Sirius Fingerprint Class#

class expectmine.steps.steps.sirius_fingerprint.SiriusFingerprint(**kwargs: Dict[Any, Any])[source]#

Bases: BaseStep

Step which takes .mgf as input and creates CSI:FingerID as output.

IMPORTANT: This step requires the env variables SIRIUS_USERNAME and SIRIUS_PASSWORD to be set before execution.

classmethod can_run(input_files: list[str]) → bool[source]#

Indicates weather the step can run on a given list of inputs. This method is used for the autosuggestion of possible next steps.

Parameters:: input_files (list[str]) – List of input files for the step
Example:

>>> can_run(["test.mzml", "test2.mzml", "data.txt"])
False

>>> can_run(["test.mzml", "test2.mzml"])
True

classmethod citation_and_disclaimer() → str[source]#

Generates all necessary citations and disclaimers.

Returns:: A multiline string with necessary citation and disclaimers.
Return type:: string

install(persistent_store: BaseStore, io: BaseIo, logger: BaseLogger)[source]#

Verifies that all necessary prerequisites to the method have been properly installed. If not the method can take action and install the files, methods or executables on its own.

Parameters:

persistent_store (BaseStore) – Persistent store which saves all step necessary parameters. The data stored will be available to all executions of the same step.
io (BaseIo) – Gives the step access to query data from the user.
logger (BaseLogger) – Gives the step access to log information about its execution.

Example:

>>> install(Store(...), Io(...), Logger(...))

metadata(persistent_store: BaseStore, volatile_store: BaseStore) → dict[str, object][source]#

Produces metadata about the past run.

Parameters:

persistent_store – Persistent store which saves all step necessary parameters. The data stored will be available to all executions of the same step.
volatile_store (BaseStore) – Volatile store which saves all step necessary execution parameters. The data stored will only be available to this instance of the step.

Returns:

Dict with all metadata in it.

Return type:

dict[str, object]

Example:

>>> metadata(Store(...), Store(...))
{ "python": 3.10 }

classmethod output_filetypes(input_files: list[str]) → list[str][source]#

Returns a list of possible output file-extensions.

NOTE: This method currently under development and can return an over or under-defined set of file extensions. Also, we currently do not rely on internal state to narrow the list of possible output file formats

Parameters:: input_files (list[str]) – List of input files for the step
Returns:: A list of output files for the step.
Return type:: list[str]
Example:

>>> output_filetypes(["test.mzml", "test2.mzml"])
["test.txt", "test2.txt"]

run(input_files: list[Path], output_path: Path, persistent_store: BaseStore, volatile_store: BaseStore, logger: BaseLogger) → list[Path][source]#

Processes the input_files given the parameters set in install and setup. The step will write to output_path.

Parameters:

input_files (list[Path]) – List of input files for the step.
output_path (Path) – Scoped folder where step will write to.
persistent_store – Persistent store which saves all step necessary parameters. The data stored will be available to all executions of the same step.
volatile_store (BaseStore) – Volatile store which saves all step necessary execution parameters. The data stored will only be available to this instance of the step.
logger (BaseLogger) – Gives the step access to log information about its execution.

Returns:

List of all files produced.

Return type:

list[Path]

Example:

>>> run(["foo.txt, bar.txt"], Path(), Store(...), Store(...), Logger(...))

setup(volatile_store: BaseStore, io: BaseIo, logger: BaseLogger)[source]#

Sets the step up to run with a specific configuration only available to this step instance. Purpose of this method is to set parameters for the step to correctly process the input data.

Parameters:

volatile_store (BaseStore) – Volatile store which saves all step necessary execution parameters. The data stored will only be available to this instance of the step.
io (BaseIo) – Gives the step access to query data from the user.
logger (BaseLogger) – Gives the step access to log information about its execution.

Example:

>>> setup(Store(...), Io(...), Logger(...))

classmethod step_name() → str[source]#

Returns the name of the step instance.

Example:

>>> step_name()
"BaseStep"