sbol2.config

Module Contents

Classes

FileFormats	Generic enumeration.
ConfigOptions	Generic enumeration.
Config	A class which contains global configuration variables

Functions

setHomespace(ns)
getHomespace()
hasHomespace()
setFileFormat(file_format)
getFileFormat()
parseClassName(uri)
parseNamespace(uri)
parseURLDomain(url)
parsePropertyName(uri)
string_equal(str1: Any, str2: Any) → bool	Converts the two arguments to str and compares them, returning

Attributes

options
valid_options
extension_namespaces
home
SBOLCompliantTypes
catch_exceptions
file_format

class sbol2.config.FileFormats

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

JSON = json

NTRIPLES = ntriples

RDFXML = rdfxml

class sbol2.config.ConfigOptions

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

HOMESPACE = homespace

SBOL_COMPLIANT_URIS = sbol_compliant_uris

SBOL_TYPED_URIS = sbol_typed_uris

SERIALIZATION_FORMAT = serialization_format

VALIDATE = validate

VALIDATE_ONLINE = validate_online

VALIDATOR_URL = validator_url

JAVA_LOCATION = java_location

LANGUAGE = language

TEST_EQUALITY = test_equality

CHECK_URI_COMPLIANCE = check_uri_compliance

CHECK_COMPLETENESS = check_completeness

CHECK_BEST_PRACTICES = check_best_practices

FAIL_ON_FIRST_ERROR = fail_on_first_error

PROVIDE_DETAILED_STACK_TRACE = provide_detailed_stack_trace

URI_PREFIX = uri_prefix

SUBSET_URI = subset_uri

VERSION = version

INSERT_TYPE = insert_type

MAIN_FILE_NAME = main_file_name

DIFF_FILE_NAME = diff_file_name

RETURN_FILE = return_file

VERBOSE = verbose

sbol2.config.options

sbol2.config.valid_options

sbol2.config.extension_namespaces

sbol2.config.home

sbol2.config.SBOLCompliantTypes = 1

sbol2.config.catch_exceptions = 0

sbol2.config.file_format = rdfxml

class sbol2.config.Config

A class which contains global configuration variables for the libSBOL environment.

Configuration variables are accessed through the setOption and getOption methods.

SBOL_DATA_MODEL_REGISTER

static register_extension_class(builder, type_uri)

Register an extension class and its namespace, so custom data can be embedded into and read from SBOL files.

Parameters

• builder – A no-argument constructor

• type_uri – An RDF type URI for the extension class

static setHomespace(ns)

Setting the Homespace has several advantages. It simplifies object creation and retrieval from Documents. In addition, it serves as a way for a user to claim ownership of new objects. Generally users will want to specify a Homespace that corresponds to their organization’s web domain. :param ns: The namespace to use as the Homespace :return: None

static getHomespace()

Returns

The Homespace (a string representing the default namespace).

static hasHomespace()

Returns

True if Homespace is set, False otherwise.

static setFileFormat(_file_format)

Parameters

_file_format – The file format to use.

Returns

None

static getFileFormat()

Returns

The file format.

static setOption(option, val)

Configure options for libSBOL. Access online validation and conversion.

Option | Description | Values | # noqa

:————————— | :———————————————————————– | :————– |

homespace | Enable validation and conversion requests through the online validator | http://examples.org |

sbol_compliant_uris | Enables autoconstruction of SBOL-compliant URIs from displayIds | True or False |

sbol_typed_uris | Include the SBOL type in SBOL-compliant URIs | True or False |

output_format | File format for serialization | True or False |

validate | Automatic validation | True or False |

validate_online | Use online (not local) validator for validation and conversion requests | True or False, defaults to True |

validator_url | The http request endpoint for online validation and conversion | A valid URL, set to<br>https://validator.sbolstandard.org/validate/ by default |

java_location | Path to Java executable for offline validation and conversion | A valid URL, set to<br>/usr/bin/java by default |

language | File format for conversion | SBOL2, SBOL1, FASTA, GenBank |

test_equality | Report differences between two files | True or False |

check_uri_compliance | If set to false, URIs in the file will not be checked for compliance<br>with the SBOL specification | True or False |

check_completeness | If set to false, not all referenced objects must be described within<br>the given main_file | True or False |

check_best_practices | If set to true, the file is checked for the best practice rules set<br>in the SBOL specification | True or False |

fail_on_first_error | If set to true, the validator will fail at the first error | True or False |

provide_detailed_stack_trace | If set to true (and failOnFirstError is true) the validator will<br>provide a stack trace for the first validation error | True or False |

uri_prefix | Required for conversion from FASTA and GenBank to SBOL1 or SBOL2,<br>used to generate URIs | True or False |

version | Adds the version to all URIs and to the document | A valid Maven version string |

return_file | Whether or not to return the file contents as a string | True or False |

Parameters

• option – The option key

• val – The option value (str or bool expected)

Returns

None

static getOption(option)

Get current option value for online validation and conversion

Parameters

option – The option key

Returns

The option value

sbol2.config.setHomespace(ns)

sbol2.config.getHomespace()

sbol2.config.hasHomespace()

sbol2.config.setFileFormat(file_format)

sbol2.config.getFileFormat()

sbol2.config.parseClassName(uri)

sbol2.config.parseNamespace(uri)

sbol2.config.parseURLDomain(url)

sbol2.config.parsePropertyName(uri)

sbol2.config.string_equal(str1: Any, str2: Any) → bool

Converts the two arguments to str and compares them, returning the result. This helps when comparing a str with a rdflib.URIRef or a rdflib.Literal.