diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 1a1aa2ab9..d934d7947 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,12 +6,29 @@ dcicutils Change Log ---------- +8.14.0 +====== +* Minor updates to the view-portal-object dev/troubleshooting utility script. +* Changed from typing_extensions import Literal to import from typing; + odd Python 3.12 issue but only in GitHub Actions (observed for submitr). +* Added tomli dependency in pyproject.toml (came up in submitr GA for Pyhthon 3.12). +* Change to structured_data.py to NOT silently convert a string + representing a floating point number to an integer. +* Changes in structured_data.py for validator hook. +* Added to_number function to misc_utils. +* Added run_concurrently function to misc_utils. +* Changed misc_utils.to_enum to default to non-fuzzy (prefix) match, for structured_data, + i.e for smaht-submitr to match on (case-insensitive) full enum namess. +* Changed dcicutils.structured_data.Schema._map_function_date/time to + report malformed dates, e.g. "6/29/2024" rather than "2024-06-29". + + 8.13.3 ====== * N.B. Accidentially tagged/pushed 8.13.1 -> PLEASE IGNORE VERSION: 8.13.1 (subsequently yanked). And then to correct (while no permission to delete above) pushed unofficial 8.13.2. * Fallout from Python 3.12 support. - - Though dcicutils is not dependent on numpy, elasticsearch tries to import it, + - Though dcicutils is not dependent on numpy, elasticsearch *tries* to import it, and if it is installed and if it is a version greater than 1.x, we get this error: AttributeError: `np.float_` was removed in the NumPy 2.0 release. Use `np.float64` instead. So added a hack in hack_for_elasticsearch_numpy_usage.py for this specific case; diff --git a/dcicutils/common.py b/dcicutils/common.py index a390db668..45f32cb33 100644 --- a/dcicutils/common.py +++ b/dcicutils/common.py @@ -3,8 +3,7 @@ import re from tempfile import TemporaryFile -from typing import Dict, Union, Tuple, List, Any -from typing_extensions import Literal +from typing import Dict, Union, Tuple, List, Any, Literal # ===== Useful constants ===== diff --git a/dcicutils/license_utils.py b/dcicutils/license_utils.py index ab9aa9d76..3f085067c 100644 --- a/dcicutils/license_utils.py +++ b/dcicutils/license_utils.py @@ -7,17 +7,20 @@ import os import re import subprocess +import sys import warnings try: import piplicenses except ImportError: # pragma: no cover - not worth unit testing this case - raise Exception("The dcicutils.license_utils module is intended for use at development time, not runtime." - " It does not export a requirement for the pip-licenses library," - " but to use this in your unit tests, you are expected to assure a dev dependency on that library" - " as part of the [tool.poetry.dependencies] section of your pyproject.toml file." - " If you are trying to manually evaluate the utility of this library, you can" - " do 'pip install pip-licenses' and then retry importing this library.") + if not ((sys.version_info[0] == 3) and (sys.version_info[1] >= 12)): + # For some reason for with Python 3.12 this gets triggered at least for submitr (TODO: track down further). + raise Exception("The dcicutils.license_utils module is intended for use at development time, not runtime." + " It does not export a requirement for the pip-licenses library," + " but to use this in your unit tests, you are expected to assure a dev dependency on that" + " library as part of the [tool.poetry.dependencies] section of your pyproject.toml file." + " If you are trying to manually evaluate the utility of this library, you can" + " do 'pip install pip-licenses' and then retry importing this library.") # or you can comment out the above raise of Exception and instead execute: # # subprocess.check_output('pip install pip-licenses'.split(' ')) diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py index e830e55e5..5de86755e 100644 --- a/dcicutils/misc_utils.py +++ b/dcicutils/misc_utils.py @@ -3,8 +3,10 @@ """ from collections import namedtuple +from typing import Iterable # would prefer this but error from Python 3.8: from collections.abc import Iterable import appdirs from copy import deepcopy +import concurrent.futures import contextlib import datetime import functools @@ -984,23 +986,159 @@ def str_to_bool(x: Optional[str]) -> Optional[bool]: raise ValueError(f"An argument to str_or_bool must be a string or None: {x!r}") -def to_integer(value: str, fallback: Optional[Any] = None) -> Optional[Any]: - try: - return int(value) - except Exception: - try: - return int(float(value)) - except Exception: - pass - return fallback +def to_integer(value: str, + allow_commas: bool = False, + allow_multiplier_suffix: bool = False, + fallback: Optional[Union[int, float]] = None) -> Optional[int]: + """ + Converts the given string value to an int or None or the given fallback value if malformed. + See comments in to_number for details on the other arguments. + """ + return to_number(value, fallback=fallback, as_float=False, + allow_commas=allow_commas, + allow_multiplier_suffix=allow_multiplier_suffix) -def to_float(value: str, fallback: Optional[Any] = None) -> Optional[Any]: - try: - return float(value) - except Exception: +def to_float(value: str, + allow_commas: bool = False, + allow_multiplier_suffix: bool = False, + fallback: Optional[Union[int, float]] = None) -> Optional[int]: + """ + Converts the given string value to a float or None or the given fallback value if malformed. + See comments in to_number for details on the other arguments. + """ + return to_number(value, fallback=fallback, as_float=True, + allow_commas=allow_commas, + allow_multiplier_suffix=allow_multiplier_suffix) + + +_TO_NUMBER_POWER_OF_TEN_FOR_NOTHING = 0 +_TO_NUMBER_POWER_OF_TEN_FOR_K = 3 +_TO_NUMBER_POWER_OF_TEN_FOR_M = 6 +_TO_NUMBER_POWER_OF_TEN_FOR_G = 9 +_TO_NUMBER_POWER_OF_TEN_FOR_T = 12 + +_TO_NUMBER_MULTIPLIER_SUFFIXES = { + "K": _TO_NUMBER_POWER_OF_TEN_FOR_K, + "KB": _TO_NUMBER_POWER_OF_TEN_FOR_K, + "M": _TO_NUMBER_POWER_OF_TEN_FOR_M, + "MB": _TO_NUMBER_POWER_OF_TEN_FOR_M, + "G": _TO_NUMBER_POWER_OF_TEN_FOR_G, + "GB": _TO_NUMBER_POWER_OF_TEN_FOR_G, + "T": _TO_NUMBER_POWER_OF_TEN_FOR_T, + "TB": _TO_NUMBER_POWER_OF_TEN_FOR_T, + # B means bytes or bases and BP means base pairs; this needs to be last. + "B": _TO_NUMBER_POWER_OF_TEN_FOR_NOTHING, + "BP": _TO_NUMBER_POWER_OF_TEN_FOR_NOTHING +} + + +def to_number(value: str, + as_float: bool = False, + allow_commas: bool = False, + allow_multiplier_suffix: bool = False, + fallback: Optional[Union[int, float]] = None) -> Optional[Union[int, float]]: + """ + Converts the given string value to an int, or float if as_float is True, + or None or the given fallback value if malformed. + + If allow_commas is True then allows appropriately placed commas (i.e. every three digits). + + If allow_multiplier_suffix is True allows any of the multiplier suffixes K, KB; M, MB; + or G, GB; or T, TB; all case-insensitive; which will multiply the value by a thousand; + a million; a billion; or a trillion; respectively. + + If as_float is True then value is parsed and returned as a float rather than int. + + Note that even if as_float is False, values that might LOOK like a float, can be + an int, for example, "1.5K", returns 1500 as an int since it is; but "1.5002K" + is malformed, since 1.5002K is equivalent to 1500.2 which is not an int. + """ + + if not (isinstance(value, str) and (value := value.strip())): + # Just in case the value is already the actual/desired return type. + if as_float is True: + return float(value) if isinstance(value, (float, int)) else fallback + else: + return value if isinstance(value, int) else fallback + + value_multiplier = _TO_NUMBER_POWER_OF_TEN_FOR_NOTHING + value_fraction = None + value_negative = False + + if value.startswith("-"): + if not (value := value[1:].strip()): + return fallback + value_negative = True + elif value.startswith("+"): + if not (value := value[1:].strip()): + return fallback + + if allow_multiplier_suffix is True: + value_upper = value.upper() + for suffix in _TO_NUMBER_MULTIPLIER_SUFFIXES: + if value_upper.endswith(suffix): + value_multiplier = _TO_NUMBER_MULTIPLIER_SUFFIXES[suffix] + if not (value := value[:-len(suffix)].strip()): + return fallback + break + + if (allow_multiplier_suffix is True) or (as_float is True): + # Allow for example "1.5K" to mean 1500 (int). + if (dot_index := value.rfind(".")) >= 0: + if value_fraction := value[dot_index + 1:].strip(): + if not value_fraction.isdigit(): + return fallback + if not (value := value[:dot_index].strip()): + if not value_fraction: + return fallback + value = "0" + elif (as_float is not True) and (value_dot_zeros_suffix := re.search(r"\.0*$", value)): + # Allow for example "123.00" to mean 123 (int). + value = value[:value_dot_zeros_suffix.start()] + + if (allow_commas is True) and ("," in value): + # Make sure any commas are properly placed/spaced. + if not re.fullmatch(r"(-?\d{1,3}(,\d{3})*)", value): + return fallback + value = value.replace(",", "") + + if not value.isdigit(): return fallback + if value_multiplier != _TO_NUMBER_POWER_OF_TEN_FOR_NOTHING: + # We do string manipulation for the (power of ten) multiplier and NOT normal multiplicative + # arithmetic because this can EASILY yield UNEXPECTED floating point related INACCURACIES. + # E.g. to_integer("1.5678K", allow_multiplier_suffix=True) would yield 1567.8000000000002 + # rather than 1567.8 if (we simply did 1.5678 * 1000.0); also tried multiplying by 10 at + # a time, and using Decimal, which obviated some, but not all, of the idiosyncrasies. + if value_fraction: + for _ in range(value_multiplier): + if value_fraction: + value += value_fraction[0] + value_fraction = value_fraction[1:] + else: + value += "0" + if value_fraction: + if as_float is not True: + # Left over fraction for int with multiplier, e.g. "1.2345K" -> 1234.5. + return fallback + value = float(f"{value}.{value_fraction}") + else: + value = float(value) if as_float else int(value) + else: + value = value + ("0" * value_multiplier) + value = float(value) if as_float else int(value) + elif as_float is True: + if value_fraction: + value = float(f"{value}.{value_fraction}") + else: + value = float(value) + else: + value = int(value) + + return -value if value_negative else value + def to_boolean(value: str, fallback: Optional[Any]) -> Optional[Any]: if isinstance(value, str) and (value := value.strip().lower()): @@ -1011,12 +1149,14 @@ def to_boolean(value: str, fallback: Optional[Any]) -> Optional[Any]: return fallback -def to_enum(value: str, enumerators: List[str]) -> Optional[str]: +def to_enum(value: str, enumerators: List[str], fuzzy: bool = False) -> Optional[str]: matches = [] if isinstance(value, str) and (value := value.strip()) and isinstance(enumerators, List): enum_specifiers = {str(enum).lower(): enum for enum in enumerators} if (enum_value := enum_specifiers.get(lower_value := value.lower())) is not None: return enum_value + if fuzzy is not True: + return value for enum_canonical, _ in enum_specifiers.items(): if enum_canonical.startswith(lower_value): matches.append(enum_canonical) @@ -2778,3 +2918,8 @@ def create_short_uuid(length: Optional[int] = None, upper: bool = False): if upper is True: value = value.upper() return value + + +def run_concurrently(functions: Iterable[Callable], nthreads: int = 4) -> None: + with concurrent.futures.ThreadPoolExecutor(max_workers=nthreads) as executor: + concurrent.futures.as_completed([executor.submit(f) for f in functions]) diff --git a/dcicutils/qa_checkers.py b/dcicutils/qa_checkers.py index 6eaa13640..c5f704178 100644 --- a/dcicutils/qa_checkers.py +++ b/dcicutils/qa_checkers.py @@ -6,8 +6,7 @@ import warnings from collections import defaultdict -from typing import Optional, List, Dict, Type -from typing_extensions import Literal +from typing import Optional, List, Dict, Type, Literal from .contribution_utils import Contributions from .lang_utils import conjoined_list, n_of, there_are from .misc_utils import PRINT, remove_prefix, remove_suffix, getattr_customized, CustomizableProperty diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py index ac18f3b19..5aadcba6b 100644 --- a/dcicutils/qa_utils.py +++ b/dcicutils/qa_utils.py @@ -25,8 +25,7 @@ from botocore.exceptions import ClientError from collections import defaultdict from json import dumps as json_dumps, loads as json_loads -from typing import Any, Optional, List, DefaultDict, Union, Type, Dict -from typing_extensions import Literal +from typing import Any, Optional, List, DefaultDict, Union, Type, Dict, Literal from unittest import mock from . import misc_utils as misc_utils_module, command_utils as command_utils_module from .common import S3StorageClass diff --git a/dcicutils/s3_utils.py b/dcicutils/s3_utils.py index c5d200243..c09cbec07 100644 --- a/dcicutils/s3_utils.py +++ b/dcicutils/s3_utils.py @@ -5,8 +5,7 @@ import os from io import BytesIO -from typing import Optional, Any, Union -from typing_extensions import Literal +from typing import Optional, Any, Union, Literal from zipfile import ZipFile from .base import get_beanstalk_real_url from .common import ( diff --git a/dcicutils/scripts/update_portal_object.py b/dcicutils/scripts/update_portal_object.py index 0918b8f26..c5b29255b 100644 --- a/dcicutils/scripts/update_portal_object.py +++ b/dcicutils/scripts/update_portal_object.py @@ -13,6 +13,7 @@ import io import json import os +import re import sys from typing import Callable, List, Optional, Tuple, Union from dcicutils.command_utils import yes_or_no @@ -162,14 +163,18 @@ def usage(message: Optional[str] = None) -> None: explicit_schema_name=explicit_schema_name, update_function=patch_data, update_action_name="PATCH", + patch_delete_fields=args.delete, confirm=args.confirm, verbose=args.verbose, quiet=args.quiet, debug=args.debug) + args.delete = None if args.upsert: _post_or_patch_or_upsert(portal=portal, file_or_directory=args.upsert, explicit_schema_name=explicit_schema_name, update_function=upsert_data, update_action_name="UPSERT", + patch_delete_fields=args.delete, confirm=args.confirm, verbose=args.verbose, quiet=args.quiet, debug=args.debug) + args.delete = None if args.delete: if not portal.get_metadata(args.delete, raise_exception=False): @@ -190,6 +195,7 @@ def usage(message: Optional[str] = None) -> None: def _post_or_patch_or_upsert(portal: Portal, file_or_directory: str, explicit_schema_name: str, update_function: Callable, update_action_name: str, + patch_delete_fields: Optional[str] = None, confirm: bool = False, verbose: bool = False, quiet: bool = False, debug: bool = False) -> None: @@ -202,6 +208,7 @@ def is_schema_name_list(portal: Portal, keys: list) -> bool: return False def post_or_patch_or_upsert(portal: Portal, file: str, schema_name: Optional[str], + patch_delete_fields: Optional[str] = None, confirm: bool = False, verbose: bool = False, quiet: bool = False, debug: bool = False) -> None: @@ -213,8 +220,9 @@ def post_or_patch_or_upsert(portal: Portal, file: str, schema_name: Optional[str if isinstance(schema_name, str) and schema_name: if debug: _print(f"DEBUG: File ({file}) contains an object of type: {schema_name}") - update_function(portal, data, schema_name, confirm=confirm, - file=file, verbose=verbose, debug=debug) + update_function(portal, data, schema_name, file=file, + patch_delete_fields=patch_delete_fields, + confirm=confirm, verbose=verbose, debug=debug) elif is_schema_name_list(portal, list(data.keys())): if debug: _print(f"DEBUG: File ({file}) contains a dictionary of schema names.") @@ -223,8 +231,9 @@ def post_or_patch_or_upsert(portal: Portal, file: str, schema_name: Optional[str if debug: _print(f"DEBUG: Processing {update_action_name}s for type: {schema_name}") for index, item in enumerate(schema_data): - update_function(portal, item, schema_name, confirm=confirm, - file=file, index=index, verbose=verbose, debug=debug) + update_function(portal, item, schema_name, file=file, index=index, + patch_delete_fields=patch_delete_fields, + confirm=confirm, verbose=verbose, debug=debug) else: _print(f"WARNING: File ({file}) contains schema item which is not a list: {schema_name}") else: @@ -233,8 +242,9 @@ def post_or_patch_or_upsert(portal: Portal, file: str, schema_name: Optional[str if debug: _print(f"DEBUG: File ({file}) contains a list of objects of type: {schema_name}") for index, item in enumerate(data): - update_function(portal, item, schema_name, confirm=confirm, - file=file, index=index, verbose=verbose, debug=debug) + update_function(portal, item, schema_name, file=file, index=index, + patch_delete_fields=patch_delete_fields, + confirm=confirm, verbose=verbose, debug=debug) if debug: _print(f"DEBUG: Processing {update_action_name} file done: {file}") @@ -248,14 +258,17 @@ def post_or_patch_or_upsert(portal: Portal, file: str, schema_name: Optional[str _print(f"ERROR: Schema cannot be inferred from file name and --schema not specified: {file}") continue post_or_patch_or_upsert(portal, file_and_schema[0], schema_name=schema_name, + patch_delete_fields=patch_delete_fields, confirm=confirm, quiet=quiet, verbose=verbose, debug=debug) elif os.path.isfile(file := file_or_directory): if ((schema_name := _get_schema_name_from_schema_named_json_file_name(portal, file)) or (schema_name := explicit_schema_name)): # noqa post_or_patch_or_upsert(portal, file, schema_name=schema_name, + patch_delete_fields=patch_delete_fields, confirm=confirm, quiet=quiet, verbose=verbose, debug=debug) else: post_or_patch_or_upsert(portal, file, schema_name=schema_name, + patch_delete_fields=patch_delete_fields, confirm=confirm, quiet=quiet, verbose=verbose, debug=debug) # _print(f"ERROR: Schema cannot be inferred from file name and --schema not specified: {file}") # return @@ -263,9 +276,10 @@ def post_or_patch_or_upsert(portal: Portal, file: str, schema_name: Optional[str _print(f"ERROR: Cannot find file or directory: {file_or_directory}") -def post_data(portal: Portal, data: dict, schema_name: str, confirm: bool = False, +def post_data(portal: Portal, data: dict, schema_name: str, file: Optional[str] = None, index: int = 0, - verbose: bool = False, debug: bool = False) -> None: + patch_delete_fields: Optional[str] = None, # unused here + confirm: bool = False, verbose: bool = False, debug: bool = False) -> None: if not (identifying_path := portal.get_identifying_path(data, portal_type=schema_name)): if isinstance(file, str) and isinstance(index, int): _print(f"ERROR: Item for POST has no identifying property: {file} (#{index + 1})") @@ -289,9 +303,10 @@ def post_data(portal: Portal, data: dict, schema_name: str, confirm: bool = Fals return -def patch_data(portal: Portal, data: dict, schema_name: str, confirm: bool = False, +def patch_data(portal: Portal, data: dict, schema_name: str, file: Optional[str] = None, index: int = 0, - verbose: bool = False, debug: bool = False) -> None: + patch_delete_fields: Optional[str] = None, + confirm: bool = False, verbose: bool = False, debug: bool = False) -> None: if not (identifying_path := portal.get_identifying_path(data, portal_type=schema_name)): if isinstance(file, str) and isinstance(index, int): _print(f"ERROR: Item for PATCH has no identifying property: {file} (#{index + 1})") @@ -306,6 +321,8 @@ def patch_data(portal: Portal, data: dict, schema_name: str, confirm: bool = Fal if verbose: _print(f"PATCH {schema_name} item: {identifying_path}") try: + if delete_fields := _parse_delete_fields(patch_delete_fields): + identifying_path += f"?delete_fields={delete_fields}" portal.patch_metadata(identifying_path, data) if debug: _print(f"DEBUG: PATCH {schema_name} item OK: {identifying_path}") @@ -315,9 +332,10 @@ def patch_data(portal: Portal, data: dict, schema_name: str, confirm: bool = Fal return -def upsert_data(portal: Portal, data: dict, schema_name: str, confirm: bool = False, +def upsert_data(portal: Portal, data: dict, schema_name: str, file: Optional[str] = None, index: int = 0, - verbose: bool = False, debug: bool = False) -> None: + patch_delete_fields: Optional[str] = None, + confirm: bool = False, verbose: bool = False, debug: bool = False) -> None: if not (identifying_path := portal.get_identifying_path(data, portal_type=schema_name)): if isinstance(file, str) and isinstance(index, int): _print(f"ERROR: Item for UPSERT has no identifying property: {file} (#{index + 1})") @@ -330,7 +348,12 @@ def upsert_data(portal: Portal, data: dict, schema_name: str, confirm: bool = Fa if verbose: _print(f"{'PATCH' if exists else 'POST'} {schema_name} item: {identifying_path}") try: - portal.post_metadata(schema_name, data) if not exists else portal.patch_metadata(identifying_path, data) + if not exists: + portal.post_metadata(schema_name, data) + else: + if delete_fields := _parse_delete_fields(patch_delete_fields): + identifying_path += f"?delete_fields={delete_fields}" + portal.patch_metadata(identifying_path, data) if debug: _print(f"DEBUG: UPSERT {schema_name} item OK: {identifying_path}") except Exception as e: @@ -396,6 +419,14 @@ def _file_names_to_ordered_file_and_schema_names(portal: Portal, return ordered_results +def _parse_delete_fields(value: str) -> str: + if not isinstance(value, str): + value = [] + else: + value = list(set([part.strip() for part in re.split(r'[,;|\s]+', value) if part.strip()])) + return ",".join(value) + + def _get_schema_name_from_schema_named_json_file_name(portal: Portal, value: str) -> Optional[str]: try: if not value.endswith(".json"): diff --git a/dcicutils/scripts/view_portal_object.py b/dcicutils/scripts/view_portal_object.py index bc28ccc12..90f459303 100644 --- a/dcicutils/scripts/view_portal_object.py +++ b/dcicutils/scripts/view_portal_object.py @@ -114,16 +114,13 @@ def main(): help="Copy object data to clipboard.") parser.add_argument("--output", required=False, help="Output file.", type=str) parser.add_argument("--indent", required=False, default=False, help="Indent output.", type=int) - parser.add_argument("--details", action="store_true", required=False, default=False, help="Detailed output.") - parser.add_argument("--more-details", action="store_true", required=False, default=False, - help="More detailed output.") + parser.add_argument("--summary", action="store_true", required=False, default=False, + help="Summary output (for schema only).") + parser.add_argument("--terse", action="store_true", required=False, default=False, help="Terse output.") parser.add_argument("--verbose", action="store_true", required=False, default=False, help="Verbose output.") parser.add_argument("--debug", action="store_true", required=False, default=False, help="Debugging output.") args = parser.parse_args() - if args.more_details: - args.details = True - portal = _create_portal(ini=args.ini, env=args.env or os.environ.get("SMAHT_ENV"), server=args.server, app=args.app, verbose=args.verbose, debug=args.debug) @@ -143,9 +140,8 @@ def main(): _output_file = io.open(args.output, "w") if args.uuid and ((args.uuid.lower() == "schemas") or (args.uuid.lower() == "schema")): - _print_all_schema_names(portal=portal, details=args.details, - more_details=args.more_details, all=args.all, - tree=args.tree, raw=args.raw, raw_yaml=args.yaml) + _print_all_schema_names(portal=portal, terse=args.terse, all=args.all, + tree=args.tree, summary=args.summary, yaml=args.yaml) return elif args.uuid and (args.uuid.lower() == "info"): if consortia := portal.get_metadata("/consortia?limit=1000"): @@ -182,7 +178,7 @@ def main(): if schema: if args.copy: pyperclip.copy(json.dumps(schema, indent=4)) - if not args.raw: + if args.summary: if parent_schema_name := _get_parent_schema_name(schema): if schema.get("isAbstract") is True: _print_output(f"{schema_name} | parent: {parent_schema_name} | abstract") @@ -190,8 +186,8 @@ def main(): _print_output(f"{schema_name} | parent: {parent_schema_name}") else: _print_output(schema_name) - _print_schema(schema, details=args.details, more_details=args.details, - all=args.all, raw=args.raw, raw_yaml=args.yaml) + _print_schema(schema, terse=args.terse, + all=args.all, summary=args.summary, yaml=args.yaml) return data = _get_portal_object(portal=portal, uuid=args.uuid, raw=args.raw, inserts=args.inserts, @@ -276,9 +272,26 @@ def _get_portal_object(portal: Portal, uuid: str, (isinstance(results_type := response.get("@type"), list) and results_type) and (isinstance(results_type := results_type[0], str) and results_type.endswith("SearchResults")) and (results_type := results_type[0:-len("SearchResults")])): # noqa + # For search results, the type (from XyzSearchResults, above) may not be precisely correct for + # each of the results; it may be the supertype (e.g. QualityMetric vs QualityMetricWorkflowRun); + # so for types which are supertypes (gotten via Portal.get_schemas_super_type_map) we actually + # lookup each result individually to determine its actual precise type. + if not ((supertypes := portal.get_schemas_super_type_map()) and (subtypes := supertypes.get(results_type))): + subtypes = None + response = {} for result in results: result.pop("schema_version", None) - response = {f"{results_type}": results} + if (subtypes and + (result_uuid := result.get("uuid")) and + (individual_result := portal.get_metadata(result_uuid, raise_exception=False)) and + isinstance(result_type:= individual_result.get("@type"), list) and result_type and result_type[0]): # noqa + result_type = result_type[0] + else: + result_type = results_type + if response.get(result_type): + response[result_type].append(result) + else: + response[result_type] = [result] # Get the result as non-raw so we can get its type. elif ((response_cooked := portal.get(path, database=database)) and (isinstance(response_type := response_cooked.json().get("@type"), list) and response_type)): @@ -332,19 +345,19 @@ def _get_schema_name_from_schema_named_json_file_name(portal: Portal, value: str return False -def _print_schema(schema: dict, details: bool = False, more_details: bool = False, all: bool = False, - raw: bool = False, raw_yaml: bool = False) -> None: - if raw: - if raw_yaml: +def _print_schema(schema: dict, terse: bool = False, all: bool = False, + summary: bool = False, yaml: bool = False) -> None: + if summary is not True: + if yaml: _print_output(yaml.dump(schema)) else: _print_output(json.dumps(schema, indent=4)) return - _print_schema_info(schema, details=details, more_details=more_details, all=all) + _print_schema_info(schema, terse=terse, all=all) def _print_schema_info(schema: dict, level: int = 0, - details: bool = False, more_details: bool = False, all: bool = False, + terse: bool = False, all: bool = False, required: Optional[List[str]] = None) -> None: if not schema or not isinstance(schema, dict): return @@ -396,7 +409,7 @@ def _print_schema_info(schema: dict, level: int = 0, _print_output(f" - {reference_property['name']}: {reference_property['ref']}") if schema.get("additionalProperties") is True: _print_output(f" - additional properties are allowed") - if not more_details: + if terse: return if properties := (schema.get("properties") if level == 0 else schema): if level == 0: @@ -422,8 +435,7 @@ def _print_schema_info(schema: dict, level: int = 0, if property.get("calculatedProperty"): suffix += f" | calculated" _print_output(f"{spaces}- {property_name}: {property_type}{suffix}") - _print_schema_info(object_properties, level=level + 1, - details=details, more_details=more_details, all=all, + _print_schema_info(object_properties, level=level + 1, terse=terse, all=all, required=property.get("required")) elif property_type == "array": suffix = "" @@ -447,7 +459,7 @@ def _print_schema_info(schema: dict, level: int = 0, suffix = "" _print_output(f"{spaces}- {property_name}: array of object{suffix}") _print_schema_info(property_items.get("properties"), level=level + 1, - details=details, more_details=more_details, all=all, + terse=terse, all=all, required=property_items.get("required")) elif property_type == "array": # This (array-of-array) never happens to occur at this time (February 2024). @@ -523,13 +535,13 @@ def _print_schema_info(schema: dict, level: int = 0, def _print_all_schema_names(portal: Portal, - details: bool = False, more_details: bool = False, all: bool = False, - tree: bool = False, raw: bool = False, raw_yaml: bool = False) -> None: + terse: bool = False, all: bool = False, + tree: bool = False, summary: bool = False, yaml: bool = False) -> None: if not (schemas := _get_schemas(portal)): return - if raw: - if raw_yaml: + if summary is not True: + if yaml: _print_output(yaml.dump(schemas)) else: _print_output(json.dumps(schemas, indent=4)) @@ -550,8 +562,8 @@ def _print_all_schema_names(portal: Portal, _print_output(f"{schema_name} | abstract") else: _print_output(schema_name) - if details: - _print_schema(schemas[schema_name], details=details, more_details=more_details, all=all) + if not terse: + _print_schema(schemas[schema_name], terse=terse, all=all) def _get_parent_schema_name(schema: dict) -> Optional[str]: diff --git a/dcicutils/structured_data.py b/dcicutils/structured_data.py index 2d058a588..8bb134432 100644 --- a/dcicutils/structured_data.py +++ b/dcicutils/structured_data.py @@ -57,7 +57,7 @@ def __init__(self, file: Optional[str] = None, portal: Optional[Union[VirtualApp ref_lookup_nocache: bool = False, norefs: bool = False, merge: bool = False, progress: Optional[Callable] = None, - row_reader_hook: Optional[Callable] = None, + validator_hook: Optional[Callable] = None, debug_sleep: Optional[str] = None) -> None: self._progress = progress if callable(progress) else None self._data = {} @@ -76,7 +76,7 @@ def __init__(self, file: Optional[str] = None, portal: Optional[Union[VirtualApp self._autoadd_properties = autoadd if isinstance(autoadd, dict) and autoadd else None self._norefs = True if norefs is True else False self._merge = True if merge is True else False # New merge functionality (2024-05-25) - self._row_reader_hook = row_reader_hook if callable(row_reader_hook) else None # Testing support (2024-06-12) + self._validator_hook = validator_hook if callable(validator_hook) else None # Testing support (2024-06-12) self._debug_sleep = None if debug_sleep: try: @@ -379,8 +379,14 @@ def _load_reader(self, reader: RowReader, type_name: str) -> None: structured_row_template = _StructuredRowTemplate(reader.header, schema) structured_row = structured_row_template.create_row() for column_name, value in row.items(): - if self._row_reader_hook: - value = self._row_reader_hook(reader.sheet_name, column_name, value) + if self._validator_hook: + value, validator_error = ( + self._validator_hook(self, type_name, column_name, reader.row_number, value)) + if validator_error: + self._note_error({ + "src": create_dict(type=schema_name, row=reader.row_number), + "error": validator_error + }, "validation") structured_row_template.set_value(structured_row, column_name, value, reader.file, reader.row_number) if self._autoadd_properties: self._add_properties(structured_row, self._autoadd_properties, schema) @@ -526,6 +532,18 @@ def _note_issue(self, issues: dict, item: Optional[Union[dict, List[dict]]], gro issues[group] = [] issues[group].extend(item) + def note_validation_error(self, validation_error: str, + schema_name: Optional[str] = None, row_number: Optional[int] = None) -> None: + if isinstance(validation_error, str) and validation_error: + if isinstance(schema_name, str) and schema_name: + if isinstance(row_number, int): + src = create_dict(type=schema_name, row=row_number) + else: + src = create_dict(type=schema_name) + else: + src = None + self._note_error({"src": src, "error": validation_error}, "validation") + class _StructuredRowTemplate: @@ -705,13 +723,23 @@ def map_enum(value: str, enum_specifiers: dict, src: Optional[str]) -> Any: return lambda value, src: map_enum(value, typeinfo.get("enum", []), src) def _map_function_integer(self, typeinfo: dict) -> Callable: - def map_integer(value: str, src: Optional[str]) -> Any: - return to_integer(value, value) + allow_commas = typeinfo.get("allow_commas") is True + allow_multiplier_suffix = typeinfo.get("allow_multiplier_suffix") is True + def map_integer(value: str, src: Optional[str]) -> Any: # noqa + nonlocal allow_commas, allow_multiplier_suffix + return to_integer(value, fallback=value, + allow_commas=allow_commas, + allow_multiplier_suffix=allow_multiplier_suffix) return map_integer def _map_function_number(self, typeinfo: dict) -> Callable: - def map_number(value: str, src: Optional[str]) -> Any: - return to_float(value, value) + allow_commas = typeinfo.get("allow_commas") is True + allow_multiplier_suffix = typeinfo.get("allow_multiplier_suffix") is True + def map_number(value: str, src: Optional[str]) -> Any: # noqa + nonlocal allow_commas, allow_multiplier_suffix + return to_float(value, fallback=value, + allow_commas=allow_commas, + allow_multiplier_suffix=allow_multiplier_suffix) return map_number def _map_function_string(self, typeinfo: dict) -> Callable: @@ -721,14 +749,16 @@ def map_string(value: str, src: Optional[str]) -> str: def _map_function_date(self, typeinfo: dict) -> Callable: def map_date(value: str, src: Optional[str]) -> str: - value = normalize_date_string(value) - return value if value is not None else "" + if not (parsed_value := normalize_date_string(value)): + return value + return parsed_value return map_date def _map_function_datetime(self, typeinfo: dict) -> Callable: def map_datetime(value: str, src: Optional[str]) -> str: - value = normalize_datetime_string(value) - return value if value is not None else "" + if not (parsed_value := normalize_datetime_string(value)): + return value + return parsed_value return map_datetime def _map_function_ref(self, typeinfo: dict) -> Callable: diff --git a/poetry.lock b/poetry.lock index b7b40dcc7..0f853563a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -83,18 +83,18 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.34.136" +version = "1.34.147" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.34.136-py3-none-any.whl", hash = "sha256:d41037e2c680ab8d6c61a0a4ee6bf1fdd9e857f43996672830a95d62d6f6fa79"}, - {file = "boto3-1.34.136.tar.gz", hash = "sha256:0314e6598f59ee0f34eb4e6d1a0f69fa65c146d2b88a6e837a527a9956ec2731"}, + {file = "boto3-1.34.147-py3-none-any.whl", hash = "sha256:e1cef9a1a301866bcdee32ae0c699465eb2345f9a8e613a5835821430165ff6d"}, + {file = "boto3-1.34.147.tar.gz", hash = "sha256:9ec1c6ab22588242a47549f51a63dfc7c21fdf95a94820fc6e629ab060c38bd9"}, ] [package.dependencies] -botocore = ">=1.34.136,<1.35.0" +botocore = ">=1.34.147,<1.35.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -103,14 +103,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.136" -description = "Type annotations for boto3 1.34.136 generated with mypy-boto3-builder 7.24.0" +version = "1.34.147" +description = "Type annotations for boto3 1.34.147 generated with mypy-boto3-builder 7.25.0" category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.34.136-py3-none-any.whl", hash = "sha256:5826c22c10fc9032376bbee436d1b23b111e5fb1f13c75ecde8727151191f057"}, - {file = "boto3_stubs-1.34.136.tar.gz", hash = "sha256:ecbce782ae19037d1f26673cfc30358493c9658ea0af06dd58a999be963ab275"}, + {file = "boto3_stubs-1.34.147-py3-none-any.whl", hash = "sha256:6a5b276eb3414b370a084561f23d610a1e8c8e7630f6fe463523fc06766bc887"}, + {file = "boto3_stubs-1.34.147.tar.gz", hash = "sha256:3a483d2a55b247029d6e5e04002153984353c0c19882607af7e37038a7ce72b0"}, ] [package.dependencies] @@ -123,7 +123,7 @@ accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)"] account = ["mypy-boto3-account (>=1.34.0,<1.35.0)"] acm = ["mypy-boto3-acm (>=1.34.0,<1.35.0)"] acm-pca = ["mypy-boto3-acm-pca (>=1.34.0,<1.35.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)", "mypy-boto3-account (>=1.34.0,<1.35.0)", "mypy-boto3-acm (>=1.34.0,<1.35.0)", "mypy-boto3-acm-pca (>=1.34.0,<1.35.0)", "mypy-boto3-amp (>=1.34.0,<1.35.0)", "mypy-boto3-amplify (>=1.34.0,<1.35.0)", "mypy-boto3-amplifybackend (>=1.34.0,<1.35.0)", "mypy-boto3-amplifyuibuilder (>=1.34.0,<1.35.0)", "mypy-boto3-apigateway (>=1.34.0,<1.35.0)", 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"pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "shortuuid" @@ -1989,7 +1994,7 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2035,14 +2040,14 @@ docs = ["Sphinx (>=1.3.1)", "docutils", "pylons-sphinx-themes"] [[package]] name = "types-awscrt" -version = "0.20.12" +version = "0.21.2" description = "Type annotations and code completion for awscrt" category = "dev" optional = false python-versions = "<4.0,>=3.7" files = [ - {file = "types_awscrt-0.20.12-py3-none-any.whl", hash = "sha256:521ce54cc4dad9fe6480556bb0f8315a508106938ba1f2a0baccfcea7d4a4dee"}, - {file = "types_awscrt-0.20.12.tar.gz", hash = "sha256:0beabdde0205dc1da679ea464fd3f98b570ef4f0fc825b155a974fb51b21e8d9"}, + {file = "types_awscrt-0.21.2-py3-none-any.whl", hash = "sha256:0839fe12f0f914d8f7d63ed777c728cb4eccc2d5d79a26e377d12b0604e7bf0e"}, + {file = "types_awscrt-0.21.2.tar.gz", hash = "sha256:84a9f4f422ec525c314fdf54c23a1e73edfbcec968560943ca2d41cfae623b38"}, ] [[package]] @@ -2277,4 +2282,4 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.13" -content-hash = "6d3f00c8a5e582bd82576dbfd357cd86065acac7b175e6938d75dd37ef9918e8" +content-hash = "45bd3f78d7d134a4e8ec30f529e286d963e5612daea5287174a43d1d3069afc2" diff --git a/pyproject.toml b/pyproject.toml index 5f9b51c6f..c47099bb5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicutils" -version = "8.13.3" +version = "8.14.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" authors = ["4DN-DCIC Team "] license = "MIT" @@ -39,8 +39,8 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.8.1,<3.13" -boto3 = "^1.34.136" -botocore = "^1.34.136" +boto3 = "^1.34.147" +botocore = "^1.34.147" # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version. # This value is intentionally pinned and must not be changed casually. elasticsearch = "7.13.4" @@ -63,7 +63,7 @@ pyperclip = "^1.8.2" PyYAML = "^6.0.1" # N.B. 2024-06-30: Updating (via poetry update) from requests 2.31.0 (2023-05-22) # to 2.32.3 (2024-05-29) causes utils GA/CI to fail (on test_ecr_utils_workflow) for some reason. -requests = "^2.21.0" +requests = "2.31.0" rfc3986 = "^1.4.0" shortuuid = "^1.0.13" structlog = "^19.2.0" @@ -75,8 +75,8 @@ webtest = "^2.0.34" [tool.poetry.dev-dependencies] -boto3-stubs = "^1.34.136" -botocore-stubs = "^1.34.136" +boto3-stubs = "^1.34.147" +botocore-stubs = "^1.34.147" coverage = "^7.5.4" # Loaded manually in GA workflow for coverage because a dependency on 2to3 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023 diff --git a/test/data_files/structured_data/submission_test_file_from_doug_20231130.xlsx b/test/data_files/structured_data/submission_test_file_from_doug_20231130.xlsx index a787c009e..59f39a9a1 100644 Binary files a/test/data_files/structured_data/submission_test_file_from_doug_20231130.xlsx and b/test/data_files/structured_data/submission_test_file_from_doug_20231130.xlsx differ diff --git a/test/test_misc_utils.py b/test/test_misc_utils.py index 0f2af3c70..e0c414d61 100644 --- a/test/test_misc_utils.py +++ b/test/test_misc_utils.py @@ -31,7 +31,7 @@ ObsoleteError, CycleError, TopologicalSorter, keys_and_values_to_dict, dict_to_keys_and_values, is_c4_arn, deduplicate_list, chunked, parse_in_radix, format_in_radix, managed_property, future_datetime, MIN_DATETIME, MIN_DATETIME_UTC, INPUT, builtin_print, map_chunked, to_camel_case, json_file_contents, - pad_to, JsonLinesReader, split_string, merge_objects, to_integer, + pad_to, JsonLinesReader, split_string, merge_objects, to_float, to_integer, load_json_from_file_expanding_environment_variables, create_readonly_object ) from dcicutils.qa_utils import ( @@ -3701,14 +3701,171 @@ def test_merge_objects_9(): def test_to_integer(): - assert to_integer("17") == 17 - assert to_integer("17.0") == 17 - assert to_integer("17.1") == 17 - assert to_integer("17.9", "123") == 17 + assert to_integer("0") == 0 - assert to_integer("0.0") == 0 - assert to_integer("asdf") is None - assert to_integer("asdf", "myfallback") == "myfallback" + assert to_integer("00") == 0 + assert to_integer("1") == 1 + assert to_integer("01") == 1 + assert to_integer("123") == 123 + assert to_integer("123.0") == 123 + assert to_integer("123.00000") == 123 + assert to_integer(" 1234567890 ") == 1234567890 + + assert to_integer("+0") == 0 + assert to_integer("+1") == 1 + assert to_integer("+123") == 123 + assert to_integer("+123.0") == 123 + assert to_integer("+123.00000") == 123 + assert to_integer("+ 1234567890 ") == 1234567890 + + assert to_integer("-0") == 0 + assert to_integer("-1") == -1 + assert to_integer("-123") == -123 + assert to_integer("-123.0") == -123 + assert to_integer("-123.00000") == -123 + assert to_integer("- 1234567890 ") == -1234567890 + + assert to_integer("1K", allow_multiplier_suffix=True) == 1000 + assert to_integer("2KB", allow_multiplier_suffix=True) == 2000 + assert to_integer("3Kb", allow_multiplier_suffix=True) == 3000 + assert to_integer("4kb", allow_multiplier_suffix=True) == 4000 + assert to_integer("5 kb", allow_multiplier_suffix=True) == 5000 + assert to_integer("6.00kB", allow_multiplier_suffix=True) == 6000 + assert to_integer("9KB", allow_multiplier_suffix=True) == 9000 + assert to_integer("12KB", allow_multiplier_suffix=True) == 12000 + assert to_integer("15K", allow_multiplier_suffix=True) == 15000 + assert to_integer("1.5K", allow_multiplier_suffix=True) == 1500 + assert to_integer("15.K", allow_multiplier_suffix=True) == 15000 + assert to_integer("15.0K", allow_multiplier_suffix=True) == 15000 + assert to_integer("15.01K", allow_multiplier_suffix=True) == 15010 + assert to_integer(" 15.01 K ", allow_multiplier_suffix=True) == 15010 + assert to_integer("15.012 KB", allow_multiplier_suffix=True) == 15012 + assert to_integer("25k", allow_multiplier_suffix=True) == 25000 + assert to_integer("35Kb", allow_multiplier_suffix=True) == 35000 + assert to_integer("-35Kb", allow_multiplier_suffix=True) == -35000 + assert to_integer("0K", allow_multiplier_suffix=True) == 0 + assert to_integer("1M", allow_multiplier_suffix=True) == 1000000 + assert to_integer("2G", allow_multiplier_suffix=True) == 2000000000 + assert to_integer("2.123456G", allow_multiplier_suffix=True) == 2123456000 + assert to_integer("345T", allow_multiplier_suffix=True) == 345000000000000 + assert to_integer("4.000000001230TB", allow_multiplier_suffix=True) == 4000000001230 + assert to_integer("0M", allow_multiplier_suffix=True) == 0 + + assert type(to_integer("4.000000001230TB", allow_multiplier_suffix=True)) == int + + assert to_integer("1,234", allow_commas=True) == 1234 + assert to_integer("12,345", allow_commas=True) == 12345 + assert to_integer("123,456", allow_commas=True) == 123456 + assert to_integer("1,234,567", allow_commas=True) == 1234567 + + assert to_integer("1,234K", allow_multiplier_suffix=True, allow_commas=True) == 1234000 + assert to_integer("1,234M", allow_multiplier_suffix=True, allow_commas=True) == 1234000000 + assert to_integer("1,234G", allow_multiplier_suffix=True, allow_commas=True) == 1234000000000 + assert to_integer("-1,234G", allow_multiplier_suffix=True, allow_commas=True) == -1234000000000 + assert to_integer("1,234,567T", allow_multiplier_suffix=True, allow_commas=True) == 1234567000000000000 + assert to_integer("-1,234,567T", allow_multiplier_suffix=True, allow_commas=True) == -1234567000000000000 + + assert to_integer(4321) == 4321 + assert to_integer(4321 + 9) == 4330 + + +def test_to_integer_errors(): + + assert to_integer("") is None + assert to_integer(" ") is None + assert to_integer(None) is None + assert to_integer([]) is None + assert to_integer({}) is None + assert to_integer(datetime_module.datetime.now()) is None + + assert to_integer("abc") is None + assert to_integer("123 456") is None + assert to_integer("1.2") is None + assert to_integer("123K") is None + assert to_integer("123 K") is None + assert to_integer("123K B") is None + assert to_integer("++123") is None + assert to_integer("--123") is None + assert to_integer("+-123") is None + assert to_integer("123,456") is None + + assert to_integer("K2", allow_multiplier_suffix=True) is None + assert to_integer("2KK", allow_multiplier_suffix=True) is None + assert to_integer(".", allow_multiplier_suffix=True) is None + assert to_integer(".K", allow_multiplier_suffix=True) is None + assert to_integer("1.5001K", allow_multiplier_suffix=True) is None + assert to_integer(".5001K", allow_multiplier_suffix=True) is None + assert to_integer("123P", allow_multiplier_suffix=True) is None + assert to_integer("1,234M", allow_multiplier_suffix=True) is None + assert to_integer("4.0000000012309TB", allow_multiplier_suffix=True) is None # 4000000001230.9 + + assert to_integer("12,345") is None + assert to_integer(",", allow_commas=True) is None + assert to_integer("1,", allow_commas=True) is None + assert to_integer("123,", allow_commas=True) is None + assert to_integer(",123", allow_commas=True) is None + assert to_integer("123,45", allow_commas=True) is None + assert to_integer("12,4356", allow_commas=True) is None + assert to_integer("12,,456", allow_commas=True) is None + assert to_integer("1,234,5678", allow_commas=True) is None + + +def test_to_float(): + + assert to_float("789") == 789.0 + assert to_float("1234.0567") == 1234.0567 + assert to_float("1234.0") == 1234.0 + assert to_float(".1234") == 0.1234 + assert to_float("1234.") == 1234.0 + assert to_float("1.5K", allow_multiplier_suffix=True) == 1500 + assert to_float("1.5678K", allow_multiplier_suffix=True) == 1567.8 + assert to_float("1.56789K", allow_multiplier_suffix=True) == 1567.89 + assert to_float("1.567898K", allow_multiplier_suffix=True) == 1567.898 + assert to_float("1.0K", allow_multiplier_suffix=True) == 1000 + assert to_float("1.K", allow_multiplier_suffix=True) == 1000 + assert to_float(".2K", allow_multiplier_suffix=True) == 200 + assert to_float(".2M", allow_multiplier_suffix=True) == 200000 + assert to_float("3.M", allow_multiplier_suffix=True) == 3000000 + assert to_float("0.9G", allow_multiplier_suffix=True) == 900000000 + assert to_float("1.9G", allow_multiplier_suffix=True) == 1900000000 + assert to_float("4.0000000012309TB", allow_multiplier_suffix=True) == 4000000001230.9 + assert to_float(4321.1234) == 4321.1234 + + assert to_float("1,234.K", allow_commas=True, allow_multiplier_suffix=True) == 1234000 + assert to_float("12,345.K", allow_commas=True, allow_multiplier_suffix=True) == 12345000 + assert to_float("12,345.0K", allow_commas=True, allow_multiplier_suffix=True) == 12345000 + assert to_float("12,345.06K", allow_commas=True, allow_multiplier_suffix=True) == 12345060 + assert to_float("12,345.06789K", allow_commas=True, allow_multiplier_suffix=True) == 12345067.89 + assert to_float("123,456.9876G", allow_commas=True, allow_multiplier_suffix=True) == 123456987600000 + assert to_float("123,456.9876G", allow_commas=True, allow_multiplier_suffix=True) == 123456987600000.0 + assert to_float("123,456.123498765G", allow_commas=True, allow_multiplier_suffix=True) == 123456123498765.0 + assert to_float("123,456.1234987656G", allow_commas=True, allow_multiplier_suffix=True) == 123456123498765.6 + assert to_float("123,456.1234987656Tb", allow_commas=True, allow_multiplier_suffix=True) == 123456123498765600 + assert to_float("123,456.g", allow_commas=True, allow_multiplier_suffix=True) == 123456 * 1000 * 1000 * 1000 + assert to_float("0.0m", allow_commas=True, allow_multiplier_suffix=True) == 0 + + assert type(to_float("789")) == float + assert type(to_float("1.5K", allow_multiplier_suffix=True)) == float + assert type(to_float("123,456.9876G", allow_commas=True, allow_multiplier_suffix=True)) == float + + +def test_to_float_errors(): + + assert to_float("") is None + assert to_float(" ") is None + assert to_float(None) is None + assert to_float([]) is None + assert to_float({}) is None + assert to_float(datetime_module.datetime.now()) is None + assert to_float({}, fallback="123") == "123" + + assert to_float("abc") is None + assert to_float("123 456") is None + assert to_float("123.456K") is None + assert to_float("123,456") is None + assert to_float(".") is None + assert to_float(".M", allow_multiplier_suffix=True) is None + assert to_float("M", allow_multiplier_suffix=True) is None def test_load_json_from_file_expanding_environment_variables(): diff --git a/test/test_qa_utils.py b/test/test_qa_utils.py index 6e9c606bf..44c88bf33 100644 --- a/test/test_qa_utils.py +++ b/test/test_qa_utils.py @@ -31,8 +31,7 @@ ) # The following line needs to be separate from other imports. It is PART OF A TEST. from dcicutils.qa_utils import notice_pytest_fixtures # Use care if editing this line. It is PART OF A TEST. -from typing import List, Dict -from typing_extensions import Literal +from typing import List, Dict, Literal from unittest import mock from .fixtures.sample_fixtures import MockMathError, MockMath, math_enabled