Protocol

The protocol module helps extracting information from a MultispeQ protocol for a subsequent analysis of the MultispeQ data based on settings and information within the used protocol.

The provided protocol can either be from a local resource like a file or a variable, or from an online project’s information.

Protocol

Functions to work with MultispeQ protocols. This includes getting the protocol from the project information and extracting information from the protocol code including subprotocols by their labels or positions within the protocol.

get_protocol(project=None, index=0)

Return the protocol for a project given the project information. A project’s protocol for a MultispeQ is a list of protocols. This function is returning a single protocol from the list.

Parameters:

• project (dict) – Project information as returned by jii_multispeq.project.get()

• index (int) – Protocol position in list of project protocols. The default protocol position is 0.

Returns:

The code of the selected protocol.

Return type:

dict

Raises:

• ValueError – if no project information is provided

• KeyError – if the key protocol_json is missing in the project information

• ValueError – if the protocol_json value is not formatted properly

• ValueError – if the provided index is not an integer

• IndexError – if the provided index is out of range

get_protocol_name(project=None, index=0)

Get the protocol name from the provided Project. The PhotosynQ_Py library is creating a dictionary of data frames, with the keys being the protocol names. Most projects have only one protocol, but some projects in the past had multiple.

Parameters:

• project (dict) – Project information as returned by jii_multispeq.project.get()

• index (int) – Protocol position in list of project protocols. The default protocol position is 0.

Returns:

a string with the protocol name

Return type:

string

Raises:

• ValueError – if no project information is provided

• KeyError – if the protocols key is missing in the project information

• IndexError – if provided index is out of range for the protocols list

get_subprotocol_labels(protocol=None)

Returns a list of labels for each subprotocol. In case a sub-protocol has no label, None is returned.

Parameters:

protocol (dict) – Protocol as returned by jii_multispeq.protocol.get_protocol()

Returns:

list of sub-protocols label

Return type:

list[str]

Raises:

• ValueError – If no protocol is provided

• ValueError – If the provided protocol is not a dictionary

• KeyError – If the _protocol_set_ key is missing in the provided protocol

get_subprotocols_by_label(protocol=None, label='')

Returns a list of sub_protocols in a protocol with given label value label is the desired label. If the protocol does not have labels, will be ignored. protocol is the protocol to be seaerched.

Parameters:

• protocol (dict) – Protocol as returned by jii_multispeq.protocol.get_protocol()

• label (string) – Protocol label to search

Returns:

list of sub-protocols with matching label

Return type:

list[dict]

Raises:

• ValueError – If no protocol is provided

• ValueError – If the provided protocol is not a dictionary

• KeyError – If the _protocol_set_ key is missing in the provided protocol

get_subprotocol_by_index(protocol=None, index=0)

Returns a list of sub_protocols in a protocol with given label value label is the desired label. If the protocol does not have labels, will be ignored. protocol is the protocol to be seaerched.

Parameters:

• project_json – project information file

• subidx – index of the selected sub-protocol

• index – protocol position in the list of protocols (default: 0)

Returns:

single sub-protocol as a dictionary

Return type:

dict

Raises:

• ValueError – If no protocol is provided

• ValueError – If the provided protocol is not a dictionary

• KeyError – If the _protocol_set_ key is missing in the provided protocol

• ValueError – If provided index is not an integer

• IndexError – If provided index is out of range

Variable Arrays

MultispeQ protocols can contain a so called v_arrays that allow to define values as variabls, which can be used throughout the protocol, so the value itself doesn’t need to be repeated multiple times throughout the protocol. The functions allow to access the v_arrays themselfs as well as accessing specific variable values, so they can be available for the later data analysis.

get_v_arrays(protocol=None)

Get the v_arrays (variable arrays) from a given protocol. See get_protocol() on how to extract a single protocol.

Parameters:

protocol (dict) – Single MultispeQ Protocol

Returns:

v_arrays content

Return type:

dict

Raises:

• ValueError – If no protocol is provided.

• ValueError – If protocol is not provided as a dictionary.

• Exception – If the provided protocol doesn’t have a v_arrays.