nidm package¶
Subpackages¶
Submodules¶
nidm.app module¶
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class
nidm.app.
apiDoQuery
[source]¶ 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
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endpoint
= 'apidoquery'¶
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mediatypes
(resource_cls)¶
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methods
= ['GET']¶
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class
nidm.app.
apiIndex
[source]¶ Bases:
flask_restful.Resource
Main view for REST API to display all available queries
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endpoint
= 'apiindex'¶
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mediatypes
(resource_cls)¶
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methods
= ['GET']¶
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nidm.experiment module¶
nidm.query module¶
query: part of the nidm-api general functions to work with query data structures for nidm-queries
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nidm.query.
do_query
(ttl_file, query, rdf_format='turtle', serialize_format='csv', output_df=True)[source]¶
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nidm.query.
download_queries
(destination)[source]¶ Download queries repo to a destination Parameters ========== destination:
the full path to download the repo to
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nidm.query.
find_queries
(query_folders, search_pattern='*.json')[source]¶ 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
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nidm.query.
format_sparql
(sparql_text)[source]¶ split sparql text into a list, and extract parameter options from select.
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nidm.query.
generate_query_template
(output_dir=None, template_path=None, fields=None)[source]¶ - 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
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nidm.query.
get_query_directory
(tmpdir=None)[source]¶ get_query_directory: Download queries repo to tmp directory Parameters ========== tmpdir: str
path to directory to download queries to
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nidm.query.
make_lookup
(query_list, key_field)[source]¶ 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
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nidm.query.
read_queries
(query_paths)[source]¶ 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
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nidm.query.
save_query_template
(template, output_dir)[source]¶ 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
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nidm.query.
validate_queries
(query_dir, queries=None, components=['sparql'])[source]¶ 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.utils module¶
utils: part of the nidm-api general functions for the api
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nidm.utils.
clean_fields
(mydict)[source]¶ 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
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nidm.utils.
find_directories
(root, fullpath=True)[source]¶ Return directories at one level specified by user (not recursive)
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nidm.utils.
get_query_template
()[source]¶ get_standard_template returns the full path to the standard template for queries
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nidm.utils.
has_internet_connectivity
()[source]¶ Checks for internet connectivity by way of trying to retrieve google IP address. Returns True/False
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nidm.utils.
load_json
(json_path)[source]¶ returns a loaded json file Parameters ========== json_path: str
full path to json file to load- thejson: json (dict)
- loaded json (dict)