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neurostore-sdk

Create studysets for meta-analysis

This Python package is automatically generated by the OpenAPI Generator project:

  • API version: 1.2
  • Package version: 1.2
  • Generator version: 7.27.0
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen For more information, please visit https://github.com/jdkent

Requirements.

Python 3.11+

Packaging uses standard [project] metadata and [dependency-groups] (PEP 621/735). Install the package with python -m pip install .; install development dependencies with Poetry 2.2 or newer using poetry install, or pip 25.1 or newer using python -m pip install --group dev. The latter installs the group, not the package.

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/neurostuff/neurostore-python-sdk.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/neurostuff/neurostore-python-sdk.git)

Then import the package:

import neurostore_sdk

From a local checkout

pip install .

Then import the package:

import neurostore_sdk

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:


import neurostore_sdk
from neurostore_sdk.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://neurostore.org/api
# See configuration.py for a list of all supported configuration parameters.
configuration = neurostore_sdk.Configuration(
    host = "https://neurostore.org/api"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure Bearer authorization: JSON-Web-Token
configuration = neurostore_sdk.Configuration(
    access_token = os.environ["BEARER_TOKEN"]
)


# Enter a context with an instance of the API client
with neurostore_sdk.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = neurostore_sdk.ReviewApi(api_client)
    id = 'id_example' # str | The base study (paper).

    try:
        # The users a paper is assigned to
        api_response = api_instance.review_base_studies_id_assignments_get(id)
        print("The response of ReviewApi->review_base_studies_id_assignments_get:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling ReviewApi->review_base_studies_id_assignments_get: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to https://neurostore.org/api

Class Method HTTP request Description
ReviewApi review_base_studies_id_assignments_get GET /review/base-studies/{id}/assignments The users a paper is assigned to
ReviewApi review_base_studies_id_assignments_user_id_delete DELETE /review/base-studies/{id}/assignments/{user_id} Release a paper from a reviewer
ReviewApi review_base_studies_id_assignments_user_id_put PUT /review/base-studies/{id}/assignments/{user_id} Assign a paper to a reviewer, or reassign it
ReviewApi review_exports_post POST /review/exports/ Export the reviews that match the filters as a zip of layout trees
ReviewApi review_imports_pipeline_post POST /review/imports/pipeline Load the records of a pipeline run already in neurostore for review
ReviewApi review_imports_post POST /review/imports/ Load the papers of a study_schema layout zip for review
ReviewApi review_me_get GET /review/me The caller, as a reviewer
ReviewApi review_reviewers_get GET /review/reviewers/ The admin-reviewers, to assign papers to
ReviewApi review_reviews_id_export_get GET /review/reviews/{id}/export Export one review as a study_schema layout zip
ReviewApi review_reviews_id_get GET /review/reviews/{id} One reviewer's review of a paper
ReviewApi review_reviews_id_ops_post POST /review/reviews/{id}/ops Apply a batch of the owner's ops to their review
ReviewApi review_reviews_id_patch PATCH /review/reviews/{id} Submit, reopen, set aside, or mark as the reference review
ReviewApi review_schemas_name_get GET /review/schemas/{name} One JSON Schema of the review API
ReviewApi review_sources_get GET /review/sources/ List papers loaded for review, with each reviewer's progress
ReviewApi review_sources_id_bundle_get GET /review/sources/{id}/bundle Everything the review app needs to open one paper for the caller
ReviewApi review_sources_id_review_put PUT /review/sources/{id}/review Start the caller's review of a paper
StoreApi analyses_get GET /analyses/ GET list of analyses
StoreApi analyses_id_delete DELETE /analyses/{id} DELETE an analysis
StoreApi analyses_id_get GET /analyses/{id} GET an analysis
StoreApi analyses_id_put PUT /analyses/{id} PUT/update an analysis
StoreApi analyses_post POST /analyses/ POST/create an analysis
StoreApi analysis_queries_post POST /analysis-queries/ Select analyses by what their extraction records say
StoreApi analysis_terms_get GET /analysis-terms/ The values an analysis query field takes
StoreApi annotation_analyses_get GET /annotation-analyses/ Get annotation analyses
StoreApi annotation_analyses_id_get GET /annotation-analyses/{id} Your GET endpoint
StoreApi annotation_analyses_id_put PUT /annotation-analyses/{id} Your PUT endpoint
StoreApi annotation_analyses_post POST /annotation-analyses/ Your POST endpoint
StoreApi annotations_get GET /annotations/ Your GET endpoint
StoreApi annotations_id_delete DELETE /annotations/{id} DELETE an annotation
StoreApi annotations_id_get GET /annotations/{id} Your GET endpoint
StoreApi annotations_id_put PUT /annotations/{id} Update an annotation
StoreApi annotations_post POST /annotations/ Post Annotation
StoreApi api_keys_get GET /api-keys/ List your API keys
StoreApi api_keys_id_delete DELETE /api-keys/{id} Revoke an API key
StoreApi api_keys_introspect_get GET /api-keys/introspect Describe the API key making the request
StoreApi api_keys_post POST /api-keys/ Create an API key
StoreApi base_studies_get GET /base-studies/
StoreApi base_studies_id_delete DELETE /base-studies/{id} Delete a base study
StoreApi base_studies_id_get GET /base-studies/{id} Your GET endpoint
StoreApi base_studies_id_put PUT /base-studies/{id}
StoreApi base_studies_post POST /base-studies/
StoreApi conditions_get GET /conditions/ GET Conditions
StoreApi conditions_id_delete DELETE /conditions/{id} DELETE a condition
StoreApi conditions_id_get GET /conditions/{id} GET a condition
StoreApi conditions_id_put PUT /conditions/{id} PUT/update a condition
StoreApi conditions_post POST /conditions/ POST/Create a condition
StoreApi data_sources_get GET /data-sources/ GET data sources
StoreApi data_sources_id_delete DELETE /data-sources/{id} DELETE a data source
StoreApi data_sources_id_get GET /data-sources/{id} GET a data source
StoreApi data_sources_id_put PUT /data-sources/{id} PUT/update a data source
StoreApi data_sources_post POST /data-sources/ POST/Create a data source
StoreApi images_get GET /images/ GET a list of images
StoreApi images_id_delete DELETE /images/{id} DELETE an image
StoreApi images_id_get GET /images/{id} GET an image
StoreApi images_id_put PUT /images/{id} PUT/update an image
StoreApi images_post POST /images/ POST/create an image
StoreApi journals_get GET /journals/ GET journals
StoreApi journals_id_get GET /journals/{id} GET a journal
StoreApi neurostore_studyset_releases_get GET /neurostore-studyset-releases/ GET NeuroStore studyset release list
StoreApi neurostore_studyset_releases_version_download_get GET /neurostore-studyset-releases/{version}/download Download NeuroStore studyset release tarball
StoreApi neurostore_studyset_releases_version_get GET /neurostore-studyset-releases/{version} GET NeuroStore studyset release manifest
StoreApi pipeline_configs_get GET /pipeline-configs/ GET a list of pipeline configs
StoreApi pipeline_configs_id_delete DELETE /pipeline-configs/{id} DELETE a pipeline config by ID
StoreApi pipeline_configs_id_get GET /pipeline-configs/{id} GET a pipeline config by ID
StoreApi pipeline_configs_id_put PUT /pipeline-configs/{id} PUT/update a pipeline config by ID
StoreApi pipeline_configs_post POST /pipeline-configs/ POST/create a pipeline config
StoreApi pipeline_embeddings_get GET /pipeline-embeddings/ List pipeline embeddings
StoreApi pipeline_embeddings_id_get GET /pipeline-embeddings/{id} Get a pipeline embedding by id
StoreApi pipeline_study_results_get GET /pipeline-study-results/ GET a list of pipeline run results
StoreApi pipeline_study_results_pipeline_study_result_id_delete DELETE /pipeline-study-results/{pipeline_study_result_id} DELETE a pipeline run result by ID
StoreApi pipeline_study_results_pipeline_study_result_id_get GET /pipeline-study-results/{pipeline_study_result_id} GET a pipeline run result by ID
StoreApi pipeline_study_results_pipeline_study_result_id_put PUT /pipeline-study-results/{pipeline_study_result_id} PUT/update a pipeline run result by ID
StoreApi pipeline_study_results_post POST /pipeline-study-results/ POST/create a pipeline run result
StoreApi pipelines_get GET /pipelines/ GET a list of pipelines
StoreApi pipelines_id_delete DELETE /pipelines/{id} DELETE a pipeline by ID
StoreApi pipelines_id_get GET /pipelines/{id} GET a pipeline by ID
StoreApi pipelines_id_put PUT /pipelines/{id} PUT/update a pipeline by ID
StoreApi pipelines_post POST /pipelines/ POST/create a pipeline
StoreApi points_get GET /points/ Get Points
StoreApi points_id_delete DELETE /points/{id} DELETE a point
StoreApi points_id_get GET /points/{id} GET a point
StoreApi points_id_put PUT /points/{id} PUT/update a point
StoreApi points_post POST /points/ POST Points
StoreApi query_dataset_get GET /query/{dataset} Run an aggregate query over one dataset
StoreApi query_get GET /query/ The datasets a public query reads
StoreApi studies_get GET /studies/ GET a list of studies
StoreApi studies_id_delete DELETE /studies/{id} DELETE a study
StoreApi studies_id_get GET /studies/{id} GET a study
StoreApi studies_id_put PUT /studies/{id} PUT/update a study
StoreApi studies_post POST /studies/ POST/create a study
StoreApi study_schema_uploads_post POST /study-schema-uploads/ Store a coordinate parse, a revision, an extraction record, or a parse with its record
StoreApi studysets_get GET /studysets/ GET a list of studysets
StoreApi studysets_id_delete DELETE /studysets/{id} DELETE a studyset
StoreApi studysets_id_get GET /studysets/{id} GET a studyset
StoreApi studysets_id_put PUT /studysets/{id} PUT/update a studyset
StoreApi studysets_post POST /studysets/ POST/create a studyset
StoreApi tables_get GET /tables/ GET list of tables
StoreApi tables_id_delete DELETE /tables/{id} DELETE a table
StoreApi tables_id_get GET /tables/{id} GET a table
StoreApi tables_id_put PUT /tables/{id} PUT/update a table
StoreApi tables_post POST /tables/ POST/create a table
StoreApi users_get GET /users/ Your GET endpoint
StoreApi users_id_get GET /users/{id} Individual User Profile
StoreApi users_id_put PUT /users/{id} Update Individual Profile
StoreApi users_post POST /users/

Documentation For Models

Documentation For Authorization

Authentication schemes defined for the API:

JSON-Web-Token

  • Type: Bearer authentication

Author

jamesdkent21@gmail.com

Request headers

Header names are compared case-insensitively in all Python client libraries. Request headers are copied; supplying _headers does not change the caller's dict or the client's shared defaults. The public _headers argument retains its dict validation and existing value serialization. Pydantic can coerce mappings such as HTTPX Headers to a dict, combining repeated fields into a single value; _headers does not provide a repeated-field or list-of-pairs API.

Precedence, from lowest to highest:

  1. _headers (within one dict, the last inserted case variant wins).
  2. Explicit OpenAPI header parameters and generated Content-Type (or _content_type). Generated Accept is added only when neither _headers nor explicit header parameters contain an Accept case variant.
  3. ApiClient.default_headers (including headers set with set_default_header).
  4. The client's cookie setting, for Cookie.
  5. Authentication headers. A non-empty _request_auth replaces configured authentication for that call; {} retains configured authentication. Cookie authentication appends to the selected Cookie value.

This retains the existing precedence for identically spelled names and extends it to case variants. To override a generated content type, use _content_type; client defaults still take precedence over it. The winning header's spelling and value are retained for replacements. Cookie authentication uses the canonical Cookie spelling and appends its value. Values containing legitimate comma-separated lists are not split or deduplicated. This does not remove duplicate values inside a header or change the handling of repeated fields supplied directly to the transport.

Neurostuff SDK Helpers

The generator adds two helper modules to reduce import friction:

  1. sdk.py: a single facade for endpoint groups.
  2. auth.py: Auth0 refresh-token exchange + automatic bearer token refresh.

Minimal usage

from neurostore_sdk.sdk import SDK

sdk = SDK(host="https://example.org/api", access_token="<access-token>")
studysets_api = sdk.studysets
result = studysets_api.studysets_get()

Auth0 refresh-token usage

from neurostore_sdk.sdk import SDK

sdk = SDK.from_auth0_refresh_token(
    domain="your-tenant.us.auth0.com",
    client_id="<auth0-client-id>",
    refresh_token="<auth0-refresh-token>",
    audience="<optional-audience>",
)

# Access token is exchanged and refreshed automatically per request.
users = sdk.users.users_get()

You can also use environment variables: AUTH0_DOMAIN, AUTH0_CLIENT_ID, AUTH0_REFRESH_TOKEN, plus optional AUTH0_AUDIENCE, AUTH0_CLIENT_SECRET, AUTH0_SCOPE.

sdk = SDK.from_auth0_env(prefix="AUTH0")

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