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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: 7.17.0
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen For more information, please visit https://github.com/jdkent

Requirements.

Python 3.9+

Installation & Usage

pip install

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

pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git)

Then import the package:

import neurostore_sdk

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

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 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 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 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 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 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

[email protected]

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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