Welcome to harvdev-utils’s documentation!¶
Please refer to the sections below for information regarding common Python functions used by FlyBase developers at Harvard.
Modules for converting special characters¶
harvdev_utils init file.
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harvdev_utils.sgml_to_plain_text(input_string)[source]¶ Convert FlyBase SGML to plain text Greek words.
e.g. “&agr; -> alpha”
Parameters: arg1 (str) – The “input_string” containing characters to be converted. Returns: The same string as the input with the SGML characters converted. Return type: str Raises: KeyError– If the regex matches for a set of SGML characters but there is no exact matching SGML.
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harvdev_utils.sgml_to_unicode(input_string)[source]¶ Convert FlyBase SGML to Greek characters in unicode.
e.g. “&agr;” -> “\u03B1”
Parameters: arg1 (str) – The “input_string” containing FB SGML characters to be converted. Returns: The same string as the input with the SGML characters converted to unicode. Return type: str Raises: KeyError– If the regex matches for a set of SGML characters but there is no exact matching SGML.
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harvdev_utils.unicode_to_plain_text(input_string)[source]¶ Convert Greek unicode to plain text Greek words.
e.g. “\u03B1” -> “alpha”
Parameters: arg1 (str) – The “input_string” containing Greek unicode characters to be converted. Returns: The same string as the input with the Greek unicode characters transliterated. Return type: str Raises: KeyError– If the regex matches for a set of unicode characters but there is no exact matching plain text.
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harvdev_utils.sub_sup_to_sgml(input_string)[source]¶ Convert bracket characters to up and down flags.
e.g. “[hello]” -> “<up>hello</up>”
Parameters: arg1 (str) – The “input_string” containing bracket characters to be converted. Returns: The same string as the input with the bracket characters converted to up and down flags. Return type: str
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harvdev_utils.get_or_create(session: sqlalchemy.orm.session.Session, model, **kwargs)[source]¶ Parameters: - session – The current session in use by SQL Alchemy
- model – The table to be queried.
- kwargs – Values for the table used for lookup (e.g. name=’awesome gene’)
Returns: Both an SQL Alchemy object and True (if new object created) or False (if object retrieved)