nidm package

Subpackages

• nidm.script package
  • Submodules
  • nidm.script.post_install module
  • Module contents
• nidm.templates package
  • Module contents

Submodules

nidm.app module

class nidm.app.NIDMServer(*args, **kwargs)

Bases: flask.app.Flask

class nidm.app.apiDoQuery

Bases: flask_restful.Resource

return result of query on ttl file Paramters ========= qid: str

the uid associated with the query

ttl: str

the url of the turtle file

endpoint = 'apidoquery'

get(qid, output_format)

mediatypes(resource_cls)

methods = ['GET']

class nidm.app.apiIndex

Bases: flask_restful.Resource

Main view for REST API to display all available queries

endpoint = 'apiindex'

get()

mediatypes(resource_cls)

methods = ['GET']

class nidm.app.apiQueryMeta

Bases: flask_restful.Resource

return complete meta data for specific query

endpoint = 'apiquerymeta'

get(qid)

mediatypes(resource_cls)

methods = ['GET']

nidm.app.generateQuery()

nidm.app.newQuery()

nidm.app.previewQuery()

nidm.app.start(port=8088)

nidm.experiment module

nidm.query module

query: part of the nidm-api general functions to work with query data structures for nidm-queries

class nidm.query.Queries(components=['experiment', 'results', 'workflow'])

nidm.query.do_query(ttl_file, query, rdf_format='turtle', serialize_format='csv', output_df=True)

nidm.query.download_queries(destination)

Download queries repo to a destination Parameters ========== destination:

the full path to download the repo to

nidm.query.find_queries(query_folders, search_pattern='*.json')

searches one or more folders for valid queries, meaning json files. In the case of multiple directories, will append the folder name as a variable to indicate the type Parameters ========== query_folders: list or str

one or more full paths to directories with json objects

search_pattern: str

pattern for glob to use to find query objects default is “*.json”

queries: list

a list of full paths to query object files

nidm.query.format_sparql(sparql_text)

split sparql text into a list, and extract parameter options from select.

nidm.query.generate_query_template(output_dir=None, template_path=None, fields=None)

output_dir: str

full path to output directory for json data structure. if none specified, will not save the data structure

template_path: str

path to json file to use as a template. Only should be specified if the user has reason to use a custom template default is the standard provided by nidm-api.

fields: dict (optional)

a dictionary with fields that correspond to template keys. if provided, template will be filled with keys. Possible values include

template: json (dict)

A python dictionary (json) that can be filled with new query information

nidm.query.get_query_directory(tmpdir=None)

get_query_directory: Download queries repo to tmp directory Parameters ========== tmpdir: str

path to directory to download queries to

nidm.query.make_lookup(query_list, key_field)

returns dict object to quickly look up query based on uid Parameters ========== query_list: list

a list of query (dict objects)

key_field: str

the key in the dictionary to base the lookup key

query_dict: dict

dict (json) with key as “key_field” from query_list

nidm.query.read_queries(query_paths)

Read in a list of query (json) objects. Parameters ========== query_paths: list a list of full paths to query objects to read Returns ======= queries_: list

dict to be served as json describing queries available a “type” variable is added to indicate folder query was found in

nidm.query.save_query_template(template, output_dir)

generate_query_template Parameters ========== output_dir: string path

full path to output directory for json data structure. the template filename is generated from the uid variable

success: boolean

True if save was successful, false otherwise

nidm.query.validate_queries(query_dir, queries=None, components=['sparql'])

returns json object with query data structures, and a field ‘valid’ to describe if query was valid Parameters ========== queries: list

a list of full paths to json files, each a query

query_dir: str

full path to a nidm-query repo

components: folders to include corresponding to nidm

query language (currently only option is sparql)

queries: json

dict (json) with all read in queries available

from nidm-query, provided by API

nidm.results module

nidm.scripts module

script.py: part of nidmapi package Runtime executable

nidm.scripts.main()

nidm.utils module

utils: part of the nidm-api general functions for the api

nidm.utils.clean_fields(mydict)

Ensures that keys and values of dictionary are in utf-8 so rendering in javascript is clean. Paramters ========= mydict: dict

dictionary to clean

newdict: dict

dictionary with all fields encoded in utf-8

nidm.utils.copy_directory(src, dest)

Copy an entire directory recursively

nidm.utils.find_directories(root, fullpath=True)

Return directories at one level specified by user (not recursive)

nidm.utils.find_subdirectories(basepath)

Return directories (and sub) starting from a base

nidm.utils.get_installdir()

returns installation directory of nidm-api

nidm.utils.get_query_template()

get_standard_template returns the full path to the standard template for queries

nidm.utils.get_template(template_file)

get_template: read in and return a template file

nidm.utils.has_internet_connectivity()

Checks for internet connectivity by way of trying to retrieve google IP address. Returns True/False

nidm.utils.is_type(var, types=[<type 'int'>, <type 'float'>, <type 'list'>])

Check type

nidm.utils.load_json(json_path)

returns a loaded json file Parameters ========== json_path: str

full path to json file to load

thejson: json (dict)

loaded json (dict)

nidm.utils.remove_unicode_dict(input_dict, encoding='utf-8')

remove unicode keys and values from dict, encoding in utf8

nidm.utils.save_template(output_file, html_snippet)

nidm.utils.set_permissions(path, permission=128)

nidm.utils.sub_template(template, template_tag, substitution)

make a substitution for a template_tag in a template

nidm.workflow module

Module contents