biosimulators_utils.utils package#

Submodules#

biosimulators_utils.utils.core module#

Miscellaneous utilities

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
Copyright:: 2020, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.utils.core.are_lists_equal(a, b)[source]#

Determine if two lists are equal, optionally up to the order of the elements

Parameters:

a (list) – first list
b (list) – second list

Returns:

True, if lists are equal

Return type:

bool

biosimulators_utils.utils.core.assert_exception(success, exception)[source]#

Raise an error if success is False

Parameters:

success (bool) –
exception (Exception) –

Raises:

Exception –

biosimulators_utils.utils.core.flatten_nested_list_of_strings(nested_list, prefix='- ', indent=' ')[source]#

Flatten a nested list of strings

Parameters:

nested_list (nested list of str) – nested list of string
prefix (str, optional) – prefix
indentation (str, optional) – indentation

Returns:

flattened string

Return type:

str

biosimulators_utils.utils.core.format_float(val)[source]#

Format a float in scientific notation

Parameters:: val (float) – value
Returns:: value formatted as a string
Return type:: str

biosimulators_utils.utils.core.format_value(val, type)[source]#

Format a value as a string (e.g., for use with an attribute of an XML object)

Parameters:

val (object) – value
type (ValueType) – type

Returns:

string representation of the value

Return type:

str

biosimulators_utils.utils.core.none_sorted(arr, key=None)[source]#

Sort an error that contains None

Parameters:: arr (list) – array
Returns:: sorted array
Return type:: list

biosimulators_utils.utils.core.pad_arrays_to_consistent_shapes(arrays)[source]#

Pad a list of NumPy arrays to a consistent shape

Parameters:: arrays (list of numpy.ndarray) – list of NumPy arrays
Returns:: list of padded arrays
Return type:: list of numpy.ndarray

biosimulators_utils.utils.core.parse_value(str_val, type)[source]#

Parse the string representation of a value (e.g., for use with an attribute of an XML object)

Parameters:

str_val (str) – string representation of the value
type (ValueType) – type

Returns:

Python representation of the value

Return type:

object

biosimulators_utils.utils.core.patch_dict(dictionary: dict, patch: dict)[source]#

Recursively patch the attributes of a dictionary

Parameters:

dictionary (dict) – dictionary
patch (dict) – patch

biosimulators_utils.utils.core.raise_errors_warnings(errors, warnings=None, error_summary=None, warning_summary=None)[source]#

Raises errors and warnings

Parameters:

errors (nested list of str) – errors
warnings (nested list of str) – warnings
error_summary (str, optional) – summary of errors
warning_summary (str, optional) – summary of warnings

Raises:

ValueError – if errors

biosimulators_utils.utils.core.validate_str_value(str_val, type)[source]#

Determine if a value is a valid string representation of type type

Parameters:

str_val (str) – string representation of a value
type (ValueType) – type

Returns:

True, if a value is a valid string representation of type type

Return type:

bool

biosimulators_utils.utils.core.validate_value(val, type)[source]#

Determine if a value is a valid instance of type type

Parameters:

val (object) – value
type (ValueType) – type

Returns:

True, if a value is a valid instance of type type

Return type:

bool

biosimulators_utils.utils.identifiers_org module#

Utilities for working with Identifiers.org

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-08-04
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

class biosimulators_utils.utils.identifiers_org.IdentifiersOrgCountry(code: str, name: str)[source]#

Bases: object

code: str[source]#

name: str[source]#

class biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution(id: int, name: str, home_url: str, description: str, ror_id: str, country: biosimulators_utils.utils.identifiers_org.IdentifiersOrgCountry)[source]#

Bases: object

country: IdentifiersOrgCountry[source]#

description: str[source]#

home_url: str[source]#

id: int[source]#

name: str[source]#

ror_id: str[source]#

class biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace(id: int, mir_id: str, prefix: str, name: str, description: str, pattern: _regex.Pattern, embedded_in_lui: bool, sample_id: str, resources: List[biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource], deprecated: bool, deprecated_date: datetime.datetime, created: datetime.datetime, modified: datetime.datetime)[source]#

Bases: object

created: datetime[source]#

deprecated: bool[source]#

deprecated_date: datetime[source]#

description: str[source]#

embedded_in_lui: bool[source]#

id: int[source]#

mir_id: str[source]#

modified: datetime[source]#

name: str[source]#

pattern: Pattern[source]#

prefix: str[source]#

resources: List[IdentifiersOrgNamespaceResource][source]#

sample_id: str[source]#

class biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource(id: int, mir_id: str, name: str, description: str, url_pattern: str, official: bool, provider_code: str, sample_id: str, home_url: str, institution: biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution, country: biosimulators_utils.utils.identifiers_org.IdentifiersOrgCountry, deprecated: bool, deprecated_date: datetime.datetime)[source]#

Bases: object

country: IdentifiersOrgCountry[source]#

deprecated: bool[source]#

deprecated_date: datetime[source]#

description: str[source]#

home_url: str[source]#

id: int[source]#

institution: IdentifiersOrgInstitution[source]#

mir_id: str[source]#

name: str[source]#

official: bool[source]#

provider_code: str[source]#

sample_id: str[source]#

url_pattern: str[source]#

exception biosimulators_utils.utils.identifiers_org.InvalidIdentifiersOrgUri[source]#

Bases: Exception

An invalid Identifers.org URI

biosimulators_utils.utils.identifiers_org.download_identifiers_org_namespaces()[source]#

Get the namespaces registered with Identifiers.org.

Returns:

dictionary that maps the prefix of each Identifiers.org namespace or: a tuple of its provider code and its prefix to its attributes

Return type:

dict

biosimulators_utils.utils.identifiers_org.get_identifiers_org_namespace(prefix)[source]#

Get an Identifiers.org namespace

Parameters:: prefix (str) – prefix (e.g., biosimulators) or /-separated tuple of a provider code and prefix (e.g, icahn/biosimulators)
Returns:: namespace
Return type:: IdentifiersOrgNamespace
Raises:: InvalidIdentifiersOrgUri – if the prefix is not defined

biosimulators_utils.utils.identifiers_org.get_identifiers_org_namespaces(reload=False)[source]#

Get the namespaces registered with Identifiers.org.

Parameters:

reload (bool, optional) – whether to reload the namespaces from the Identifiers.org API

Returns:

dictionary that maps the prefix of each Identifiers.org namespace or: a tuple of its provider code and its prefix to its attributes

Return type:

dict

biosimulators_utils.utils.identifiers_org.validate_identifiers_org_uri(uri)[source]#

Determine whether a URI is a validate for one of the namespaces registered with Identifiers.org

Raises:: InvalidIdentifiersOrgUri – if the URI is not a valid with one of the namespaces registered with Identifiers.org

biosimulators_utils.utils.logging module#

Utilities for logging

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2020-12-06
License:: MIT

biosimulators_utils.utils.logging.get_logger(name='log', filename_pattern='~/.biosimulators-utils/logs/{}.log')[source]#

Get a logger

Parameters:

name (str, optional) – name
filename_pattern (str, optional) – pattern for paths for log files

Returns:

logger

Return type:

logging.Logger