API documentation¶

main.py¶

Main functions used by ToolDog.

tooldog.main.analyse(biotool, args)[source]¶

Run analysis of the source code from bio.tools or given locally.

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object. args (`argparse.ArgumentParser`) – Parsed arguments.

tooldog.main.annotate(biotool, args, existing_desc=None)[source]¶

Run annotation (generated by analysis or existing_desc).

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object. args (`argparse.ArgumentParser`) – Parsed arguments. existing_desc (STRING) – Existing tool descriptor path.

tooldog.main.config_logger(write_logs, log_level, log_file, verbose)[source]¶

Initialize the logger for ToolDog. By default, only WARNING, ERROR and CRITICAL are written on STDERR. You can also write logs to a log file.

Parameters:	write_logs (BOOLEAN) – Decide to write logs to output log file. log_level (STRING) – Select the level of logs. ‘debug’, ‘info’ or ‘warn’. Other value is considered as ‘warn’. log_file (STRING) – path to output log file.
Returns:	Config dictionnary for logger.
Return type:	DICT

tooldog.main.json_from_biotools(tool_id, tool_version='latest')[source]¶

Import JSON of a tool from https://bio.tools.

Parameters:	tool_id (STRING) – ID of the tool. tool_version (STRING) – Version of the tool.
Returns:	dictionnary corresponding to the JSON from https://bio.tools.
Return type:	DICT

tooldog.main.json_from_file(json_file)[source]¶

Import JSON of a tool from a local JSON file.

Parameters:	json_file (STRING) – path to the file
Returns:	dictionnary corresponding to the JSON.
Return type:	DICT

tooldog.main.json_to_biotool(json_file)[source]¶

Takes JSON file from bio.tools description and loads its content to tooldog.model.Biotool object.

Parameters:	json_file (DICT) – dictionnary of JSON file from bio.tools description.
Returns:	Biotool object.
Return type:	`tooldog.biotool_model.Biotool`

tooldog.main.parse_arguments()[source]¶: Defines parser for ToolDog.

tooldog.main.run()[source]¶: Running function called by tooldog command line.

tooldog.main.write_cwl(biotool, outfile=None, existing_tool=None)[source]¶

This function uses tooldog.cwl.CwlToolGen to write CWL using cwlgen. CWL is generated on STDOUT by default.

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object. outfile (STRING) – path to output file to write the CWL. existing_tool (STRING) – local path to existing CWL tool description.

tooldog.main.write_xml(biotool, outfile=None, galaxy_url=None, edam_url=None, mapping_json=None, existing_tool=None, inout_biotool=False)[source]¶

This function uses tooldog.galaxy.GalaxyToolGen to write XML using galaxyxml library.

Parameters:

biotool (tooldog.biotool_model.Biotool) – Biotool object.
outfile (STRING) – path to output file to write the XML.
galaxy_url (STRING) – link to galaxy instance.
edam_url (STRING) – link to EDAM owl.
mapping_json (STRING) – local JSON mapping between EDAM and Galaxy datatypes.
existing_tool (STRING) – local path to existing Galaxy XML tool description.
inout_biotool (BOOLEAN) – add input and outputs description from https://bio.tools.

biotool_model.py¶

Model used to process information contained in JSON from https://bio.tools description.

The content of a description on https://bio.tools is contained in a JSON file and this model aims to store the different information.

class tooldog.biotool_model.Biotool(name, tool_id, version, description, homepage)[source]¶

This class correspond to an entry from https://bio.tools.

__init__(name, tool_id, version, description, homepage)[source]¶

Parameters:	name (STRING) – Name of the tool. tool_id (STRING) – ID of the tool entry. version (STRING) – Version of the tool entry. description (STRING) – Description of the tool entry. homepage (STRING) – URL to homepage.

tooldog.biotool_model.Biotool object is also initialized with two empty list of objects:

functions: list of tooldog.biotool_model.Function
topics: list of tooldog.biotool_model.Topic

More information (tooldog.biotool_model.Informations object) can be specified using tooldog.biotool_model.Biotool.set_informations().

add_functions(functions)[source]¶

Add tooldog.biotool_model.Function objects to the list of functions of the Biotool object.

Parameters:	functions (LIST of DICT) – list of functions description from https://bio.tools.

add_topics(topics)[source]¶

Add tooldog.biotool_model.Topic objects to the list of topics of the Biotool object.

Parameters:	topics (LIST of DICT) – list of topics description from https://bio.tools.

generate_cwl_doc()[source]¶

Generate a doc from the different informations found on the tool.

Returns:	a doc for CWL tool description.
Return type:	STRING

generate_galaxy_help()[source]¶

Generate a help message from the different informations found on the tool.

Returns:	a help message for Galaxy XML.
Return type:	STRING

set_informations(tool_credits, contacts, publications, docs, language, links, download)[source]¶

Add an tooldog.biotool_model.Informations object to the Biotool.

Parameters:	tool_credits (LIST of DICT) – list of different tool_credits. contacts (LIST of DICT) – list of different contacts. publications (LIST of DICT) – list of different IDs for publications. doc (LIST of DICT) – list of different documentations.

class tooldog.biotool_model.Contact(contact)[source]¶

Class to store one contact information.

__init__(contact)[source]¶

Parameters:	contact (DICT) – contact part of the JSON from http://bio.tools.

class tooldog.biotool_model.Credit(credit)[source]¶

Class to store a credit information.

__init__(credit)[source]¶

Parameters:	credit (DICT) – credit part of the JSON from http://bio.tools.

class tooldog.biotool_model.Data(data_type, formats, description=None)[source]¶

Data described by EDAM ontology.

__init__(data_type, formats, description=None)[source]¶

Parameters:	data_type (DICT) – EDAM ontology for the data type with uri and term. formats (LIST of DICT) – EDAM ontology for data formats with uri and term. description (STRING) – description of the data (DEPRECATED)

class tooldog.biotool_model.DataType(edam)[source]¶

EDAM data associated to either input or output.

__init__(edam)[source]¶

Parameters:	edam (DICT) – EDAM ontology with uri and term.

class tooldog.biotool_model.Documentation(documentation)[source]¶

Class to store one documentation information.

__init__(documentation)[source]¶

Parameters:	documentation (DICT) – documentation part of the JSON from http://bio.tools.

class tooldog.biotool_model.Edam(edam)[source]¶

Edam annotation with the uri and its corresponding term.

__init__(edam)[source]¶

Parameters:	edam (DICT) – EDAM ontology with uri and term.

get_edam_id()[source]¶

Get the EDAM id from the uri.

Returns:	EDAM id from the uri.
Return type:	STRING

class tooldog.biotool_model.Format(edam)[source]¶

EDAM format associated to either input or output.

__init__(edam)[source]¶

Parameters:	edam (DICT) – EDAM ontology with uri and term.

class tooldog.biotool_model.Function(edams)[source]¶

Correspond to one function of the entry with the corresponding inputs and outputs.

__init__(edams)[source]¶

Parameters:	edams (LIST of DICT) – EDAM ontology for operation(s) with uri and term.

tooldog.biotool_model.Function object is initialized with two empty list of objects:

inputs: list of tooldog.biotool_model.Input
outputs: list of tooldog.biotool_model.Output

add_inputs(inputs)[source]¶

Add inputs to the tooldog.biotool_model.Function object.

Parameters:	inputs (LIST of DICT) – inputs part of one function from http://bio.tools.

add_outputs(outputs)[source]¶

Add outputs to the tooldog.biotool_model.Function object.

Parameters:	outputs (LIST of DICT) – inputs part of one function from http://bio.tools.

class tooldog.biotool_model.Informations[source]¶

Class to describe different information concerning a bio.tool entry.

__init__()[source]¶

tooldog.biotool_model.Informations object is initialized with four empty list of objects:

publications: list of tooldog.biotool_model.Publication
documentations: list of tooldog.biotool_model.Documentation
contacts: list of tooldog.biotool_model.Contact
tool_credits: list of tooldog.biotool_model.Credit
language: list of coding language
link: list of tooldog.biotool_model.Link

class tooldog.biotool_model.Input(data_type, formats, description=None)[source]¶

Input of a described function.

__init__(data_type, formats, description=None)[source]¶

Parameters:	data_type (DICT) – EDAM ontology for the data type with uri and term. formats (LIST of DICT) – EDAM ontology for data formats with uri and term. description (STRING) – description of the data (DEPRECATED)

class tooldog.biotool_model.Link(link)[source]¶

Class to store download and links content.

__init__(link)[source]¶

Parameters:	link (DICT) – links or download content of the JSON from http://bio.tools.

class tooldog.biotool_model.Operation(edam)[source]¶

EDAM operation associated to a function.

__init__(edam)[source]¶

Parameters:	edam (DICT) – EDAM ontology with uri and term.

class tooldog.biotool_model.Output(data_type, formats, description=None)[source]¶

Output of a described function.

__init__(data_type, formats, description=None)[source]¶

Parameters:	data_type (DICT) – EDAM ontology for the data type with uri and term. formats (LIST of DICT) – EDAM ontology for data formats with uri and term. description (STRING) – description of the data (DEPRECATED)

class tooldog.biotool_model.Publication(publication)[source]¶

Class to store one publication information.

__init__(publication)[source]¶

Parameters:	publication (DICT) – publication part of the JSON from http://bio.tools.

class tooldog.biotool_model.Topic(edam)[source]¶

EDAM topic associated to the entry.

__init__(edam)[source]¶

Parameters:	edam (DICT) – EDAM ontology with uri and term.

analyse/code_collector.py¶

class tooldog.analyse.code_collector.CodeCollector(biotool)[source]¶

Class to download source code from a https://bio.tools entry

__init__(biotool)[source]¶

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object

get_source()[source]¶: Retrieve source code of the tool using links provided in https://bio.tools

analyse/container.py¶

Wrapper for docker-py low-level client API. Allow creating container and using it within with statement.

class tooldog.analyse.container.Container(image, command, environment=None)[source]¶

Class to represent docker container and expose simple API to it.

__enter__()[source]¶: Start the container and make a with context.

__exit__(exc_type, exc_val, exc_tb)[source]¶: Stop the container and clean up.

__init__(image, command, environment=None)[source]¶

Create the container. Not the same as docker run, need to be started after the creation.

Parameters:	image (STRING) – the image to run command (STRING or LIST) – the command to be run in the container environment (DICT or LIST) – A dictionary or a list of strings in the following format {“TEST”: “123”} or [“TEST=123”]. mount (STRING) – absolute path to file to mount

exec(command)[source]¶

Execute the command inside container cid

Parameters:	command (str) – String representation of bash command
Returns:	Returns a generator of output of the result of running bash command in bytes
Return type:	iter

inspect()[source]¶

Returns:	Description of the container ans its status
Return type:	DICT

kill()[source]¶: Kill the container.

logs()[source]¶

Returns:	Returns a stream of the STDOUT and STDERR
Return type:	iter

pull(image)[source]¶: Pull image :param image: the image to pull :type image: STRING

remove()[source]¶: Remove the container and associated volumes.

run(image, command, environment=None)[source]¶: Do real work of __init__.

start()[source]¶: Start the container.

stop()[source]¶: Stop the container.

analyse/tool_analyzer.py¶

class tooldog.analyse.tool_analyzer.ToolAnalyzer(biotool, gen_format, language=None, source_code=None)[source]¶

Class to perform appropriate source code analysis of a tool.

__init__(biotool, gen_format, language=None, source_code=None)[source]¶

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object gen_format (STRING) – tool descriptor language (Galaxy XML or CWL) language (STRING) – language of the tool source_code (STRING) – path to source code

get_source()[source]¶: Get source code to give to analyzer.

run_analysis()[source]¶: Method to run analysis of source code of the entry.

set_language()[source]¶: Set the language attribute of the object based on the https://bio.tools description.

analyse/language_analyzer.py¶

class tooldog.analyse.language_analyzer.LanguageAnalyzer(biotool)[source]¶

This should be the abstract class for all analyzer.

__init__(biotool)[source]¶

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object

analyse()[source]¶: Run source code analysis.

class tooldog.analyse.language_analyzer.PythonAnalyzer(gen_format, source_code)[source]¶

Object to specifically analyze Python source code.

__init__(gen_format, source_code)[source]¶

Parameters:	gen_format (STRING) – tool description language (Galaxy XML or CWL) source_code (STRING) – path to source code.

analyse()[source]¶: Run source code analysis.

annotate/galaxy.py¶

Generation of XML for Galaxy from https://bio.tools based on the Tooldog model using galaxyxml library.

class tooldog.annotate.galaxy.GalaxyToolGen(biotool, galaxy_url=None, edam_url=None, mapping_json=None, existing_tool=None)[source]¶

Class to support generation of XML from tooldog.biotool_model.Biotool object.

__init__(biotool, galaxy_url=None, edam_url=None, mapping_json=None, existing_tool=None)[source]¶

Initialize a [Tool] object from galaxyxml with the minimal information (a name, an id, a version, a description, the command, the command version and a help).

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object of an entry from https://bio.tools.

add_citation(publication)[source]¶

Add publication(s) to the tool (XML: <citations>).

Parameters:	publication (`tooldog.biotool_model.Publication`) – Publication object.

add_edam_operation(operation)[source]¶

Add the EDAM operation to the tool (XML: <edam_operations>).

Parameters:	topic (`tooldog.biotool_model.Operation`) – Operation object.

add_edam_topic(topic)[source]¶

Add the EDAM topic to the tool (XML: <edam_topics>).

Parameters:	topic (`tooldog.biotool_model.Topic`) – Topic object.

add_input_file(input_obj)[source]¶

Add an input to the tool (XML: <inputs>).

Parameters:	input_obj (`tooldog.biotool_model.Input`) – Input object.

add_output_file(output)[source]¶

Add an output to the tool (XML: <outputs>).

Parameters:	output (`tooldog.biotool_model.Output`) – Output object.

write_xml(out_file=None, index=None, keep_old_command=False)[source]¶

Write CWL to STDOUT or out_file(s).

Parameters:	out_file (STRING) – path to output file. index (INT) – Index in case more than one function is described.

annotate/cwl.py¶

Generation of CWL tool from https://bio.tools based on the ToolDog model using cwlgen library.

class tooldog.annotate.cwl.CwlToolGen(biotool, existing_tool=None)[source]¶

Class to support generation of CWL from tooldog.biotool_model.Biotool object.

__init__(biotool, existing_tool=None)[source]¶

Initialize a [CommandLineTool] object from cwlgen.

Parameters:	biotool (`tooldog.biotool_model.Biotool`) – Biotool object of an entry from https://bio.tools.

add_edam_operation(operation)[source]¶

Add the EDAM operation to the tool (CWL: s:operation).

Parameters:	operation (`tooldog.biotool_model.Operation`) – Operation object.

add_edam_topic(topic)[source]¶

Add the EDAM topic to the tool (CWL: s:topic).

Parameters:	topic (`tooldog.biotool_model.Topic`) – Topic object.

add_input_file(input_obj)[source]¶

Add an input to the CWL tool.

Parameters:	input_obj (`tooldog.biotool_model.Input`) – Input object.

add_output_file(output)[source]¶

Add an output to the CWL tool.

Parameters:	output (`tooldog.biotool_model.Output`) – Output object.

add_publication(publication)[source]¶

Add publication to the tool (CWL: s:publication).

Parameters:	publication (`tooldog.biotool_model.Publication`) – Publication object.

write_cwl(out_file=None, index=None)[source]¶

Write CWL to STDOUT or out_file(s).

Parameters:	out_file (STRING) – path to output file. index (INT) – Index in case more than one function is described.

annotate/edam_to_galaxy.py¶

Gather different information from a Galaxy server (by default https://usegalaxy.org) and EDAM ontology (by default from http://edamontology.org/EDAM.owl)

class tooldog.annotate.edam_to_galaxy.EdamInfo(edam_url)[source]¶

Contains the given EDAM ontology.

It is also possible to generate several dictionnaries to help interrogating the ontology for a faster access.

__init__(edam_url)[source]¶

Parameters:	edam_url (STRING) – path to EDAM.owl file

All the EDAM ontology will be contained in a dictionnary (self.edam_ontology).

generate_hierarchy()[source]¶

Generates two dictionnaries of the EDAM hierarchy (format and data) with the following structure:

DICT[edam_uri] -> LIST of edam_uri from parents

The dictionnary can be accessed via self.edam_format_hierarchy

class tooldog.annotate.edam_to_galaxy.EdamToGalaxy(galaxy_url=None, edam_url=None, mapping_json=None)[source]¶

Class to make the link between EDAM ontology terms (edam_format and edam_data) and Galaxy datatypes.

__init__(galaxy_url=None, edam_url=None, mapping_json=None)[source]¶

Parameters:	galaxy_url (STRING) – URL of the galaxy instance. edam_url (STRING) – path to EDAM.owl file (URL or local path). mapping_json (STRING) – path to personnalized EDAM mapping to Galaxy.

export_info(export_file)[source]¶

Method to export mapping of this object to a JSON file.

Parameters:	export_file (STRING) – path to the file.

generate_mapping()[source]¶

Generates mapping between edam_format and edam_data to Galaxy datatypes based on the information of the Galaxy instance and the EDAM ontology.

Every edam_format and edam_data will be given a datatype.

get_datatype(edam_data=None, edam_format=None)[source]¶: Get datatype from EDAM terms. :param edam_data: EDAM data term. :type edam_data: STRING :param edam_format: EDAM format term. :type edam_format: STRING :return: datatype corresponding to given EDAM ontologies. :rtype: STRING

load_local_mapping(local_file)[source]¶

Method to load (from JSON file) mapping previously generated and exported in the local_file.

Parameters:	local_file (STRING) – path to the mapping local file.

class tooldog.annotate.edam_to_galaxy.GalaxyInfo(galaxy_url)[source]¶

Class to gather different information about a Galaxy instance.

By default, if the galaxy_url is None, information is loaded from local files located in the data/ folder corresponding to https://usegalaxy.org.

__init__(galaxy_url)[source]¶

Parameters:	galaxy_url (STRING) – URL of the Galaxy instance.

tooldog.edam_to_galaxy.GalaxyInfo object is initialized with several information from the given Galaxy instance. It contains:

Parameters:	self.version (STRING) – version of the Galaxy instance. self.edam_formats (DICT) – mapping edam_format to LIST of extension of datatypes. self.edam_data (DICT) – mapping edam_data to LIST of extension of datatypes. self.hierarchy – class_to_classes part of the /api/mapping.json which maps

the parental classes of each classes. :type self.hierarchy: DICT :param self.class_names: ext_to_class_name part of the /api/mapping.json which maps the extension of a datatype to its class in Galaxy. :type self.class_names: DICT

select_root(datatypes)[source]¶

Select the root datatype from all given datatypes.

Parameters:	datatypes (list of STRING) – list of different datatypes.
Returns:	root datatype.
Return type:	STRING