pybiouml

class src.pybiouml.pybiouml.PyBiouml[source]

This library is a python API interface for using BioUML Web service

analysis(analysis_name, wait=True, verbose=True, parameters=None, **params)[source]

Method for run BioUML analysis, optionally tracking progress

Parameters:

  • analysis_name (str) – name of BioUML analysis to run, use PyBiouml.analysis_list to get the list of possible values

  • wait (bool) – whether to wait for analysis completion or return immediately

  • verbose (bool) – print messages and progress from BioUML analysis, only meaningful if wait is TRUE

  • parameters (dict) – a dictionary of parameters to BioUML analysis, use PyBiouml.analysis_parameters to get the table of parameters. Default None, this method can take parameters through **params.

  • params – parameters to BioUML analysis, use PyBiouml.analysis_parameters to get the table of parameters. Collect any other parameters which are give to the method and return a dictionary with them.

Returns:

job_id: return a job id of started work, that can be passed to PyBiouml.job_info and PyBiouml.job_wait.

Return type:

str

analysis_list()[source]

Method that fetches list of available analyses from current BioUML server

Returns:

DataFrame table of analysis with two column ’Group’ and ’Name’.

Return type:

pandas.DataFrame

analysis_parameters(analysis_name)[source]

Get BioUML analysis parameters names and description

Parameters:

analysis_name (str) – me of BioUML analysis, , use PyBiouml.analysis_list to get the list of possible values

Returns:

DataFrame which contains row with names corresponding to parameter names and one column ’description’ with parameter description

Return type:

pandas.DataFrame

as_tree(params_dictionary)[source]

Service method for parsing dictionary with parameters to json, which can be used by BioUML Web service.

Parameters:

params_dictionary (dict) – dictionary with parameters

Returns:

parameters in json format

export(path, exporter_params=None, exporter='Tab-separated text (*.txt)', target_file='biouml.out')[source]

Method exports data from BioUML server to local file in given format

Parameters:

  • path (str) – path in BioUML repository.

  • exporter_params – dictionary of parameters to exporter. Default None.

  • exporter (str) – character string specifying format, PyBiouml_exporters provides possible values.

  • target_file (str) – a character string naming a file to export to. Default biouml.out

export_parameters(path, exporter)[source]

Method get BioUML export parameters

Parameters:

  • path (str) – path to data element in BioUML repository to export

  • exporter (str) – name of BioUML exporter, use PyBiouml.exporters to get the table of possible values

Returns:

DataFrame which contains row with names corresponding to parameter names and one column ’description’ with parameter description

Return type:

pandas.DataFrame

exporters()[source]

Method fetches the list of exporters from BioUML server, these exporters can be used in PyBiouml.export method

Returns:

list with expoters

get(path)[source]

Method fetches table data from BioUML server.

Parameters:

path (str) – Path to table in BioUML repository.

Return crafted_table:

return DataFrame representation of BioUML table from path.

Rtype crafted_table:

pandas.DataFrame

get_connection()[source]

Service method for creation a connection with BioUML Web Service, which checks if user was logged into BioUML

Return connection:

connection link

get_stats()[source]

Retrieve statistics for all requests

Returns:

List of statistics dictionaries

import_parameters(path, importer)[source]

Method Get BioUML import parameters

Parameters:

  • path (str) – path to data element in BioUML repository to import

  • importer (str) – name of BioUML importer, use biouml.importers to get the list of possible values

Returns:

DataFrame which contains row with names corresponding to parameter names and one column ’description’ with parameter description

Return type:

pandas.DataFrame

importers()[source]

Method fetches the list of importers from BioUML server, these importers can be used in PyBiouml.to_import method

Returns:

list with expoters

job_info(job_id)[source]

Method info fetches info about BioUML job.

Parameters:

job_id (str) – ID of job usually returned from PyBiouml.analysis

Returns:

info: json with information about requested process (status, results, values, percent)

job_wait(job_id, verbose=True)[source]

Waits for BioUML job completion

Parameters:

  • job_id – ID of job usually returned from biouml.analysis

  • verbose – print messages and progress from BioUML job

Returns:

json with information about requested process (status, results, values, percent)

login(url='http://localhost:8080/biouml', user='', password='')[source]

Method which LogintoBioUMLserver. Theconnectionwillbesavedinglobaloptionsundernamebiouml_connection for future reuse.

Parameters:

  • url (str) – URLof running biouml server. Default it is http://localhost:8080/biouml, like an example of local biouml service.

  • user (str) – BioUML user, empty string for anonymous login.

  • password (str) – password.

logout()[source]

Method which Logouts from BioUML server.

ls(path, extended=False)[source]

Method lists children data elements by path in BioUML repository.

Parameters:

  • path (str) – path to data collection in BioUML repository.

  • extended (bool) – whether to return additional attributes for each children.

Returns:

df: If extended is False a DataFrame with child names, otherwise a DataFrame wich contains row with names corresponding to child names and columns hasChildren and type.

Return type:

pandas.DataFrame

next_job_id()[source]

Service method for creation a new job id.

Returns:

job_id

Return type:

str

parameters(server_path, **params)[source]

Service method, which create a request to get parameters

Parameters:

  • server_path (str) – path to target of the request for which need to take parameters

  • params – This parameter collect any other parameters which are give to the method and return a dictionary with them.

Returns:

DataFrame with all parameters

Return type:

pandas.DataFrame

put(path, value)[source]

Method to put usere’s table on BioUML Web Service.

Parameters:

  • path (str) – path to repository for table.

  • value (DataFrame) – pandas DataFrame table to put

query(servers_path, data, file=None, binary=False)[source]

Service method for making post request with time and size logging

Returns:

result of post request

query_json(server_path, reconnect=True, parameters=None, **params)[source]

Service method for json return of connection with time and size logging

Parameters:

  • server_path (str) – path to required server.

  • reconnect (bool) – try to reconnect or not.

  • parameters (dict) – a dictionary with parameters for connection. Default None, this method can take parameters through **params.

  • params – This parameter collect any other parameters which are give to the method and return a dictionary with them.

Return json_content:

return a result of the request in json format.

Rtype json_content:

json

reconnect()[source]

Service method for reconnection to BioUML web service

to_import(file, parentPath, importer, importer_params=None)[source]

Method imports file to BioUML repository.

Parameters:

  • file – The name of file to import.

  • parentPath (str) – Path to folder in BioUML repository.

  • importer (str) – character string specifying format, PyBiouml.importers() provides list of posible values

  • importer_params – dictionary of parameters to importer

Returns:

Resulting path in BioUML repository

Return type:

str

workflow(path, parameters=None, wait=True, verbose=True)[source]

Method run BioUML workflow optionaly tracking progress.

Parameters:

  • path (str) – path to BioUML workflow

  • parameters – list of parameters to BioUML workflow.

  • wait (bool) – whether to wait for workflow completion or return immediately

  • verbose (bool) – print messages and progress from BioUML workflow, only meaningful if wait is TRUE

Returns:

job_id: return a job id of started work, that can be passed to PyBiouml.job_info and PyBiouml.job_wait.

Return type:

str