caosadvancedtools.utils module#

caosadvancedtools.utils.check_win_path(path: str, filename: str = None)#

check whether ‘/’ are in the path but no ‘’.

If that is the case, it is likely, that the path is not a Windows path.

Parameters:

  • path (str) – Path to be checked.

  • filename (str) – If the path is located in a file, this parameter can be used to direct the user to the file where the path is located.

creates a string that contains the code for an html link to the provided entity.

The text of the link is the entity name if one exists and the id otherwise.

Parameters:

  • entity (db.Entity) – the entity object to which the link will point

  • base_url (str) – optional, by default, the url starts with ‘/Entity’ and thus is relative. You can provide a base url that will be prefixed.

Returns:

the string containing the html code

Return type:

str

caosadvancedtools.utils.find_records_that_reference_ids(referenced_ids, rt='', step_size=50)#

Returns a list with ids of records that reference entities with supplied ids

Sometimes a file or folder will be referenced in a README.md (e.g. in an Analysis) but not those files shall be referenced but the corresponding object (e.g. the Experiment). Thus the ids of all Records (of a suitable type) are collected that reference one or more of the supplied ids. This is done in chunks as the ids are passed in the header of the http request.

caosadvancedtools.utils.get_referenced_files(glob: str, prefix: str = None, filename: str = None, location: str = None)#

queries the database for files referenced by the provided glob

Parameters:

  • glob (str) – the glob referencing the file(s)

  • prefix (str, optional) – the glob can be relative to some path, in that case that path needs to be given as prefix

  • filename (str, optional) – the file in which the glob is given (used for error messages)

  • location (str, optional) – the location in the file in which the glob is given (used for error messages)

caosadvancedtools.utils.read_field_as_list(field)#

E.g. in yaml headers entries can be single values or list. To simplify the work with those values, this function puts single values in a list.

caosadvancedtools.utils.replace_path_prefix(path, old_prefix, new_prefix)#

Replaces the prefix old_prefix in path with new_prefix.

Raises a RuntimeError when the path does not start with old_prefix.

caosadvancedtools.utils.return_field_or_property(value, prop=None)#

returns value itself of a property.

Typical in yaml headers is that a field might sometimes contain a single value and other times a dict itself. This function either returns the single value or (in case of dict as value) a value of the dict.

caosadvancedtools.utils.set_log_level(level=10)#
caosadvancedtools.utils.string_to_person(person)#

Creates a Person Record from a string.

The following formats are supported: - <Firstname> <Lastname> <*> - <Lastname(s)>,<Firstname(s)>,<*>

The part after the name can be used for an affiliation for example.