Type:
if self.options is not None:
if len(self.options) > 0:
literal_options: List[Type] = [cast_as_type(Literal[o.value]) for o in self.options]
py_type = union_type(literal_options)
else:
py_type = type(None)
else:
py_type = StrictStr
if self.multiple:
if allow_connections:
py_type = list_type(allow_connected_value(py_type))
else:
py_type = list_type(py_type)
elif allow_connections:
py_type = allow_connected_value(py_type)
return py_type
@property
def py_type(self) -> Type:
return optional_if_needed(self.py_type_if_required(), self.optional or self.multiple)
@property
def py_type_workflow_step(self) -> Type:
# this is always optional in this context
return optional(self.py_type_if_required())
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
validators = {}
requires_value = self.request_requires_value
py_type = None
if state_representation == "workflow_step":
py_type = self.py_type_workflow_step
elif state_representation == "workflow_step_linked":
py_type = self.py_type_if_required(allow_connections=True)
py_type = optional_if_needed(py_type, self.optional or self.multiple)
elif state_representation == "test_case_xml":
# in a YAML test case representation this can be string, in XML we are still expecting a comma separated string
py_type = self.py_type_if_required(allow_connections=False)
if self.multiple:
validators = {"from_string": field_validator(self.name, mode="before")(SelectParameterModel.split_str)}
py_type = optional_if_needed(py_type, self.optional)
elif state_representation in ("job_internal", "job_runtime"):
requires_value = True
py_type = self.py_type
else:
py_type = self.py_type
py_type = decorate_type_with_validators_if_needed(py_type, self.validators)
return dynamic_model_information_from_py_type(
self, py_type, validators=validators, requires_value=requires_value
)
@property
def has_selected_static_option(self):
return self.options is not None and any(o.selected for o in self.options)
@property
def default_value(self) -> Optional[str]:
if self.options:
for option in self.options:
if option.selected:
return option.value
# single value pick up first value
if not self.optional:
return self.options[0].value
return None
@property
def request_requires_value(self) -> bool:
# API will allow an empty value and just grab the first static option
# see API Tests -> test_tools.py -> test_select_first_by_default
# If it is multiple - it will also always just allow null regardless of
# optional - see test_select_multiple_null_handling
return False
@property
def dynamic_options(self) -> bool:
return self.options is None
class GenomeBuildParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_genomebuild"] = "gx_genomebuild"
type: Literal["genomebuild"]
multiple: bool
@property
def py_type(self) -> Type:
py_type: Type = StrictStr
if self.multiple:
py_type = list_type(py_type)
return optional_if_needed(py_type, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
# it seems to always just pick values currently - an empty multiple or optional comes through as null
# and empty single non-optional input comes through as "?"". See gx_genomebuild*.xml tools.
return False
DrillDownHierarchyT = Literal["recurse", "exact"]
def drill_down_possible_values(
options: List[DrillDownOptionsDict], multiple: bool, hierarchy: DrillDownHierarchyT
) -> List[str]:
possible_values = []
def add_value(option: str, is_leaf: bool):
if not multiple and not is_leaf and hierarchy == "recurse":
return
possible_values.append(option)
def walk_selection(option: DrillDownOptionsDict):
child_options = option["options"]
is_leaf = not child_options
add_value(option["value"], is_leaf)
if not is_leaf:
for child_option in child_options:
walk_selection(child_option)
for option in options:
walk_selection(option)
return possible_values
class DrillDownParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_drill_down"] = "gx_drill_down"
type: Literal["drill_down"]
options: Optional[List[DrillDownOptionsDict]] = None
multiple: bool
hierarchy: DrillDownHierarchyT
@property
def py_type(self) -> Type:
if self.options is not None:
literal_options: List[Type] = [
cast_as_type(Literal[o])
for o in drill_down_possible_values(self.options, self.multiple, self.hierarchy)
]
py_type = union_type(literal_options)
else:
py_type = StrictStr
if self.multiple:
py_type = list_type(py_type)
return py_type
@property
def py_type_test_case_xml(self) -> Type:
base_model = str
return optional_if_needed(base_model, not self.request_requires_value)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
py_type = self.py_type_test_case_xml if state_representation == "test_case_xml" else self.py_type
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
options = self.options
if options:
# if any of these are selected, they seem to serve as defaults - check out test_tools -> test_drill_down_first_by_default
return not any_drill_down_options_selected(options)
else:
# I'm not sure how to handle dynamic options... they might or might not be required?
# do we need to default to assuming they're not required?
return False
@property
def default_option(self) -> Optional[str]:
options = self.options
if options:
selected_options = selected_drill_down_options(options)
if len(selected_options) > 0:
return selected_options[0]
return None
@property
def default_options(self) -> Optional[List[str]]:
options = self.options
if options:
selected_options = selected_drill_down_options(options)
return selected_options
return None
def any_drill_down_options_selected(options: List[DrillDownOptionsDict]) -> bool:
for option in options:
selected = option.get("selected")
if selected:
return True
child_options = option.get("options", [])
if any_drill_down_options_selected(child_options):
return True
return False
def selected_drill_down_options(options: List[DrillDownOptionsDict]) -> List[str]:
selected_options: List[str] = []
for option in options:
selected = option.get("selected")
value = option.get("value")
if selected and value:
selected_options.append(value)
child_options = option.get("options", [])
selected_options.extend(selected_drill_down_options(child_options))
return selected_options
class DataColumnParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_data_column"] = "gx_data_column"
type: Literal["data_column"]
multiple: bool
value: Optional[Union[int, List[int]]] = None
@staticmethod
def split_str(cls, data: Any) -> Any:
if isinstance(data, str):
return [int(x.strip()) for x in data.split(",")]
elif isinstance(data, int):
return [data]
return data
@property
def py_type(self) -> Type:
py_type: Type = StrictInt
if self.multiple:
py_type = list_type(py_type)
return optional_if_needed(py_type, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
if state_representation == "test_case_xml":
if self.multiple:
validators = {
"from_string": field_validator(self.name, mode="before")(DataColumnParameterModel.split_str)
}
else:
validators = {}
requires_value = self.request_requires_value
return dynamic_model_information_from_py_type(
self, self.py_type, validators=validators, requires_value=requires_value
)
else:
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return self.multiple and not (self.optional or self.value)
class GroupTagParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_group_tag"] = "gx_group_tag"
type: Literal["group_tag"]
multiple: bool
@property
def py_type(self) -> Type:
py_type: Type = StrictStr
if self.multiple:
py_type = list_type(py_type)
return optional_if_needed(py_type, self.optional)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
@property
def request_requires_value(self) -> bool:
return not self.optional
class BaseUrlParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_baseurl"] = "gx_baseurl"
type: Literal["baseurl"]
@property
def py_type(self) -> Type:
return HttpUrl
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return dynamic_model_information_from_py_type(self, self.py_type)
@property
def request_requires_value(self) -> bool:
return True
DiscriminatorType = Union[bool, str]
def cond_test_parameter_default_value(
test_parameter: Union["BooleanParameterModel", "SelectParameterModel"],
) -> Optional[DiscriminatorType]:
default_value: Optional[DiscriminatorType] = None
if isinstance(test_parameter, BooleanParameterModel):
default_value = test_parameter.value
elif isinstance(test_parameter, SelectParameterModel):
select_default_value = test_parameter.default_value
if select_default_value is not None:
default_value = select_default_value
return default_value
class ConditionalWhen(StrictModel):
discriminator: DiscriminatorType
parameters: List["ToolParameterT"]
is_default_when: bool
class ConditionalParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_conditional"] = "gx_conditional"
type: Literal["conditional"]
test_parameter: Union[BooleanParameterModel, SelectParameterModel]
whens: List[ConditionalWhen]
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
is_boolean = isinstance(self.test_parameter, BooleanParameterModel)
test_param_name = self.test_parameter.name
test_info = self.test_parameter.pydantic_template(state_representation)
extra_validators = test_info.validators
if state_representation in ("job_internal", "job_runtime"):
test_parameter_requires_value = True
else:
test_parameter_requires_value = self.test_parameter.request_requires_value
when_types: List[Type[BaseModel]] = []
default_type = None
for when in self.whens:
discriminator = when.discriminator
parameters = when.parameters
if test_parameter_requires_value:
initialize_test = ...
else:
initialize_test = None
tag = str(discriminator) if not is_boolean else str(discriminator).lower()
extra_kwd = {test_param_name: (Literal[when.discriminator], initialize_test)}
when_types.append(
cast(
Type[BaseModel],
Annotated[
create_field_model(
parameters,
f"When_{test_param_name}_{discriminator}",
state_representation,
extra_kwd=extra_kwd,
extra_validators=extra_validators,
),
Tag(tag),
],
)
)
# job_internal requires parameters are filled in - so don't allow the absent branch
# here that most other state representations allow
if state_representation not in ("job_internal", "job_runtime"):
if when.is_default_when:
extra_kwd = {}
default_type = create_field_model(
parameters,
f"When_{test_param_name}___absent",
state_representation,
extra_kwd=extra_kwd,
extra_validators={},
)
when_types.append(cast(Type[BaseModel], Annotated[default_type, Tag("__absent__")]))
def model_x_discriminator(v: Any) -> Optional[str]:
# returning None causes a validation error, this is what we would want if
# if the conditional state is not a dictionary.
if not isinstance(v, dict):
return None
if test_param_name not in v:
return "__absent__"
else:
test_param_val = v[test_param_name]
if test_param_val is True:
return "true"
elif test_param_val is False:
return "false"
else:
return str(test_param_val)
py_type: Type
if len(when_types) > 1:
cond_type = union_type(when_types)
class ConditionalType(RootModel):
root: cond_type = Field(..., discriminator=Discriminator(model_x_discriminator)) # type: ignore[valid-type]
if default_type is not None:
initialize_cond = None
else:
initialize_cond = ...
py_type = ConditionalType
else:
py_type = when_types[0]
# a better check here would be if any of the parameters below this have a required value,
# in the case of job_internal though this is correct
if state_representation in ("job_internal", "job_runtime"):
initialize_cond = ...
else:
initialize_cond = None
return DynamicModelInformation(
self.name,
(py_type, initialize_cond),
{},
)
@property
def request_requires_value(self) -> bool:
return False # TODO
class RepeatParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_repeat"] = "gx_repeat"
type: Literal["repeat"]
parameters: List["ToolParameterT"]
min: Optional[int] = None
max: Optional[int] = None
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
# Maybe validators for min and max...
instance_class: Type[BaseModel] = create_field_model(
self.parameters, f"Repeat_{self.name}", state_representation
)
min_length = self.min
max_length = self.max
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
elif _is_landing_request(state_representation):
requires_value = False
min_length = 0 # in a landing request - parameters can be partially filled
initialize_repeat: Any
if requires_value:
initialize_repeat = ...
else:
initialize_repeat = None
class RepeatType(RootModel):
root: List[instance_class] = Field(initialize_repeat, min_length=min_length, max_length=max_length) # type: ignore[valid-type]
return DynamicModelInformation(
self.name,
(RepeatType, initialize_repeat),
{},
)
@property
def request_requires_value(self) -> bool:
if self.min is None or self.min == 0:
return False
# so we know we need at least one value, but maybe none of the parameters in the list
# are required
for parameter in self.parameters:
if parameter.request_requires_value:
return True
return False
class SectionParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["gx_section"] = "gx_section"
type: Literal["section"]
parameters: List["ToolParameterT"]
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
instance_class: Type[BaseModel] = create_field_model(
self.parameters, f"Section_{self.name}", state_representation
)
requires_value = self.request_requires_value
if state_representation in ("job_internal", "job_runtime"):
requires_value = True
if requires_value:
initialize_section = ...
else:
initialize_section = None
return DynamicModelInformation(
self.name,
(instance_class, initialize_section),
{},
)
@property
def request_requires_value(self) -> bool:
any_request_parameters_required = False
for parameter in self.parameters:
if parameter.request_requires_value:
any_request_parameters_required = True
break
return any_request_parameters_required
LiteralNone: Type = Literal[None] # type: ignore[assignment]
class CwlNullParameterModel(BaseToolParameterModelDefinition):
parameter_type: Literal["cwl_null"] = "cwl_null"
@property
def py_type(self) -> Type:
return LiteralNone
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return DynamicModelInformation(
self.name,
(self.py_type, ...),
{},
)
@property
def request_requires_value(self) -> bool:
return False
class CwlStringParameterModel(BaseToolParameterModelDefinition):
parameter_type: Literal["cwl_string"] = "cwl_string"
@property
def py_type(self) -> Type:
return StrictStr
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return DynamicModelInformation(
self.name,
(self.py_type, ...),
{},
)
@property
def request_requires_value(self) -> bool:
return True
class CwlIntegerParameterModel(BaseToolParameterModelDefinition):
parameter_type: Literal["cwl_integer"] = "cwl_integer"
@property
def py_type(self) -> Type:
return StrictInt
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return DynamicModelInformation(
self.name,
(self.py_type, ...),
{},
)
@property
def request_requires_value(self) -> bool:
return True
class CwlFloatParameterModel(BaseToolParameterModelDefinition):
parameter_type: Literal["cwl_float"] = "cwl_float"
@property
def py_type(self) -> Type:
return union_type([StrictFloat, StrictInt])
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return DynamicModelInformation(
self.name,
(self.py_type, ...),
{},
)
@property
def request_requires_value(self) -> bool:
return True
class CwlBooleanParameterModel(BaseToolParameterModelDefinition):
parameter_type: Literal["cwl_boolean"] = "cwl_boolean"
@property
def py_type(self) -> Type:
return StrictBool
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return DynamicModelInformation(
self.name,
(self.py_type, ...),
{},
)
@property
def request_requires_value(self) -> bool:
return True
class CwlUnionParameterModel(BaseToolParameterModelDefinition):
parameter_type: Literal["cwl_union"] = "cwl_union"
parameters: List["CwlParameterT"]
@property
def py_type(self) -> Type:
union_of_cwl_types: List[Type] = []
for parameter in self.parameters:
union_of_cwl_types.append(parameter.py_type)
return union_type(union_of_cwl_types)
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return DynamicModelInformation(
self.name,
(self.py_type, ...),
{},
)
@property
def request_requires_value(self) -> bool:
return False # TODO:
class CwlFileParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["cwl_file"] = "cwl_file"
@property
def py_type(self) -> Type:
return DataRequest
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return dynamic_model_information_from_py_type(self, self.py_type)
@property
def request_requires_value(self) -> bool:
return True
class CwlDirectoryParameterModel(BaseGalaxyToolParameterModelDefinition):
parameter_type: Literal["cwl_directory"] = "cwl_directory"
@property
def py_type(self) -> Type:
return DataRequest
def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
return dynamic_model_information_from_py_type(self, self.py_type)
@property
def request_requires_value(self) -> bool:
return True
CwlParameterT = Union[
CwlIntegerParameterModel,
CwlFloatParameterModel,
CwlStringParameterModel,
CwlBooleanParameterModel,
CwlNullParameterModel,
CwlFileParameterModel,
CwlDirectoryParameterModel,
CwlUnionParameterModel,
]
GalaxyParameterT = Union[
TextParameterModel,
IntegerParameterModel,
FloatParameterModel,
BooleanParameterModel,
HiddenParameterModel,
SelectParameterModel,
DataParameterModel,
DataCollectionParameterModel,
DataColumnParameterModel,
DirectoryUriParameterModel,
RulesParameterModel,
DrillDownParameterModel,
GroupTagParameterModel,
BaseUrlParameterModel,
GenomeBuildParameterModel,
ColorParameterModel,
ConditionalParameterModel,
RepeatParameterModel,
SectionParameterModel,
]
ToolParameterT = Union[
CwlParameterT,
GalaxyParameterT,
]
class ToolParameterModel(RootModel):
root: ToolParameterT = Field(..., discriminator="parameter_type")
class GalaxyToolParameterModel(RootModel):
root: GalaxyParameterT = Field(..., discriminator="type")
ConditionalWhen.model_rebuild()
ConditionalParameterModel.model_rebuild()
RepeatParameterModel.model_rebuild()
CwlUnionParameterModel.model_rebuild()
class ToolParameterBundle(Protocol):
"""An object having a dictionary of input models (i.e. a 'Tool')"""
parameters: List[ToolParameterT]
class ToolParameterBundleModel(BaseModel):
parameters: List[ToolParameterT]
def to_simple_model(input_parameter: Union[ToolParameterModel, ToolParameterT]) -> ToolParameterT:
if input_parameter.__class__ == ToolParameterModel:
assert isinstance(input_parameter, ToolParameterModel)
return input_parameter.root
else:
return cast(ToolParameterT, input_parameter)
def simple_input_models(parameters: Union[List[ToolParameterModel], List[ToolParameterT]]) -> Iterable[ToolParameterT]:
return [to_simple_model(m) for m in parameters]
def create_model_strict(*args, **kwd) -> Type[BaseModel]:
# proteted_namespaces here prevents tool with model_ parameter names from issueing warnings
model_config = ConfigDict(extra="forbid", protected_namespaces=())
return create_model(*args, __config__=model_config, **kwd)
def create_model_factory(state_representation: StateRepresentationT):
def create_method(tool: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
return create_field_model(tool.parameters, name or DEFAULT_MODEL_NAME, state_representation)
return create_method
create_request_model = create_model_factory("request")
create_request_internal_model = create_model_factory("request_internal")
create_request_internal_dereferenced_model = create_model_factory("request_internal_dereferenced")
create_landing_request_model = create_model_factory("landing_request")
create_landing_request_internal_model = create_model_factory("landing_request_internal")
create_job_internal_model = create_model_factory("job_internal")
create_job_runtime_model = create_model_factory("job_runtime")
create_test_case_model = create_model_factory("test_case_xml")
create_workflow_step_model = create_model_factory("workflow_step")
create_workflow_step_linked_model = create_model_factory("workflow_step_linked")
def create_field_model(
tool_parameter_models: Union[List[ToolParameterModel], List[ToolParameterT]],
name: str,
state_representation: StateRepresentationT,
extra_kwd: Optional[Mapping[str, tuple]] = None,
extra_validators: Optional[ValidatorDictT] = None,
) -> Type[BaseModel]:
kwd: Dict[str, tuple] = {}
if extra_kwd:
kwd.update(extra_kwd)
model_validators = (extra_validators or {}).copy()
for input_model in tool_parameter_models:
input_model = to_simple_model(input_model)
pydantic_request_template = input_model.pydantic_template(state_representation)
input_name = pydantic_request_template.name
kwd[input_name] = pydantic_request_template.definition
input_validators = pydantic_request_template.validators
for validator_name, validator_callable in input_validators.items():
model_validators[f"{input_name}_{validator_name}"] = validator_callable
pydantic_model = create_model_strict(name, __validators__=model_validators, **kwd)
return pydantic_model
def _is_landing_request(state_representation: StateRepresentationT):
return state_representation in ["landing_request", "landing_request_internal"]
|