allensdk.api.api module¶
- class allensdk.api.api.Api(api_base_url_string=None)[source]¶
Bases:
object
- cleanup_truncated_file(file_path)[source]¶
Helper for removing files.
- Parameters:
- file_pathstring
Absolute path including the file name to remove.
- construct_well_known_file_download_url(well_known_file_id)[source]¶
Join data api endpoint and id.
- Parameters:
- well_known_file_idinteger or string representing an integer
well known file id
- Returns:
- string
the well-known-file download url for the current api api server
See also
retrieve_file_over_http
Can be used to retrieve the file from the url.
- default_api_url = 'http://api.brain-map.org'¶
- do_query(url_builder_fn, json_traversal_fn, *args, **kwargs)[source]¶
Bundle an query url construction function with a corresponding response json traversal function.
- Parameters:
- url_builder_fnfunction
A function that takes parameters and returns an rma url.
- json_traversal_fnfunction
A function that takes a json-parsed python data structure and returns data from it.
- postboolean, optional kwarg
True does an HTTP POST, False (default) does a GET
- argsarguments
Arguments to be passed to the url builder function.
- kwargskeyword arguments
Keyword arguments to be passed to the rma builder function.
- Returns:
- any type
The data extracted from the json response.
Examples
- do_rma_query(rma_builder_fn, json_traversal_fn, *args, **kwargs)[source]¶
Bundle an RMA query url construction function with a corresponding response json traversal function.
- ..note:: Deprecated in AllenSDK 0.9.2
do_rma_query will be removed in AllenSDK 1.0, it is replaced by do_query because the latter is more general.
- Parameters:
- rma_builder_fnfunction
A function that takes parameters and returns an rma url.
- json_traversal_fnfunction
A function that takes a json-parsed python data structure and returns data from it.
- argsarguments
Arguments to be passed to the rma builder function.
- kwargskeyword arguments
Keyword arguments to be passed to the rma builder function.
- Returns:
- any type
The data extracted from the json response.
Examples
- download_url = 'http://download.alleninstitute.org'¶
- json_msg_query(url, dataframe=False)[source]¶
- Common case where the url is fully constructed
and the response data is stored in the ‘msg’ field.
- Parameters:
- urlstring
Where to get the data in json form
- dataframeboolean
True converts to a pandas dataframe, False (default) doesn’t
- Returns:
- dict or DataFrame
returned data; type depends on dataframe option
- load_api_schema()[source]¶
Download the RMA schema from the current RMA endpoint
- Returns:
- dict
the parsed json schema message
Notes
This information and other Allen Brain Atlas Data Portal Data Model documentation is also available as a Class Hierarchy and Class List.
- read_data(parsed_json)[source]¶
Return the message data from the parsed query.
- Parameters:
- parsed_jsondict
A python structure corresponding to the JSON data returned from the API.
Notes
See API Response Formats - Response Envelope for additional documentation.
- retrieve_file_over_http(url, file_path, zipped=False)[source]¶
Get a file from the data api and save it.
- Parameters:
- urlstring
Url[R099781a1d33c-1]_ from which to get the file.
- file_pathstring
Absolute path including the file name to save.
- zippedbool, optional
If true, assume that the response is a zipped directory and attempt to extract contained files into the directory containing file_path. Default is False.
See also
construct_well_known_file_download_url
Can be used to construct the url.
References
[1]Allen Brain Atlas Data Portal: Downloading a WellKnownFile.
- retrieve_parsed_json_over_http(url, post=False)[source]¶
Get the document and put it in a Python data structure
- Parameters:
- urlstring
Full API query url.
- postboolean
True does an HTTP POST, False (default) encodes the URL and does a GET
- Returns:
- dict
Result document as parsed by the JSON library.
- retrieve_xml_over_http(url)[source]¶
Get the document and put it in a Python data structure
- Parameters:
- urlstring
Full API query url.
- Returns:
- string
Unparsed xml string.
- allensdk.api.api.stream_file_over_http(url, file_path, timeout=(9.05, 31.1))[source]¶
Supply an http get request and stream the response to a file.
- Parameters:
- urlstr
Send the request to this url
- file_pathstr
Stream the response to this path
- timeoutfloat or tuple of float, optional
Specify a timeout for the request. If a tuple, specify seperate connect and read timeouts.
- allensdk.api.api.stream_zip_directory_over_http(url, directory, members=None, timeout=(9.05, 31.1))[source]¶
Supply an http get request and stream the response to a file.
- Parameters:
- urlstr
Send the request to this url
- directorystr
Extract the response to this directory
- memberslist of str, optional
Extract only these files
- timeoutfloat or tuple of float, optional
Specify a timeout for the request. If a tuple, specify seperate connect and read timeouts.