General Helper Functions

user_errors_group

autoprotocol_utilities.misc_helpers.user_errors_group(error_msgs, info=None)

Takes a list error messages and neatly displays as a single UserError

Will automatically remove instances of None and only report errors if list is not empty.

Parameters:error_msgs (list) – List of strings that are the error messages Raises:ValueError – If error_msgs is not of type list

char_limit

autoprotocol_utilities.misc_helpers.char_limit(label, length=22, trunc=False, clip=False)

Enforces a string limit on the label provided

Can either throw an error message if length is exceeded or correct the string and return the corrected string.

Parameters:

• label (str) – String to test.
• length (int, optional) – Maximum label length for this string. Default: 22.
• trunc (bool, optional) – Truncate the label if it is too long. Default: False.
• clip (bool, optional) – Clip the label (remove from beginning of the string) if it is too long Default: False. If both trunc and clip are True, trunc will take effect and not clip.

Returns:

label (str) and error_message (string) that is empty on success label is the unmodified, truncated to clipped label as indicated

Return type:

namedtuple

Raises:

ValueError – If label is not of type string

det_new_group

autoprotocol_utilities.misc_helpers.det_new_group(i, base=0)

Determine if new_group should be added to pipetting operation.

Helper to determine if new_group should be added. Returns true when ‘i’ matches the base, which defaults to 0.

Parameters:

• i (int) – The iteration you are on.
• base (int, optional) – The value at which you want to trigger a new group. Default: 0.

Returns:

True if iteration equals base case.

Return type:

bool

Raises:

• ValueError – If i is not of type integer
• ValueError – If base is not of type integer

printdatetime

autoprotocol_utilities.misc_helpers.printdatetime()

Generate a datetime string.

Returns:The current date and time formatted as: YYYY-MM-DD_HH-MM-SS Return type:str

printdate

autoprotocol_utilities.misc_helpers.printdate()

Generate a date string.

Returns:The current date formatted as: YYYY-MM-DD Return type:str

make_list

autoprotocol_utilities.misc_helpers.make_list(my_str, integer=False)

Return a list of strings (or ints) from a string containing comma separated elements.

Parameters:

• my_str (str) – String with individual elements separated by comma.
• interger (bool) – If true list of integers instead of list of strings is returned. Default: False.

Returns:

List of strings or integers

Return type:

list

Raises:

ValueError – If my_str is not of type string

flatten_list

autoprotocol_utilities.misc_helpers.flatten_list(l)

Flatten a list recursively without for loops or additional modules

Example Usage:

from autoprotocol_utilities.misc_helpers import flatten_list

l = [-1, 0, [1,2], "string", [3, [4, 5]]]
flatten_list(l)

Returns:

[-1, 0, 1, 2, 'string', 3, 4, 5]

Parameters:l (list, list of WellGroup) – List or list of WellGroups to flatten Returns:Flat list Return type:list Raises:ValueError – If l is not of type list

recursive_search

autoprotocol_utilities.misc_helpers.recursive_search(params, class_name=None, method=None, args={})

Recursive params checker

Iterates through all items of a passed in dict, tuple, or list and either returns everything as a list, returns an optional subset of them or calls a specified method on the subset

Example Usage:

from autoprotocol.protocol import Protocol
from autoprotocol.container import Well
from autoprotocol_utilities import recursive_search

p = Protocol()

example_container = p.ref(name="example", id=None, cont_type="96-pcr",
                          storage="ambient")

p.dispense(ref=example_container, reagent="water",
           columns=[{"column": 0, "volume": "20:microliters"},
                    {"column": 1, "volume": "10:microliters"}
                    ])

wells = example_container.wells_from(start=0, num=9, columnwise=True)

recursive_search(params=wells.wells, class_name=Well,
                 method=volume_check, args={"usage_volume": 15})

Returns:

["1 volume errors: You want to pipette 15.0 ul from a container with "
"3.0 ul dead volume (18.0 ul total). However, your aliquot: example-1,"
"only has 10.0 ul."]

Parameters:

• params (list, tuple or dict) – Structure to parse
• class_name (Class name, optional) – Optionally return only instances of a class.
• method (function, optional) – A function that will be applied to all instances found of a class, must include class name.
• args (parameters, optional) – Parameters to pass to a method, if desired.

Returns:

Will return a list of all items, or the found items of a specified class, or the response (if not None) from a method called on found items.

Return type:

list