diff --git a/.gitignore b/.gitignore index 02c0b30..e94cbe7 100644 --- a/.gitignore +++ b/.gitignore @@ -11,6 +11,7 @@ # Python **/__pycache__ +**/.pytest_cache # Logs backend/pine/backend/logs diff --git a/README.md b/README.md index f5be26d..84e3e0f 100644 --- a/README.md +++ b/README.md @@ -150,6 +150,20 @@ Once the dev stack is up and running, the following ports are accessible: 2. `./generate_documentation.sh` 3. Generated documentation can then be found in `./docs/build`. +### Backend OpenAPI Specification + +The backend API is documented using an [OpenAPI specification](https://swagger.io/specification/). +This specification covers the main REST API used by PINE. A copy of the +[Swagger UI](https://swagger.io/tools/swagger-ui/) is hosted at `http[s]:///api/ui` and +the specification itself is hosted at `http[s]:///api/openapi.yaml`. + +This specification is found in the source code at `backend/pine/backend/api/openapi.yaml`. +*NOTE* however that this file is autogenerated by the `./update_openapi.sh` script. The "base" +file is located at `backend/pine/backend/api/base.yaml` which then pulls in information from other +files. ALL changes to the backend API should result in updates to the specification, as it is *NOT* +automatically updated or generated based on code changes. The `./update_openapi.sh` script requires +Docker to run and standard Linux tools (find, grep, awk, sort) but no other dependencies. + ### Testing Data To import testing data, run the dev stack and then run: diff --git a/backend/pine/backend/admin/bp.py b/backend/pine/backend/admin/bp.py index 662ecd7..cc0d596 100644 --- a/backend/pine/backend/admin/bp.py +++ b/backend/pine/backend/admin/bp.py @@ -1,6 +1,6 @@ # (C) 2019 The Johns Hopkins University Applied Physics Laboratory LLC. -from flask import Blueprint, jsonify, request, Response +from flask import Blueprint, jsonify, request import requests from werkzeug import exceptions @@ -29,7 +29,7 @@ def get_user(user_id): """ return jsonify(users.get_user(user_id)) -@bp.route("/users//password", methods = ["POST", "PUT", "PATCH"]) +@bp.route("/users//password", methods = ["PUT"]) @auth.admin_required def update_user_password(user_id): """ @@ -48,7 +48,7 @@ def update_user_password(user_id): resp = service.put("users/" + user_id, json = user, headers = {"If-Match": etag}) return service.convert_response(resp) -@bp.route("/users/", methods = ["PUT", "PATCH"]) +@bp.route("/users/", methods = ["PUT"]) @auth.admin_required def update_user(user_id): """ @@ -98,7 +98,13 @@ def add_user(): body["_id"] = body["id"] del body["id"] - if body["description"] == None: + + # check other fields as required by eve schema + if not "firstname" in body or not body["firstname"] or "lastname" not in body or not body["lastname"]: + raise exceptions.BadRequest(description = "Missing firstname or lastname in body JSON data.") + if not "roles" in body or not body["roles"]: + raise exceptions.BadRequest(description = "Missing/empty roles in body JSON data.") + if "description" in body and body["description"] == None: del body["description"] # post to data server diff --git a/backend/pine/backend/admin/openapi.yaml b/backend/pine/backend/admin/openapi.yaml new file mode 100644 index 0000000..ef986c5 --- /dev/null +++ b/backend/pine/backend/admin/openapi.yaml @@ -0,0 +1,361 @@ +# (C) 2021 The Johns Hopkins University Applied Physics Laboratory LLC. + +openapi: "3.0.2" + +security: + - cookieAuth: [] + +tags: + - name: admin + description: > + Operations in the "admin" blueprint. These operations are generally only available when the + "eve" auth module is running and are only accessible to logged-in users that are + administrators. + +components: + + schemas: + + UserRoles: + description: The role (for permissions) of the user. + type: array + items: + type: string + enum: [administrator, user] + + NewUserData: + type: object + properties: + id: + type: string + email: + type: string + passwd: + type: string + description: + type: string + firstname: + type: string + lastname: + type: string + role: + $ref: "#/components/schemas/UserRoles" + required: + - id + - email + - passwd + - firstname + - lastname + - roles + + UpdateUserData: + type: object + properties: + _id: + type: string + _etag: + type: string + description: + type: string + firstname: + type: string + lastname: + type: string + email: + type: string + description: If this is not included, you wont be able to log in. + passwdhash: + type: string + description: Setting this manually might break the password. + role: + $ref: "#/components/schemas/UserRoles" + required: + - _id + - _etag + - firstname + - lastname + - passwdhash + - role + +paths: + + /admin/users: + get: + summary: Get All User Information + description: | + Get a list of all users (and details: id, email, password hash). + + Example: `curl -X GET http://localhost:5000/admin/users --cookie admin.cookie` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_get_users + tags: [admin] + responses: + "200": + description: Returned list of user details. + content: + application/json: + schema: + type: array + items: + $ref: "../api/components.yaml#/schemas/UserInfo" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + post: + summary: Create New User + description: | + Create a new user. + + Example: `curl -X Post http://localhost:5000/admin/users -d '{"id":"joe", "passwd":"mypass", "email":"joe@pine.jhuapl.edu", "description": "", "firstname":"joe", "lastname":"jones"}' -H "Content-type:application/json" --cookie admin.cookie` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_add_user + tags: [admin] + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/NewUserData" + responses: + "200": + description: Return id info of newly created user. + content: + application/json: + schema: + type: array + items: + $ref: "../api/components.yaml#/schemas/IDInfo" + "400": + $ref: "../api/components.yaml#/responses/InvalidInputParameters" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "409": + description: User with that ID/email already exists. + content: {application/json: {schema: {$ref: "../api/components.yaml#/schemas/ErrorResponse"}}} + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /admin/users/{user_id}: + get: + summary: Get User Details + description: | + Get details (id, email, password hash...) of a certain user. + + Example: `curl -X GET http://localhost:5000/admin/users/ada --cookie admin.cookie` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_get_user + tags: [admin] + parameters: + - $ref: "../api/components.yaml#/parameters/userIdParam" + responses: + "200": + description: Successfully found the user and returned their details. + content: + application/json: + schema: + $ref: "../api/components.yaml#/schemas/UserInfo" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "404": + description: No user found with that ID. + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + put: + summary: Update user details. + description: | + Update user details. + + Example: `curl -X PUT http://localhost:5000/admin/users/ada -d '{"_id":"ada","description":"newdesc", "firstname":"newada", "lastname":"adalast", "_etag":"1c12354ee74f5d5732231ac5034f7915fb167244", "email":"ada@pine.jhuapl.edu"}' -H "Content-type:application/json" --cookie admin.cookie` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_update_user + tags: [admin] + parameters: + - $ref: "../api/components.yaml#/parameters/userIdParam" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/UpdateUserData" + responses: + "200": + description: Successfully changed user information + content: + application/json: + schema: + $ref: "../api/components.yaml#/schemas/IDInfo" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "404": + description: No user found with that ID. + "412": + $ref: "../api/components.yaml#/responses/MismatchedEtag" + "422": + $ref: "../api/components.yaml#/responses/InvalidInputParameters" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + delete: + summary: Delete User + description: | + Delete a user. + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_delete_user + tags: [admin] + parameters: + - $ref: "../api/components.yaml#/parameters/userIdParam" + responses: + "204": + description: Successfully deleted user. + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "404": + description: No user found with that ID. + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /admin/users/{user_id}/password: + put: + summary: Update User Password + description: | + Update the password of a user. + + Example: `curl -X post http://localhost:5000/admin/users/ada/password -d '{"passwd":"newpass"}' -H "Content-type:application/json" --cookie admin.cookie` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_update_user_password + tags: [admin] + parameters: + - $ref: "../api/components.yaml#/parameters/userIdParam" + requestBody: + content: + application/json: + schema: + type: object + properties: + passwd: + type: string + required: + - passwd + responses: + "200": + description: "Successfully changed user password" + content: + application/json: + schema: + $ref: "../api/components.yaml#/schemas/IDInfo" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "404": + description: No user found with that ID. + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /admin/system/export: + get: + summary: Export Database + description: | + Export the database to a zip file. + + Example: `curl -X GET http://localhost:5000/admin/system/export --cookie admin.cookie -v --output out.zip` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_system_export + tags: [admin] + responses: + "200": + description: "Successfully exported database" + content: + application/gzip: {} + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /admin/system/import: + put: + summary: Import Database (Update) + description: | + Import the database given in request body. This will _update_ and not _replace_ the + database. + + Example: `curl -X PUT http://localhost:5000/admin/system/import --cookie admin.cookie -F "file=@/home/pine/out.zip"` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_system_import_put + tags: [admin] + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + file: + type: string + format: binary + required: + - file + responses: + "200": + $ref: "../api/components.yaml#/responses/Success" + "400": + description: The loading of data was wrong. Should be a gz, like what is exported. + content: {application/json: {schema: {$ref: "../api/components.yaml#/schemas/ErrorResponse"}}} + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "422": + description: The file argument was not present. + content: {application/json: {schema: {$ref: "../api/components.yaml#/schemas/ErrorResponse"}}} + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + post: + summary: Import Database (Replace) + description: | + Import the database given in request body. This will _replace_ and not _update_ the + database. + + Example: `curl -X POST http://localhost:5000/admin/system/import --cookie admin.cookie -F "file=@/home/pine/out.zip"` + + _Note_: this endpoint requires the logged in user to be an admin and is only relevant if + the auth module supports it. + operationId: admin_system_import_post + tags: [admin] + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + file: + type: string + format: binary + required: + - file + responses: + "200": + $ref: "../api/components.yaml#/responses/Success" + "400": + description: The loading of data was wrong. Should be a gz, like what is exported. + content: {application/json: {schema: {$ref: "../api/components.yaml#/schemas/ErrorResponse"}}} + "401": + $ref: "../api/components.yaml#/responses/NotAuthorizedOrNotAdmin" + "422": + description: The file argument was not present. + content: {application/json: {schema: {$ref: "../api/components.yaml#/schemas/ErrorResponse"}}} + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" diff --git a/backend/pine/backend/annotations/bp.py b/backend/pine/backend/annotations/bp.py index c9cf820..950bff6 100644 --- a/backend/pine/backend/annotations/bp.py +++ b/backend/pine/backend/annotations/bp.py @@ -204,7 +204,7 @@ def _add_or_update_annotation(new_annotation): return new_annotation["_id"] -@bp.route("/mine/by_document_id/", methods = ["POST", "PUT"]) +@bp.route("/mine/by_document_id/", methods = ["POST"]) def save_annotations(doc_id): """ Save new NER annotations and labels to the database as an entry for the logged in user, for the document. If there @@ -254,7 +254,7 @@ def save_annotations(doc_id): return jsonify(resp) -@bp.route("/mine/by_collection_id/", methods = ["POST", "PUT"]) +@bp.route("/mine/by_collection_id/", methods = ["POST"]) def save_collection_annotations(collection_id: str): # If you change input or output, update client modules pine.client.models and pine.client.client collection = service.get_item_by_id("collections", collection_id, params=service.params({ @@ -277,6 +277,9 @@ def save_collection_annotations(collection_id: str): skip_document_updates = json.loads(request.args.get("skip_document_updates", "false")) update_iaa = json.loads(request.args.get("update_iaa", "true")) + # Batch mode should only be used when all documents being annotated haven't been + # annotated before, otherwise eve's versioning will be messed up. + batch_mode = json.loads(request.args.get("batch_mode", "true")) # make sure all the documents actually belong to that collection collection_ids = list(documents.get_collection_ids_for(doc_annotations.keys())) @@ -284,7 +287,6 @@ def save_collection_annotations(collection_id: str): raise exceptions.Unauthorized() user_id = auth.get_logged_in_user()["id"] - # first try batch mode new_annotations = [] for (doc_id, body) in doc_annotations.items(): (doc_labels, ner_annotations) = _make_annotations(body) @@ -295,24 +297,35 @@ def save_collection_annotations(collection_id: str): "document_id": doc_id, "annotation": doc_labels + ner_annotations }) - resp = service.post("annotations", json=new_annotations) - if resp.ok: - for (i, created_annotation) in enumerate(resp.json()["_items"]): - new_annotations[i]["_id"] = created_annotation["_id"] - if not skip_document_updates: - set_document_to_annotated_by_user(new_annotations[i]["document_id"], - new_annotations[i]["creator_id"]) - log.access_flask_annotate_documents(new_annotations) - if update_iaa: - success = pineiaa.update_iaa_report_by_collection_id(collection_id) - if not success: - logger.error("Unable to update IAA report but will not return an error") - return jsonify([annotation["_id"] for annotation in new_annotations]) + + if batch_mode: + # first try batch mode (should only be done if the document doesn't have annotations already) + resp = service.post("annotations", json=new_annotations) + if resp.ok: + resp_json = resp.json() + # Changing a single document will not have _items + if "_items" in resp_json: + for (i, created_annotation) in enumerate(resp_json["_items"]): + new_annotations[i]["_id"] = created_annotation["_id"] + if not skip_document_updates: + set_document_to_annotated_by_user(new_annotations[i]["document_id"], + new_annotations[i]["creator_id"]) + else: + new_annotations[0]["_id"] = resp_json["_id"] + if not skip_document_updates: + set_document_to_annotated_by_user(new_annotations[0]["document_id"], + new_annotations[0]["creator_id"]) + log.access_flask_annotate_documents(new_annotations) + if update_iaa: + success = pineiaa.update_iaa_report_by_collection_id(collection_id) + if not success: + logger.error("Unable to update IAA report but will not return an error") + return jsonify([annotation["_id"] for annotation in new_annotations]) # fall back on individual mode added_ids = [] for annotation in new_annotations: - added_id = _add_or_update_annotation(annotation["document_id"], user_id, annotation) + added_id = _add_or_update_annotation(annotation) if added_id: added_ids.append(added_id) if update_iaa: diff --git a/backend/pine/backend/annotations/openapi.yaml b/backend/pine/backend/annotations/openapi.yaml new file mode 100644 index 0000000..f2eb309 --- /dev/null +++ b/backend/pine/backend/annotations/openapi.yaml @@ -0,0 +1,211 @@ +# (C) 2021 The Johns Hopkins University Applied Physics Laboratory LLC. + +openapi: "3.0.2" + +security: + - cookieAuth: [] + +tags: + - name: annotations + description: Operations in the "annotations" blueprint. + +components: + + schemas: + + WrappedAnnotations: + type: object + properties: + _items: + type: array + items: + $ref: "../api/components.yaml#/schemas/UserDocumentAnnotation" + _links: + $ref: "../api/components.yaml#/schemas/EveLinks" + +paths: + + /annotations/mine/by_document_id/{doc_id}: + get: + summary: Get My Document Annotations + description: | + Get a list of annotations done by the logged in user on a document. + + Example: `curl -X GET http://localhost:5000/annotations/mine/by_document_id/60d08052f2cb44c51e0af0f1 --cookie session.cookie` + operationId: annotations_get_mine + tags: [annotations] + parameters: + - $ref: "../api/components.yaml#/parameters/docIdParam" + responses: + "200": + description: Successfully found document and got annotations. + content: + application/json: + schema: + $ref: "#/components/schemas/WrappedAnnotations" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorized" + "404": + $ref: "../api/components.yaml#/responses/DocumentNotFound" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + post: + summary: Save My Annotations + description: | + Change annotations of a document. + + Example: `curl -X PUT http://localhost:5000/annotations/mine/by_document_id/60d08052f2cb44c51e0af0f1 --cookie session.cookie -H "Content-type: application/json" -d '{"doc":["sci.crypt", "talk.politics.misc"],"ner":[{"end":365,"start":346, "label":"sci.med"}, {"start":475, "end":530, "label":"alt.atheism"}]}'` + + _Note_: start or end indices in the middle of words might make the UI not show the label. + Also, invalid labels are not checked and might cause the UI to freeze. + operationId: annotations_save_mine + tags: [annotations] + parameters: + - $ref: "../api/components.yaml#/parameters/docIdParam" + - name: update_iaa + in: query + required: false + description: Whether to also update IAA reports. + schema: + type: boolean + default: true + requestBody: + description: The labels to add to the document. + required: true + content: + application/json: + schema: + $ref: "../api/components.yaml#/schemas/DocumentAnnotations" + responses: + "200": + description: Successfully found document and changed annotations (returns doc_id). + content: + application/json: + schema: + type: string + "400": + $ref: "../api/components.yaml#/responses/InvalidInputParameters" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorized" + "404": + $ref: "../api/components.yaml#/responses/DocumentNotFound" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /annotations/mine/by_collection_id/{collection_id}: + post: + summary: Set Collection Annotations + description: | + Modify annotations of certain documents in a given collection. + + Example: `curl -X POST http://localhost:5000/annotations/mine/by_collection_id/60d32ba28d34cf656fed503f --cookie session.cookie -H "Content-type: application/json" -d '{"60d32ba48d34cf656fed504b": {"doc":["sci.crypt", "talk.politics.misc"],"ner":[[0,4,"sci.med"], [0,4,"alt.atheism"]]}, "60d32ba48d34cf656fed504c": {"doc":[], "ner":[[0,4,"sci.med"]]}}'` + operationId: annotations_collection + tags: [annotations] + parameters: + - $ref: "../api/components.yaml#/parameters/collectionIdParam" + - name: batch_mode + required: true + description: | + Whether or not to send all annotations to the database as one batch or individually. + + _Note_: Batch mode should ONLY be used if all of the documents have not already been annotated. + + The versioning of eve will be messed up if batch mode annotates a document with pre-existing annotations (even if old). + + To be clear, even if a document had annotations that were deleted, using batch mode on that document will cause problems. + + Conversely, using individual mode (batch_mode = False) can always be done, but will be slower. + + Another issue with individual mode is with many documents, there will be many backend queries, possibly getting rate limited. + schema: + type: boolean + default: true + in: query + - name: update_iaa + in: query + required: false + description: Whether to also update IAA reports. + schema: + type: boolean + default: true + requestBody: + description: The labels to add to the document. + required: true + content: + application/json: + schema: + description: Mapping from document ID to annotations object. + type: object + additionalProperties: + $ref: "../api/components.yaml#/schemas/DocumentAnnotations" + example: + {"60d47b4bdbfddb3ca87c7971": {"doc": ["label1", "label2"], + "ner": [[0, 10, "label1"], [15, 18, "label2"]]}} + responses: + "200": + description: Successfully found document and changed annotations (returns annotation ids). + content: + application/json: + schema: + type: array + items: + type: string + "400": + $ref: "../api/components.yaml#/responses/InvalidInputParameters" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorized" + "404": + $ref: "../api/components.yaml#/responses/CollectionNotFound" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /annotations/others/by_document_id/{doc_id}: + get: + summary: Get Others' Document Annotations + description: | + Get a list of annotations done by everyone but me on a document. + + Example: `curl -X GET http://localhost:5000/annotations/others/by_document_id/60d08052f2cb44c51e0af0f1 --cookie session.cookie` + operationId: annotations_others + tags: [annotations] + parameters: + - $ref: "../api/components.yaml#/parameters/docIdParam" + responses: + "200": + description: Successfully found document and got annotations. + content: + application/json: + schema: + $ref: "#/components/schemas/WrappedAnnotations" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorized" + "404": + $ref: "../api/components.yaml#/responses/DocumentNotFound" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" + + /annotations/by_document_id/{doc_id}: + get: + summary: Get All Document Annotations + description: | + Get a list of annotations done by everyone on a document. + + Example: `curl -X GET http://localhost:5000/annotations/by_document_id/60d08052f2cb44c51e0af0f1 --cookie session.cookie` + operationId: annotations_all + tags: [annotations] + parameters: + - $ref: "../api/components.yaml#/parameters/docIdParam" + responses: + "200": + description: Successfully found document and got annotations. + content: + application/json: + schema: + $ref: "#/components/schemas/WrappedAnnotations" + "401": + $ref: "../api/components.yaml#/responses/NotAuthorized" + "404": + $ref: "../api/components.yaml#/responses/DocumentNotFound" + default: + $ref: "../api/components.yaml#/responses/UnexpectedServerError" diff --git a/backend/pine/backend/api/.gitignore b/backend/pine/backend/api/.gitignore new file mode 100644 index 0000000..08677c1 --- /dev/null +++ b/backend/pine/backend/api/.gitignore @@ -0,0 +1,3 @@ +# (C) 2019 The Johns Hopkins University Applied Physics Laboratory LLC. + +*.tar.gz diff --git a/backend/pine/backend/api/__init__.py b/backend/pine/backend/api/__init__.py new file mode 100644 index 0000000..79dbc53 --- /dev/null +++ b/backend/pine/backend/api/__init__.py @@ -0,0 +1,4 @@ +# (C) 2019 The Johns Hopkins University Applied Physics Laboratory LLC. + +"""This module implements all methods required for SwaggerUI to run on the +backend of PINE.""" diff --git a/backend/pine/backend/api/base.yaml b/backend/pine/backend/api/base.yaml new file mode 100644 index 0000000..223187e --- /dev/null +++ b/backend/pine/backend/api/base.yaml @@ -0,0 +1,34 @@ +# (C) 2021 The Johns Hopkins University Applied Physics Laboratory LLC. + +openapi: "3.0.2" + +info: + title: "PINE" + description: | + PINE: Pmap Interface for Nlp Experimentation + + PINE is a Natural Language Processing (NLP) tool designed for integration with the + Precision Medicine Analytics Platform (PMAP), developed at the Johns Hopkins University Applied + Physics Laboratory (JHU/APL). + + PINE consists of a web UI along with backing services. + version: "1.0.1" + contact: + name: "Michael Harrity" + email: "Michael.Harrity@jhuapl.edu" + license: + name: "AGPL-3.0" + url: https://github.com/JHUAPL/PINE/blob/master/LICENSE + +servers: + - url: http://localhost:5000 + - url: https://localhost:8888/api + - url: https://dev-nlpannotator.pm.jh.edu/api + +paths: {} + +components: + securitySchemes: + cookieAuth: + $ref: "./components.yaml#/securitySchemes/cookieAuth" + schemas: {} diff --git a/backend/pine/backend/api/bp.py b/backend/pine/backend/api/bp.py new file mode 100644 index 0000000..a622c0d --- /dev/null +++ b/backend/pine/backend/api/bp.py @@ -0,0 +1,34 @@ +# (C) 2019 The Johns Hopkins University Applied Physics Laboratory LLC. + +import logging + +from flask import redirect, render_template, request, send_file, url_for, Blueprint + +bp = Blueprint("api", __name__, url_prefix = "/api", template_folder="swagger-ui") +LOGGER = logging.getLogger(__name__) + +# Return the openapi specification for SwaggerUI +@bp.route("/openapi.yaml", methods=["GET"]) +def openapi_spec(): + # Specify statically where the openapi file is, relative path + return send_file("api/openapi.yaml", mimetype='text/yaml', as_attachment=False) + +@bp.route("/ui", methods=["GET"], strict_slashes=False) +def swagger_ui_index(): + # forward to /api/ui/index.html, taking proxy prefix into account if set + url = request.headers.get("X-Forwarded-Prefix", "") + url_for("api.swagger_ui", file="index.html") + LOGGER.info("Redirecting to {}".format(url)) + return redirect(url) + +@bp.route("/ui/", methods=["GET"]) +def swagger_ui(file: str): + if file == "index.html": + # get url for /api/openapi.yaml, taking proxy prefix into account if set + url = request.headers.get("X-Forwarded-Prefix", "") + url_for("api.openapi_spec") + LOGGER.info("Grabbing spec from {}".format(url)) + return render_template("index.html", spec_url=url) + else: + return send_file("api/swagger-ui/{}".format(file)) + +def init_app(app): + app.register_blueprint(bp) diff --git a/backend/pine/backend/api/components.yaml b/backend/pine/backend/api/components.yaml new file mode 100644 index 0000000..f691da4 --- /dev/null +++ b/backend/pine/backend/api/components.yaml @@ -0,0 +1,611 @@ +# (C) 2021 The Johns Hopkins University Applied Physics Laboratory LLC. + +securitySchemes: + + cookieAuth: + description: | + This an example command to provision and print the session key using eve: + + `curl -X POST -H "Content-Type:application/json" -d '{"username":"ada@pine.jhuapl.edu","password":"ada@pine.jhuapl.edu"}' http://localhost:5000/auth/login --cookie-jar - --output /dev/null --silent | grep -o -P "session\s.+" | sed -e 's/session\s/session=/' -` + type: apiKey + in: cookie + name: session + +parameters: + + userIdParam: + name: user_id + in: path + required: true + description: ID of the user on which to operate. + schema: + type: string + + docIdParam: + name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: + type: string + + collectionIdParam: + name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: + type: string + + pipelineIdParam: + name: pipeline_id + in: path + required: true + description: The id of the pipeline on which to operate. + schema: + type: string + + classifierIdParam: + name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: + type: string + +schemas: + + DocumentAnnotations: + type: object + properties: + doc: + description: Document-level annotations. + type: array + items: + description: Annotation label. + type: string + ner: + description: NER annotations. + type: array + items: + type: object + properties: + start: + description: Start index, inclusive. + type: integer + end: + description: End index, exclusive. + type: integer + label: + description: Annotation label. + type: string + example: + doc: ["label1", "label2"] + ner: [{"start":0, "end":10, "label":"in-text-label"}] + + AuthUser: + type: object + properties: + display_name: + type: string + id: + type: string + is_admin: + type: boolean + username: + type: string + example: + display_name: Ada Lovelace + id: ada + is_admin: false + username: ada@pine.jhuapl.edu + + AuthUserDetails: + type: object + properties: + description: + type: string + first_name: + type: string + last_name: + type: string + example: + first_name: Ada + last_name: Lovelace + description: The first computer programmer. + + EveLinks: + type: object + properties: + parent: + type: object + properties: + title: + type: string + href: + type: string + self: + type: object + properties: + title: + type: string + href: + type: string + + EveBase: + type: object + properties: + _etag: + type: string + + EveBaseWithVersion: + allOf: + - $ref: "#/schemas/EveBase" + - type: object + properties: + _version: + type: integer + _latest_version: + type: integer + + Document: + type: object + properties: + _id: + type: string + creator_id: + type: string + collection_id: + type: string + overlap: + type: integer + format: int64 + metadata: + type: object + # This means accept any type for key/val + additionalProperties: {} + text: + type: string + has_annotated: + type: object + additionalProperties: + type: boolean + + DocumentDeletionResponse: + type: object + properties: + success: + type: boolean + description: Whether the operation was successful. + changed_objs: + type: object + description: What database objects were changed during operation. + properties: + next_instances: + type: object + properties: + updated: + description: IDs of next_instance objects that were updated. + type: array + items: + type: string + annotations: + type: object + properties: + deleted: + description: IDs of annotation objects that were deleted. + type: array + items: + type: string + documents: + type: object + properties: + deleted: + description: IDs of document objects that were deleted. + type: array + items: + type: string + + UserDocumentAnnotation: + description: > + This is the log of annotations by a specific user. A document might have 0, 1, or multiple of + these based on how many users annotated. + allOf: + - $ref: "#/schemas/EveBaseWithVersion" + - type: object + properties: + _id: + type: string + creator_id: + type: string + collection_id: + type: string + document_id: + type: string + annotation: + type: array + items: + anyOf: + - type: string + example: documentlabel + description: String for labels on the entire document. + - type: array + items: + anyOf: + - type: string + - type: integer + example: + [1, 2, "textlabel"] + description: Array for individual annotations [start_index, end_index, label] + + Collection: + type: object + properties: + _id: + type: string + creator_id: + type: string + metadata: + type: object + additionalProperties: {} + configuration: + type: object + additionalProperties: {} + labels: + type: array + items: + type: string + viewers: + type: array + items: + type: string + annotators: + type: array + items: + type: string + archived: + type: boolean + + CollectionDownload: + description: Collection download is Collection with a list of all docs inside (and no eve info) + type: object + properties: + _id: + type: string + creator_id: + type: string + metadata: + type: object + additionalProperties: {} + configuration: + type: object + additionalProperties: {} + labels: + type: array + items: + type: string + viewers: + type: array + items: + type: string + annotators: + type: array + items: + type: string + archived: + type: boolean + documents: + type: array + items: + $ref: '#/components/schemas/Document' + + UserPermissions: + type: object + properties: + add_documents: + type: boolean + add_images: + type: boolean + annotate: + type: boolean + archive: + type: boolean + download_data: + type: boolean + modify_document_metadata: + type: boolean + modify_labels: + type: boolean + modify_users: + type: boolean + view: + type: boolean + + UserInfo: + type: object + properties: + _id: + type: string + _created: + type: string + description: + type: string + email: + type: string + firstname: + type: string + lastname: + type: string + passwdhash: + type: string + role: + type: array + items: + type: string + + IDInfo: + description: > + This object is returned when doing actions like modifying a document or collection. It + contains the ID of the object and some other information from the database. + allOf: + - $ref: "#/schemas/EveBase" + - type: object + properties: + _status: + type: string + _id: + type: string + _updated: + type: string + format: date-time + _created: + type: string + format: date-time + _links: + $ref: "#/schemas/EveLinks" + + ErrorResponse: + description: Error message from the server. + type: string + example: Error message from the server. + + Pipeline: + allOf: + - $ref: "#/schemas/EveBase" + - type: object + properties: + _id: + type: string + title: + type: string + description: + type: string + name: + type: string + parameters: + type: object + additionalProperties: {} + example: + cutoff: "integer" + iterations: " integer" + n_iter: "integer" + dropout: "float" + max_left: "integer" + use_class_feature: [true, false] + use_word: [true, false] + use_ngrams: [true, false] + no_mid_ngrams: [true, false] + max_ngram_length: "integer" + use_prev: [true, false] + use_next: [true, false] + use_disjunctive: [true, false] + use_sequences: [true, false] + use_prev_sequences: [true, false] + use_type_seqs: [true, false] + use_type_seqs2: [true, false] + use_type_y_sequences: [true, false] + _updated: + type: string + format: date-time + _created: + type: string + format: date-time + + CollectionMetric: + type: object + properties: + _id: + type: string + collection_id: + type: string + classifier_id: + type: string + # Not positive what elements can be in these array so leaving blank + documents: + type: array + items: {} + annotations: + type: array + items: {} + folds: + type: array + items: {} + metrics: + type: array + items: {} + _updated: + type: string + _created: + type: string + _version: + type: integer + _etag: + type: string + _links: + type: object + properties: + self: + type: object + properties: + title: + type: string + href: + type: string + + InterAnnotatorAgreement: + allOf: + - $ref: "#/schemas/EveBaseWithVersion" + - type: object + properties: + _id: + type: string + collection_id: + type: string + num_of_annotators: + type: integer + num_of_agreement_docs: + type: integer + num_of_labels: + type: integer + per_doc_agreement: + type: object + properties: + doc_id: + type: string + avg: + type: number + format: double + stddev: + type: integer + per_label_agreement: + type: array + items: + type: object + properties: + label: + type: string + avg: + type: number + format: double + stddev: + type: integer + overall_agreement: + type: object + properties: + mean: + type: number + format: double + sd: + type: integer + heatmap_data: + type: object + properties: + matrix: + type: array + items: + type: array + items: + type: number + format: float + minItems: 2 + maxItems: 2 + example: + [1, .666666] + annotators: + type: array + items: + type: string + example: + ["ada", "margaret"] + labels_per_annotator: + # Dictionary of dictionaries per annotator + type: object + additionalProperties: + # Dictionary of number of each label + type: object + additionalProperties: + type: integer + example: + {"ada": {"label1": 1, "label2": 4}, "margaret": {"label1": 3, "label2": 2}} + _updated: + type: string + format: date-time + _created: + type: string + format: date-time + +responses: + + Success: + description: Whether the operation succeeded or failed. + content: + application/json: + schema: + type: object + properties: + success: + type: boolean + + NotAuthorized: + description: > + Authentication failed: not logged in or user doesn't have the permissions for this operation. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + NotAuthorizedOrNotAdmin: + description: Authentication failed, not logged in or not an admin. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + InvalidInputParameters: + description: Input parameters are missing/invalid. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + DocumentNotFound: + description: Document with given ID was not found. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + CollectionNotFound: + description: Collection with given ID was not found. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + PipelineNotFound: + description: Pipeline with given ID was not found. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + ClassifierNotFound: + description: Classifier with given ID was not found. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + MismatchedEtag: + description: Given etag did not match the most updated stored one. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" + + UnexpectedServerError: + description: Unexpected error, check server logs. + content: + application/json: + schema: + $ref: "#/schemas/ErrorResponse" diff --git a/backend/pine/backend/api/download_swagger_ui.sh b/backend/pine/backend/api/download_swagger_ui.sh new file mode 100755 index 0000000..4258aec --- /dev/null +++ b/backend/pine/backend/api/download_swagger_ui.sh @@ -0,0 +1,22 @@ +#!/bin/bash +# (C) 2019 The Johns Hopkins University Applied Physics Laboratory LLC. + +set -ex + +if [[ $# -eq 0 ]]; then + VERSION=$(curl --silent "https://api.github.com/repos/swagger-api/swagger-ui/releases/latest" | grep '"tag_name":' | sed -E 's/.*"([^"]+)".*/\1/') + if [[ ${VERSION} = v* ]]; then + VERSION=${VERSION:1} + fi +else + VERSION="$1" +fi + +if [[ ! -f swagger-ui-${VERSION}.tar.gz ]]; then + wget "https://github.com/swagger-api/swagger-ui/archive/refs/tags/v${VERSION}.tar.gz" -O swagger-ui-${VERSION}.tar.gz +fi + +rm -rf swagger-ui/ +tar xzf swagger-ui-${VERSION}.tar.gz swagger-ui-${VERSION}/dist/ --transform "s|swagger-ui-${VERSION}/dist|swagger-ui|" +sed -i 's|https://petstore.swagger.io/v2/swagger.json|{{spec_url}}|' swagger-ui/index.html +echo ${VERSION} > swagger-ui/VERSION diff --git a/backend/pine/backend/api/openapi.yaml b/backend/pine/backend/api/openapi.yaml new file mode 100644 index 0000000..eb15cdc --- /dev/null +++ b/backend/pine/backend/api/openapi.yaml @@ -0,0 +1,4325 @@ +# (C) 2021 The Johns Hopkins University Applied Physics Laboratory LLC. + +openapi: 3.0.2 +info: + title: PINE + description: > + PINE: Pmap Interface for Nlp Experimentation + + + PINE is a Natural Language Processing (NLP) tool designed for integration + with the + + Precision Medicine Analytics Platform (PMAP), developed at the Johns Hopkins + University Applied + + Physics Laboratory (JHU/APL). + + + PINE consists of a web UI along with backing services. + version: 1.0.1 + contact: + name: Michael Harrity + email: Michael.Harrity@jhuapl.edu + license: + name: AGPL-3.0 + url: 'https://github.com/JHUAPL/PINE/blob/master/LICENSE' +servers: + - url: 'http://localhost:5000' + - url: 'https://localhost:8888/api' + - url: 'https://dev-nlpannotator.pm.jh.edu/api' +paths: + /admin/users: + get: + summary: Get All User Information + description: > + Get a list of all users (and details: id, email, password hash). + + + Example: `curl -X GET http://localhost:5000/admin/users --cookie + admin.cookie` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_get_users + tags: + - admin + responses: + '200': + description: Returned list of user details. + content: + application/json: + schema: + type: array + items: + type: object + properties: &ref_2 + _id: + type: string + _created: + type: string + description: + type: string + email: + type: string + firstname: + type: string + lastname: + type: string + passwdhash: + type: string + role: + type: array + items: + type: string + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: &ref_0 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: &ref_1 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + security: + - cookieAuth: [] + post: + summary: Create New User + description: > + Create a new user. + + + Example: `curl -X Post http://localhost:5000/admin/users -d + '{"id":"joe", "passwd":"mypass", "email":"joe@pine.jhuapl.edu", + "description": "", "firstname":"joe", "lastname":"jones"}' -H + "Content-type:application/json" --cookie admin.cookie` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_add_user + tags: + - admin + requestBody: + content: + application/json: + schema: + type: object + properties: &ref_40 + id: + type: string + email: + type: string + passwd: + type: string + description: + type: string + firstname: + type: string + lastname: + type: string + role: + description: The role (for permissions) of the user. + type: array + items: &ref_4 + type: string + enum: + - administrator + - user + required: &ref_41 + - id + - email + - passwd + - firstname + - lastname + - roles + responses: + '200': + description: Return id info of newly created user. + content: + application/json: + schema: + type: array + items: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object + and some other information from the database. + allOf: &ref_5 + - type: object + properties: &ref_8 + _etag: + type: string + - type: object + properties: + _status: + type: string + _id: + type: string + _updated: + type: string + format: date-time + _created: + type: string + format: date-time + _links: + type: object + properties: &ref_9 + parent: + type: object + properties: + title: + type: string + href: + type: string + self: + type: object + properties: + title: + type: string + href: + type: string + '400': + description: Input parameters are missing/invalid. + content: &ref_6 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '409': + description: User with that ID/email already exists. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/admin/users/{user_id}': + get: + summary: Get User Details + description: > + Get details (id, email, password hash...) of a certain user. + + + Example: `curl -X GET http://localhost:5000/admin/users/ada --cookie + admin.cookie` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_get_user + tags: + - admin + parameters: + - name: user_id + in: path + required: true + description: ID of the user on which to operate. + schema: &ref_3 + type: string + responses: + '200': + description: Successfully found the user and returned their details. + content: + application/json: + schema: + type: object + properties: *ref_2 + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '404': + description: No user found with that ID. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + put: + summary: Update user details. + description: > + Update user details. + + + Example: `curl -X PUT http://localhost:5000/admin/users/ada -d + '{"_id":"ada","description":"newdesc", "firstname":"newada", + "lastname":"adalast", + "_etag":"1c12354ee74f5d5732231ac5034f7915fb167244", + "email":"ada@pine.jhuapl.edu"}' -H "Content-type:application/json" + --cookie admin.cookie` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_update_user + tags: + - admin + parameters: + - name: user_id + in: path + required: true + description: ID of the user on which to operate. + schema: *ref_3 + requestBody: + content: + application/json: + schema: + type: object + properties: &ref_42 + _id: + type: string + _etag: + type: string + description: + type: string + firstname: + type: string + lastname: + type: string + email: + type: string + description: 'If this is not included, you wont be able to log in.' + passwdhash: + type: string + description: Setting this manually might break the password. + role: + description: The role (for permissions) of the user. + type: array + items: *ref_4 + required: &ref_43 + - _id + - _etag + - firstname + - lastname + - passwdhash + - role + responses: + '200': + description: Successfully changed user information + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '404': + description: No user found with that ID. + '412': + description: Given etag did not match the most updated stored one. + content: &ref_57 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '422': + description: Input parameters are missing/invalid. + content: *ref_6 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + delete: + summary: Delete User + description: > + Delete a user. + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_delete_user + tags: + - admin + parameters: + - name: user_id + in: path + required: true + description: ID of the user on which to operate. + schema: *ref_3 + responses: + '204': + description: Successfully deleted user. + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '404': + description: No user found with that ID. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/admin/users/{user_id}/password': + put: + summary: Update User Password + description: > + Update the password of a user. + + + Example: `curl -X post http://localhost:5000/admin/users/ada/password -d + '{"passwd":"newpass"}' -H "Content-type:application/json" --cookie + admin.cookie` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_update_user_password + tags: + - admin + parameters: + - name: user_id + in: path + required: true + description: ID of the user on which to operate. + schema: *ref_3 + requestBody: + content: + application/json: + schema: + type: object + properties: + passwd: + type: string + required: + - passwd + responses: + '200': + description: Successfully changed user password + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '404': + description: No user found with that ID. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /admin/system/export: + get: + summary: Export Database + description: > + Export the database to a zip file. + + + Example: `curl -X GET http://localhost:5000/admin/system/export --cookie + admin.cookie -v --output out.zip` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_system_export + tags: + - admin + responses: + '200': + description: Successfully exported database + content: + application/gzip: {} + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /admin/system/import: + put: + summary: Import Database (Update) + description: > + Import the database given in request body. This will _update_ and not + _replace_ the + + database. + + + Example: `curl -X PUT http://localhost:5000/admin/system/import --cookie + admin.cookie -F "file=@/home/pine/out.zip"` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_system_import_put + tags: + - admin + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + file: + type: string + format: binary + required: + - file + responses: + '200': + description: Whether the operation succeeded or failed. + content: &ref_7 + application/json: + schema: + type: object + properties: + success: + type: boolean + '400': + description: >- + The loading of data was wrong. Should be a gz, like what is + exported. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '422': + description: The file argument was not present. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + post: + summary: Import Database (Replace) + description: > + Import the database given in request body. This will _replace_ and not + _update_ the + + database. + + + Example: `curl -X POST http://localhost:5000/admin/system/import + --cookie admin.cookie -F "file=@/home/pine/out.zip"` + + + _Note_: this endpoint requires the logged in user to be an admin and is + only relevant if + + the auth module supports it. + operationId: admin_system_import_post + tags: + - admin + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + file: + type: string + format: binary + required: + - file + responses: + '200': + description: Whether the operation succeeded or failed. + content: *ref_7 + '400': + description: >- + The loading of data was wrong. Should be a gz, like what is + exported. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + '422': + description: The file argument was not present. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/annotations/mine/by_document_id/{doc_id}': + get: + summary: Get My Document Annotations + description: > + Get a list of annotations done by the logged in user on a document. + + + Example: `curl -X GET + http://localhost:5000/annotations/mine/by_document_id/60d08052f2cb44c51e0af0f1 + --cookie session.cookie` + operationId: annotations_get_mine + tags: + - annotations + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: &ref_10 + type: string + responses: + '200': + description: Successfully found document and got annotations. + content: + application/json: + schema: + type: object + properties: &ref_15 + _items: + type: array + items: + description: > + This is the log of annotations by a specific user. A + document might have 0, 1, or multiple of these based on + how many users annotated. + allOf: &ref_55 + - allOf: &ref_30 + - type: object + properties: *ref_8 + - type: object + properties: + _version: + type: integer + _latest_version: + type: integer + - type: object + properties: + _id: + type: string + creator_id: + type: string + collection_id: + type: string + document_id: + type: string + annotation: + type: array + items: + anyOf: + - type: string + example: documentlabel + description: String for labels on the entire document. + - type: array + items: + anyOf: + - type: string + - type: integer + example: + - 1 + - 2 + - textlabel + description: >- + Array for individual annotations + [start_index, end_index, label] + _links: + type: object + properties: *ref_9 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: &ref_11 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '404': + description: Document with given ID was not found. + content: &ref_12 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + post: + summary: Save My Annotations + description: > + Change annotations of a document. + + + Example: `curl -X PUT + http://localhost:5000/annotations/mine/by_document_id/60d08052f2cb44c51e0af0f1 + --cookie session.cookie -H "Content-type: application/json" -d + '{"doc":["sci.crypt", + "talk.politics.misc"],"ner":[{"end":365,"start":346, "label":"sci.med"}, + {"start":475, "end":530, "label":"alt.atheism"}]}'` + + + _Note_: start or end indices in the middle of words might make the UI + not show the label. + + Also, invalid labels are not checked and might cause the UI to freeze. + operationId: annotations_save_mine + tags: + - annotations + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + - name: update_iaa + in: query + required: false + description: Whether to also update IAA reports. + schema: + type: boolean + default: true + requestBody: + description: The labels to add to the document. + required: true + content: + application/json: + schema: + type: object + properties: &ref_13 + doc: + description: Document-level annotations. + type: array + items: + description: Annotation label. + type: string + ner: + description: NER annotations. + type: array + items: + type: object + properties: + start: + description: 'Start index, inclusive.' + type: integer + end: + description: 'End index, exclusive.' + type: integer + label: + description: Annotation label. + type: string + example: &ref_14 + doc: + - label1 + - label2 + ner: + - start: 0 + end: 10 + label: in-text-label + responses: + '200': + description: >- + Successfully found document and changed annotations (returns + doc_id). + content: + application/json: + schema: + type: string + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/annotations/mine/by_collection_id/{collection_id}': + post: + summary: Set Collection Annotations + description: > + Modify annotations of certain documents in a given collection. + + + Example: `curl -X POST + http://localhost:5000/annotations/mine/by_collection_id/60d32ba28d34cf656fed503f + --cookie session.cookie -H "Content-type: application/json" -d + '{"60d32ba48d34cf656fed504b": {"doc":["sci.crypt", + "talk.politics.misc"],"ner":[[0,4,"sci.med"], [0,4,"alt.atheism"]]}, + "60d32ba48d34cf656fed504c": {"doc":[], "ner":[[0,4,"sci.med"]]}}'` + operationId: annotations_collection + tags: + - annotations + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: &ref_21 + type: string + - name: batch_mode + required: true + description: > + Whether or not to send all annotations to the database as one batch + or individually. + + + _Note_: Batch mode should ONLY be used if all of the documents have + not already been annotated. + + + The versioning of eve will be messed up if batch mode annotates a + document with pre-existing annotations (even if old). + + + To be clear, even if a document had annotations that were deleted, + using batch mode on that document will cause problems. + + + Conversely, using individual mode (batch_mode = False) can always be + done, but will be slower. + + + Another issue with individual mode is with many documents, there + will be many backend queries, possibly getting rate limited. + schema: + type: boolean + default: true + in: query + - name: update_iaa + in: query + required: false + description: Whether to also update IAA reports. + schema: + type: boolean + default: true + requestBody: + description: The labels to add to the document. + required: true + content: + application/json: + schema: + description: Mapping from document ID to annotations object. + type: object + additionalProperties: + type: object + properties: *ref_13 + example: *ref_14 + example: + 60d47b4bdbfddb3ca87c7971: + doc: + - label1 + - label2 + ner: + - - 0 + - 10 + - label1 + - - 15 + - 18 + - label2 + responses: + '200': + description: >- + Successfully found document and changed annotations (returns + annotation ids). + content: + application/json: + schema: + type: array + items: + type: string + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: &ref_23 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/annotations/others/by_document_id/{doc_id}': + get: + summary: Get Others' Document Annotations + description: > + Get a list of annotations done by everyone but me on a document. + + + Example: `curl -X GET + http://localhost:5000/annotations/others/by_document_id/60d08052f2cb44c51e0af0f1 + --cookie session.cookie` + operationId: annotations_others + tags: + - annotations + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + responses: + '200': + description: Successfully found document and got annotations. + content: + application/json: + schema: + type: object + properties: *ref_15 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/annotations/by_document_id/{doc_id}': + get: + summary: Get All Document Annotations + description: > + Get a list of annotations done by everyone on a document. + + + Example: `curl -X GET + http://localhost:5000/annotations/by_document_id/60d08052f2cb44c51e0af0f1 + --cookie session.cookie` + operationId: annotations_all + tags: + - annotations + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + responses: + '200': + description: Successfully found document and got annotations. + content: + application/json: + schema: + type: object + properties: *ref_15 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /auth/module: + get: + summary: Get Auth Module + description: | + Get the current auth module being used (vegas or eve). + + Example: `curl -X GET http://localhost:5000/auth/module` + operationId: auth_get_module + tags: + - auth + responses: + '200': + description: Successfully got the auth module. + content: + application/json: + schema: + type: string + enum: + - eve + - vegas + /auth/flat: + get: + summary: Get Auth Is Flat + description: > + Return true if the current auth module is flat. + + + "Flat" auth means, generally, there are no administrators and + permissions are generally on + + the same "level". Collection-level permissions for viewing/annotating + still apply, however. + + + Example: `curl -X GET http://localhost:5000/auth/flat` + operationId: auth_get_flat + tags: + - auth + responses: + '200': + description: Successfully return a boolean if the auth module was flat. + content: + application/json: + schema: + type: boolean + /auth/can_manage_users: + get: + summary: Get Auth Can Manage Users + description: > + Return true if the current auth module supports managing users. + + + If `true`, the auth module can change, add, and delete users. If + `false`, users are managed + + by an external system. + + + Example: `curl -X GET http://localhost:5000/auth/flat` + operationId: auth_get_manage + tags: + - auth + responses: + '200': + description: >- + Successfully return a boolean if the auth module supports managing + users. + content: + application/json: + schema: + type: boolean + /auth/logged_in_user: + get: + summary: Get Logged In User + description: > + Get the currently logged in user (checks based on the session - need the + session cookie sent). + + If there is no user logged, in `null` is returned. + + + Example: `curl -X GET http://localhost:5000/auth/logged_in_user --cookie + session.cookie` + operationId: auth_logged_in_user + tags: + - auth + responses: + '200': + description: >- + Successfully returned the logged in user (or null if no session + cookie). + content: + application/json: + schema: + oneOf: + - type: string + nullable: true + default: null + - type: object + properties: &ref_18 + display_name: + type: string + id: + type: string + is_admin: + type: boolean + username: + type: string + example: &ref_19 + display_name: Ada Lovelace + id: ada + is_admin: false + username: ada@pine.jhuapl.edu + /auth/logged_in_user_details: + get: + summary: Get Logged In User Details + description: > + Get the currently logged in user's details. + + + Example: `curl -X GET http://localhost:5000/auth/logged_in_user_details + --cookie session.cookie` + operationId: auth_user_details + security: + - cookieAuth: [] + tags: + - auth + responses: + '200': + description: Successfully returned the logged in user details. + content: + application/json: + schema: + type: object + properties: &ref_16 + description: + type: string + first_name: + type: string + last_name: + type: string + example: &ref_17 + first_name: Ada + last_name: Lovelace + description: The first computer programmer. + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + post: + summary: Update Logged In User Details with Eve + description: | + Updates the user details for the logged in user. + + _Note_: this endpoint is only exposed if using "eve" auth module. + operationId: auth_eve_update_user_details + security: + - cookieAuth: [] + tags: + - auth_eve + requestBody: + content: + application/json: + schema: + type: object + properties: *ref_16 + example: *ref_17 + responses: + '200': + description: Successfully updated user details. + content: + application/json: + schema: + type: boolean + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + /auth/login_form: + get: + summary: Get the login form. + description: > + For auth modules that use a form to login, this endpoint will return the + information needed + + to present that form to the user and send back the necessary info in a + subsequent login + + call. + + + Example: `curl -X GET http://localhost:5000/auth/login_form` + operationId: auth_login_form + tags: + - auth + responses: + '200': + description: Successfully returned the login form. + content: + application/json: + schema: + description: Information needed to display a login form. + type: object + properties: &ref_44 + button_text: + description: Text to set in the login button. + type: string + fields: + description: Form fields to use. + type: array + items: + type: object + properties: + display: + description: Display name. + type: string + name: + description: Form name. + type: string + type: + description: Form type. + type: string + example: &ref_45 + button_text: Login + fields: + - display: Username or email + name: username + type: text + - display: Password + name: password + type: password + /auth/logout: + post: + summary: Logout + description: > + Logout of the current session. + + + Example: `curl -X POST http://localhost:5000/auth/logout --cookie + session.cookie` + operationId: auth_logout + tags: + - auth + security: + - cookieAuth: [] + responses: + '200': + description: Successfully logged out. + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + /auth/login: + post: + summary: Login User + description: > + Logs in user. How this works depends on the auth module used. + + + For eve: this takes a request body consisting of the login form data. + + + For vegas: this takes in no parameters and returns the URL the caller + should redirect to. + operationId: auth_login + tags: + - auth_eve + - auth_vegas + parameters: + - name: return_to + in: query + required: false + description: 'For vegas auth only, a URL to return to after auth flow.' + schema: + type: string + format: url + requestBody: + required: false + content: + application/json: + schema: + description: Only for eve login. + type: object + properties: &ref_46 + username: + type: string + password: + type: string + responses: + '200': + description: > + For eve: successfully logged in, returns user information. + + + For vegas: starts auth flow and returns the URL that the caller + should redirect to. + content: + application/json: + schema: + oneOf: + - type: object + properties: *ref_18 + example: *ref_19 + - type: string + format: url + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: >- + Given user doesn't exist, password isn't set, or password doesn't + match. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + /auth/users: + get: + summary: Get Eve Users + description: | + Gets all users that are registered with eve. + + _Note_: this endpoint is only exposed if using "eve" auth module. + operationId: auth_eve_users + tags: + - auth_eve + security: + - cookieAuth: [] + responses: + '200': + description: Returns all users. + content: + application/json: + schema: + type: array + items: + type: object + properties: *ref_18 + example: *ref_19 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + /auth/logged_in_user_password: + post: + summary: Update Eve User Password + description: | + Updates the password of the currently logged in eve user. + + _Note_: this endpoint is only exposed if using "eve" auth module. + operationId: auth_eve_update_password + tags: + - auth_eve + security: + - cookieAuth: [] + requestBody: + content: + application/json: + schema: + type: object + properties: &ref_47 + current_password: + type: string + new_password: + type: string + responses: + '200': + description: Successfully changed password. + content: + application/json: + schema: + type: boolean + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: 'Not logged in, or current password doesn''t match.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + /auth/authorize: + get: + summary: Authorize From Fragment + description: > + Part of the OAuth flow, this will authorize based on passed-in query + parameters. + + + _Note_: this endpoint is only exposed if using "vegas" auth module. + operationId: auth_vegas_authorize_get + tags: + - auth_vegas + parameters: + - name: fragment + in: query + required: true + description: OAuth flow fragment. + schema: + type: string + responses: + '200': + description: 'Successfully logged in, returns user information.' + content: + application/json: + schema: + type: object + properties: *ref_18 + example: *ref_19 + '400': + description: 'Fragment is not valid, or parsed token is not valid.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + post: + summary: Authorize From Token + description: > + Authorize diretly based on an obtained vegas token, outside the normal + OAuth flow. + + This is meant to make it easy to authenticate using vegas and then use + this API outside of + + the web UI. + + + _Note_: this endpoint is only exposed if using "vegas" auth module. + operationId: auth_vegas_authorize_post + tags: + - auth_vegas + requestBody: + description: Token obtained from Vegas. + required: true + content: + application/json: + schema: + description: An auth token obtained by Vegas out-of-band from PINE. + type: object + properties: &ref_48 + auth_token: + type: string + token_type: + type: string + additionalProperties: &ref_49 {} + responses: + '200': + description: 'Successfully logged in, returns user information.' + content: + application/json: + schema: + type: object + properties: *ref_18 + example: *ref_19 + '400': + description: Token is not valid. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + /collections/unarchived: + get: + summary: Get Unarchived Collections + description: > + Get all unarchived collections for logged in user. + + + Example: `curl http://localhost:5000/collections/unarchived --cookie + session.cookie` + operationId: collections_get_unarchived_all + tags: + - collections + responses: + '200': + description: Successfully retrieved relevant collections. + content: + application/json: + schema: + type: object + properties: &ref_20 + _items: + type: array + items: + type: object + properties: &ref_22 + _id: + type: string + creator_id: + type: string + metadata: + type: object + additionalProperties: {} + configuration: + type: object + additionalProperties: {} + labels: + type: array + items: + type: string + viewers: + type: array + items: + type: string + annotators: + type: array + items: + type: string + archived: + type: boolean + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/unarchived/{page}': + get: + summary: Get Paginated Unarchived Collections + description: > + Get unarchived user collections (either all or a certain page). + + + Example: `curl http://localhost:5000/collections/unarchived --cookie + session.cookie` + operationId: collections_get_unarchived_paginated + tags: + - collections + parameters: + - name: page + in: path + required: true + description: > + Optional page number for specifying which collections. "all" for + all pages or a page number. + schema: + oneOf: + - type: string + default: all + - type: integer + responses: + '200': + description: Successfully retrieved relevant collections. + content: + application/json: + schema: + type: object + properties: *ref_20 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /collections/archived: + get: + summary: Get Archived Collections + description: > + Get all archived user collections. + + + Example: `curl http://localhost:5000/collections/archived --cookie + session.cookie` + operationId: collections_get_archived_all + tags: + - collections + responses: + '200': + description: Successfully retrieved relevant collections. + content: + application/json: + schema: + type: object + properties: *ref_20 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/archived/{page}': + get: + summary: Get Paginated Archived Collections + description: > + Get archived user collections (either all or a certain page). + + + Example: `curl http://localhost:5000/collections/archived --cookie + session.cookie` + operationId: collections_get_archived_paginated + tags: + - collections + parameters: + - name: page + in: path + required: true + description: > + Optional page number for specifying which collections. "all" for + all pages or a page number. + schema: + oneOf: + - type: string + default: all + - type: integer + responses: + '200': + description: Successfully retrieved relevant collections. + content: + application/json: + schema: + type: object + properties: *ref_20 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/archive/{collection_id}': + put: + summary: Archive Collection + description: > + Archive a collection with a certain ID. + + + Example: `curl -X PUT + http://localhost:5000/collections/archive/60c7b7375b72bf4ed6523bf0 + --cookie session.cookie` + operationId: collections_archive + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully archived the chosen collection. + content: + application/json: + schema: + type: object + properties: *ref_22 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/unarchive/{collection_id}': + put: + summary: Unarchive Collection + description: > + Unarchive a collection with a certain ID. + + + Example: `curl -X PUT + http://localhost:5000/collections/unarchive/60c7b7375b72bf4ed6523bf0 + --cookie session.cookie` + operationId: collections_unarchive + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully unarchived the chosen collection. + content: + application/json: + schema: + type: object + properties: *ref_22 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/by_id/{collection_id}': + get: + summary: Get Collection + description: > + Retrieve a collection by its ID. + + + Example: `curl -X GET + http://localhost:5000/collections/by_id/60c7b7375b72bf4ed6523bf0 + --cookie session.cookie` + operationId: collections_get + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully found and rerieved the chosen collection. + content: + application/json: + schema: + type: object + properties: *ref_22 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/by_id/{collection_id}/download': + get: + summary: Download Collection Data + description: > + Download a collection's data by its ID. + + + Example: `curl -X GET + http://localhost:5000/collections/by_id/60c7b7375b72bf4ed6523bf0/download + --cookie session.cookie` + operationId: collections_download + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully found and downloaded the chosen collection. + content: + application/json: + schema: + type: object + properties: *ref_22 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/add_annotator/{collection_id}': + post: + summary: Add Collection Annotator + description: > + Add an annotator by user_id to a specific collection. + + + Example: `curl --cookie session.cookie -X POST + "http://localhost:5000/collections/add_annotator/60c7453d5b72bf4ed65239e9" + -F 'user_id="\"bob\""'` + + + Notice the quotes around the user_id value, NEEDS to be like that to + include the "" in the + + request session.cookie is a file containing: "Set-cookie: + session=.eJy...(rest of cookie)". + operationId: collections_add_annotator + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + user_id: + type: string + description: > + Note: You must put double quotation marks (`""`) around the + user_id for the backend to parse it correctly as it is a + JSON string. For example, enter `"ada"` instead of just + `ada`. + required: + - user_id + responses: + '200': + description: Successfully added the user as an annotator to the collection. + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '400': + description: 'Request malformed, probably missisng user_id arg.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + '409': + description: Specified user is already an annotator. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '500': + description: Internal server error - the form data was probably malformed. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + security: + - cookieAuth: [] + '/collections/add_viewer/{collection_id}': + post: + summary: Add Collection Viewer + description: > + Add a viewer by user_id to a specific collection. + + + Example: `curl --cookie session.cookie -X POST + "http://localhost:5000/collections/add_viewer/60c7453d5b72bf4ed65239e9" + -F 'user_id="\"bob\""'` + + + Notice the quotes around the user_id value, NEEDS to be like that to + include the "" in the + + request. session.cookie is a file containing: "Set-cookie: + session=.eJy...(rest of cookie)" + operationId: addViewerToCollection + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + user_id: + type: string + description: >- + Note: You must put double quotation marks ("") around the + user_id for the backend to parse it correctly. + + + Ex: enter "ada" instead of just ada + required: + - user_id + responses: + '200': + description: Successfully added the user as a viewer to the collection. + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '400': + description: 'Request malformed, probably missisng user_id arg.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + '409': + description: Specified user is already an viewer. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '500': + description: Internal server error - the form data was probably malformed. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + security: + - cookieAuth: [] + '/collections/add_label/{collection_id}': + post: + summary: Add Collection Label + description: > + Add a label to a specific collection. + + + Example: `curl --cookie session.cookie -X POST + "http://localhost:5000/collections/add_label/60c7453d5b72bf4ed65239e9" + -F 'new_label="\"testlabel\""'` + + + Notice the quotes around the new_label value, NEEDS to be like that to + include the "" in the + + request. session.cookie is a file containing: "Set-cookie: + session=.eJy...(rest of cookie)" + operationId: collections_add_label + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + new_label: + type: string + description: > + Note: You must put double quotation marks (`""`) around the + new_label for the backend to parse it correctly. Ex: enter + `"MyLabel"` instead of just `MyLabel` + required: + - new_label + responses: + '200': + description: Successfully added the label to the collection. + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '400': + description: 'Request malformed, probably missisng new_label arg.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + '409': + description: Specified label is already in collection. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '500': + description: Internal server error - the form data was probably malformed. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + security: + - cookieAuth: [] + /collections: + post: + summary: Create Collection + description: > + Create a new collection. + + + Example: `curl --cookie session.cookie -X POST + "http://localhost:5000/collections" -F 'collection={"creator_id":"ada", + "annotators":["ada"], "labels":["label1", + "labellll"],"metadata":{"title":"newcoll11","subject":null,"description":"describe + blahblah"}}' -F 'overlap="\".9\""' -F 'train_every="\"100\""' -F + 'pipelineId="\"5babb6ee4eb7dd2c39b9671d\""'` + + + Notice the quotes around some value, NEEDS to be like that to include + the "" in the request + + to be parsed as a JSON string. session.cookie is a file containing: + + "Set-cookie: session=.eJy...(rest of cookie)" + operationId: collections_create + tags: + - collections + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: &ref_50 + collection: + description: >- + At minimum, this must include creator_id, annotators, + viewers and labels. All other args or sub-args should be + deleted or set to null value. + + + creator_id MUST be a valid user, otherwise 500 Error will + occur. + type: object + properties: + creator_id: + type: string + annotators: + type: array + items: + type: string + viewers: + type: array + items: + type: string + labels: + type: array + items: + type: string + archived: + type: boolean + default: false + metadata: + type: object + properties: + title: + type: string + subject: + type: string + description: + type: string + publisher: + type: string + contributor: + type: string + date: + type: string + type: + type: string + format: + type: string + identifier: + type: string + source: + type: string + language: + type: string + relation: + type: string + coverage: + type: string + rights: + type: string + configuration: + type: object + properties: + allow_overlapping_ner_annotations: + type: boolean + default: true + example: + creator_id: ada + annotators: + - ada + viewers: + - ada + - margaret + labels: + - label1 + - label2 + archived: false + metadata: + title: Test + subject: testcoll + description: test collection + publisher: ada + contributor: ada + date: 1/1/21 + type: sometype + format: HTML + identifier: ABCD + source: apl + language: english + relation: family + coverage: some + rights: all of them + configuration: + allow_overlapping_ner_annotations: true + train_every: + description: Should be an integer >= 5. + type: integer + minimum: 5 + overlap: + description: > + Should be a float between 0 and 1. + + + WARNING: You MUST put double quotation marks (`""`) around + the number for the backend to + + parse it correctly. + + + Ex: enter `".5"` instead of just `.5` + type: number + format: float + minimum: 0 + maximum: 1 + pipelineId: + type: string + description: > + WARNING: You MUST put double quotation marks (`""`) around + the id for the backend to + + parse it correctly. + + + Ex: enter `"123abc..."` instead of just `123abc...` + classifierParameters: + type: string + format: object + default: null + required: &ref_51 + - collection + - train_every + - overlap + - pipelineId + responses: + '201': + description: Successfully created the collection. + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '400': + description: Request malformed. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: 'Authentication failed, not logged in.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '500': + description: Error in syntax of the request - OR Wekzeug Authentication Failure. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + security: + - cookieAuth: [] + '/collections/static_images/{collection_id}': + get: + summary: Get Collection Static Images + description: > + Retrieve all static images used in a collection. + + + Example: `curl --cookie session.cookie -X GET + "http://localhost:5000/collections/static_images/60c745395b72bf4ed6523821"` + operationId: collections_get_static_images + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: >- + Successfully found the collection and got any relevant static + images. + content: + application/json: + schema: + type: array + description: An array of static image paths. + items: + type: string + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/images/{collection_id}': + get: + summary: Get Collection Images + description: > + Retrieve all (non-static) images used in a collection. + + + Example: `curl --cookie session.cookie -X GET + "http://localhost:5000/collections/images/60c745395b72bf4ed6523821"` + operationId: collections_get_images + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully found the collection and got any relevant images. + content: + application/json: + schema: + type: array + description: An array of image paths. + items: + type: string + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/image_exists/{collection_id}/{path}': + get: + summary: Check Collection Image + description: > + Checks whether the given image exists in the given collection. + + + Example: `curl -X GET + "http://localhost:5000/collections/image_exists/60c745395b72bf4ed6523821/static%2Fapl.png" + -H "accept: application/json" --cookie session.cookie` + operationId: collections_image_exists + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + - name: path + in: path + required: true + description: >- + Path of the image to check (same as returned from + images/static_images). + schema: + type: string + example: static/apl.jpg + responses: + '200': + description: Returns whether the collection holds the image. + content: + application/json: + schema: + type: boolean + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/image/{collection_id}/{path}': + get: + summary: Get Collection Image + description: > + Download an image from a collection. + + + Example: `curl --cookie session.cookie -X GET + "http://localhost:5000/collections/image/60c745395b72bf4ed6523821/static/apl.png" + -v --output - > apl.png` + operationId: collections_image + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + - name: path + in: path + required: true + description: >- + Path of the image to download (same as returned from + images/static_images). + schema: + type: string + example: static/apl.jpg + responses: + '200': + description: Successfully found the collection and returns image data. + content: + image/*: + schema: + type: string + format: binary + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + post: + summary: Upload Collection Image + description: > + Upload an image to a collection. + + + Example: `curl --cookie session.cookie -X POST + "http://localhost:5000/collections/image/60c745395b72bf4ed6523821/static/dog.jpeg" + -F 'file=@/home/pine/Downloads/dog.jpeg'` + operationId: collections_image_upload + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + - name: path + in: path + required: true + description: > + Path to place the image at. + + + Note: This path piece should NOT start with / (Ex: static/dog.jpg, + not /static/dog.jpg). + schema: + type: string + requestBody: + content: + multipart/form-data: + schema: + type: object + properties: + file: + type: string + format: binary + required: + - file + responses: + '100': + description: 'Couldn''t read the image, probably bad permissions or bad path.' + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '200': + description: Successfully uploaded image (Will return the path). + content: + application/json: + schema: + type: string + '400': + description: Did not include the image in the request form. + content: + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/collections/user_permissions/{collection_id}': + get: + summary: Get Collection User Permissions + description: > + Get the current user permissions of a collection. + + + Example: `curl --cookie session.cookie -X GET + "http://localhost:5000/collections/user_permissions/60c745395b72bf4ed6523821" + -v` + operationId: collections_permissions + tags: + - collections + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Returns collection permissions for logged in user. + content: + application/json: + schema: + type: object + properties: &ref_27 + add_documents: + type: boolean + add_images: + type: boolean + annotate: + type: boolean + archive: + type: boolean + download_data: + type: boolean + modify_document_metadata: + type: boolean + modify_labels: + type: boolean + modify_users: + type: boolean + view: + type: boolean + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/documents/by_id/{doc_id}': + get: + summary: Get Document + description: > + Retrieve a document based on its ID. + + + Example: `curl + http://localhost:5000/documents/by_id/60c7453f5b72bf4ed65239ee --cookie + session.cookie` + operationId: documents_get + tags: + - documents + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + responses: + '200': + description: Successfully found the document based on the ID. + content: + application/json: + schema: + type: object + properties: &ref_25 + _id: + type: string + creator_id: + type: string + collection_id: + type: string + overlap: + type: integer + format: int64 + metadata: + type: object + additionalProperties: {} + text: + type: string + has_annotated: + type: object + additionalProperties: + type: boolean + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + '500': + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + delete: + summary: Delete Document + description: > + Delete a document based on its ID. + + + This endpoint deletes a document and any annotations. It also updates + any next_instances so + + that the document will not be returned for annotation in any "get next + instance" calls in + + the future. It does NOT delete document data from any pipeline models + or update any IAA + + reports or pipeline metrics. These will be updated next time they are + requested. + + + Example: `curl -X DELETE + http://localhost:5000/documents/by_id/60c7453f5b72bf4ed65239ee --cookie + session.cookie` + operationId: documents_delete + tags: + - documents + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + responses: + '200': + description: 'Deletion successful, response has IDs of changed objects.' + content: + application/json: + schema: + type: object + properties: &ref_24 + success: + type: boolean + description: Whether the operation was successful. + changed_objs: + type: object + description: What database objects were changed during operation. + properties: + next_instances: + type: object + properties: + updated: + description: IDs of next_instance objects that were updated. + type: array + items: + type: string + annotations: + type: object + properties: + deleted: + description: IDs of annotation objects that were deleted. + type: array + items: + type: string + documents: + type: object + properties: + deleted: + description: IDs of document objects that were deleted. + type: array + items: + type: string + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + '500': + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /documents/by_ids: + delete: + summary: Delete Documents + description: > + Delete documents based on their IDs. + + + This endpoint deletes documents and any associated annotations. It also + updates any next_instances so + + that the documents will not be returned for annotation in any "get next + instance" calls in + + the future. It does NOT delete document data from any pipeline models + or update any IAA + + reports or pipeline metrics. These will be updated next time they are + requested. + + + Example: `curl -X DELETE + http://localhost:5000/documents/by_ids?ids=60c7453f5b72bf4ed65239ee,60c7453f5b72bf4ed65239ef + --cookie session.cookie` + operationId: documents_delete_multiple + tags: + - documents + parameters: + - name: ids + in: query + required: true + description: 'The IDs of the document to delete, comma-separated.' + schema: + type: string + example: '60c7453f5b72bf4ed65239ee,60c7453f5b72bf4ed65239ef' + responses: + '200': + description: 'Deletion successful, response has IDs of changed objects.' + content: + application/json: + schema: + type: object + properties: *ref_24 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + '500': + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/documents/count_by_collection_id/{collection_id}': + get: + summary: Get Collection Document Count + description: > + Count the number of documents in a collection. + + + Example: `curl + http://localhost:5000/documents/count_by_collection_id/60c7453d5b72bf4ed65239e9 + --cookie session.cookie` + operationId: documents_count_by_collection + tags: + - documents + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: >- + Successfully found collection and counted number of documents + inside. + content: + application/json: + schema: + type: integer + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/documents/by_collection_id_all/{collection_id}': + get: + summary: Get All Collection Documents + description: > + Get all documents that are in a collection with a given collection id. + + + Example: `curl + http://localhost:5000/documents/by_collection_id_all/60c7453d5b72bf4ed65239e9 + --cookie session.cookie` + operationId: documents_get_by_collection + tags: + - documents + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully found collection and retrieved all related documents. + content: + application/json: + schema: + type: object + properties: &ref_26 + _items: + type: array + items: + type: object + properties: *ref_25 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/documents/by_collection_id_paginated/{collection_id}': + get: + summary: Get Paginated Collection Documents + description: > + Get a variable page of variable size of documents. + + + Example: `curl + "http://localhost:5000/documents/by_collection_id_paginated/60c7453d5b72bf4ed65239e9?page=1&pageSize=5" + --cookie session.cookie` + operationId: documents_get_by_collection_paginated + tags: + - documents + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + - name: page + in: query + required: true + description: > + The page number to get by 0 indexing (Will have documents + page_num*pageSize -> page_num*pageSize+pageSize-1 in the collection + if there are any.) + schema: + type: integer + - name: pageSize + in: query + required: true + description: The number of documents to put in each page. + schema: + type: integer + responses: + '200': + description: > + Successfully found collection and retrieved any (if any) associated + documents (Could return no documents if page number too high). + content: + application/json: + schema: + type: object + properties: *ref_26 + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/documents/user_permissions/{doc_id}': + get: + summary: Get User Document Permissions + description: > + Get the permission that the logged in user has for this document. + + + Example: `curl + http://localhost:5000/documents/user_permissions/60c7453f5b72bf4ed65239ee + --cookie session.cookie` + operationId: documents_permissions + tags: + - documents + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + responses: + '200': + description: Successfully found document and retrieved user permissions. + content: + application/json: + schema: + type: object + properties: *ref_27 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/documents/metadata/{doc_id}': + put: + summary: Update Document Metadata + description: > + Change/Replace the metadata of a certain document (does not add). + + + Example: `curl -X PUT + http://localhost:5000/documents/metadata/60c7453f5b72bf4ed65239ee -d + '{"test":"this"}' --cookie session.cookie -H + Content-Type:application/json` + + + Note: you need the content type header to specify json. + operationId: documents_update_metadata + tags: + - documents + parameters: + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + requestBody: + description: The metadata in json form in the body. + required: true + content: + application/json: + schema: + type: object + additionalProperties: {} + responses: + '200': + description: Successfully found document and changed the metadata. + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Document with given ID was not found. + content: *ref_12 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /documents: + post: + summary: Create Document + description: > + Create a new document in a collection. + + + Example: `curl -X POST http://localhost:5000/documents/ -d + '{"collection_id":"6ada", "text":"blah"}' --cookie session.cookie -H + Content-Type:application/json` + operationId: documents_create + tags: + - documents + requestBody: + required: true + content: + application/json: + schema: + oneOf: + - description: >- + Arguments for the new document (at least collection_id, + creator_id, text). + type: object + properties: &ref_28 + collection_id: + type: string + creator_id: + type: string + text: + type: string + overlap: + type: number + format: double + metadata: + type: object + additionalProperties: {} + has_annotated: + type: object + additionalProperties: + type: boolean + required: &ref_29 + - collection_id + - creator_id + - text + - type: array + items: + description: >- + Arguments for the new document (at least collection_id, + creator_id, text). + type: object + properties: *ref_28 + required: *ref_29 + responses: + '200': + description: Successfully created the new document in the collection. + content: + application/json: + schema: + description: > + This object is returned when doing actions like modifying a + document or collection. It contains the ID of the object and + some other information from the database. + allOf: *ref_5 + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/iaa_reports/by_collection_id/{collection_id}': + get: + summary: Get IAA Report for Collection + description: > + Get the Inter-Annotator Agreement for a specified collection. + + + Note: This will not error with an invalid collection ID, it will give no + items. + + + Example: `curl -X GET + http://localhost:5000/iaa_reports/by_collection_id/60df138b3f8fa7b2e1445bd7 + --cookie ~/session.cookie -v` + operationId: iaa_get + tags: + - iaa_reports + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully got collection's IAA. + content: + application/json: + schema: + type: object + properties: + _items: + type: array + items: + allOf: &ref_56 + - allOf: *ref_30 + - type: object + properties: + _id: + type: string + collection_id: + type: string + num_of_annotators: + type: integer + num_of_agreement_docs: + type: integer + num_of_labels: + type: integer + per_doc_agreement: + type: object + properties: + doc_id: + type: string + avg: + type: number + format: double + stddev: + type: integer + per_label_agreement: + type: array + items: + type: object + properties: + label: + type: string + avg: + type: number + format: double + stddev: + type: integer + overall_agreement: + type: object + properties: + mean: + type: number + format: double + sd: + type: integer + heatmap_data: + type: object + properties: + matrix: + type: array + items: + type: array + items: + type: number + format: float + minItems: 2 + maxItems: 2 + example: + - 1 + - 0.666666 + annotators: + type: array + items: + type: string + example: + - ada + - margaret + labels_per_annotator: + type: object + additionalProperties: + type: object + additionalProperties: + type: integer + example: + ada: + label1: 1 + label2: 4 + margaret: + label1: 3 + label2: 2 + _updated: + type: string + format: date-time + _created: + type: string + format: date-time + _links: + type: object + properties: *ref_9 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + post: + summary: Create IAA Report for Collection + description: > + Create an Inter-Annotator-Agreement for a collection. + + + Note: This will not error with an invalid collection ID (or not enough + annotators), it will + + return false. + + + Example: `curl -X POST + http://localhost:5000/iaa_reports/by_collection_id/60df138b3f8fa7b2e1445bd7 + --cookie ~/session.cookie -v` + operationId: iaa_create + tags: + - iaa_reports + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: | + Tried to create the IAA (success or fail). + + False means invalid collection ID or not enough annotators. + content: + application/json: + schema: + type: boolean + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /pipelines: + get: + summary: Get Pipelines + description: > + Get all pipelines. + + + Example: `curl -X GET http://localhost:5000/pipelines/ --cookie + ~/session.cookie` + operationId: pipelines_get_all + tags: + - pipelines + responses: + '200': + description: Successfully got pipelines. + content: + application/json: + schema: + type: object + properties: + _items: + type: array + items: + allOf: &ref_31 + - type: object + properties: *ref_8 + - type: object + properties: + _id: + type: string + title: + type: string + description: + type: string + name: + type: string + parameters: + type: object + additionalProperties: {} + example: + cutoff: integer + iterations: ' integer' + n_iter: integer + dropout: float + max_left: integer + use_class_feature: + - true + - false + use_word: + - true + - false + use_ngrams: + - true + - false + no_mid_ngrams: + - true + - false + max_ngram_length: integer + use_prev: + - true + - false + use_next: + - true + - false + use_disjunctive: + - true + - false + use_sequences: + - true + - false + use_prev_sequences: + - true + - false + use_type_seqs: + - true + - false + use_type_seqs2: + - true + - false + use_type_y_sequences: + - true + - false + _updated: + type: string + format: date-time + _created: + type: string + format: date-time + _links: + type: object + properties: *ref_9 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/by_id/{pipeline_id}': + get: + summary: Get Pipeline + description: > + Get the pipeline with the given ID. + + + Example: `curl -X GET + http://localhost:5000/pipelines/by_id/5babb6ee4eb7dd2c39b9671f --cookie + ~/session.cookie -v` + operationId: pipelines_get + tags: + - pipelines + parameters: + - name: pipeline_id + in: path + required: true + description: The id of the pipeline on which to operate. + schema: &ref_35 + type: string + responses: + '200': + description: Successfully got specified pipeline. + content: + application/json: + schema: + allOf: *ref_31 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Pipeline with given ID was not found. + content: &ref_36 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/classifiers/by_collection_id/{collection_id}': + get: + summary: Get Collection Classifier + description: > + Get the classifier information for a collection. + + + Example: `curl -X GET + http://localhost:5000/pipelines/classifiers/by_collection_id/60db2cacdbfddb3ca87c845d + --cookie ~/session.cookie` + operationId: pipelines_get_collection_classifier + tags: + - pipelines + parameters: + - name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + responses: + '200': + description: Successfully found collection and got information. + content: + application/json: + schema: + allOf: &ref_52 + - allOf: *ref_30 + - type: object + properties: + _id: + type: string + _created: + type: string + format: date-time + _updated: + type: string + format: date-time + annotated_document_count: + type: integer + collection_id: + type: string + labels: + type: array + items: + type: string + overlap: + type: number + format: double + parameters: + type: object + additionalProperties: {} + pipeline_id: + type: string + train_every: + type: integer + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Collection with given ID was not found. + content: *ref_23 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + /pipelines/metrics: + get: + summary: Get Collection Metrics + description: > + Get metrics for all available collections. + + + Example: `curl -X GET http://localhost:5000/pipelines/metrics --cookie + ~/session.cookie` + operationId: pipelines_get_metrics + tags: + - pipelines + responses: + '200': + description: Successfully got metrics. + content: + application/json: + schema: + type: object + properties: + _items: + type: array + items: + type: object + properties: &ref_32 + _id: + type: string + collection_id: + type: string + classifier_id: + type: string + documents: + type: array + items: {} + annotations: + type: array + items: {} + folds: + type: array + items: {} + metrics: + type: array + items: {} + _updated: + type: string + _created: + type: string + _version: + type: integer + _etag: + type: string + _links: + type: object + properties: + self: + type: object + properties: + title: + type: string + href: + type: string + _links: + type: object + properties: *ref_9 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/metrics/by_classifier_id/{classifier_id}': + get: + summary: Get Classifier Metrics + description: > + Get metric by classifier id. + + + Example: `curl -X GET + http://localhost:5000/pipelines/metrics/by_classifier_id/60df138b3f8fa7b2e1445bd8 + --cookie ~/session.cookie` + operationId: pipelines_get_classifier_metrics + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: &ref_33 + type: string + responses: + '200': + description: Successfully got metric(s). + content: + application/json: + schema: + type: object + properties: + _items: + type: array + items: + type: object + properties: *ref_32 + _links: + type: object + properties: *ref_9 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: &ref_34 + application/json: + schema: + description: Error message from the server. + type: string + example: Error message from the server. + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/next_document/by_classifier_id/{classifier_id}': + get: + summary: Get Next Document to Annotate + description: > + Get the next document id to annotate based on classifier id (or null if + no un-annotated + + documents). + + + Example: `curl -X GET + http://localhost:5000/pipelines/next_document/by_classifier_id/60df138b3f8fa7b2e1445bd8 + --cookie ~/session.cookie` + operationId: pipelines_get_next_document + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 + responses: + '200': + description: 'Got ID of next document to annotate, or null if all are complete.' + content: + application/json: + schema: + type: string + nullable: true + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: *ref_34 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/next_document/by_classifier_id/{classifier_id}/{doc_id}': + post: + summary: Advance Next Document + description: > + Advance to next document by marking the given one as annotated. + + + Example: `curl -X POST + http://localhost:5000/pipelines/next_document/by_classifier_id/60df138b3f8fa7b2e1445bd8/60df13d73f8fa7b2e1445bdd + --cookie ~/session.cookie` + + + This will still give you a valid response with an invalid document ID. + operationId: pipelines_advance_next_document + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 + - name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + responses: + '200': + description: Complete annotations on document. + content: + application/json: + schema: + type: object + properties: + body: + type: object + nullable: true + success: + type: boolean + trained: + type: boolean + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: *ref_34 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/status/{pipeline_id}': + get: + summary: Get Pipeline Status + description: > + Get the status of the pipeline with the given ID. + + + Example: `curl -X GET + http://localhost:5000/pipelines/status/60df138b3f8fa7b2e1445bd8 --cookie + ~/session.cookie` + operationId: pipelines_get_status + tags: + - pipelines + parameters: + - name: pipeline_id + in: path + required: true + description: The id of the pipeline on which to operate. + schema: *ref_35 + responses: + '200': + description: Returns the status for the given pipeline. + content: + application/json: + schema: + type: object + properties: &ref_37 + service_details: + description: Information about the pipeline service. + type: object + properties: + channel: + type: string + framework: + type: string + framework_types: + type: array + items: + type: string + name: + type: string + version: + type: string + format: version + job_id: + description: The ID of this pipeline job. + type: string + format: uuid + job_request: + description: The job request data submitted to pipelines. + type: object + properties: &ref_38 + job_id: + description: The ID of this pipeline job. + type: string + format: uuid + job_queue: + type: string + job_type: + type: string + job_data: + type: object + properties: + framework: + type: string + type: + description: The type of job. + type: string + classifier_id: + type: string + nullable: true + additionalProperties: + description: Any additional job parameters. + job_response: + description: The job request data received from pipelines. + type: object + properties: + pipeline_name: + type: string + eve_entry_point: + type: string + model_dir: + type: string + format: path + classifier: + description: Status of the classifier. + type: object + has_trained: + description: Whether the classifier has trained. + type: boolean + classifier_id: + description: Will not be present for pipeline status. + type: string + nullable: true + classifier_class: + description: Python class for this classifier. + type: string + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Pipeline with given ID was not found. + content: *ref_36 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/classifiers/status/{classifier_id}': + get: + summary: Get Classifier Status + description: > + Get the status of the classifier with the given ID. + + + Example: `curl -X GET + http://localhost:5000/pipelines/classifiers/status/60df138b3f8fa7b2e1445bd8 + --cookie ~/session.cookie` + operationId: pipelines_get_classifier_status + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 + responses: + '200': + description: Returns the status for the given classifier. + content: + application/json: + schema: + type: object + properties: *ref_37 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: *ref_34 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/running_jobs/{classifier_id}': + get: + summary: Get Classifier Running Jobs + description: > + Get any currently running jobs of the classifier with the given ID. + + + Example: `curl -X GET + http://localhost:5000/pipelines/running_jobs/60df138b3f8fa7b2e1445bd8 + --cookie ~/session.cookie` + operationId: pipelines_get_running_jobs + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 + responses: + '200': + description: Returns the all currently running jobs for the classifier. + content: + application/json: + schema: + type: array + items: + type: string + format: uuid + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: *ref_34 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/train/{classifier_id}': + post: + summary: Train Classifier + description: > + Trains the classifier based on currently annotated documents in the + collection. + + + This endpoint is _ASYNCHRONOUS_ in that it will return information about + the submitted job + + rather than any results from the job. + + + Example: `curl -X POST + http://localhost:5000/pipelines/train/60df138b3f8fa7b2e1445bd8 --cookie + session.cookie` + operationId: pipelines_train + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 + requestBody: + content: + application/json: + schema: + type: object + properties: + model_name: + description: Optional name to save the model for future reference. + type: string + responses: + '200': + description: Returns the all currently running jobs for the classifier. + content: + application/json: + schema: + type: object + properties: + request: + description: The job request data submitted to pipelines. + type: object + properties: *ref_38 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: *ref_34 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] + '/pipelines/predict/{classifier_id}': + post: + summary: Predict Using Classifier + description: > + Uses the given classifier to predict annotations for the given + document(s). + + + Example: `curl -X POST + http://localhost:5000/pipelines/predict/60df138b3f8fa7b2e1445bd8 + --cookie session.cookie` + operationId: pipelines_predict + tags: + - pipelines + parameters: + - name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 + requestBody: + content: + application/json: + schema: + description: Either document_ids or texts must be given and non-empty. + type: object + properties: &ref_53 + document_ids: + description: IDs of documents to predict annotations for. + type: array + items: + type: string + default: [] + texts: + description: Text of documents to predict annotations for. + type: array + items: + type: string + default: [] + timeout_in_s: + description: >- + If provided, will wait this long before timing out on the + job. + type: integer + default: 36000 + responses: + '200': + description: Returns the predictions and other job information. + content: + application/json: + schema: + description: Pipeline predictions and other job information. + type: object + properties: &ref_54 + job_id: + type: string + format: uuid + job_request: + description: The job request data submitted to pipelines. + type: object + properties: *ref_38 + job_response: + type: object + properties: + documents_by_id: + description: >- + Predictions in a mapping from document ID to + annotations. + type: object + additionalProperties: + type: object + properties: &ref_39 + doc: + description: Document-level annotations. + type: array + items: + description: Annotation label. + type: string + example: + - label1 + - label2 + ner: + description: 'NER annotations. [startIndex, endIndex, label].' + type: array + items: + type: array + items: + oneOf: + - type: string + - type: integer + example: + - 5 + - 10 + - label1 + texts: + description: >- + Predictions for manual texts in the same order as they + were in the input. + type: array + items: + type: object + properties: *ref_39 + '400': + description: Input parameters are missing/invalid. + content: *ref_6 + '401': + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + '404': + description: Classifier with given ID was not found. + content: *ref_34 + default: + description: 'Unexpected error, check server logs.' + content: *ref_1 + security: + - cookieAuth: [] +components: + securitySchemes: + cookieAuth: + description: > + This an example command to provision and print the session key using + eve: + + + `curl -X POST -H "Content-Type:application/json" -d + '{"username":"ada@pine.jhuapl.edu","password":"ada@pine.jhuapl.edu"}' + http://localhost:5000/auth/login --cookie-jar - --output /dev/null + --silent | grep -o -P "session\s.+" | sed -e 's/session\s/session=/' -` + type: apiKey + in: cookie + name: session + schemas: + UserRoles: + description: The role (for permissions) of the user. + type: array + items: *ref_4 + NewUserData: + type: object + properties: *ref_40 + required: *ref_41 + UpdateUserData: + type: object + properties: *ref_42 + required: *ref_43 + WrappedAnnotations: + type: object + properties: *ref_15 + LoginForm: + description: Information needed to display a login form. + type: object + properties: *ref_44 + example: *ref_45 + EveLogin: + description: Only for eve login. + type: object + properties: *ref_46 + EvePasswordChange: + type: object + properties: *ref_47 + VegasAuthToken: + description: An auth token obtained by Vegas out-of-band from PINE. + type: object + properties: *ref_48 + additionalProperties: *ref_49 + WrappedCollections: + type: object + properties: *ref_20 + NewCollection: + type: object + properties: *ref_50 + required: *ref_51 + WrappedDocuments: + type: object + properties: *ref_26 + NewDocument: + description: >- + Arguments for the new document (at least collection_id, creator_id, + text). + type: object + properties: *ref_28 + required: *ref_29 + Classifier: + allOf: *ref_52 + PipelineJobRequest: + description: The job request data submitted to pipelines. + type: object + properties: *ref_38 + PipelineOrClassifierStatus: + type: object + properties: *ref_37 + PipelinePredictParameters: + description: Either document_ids or texts must be given and non-empty. + type: object + properties: *ref_53 + PipelineDocumentPredictions: + type: object + properties: *ref_39 + PipelinePredictions: + description: Pipeline predictions and other job information. + type: object + properties: *ref_54 + ErrorResponse: + description: Error message from the server. + type: string + example: Error message from the server. + UserInfo: + type: object + properties: *ref_2 + EveBase: + type: object + properties: *ref_8 + EveLinks: + type: object + properties: *ref_9 + IDInfo: + description: > + This object is returned when doing actions like modifying a document or + collection. It contains the ID of the object and some other information + from the database. + allOf: *ref_5 + EveBaseWithVersion: + allOf: *ref_30 + UserDocumentAnnotation: + description: > + This is the log of annotations by a specific user. A document might + have 0, 1, or multiple of these based on how many users annotated. + allOf: *ref_55 + DocumentAnnotations: + type: object + properties: *ref_13 + example: *ref_14 + AuthUser: + type: object + properties: *ref_18 + example: *ref_19 + AuthUserDetails: + type: object + properties: *ref_16 + example: *ref_17 + Collection: + type: object + properties: *ref_22 + UserPermissions: + type: object + properties: *ref_27 + Document: + type: object + properties: *ref_25 + DocumentDeletionResponse: + type: object + properties: *ref_24 + InterAnnotatorAgreement: + allOf: *ref_56 + Pipeline: + allOf: *ref_31 + CollectionMetric: + type: object + properties: *ref_32 + responses: + UnexpectedServerError: + description: 'Unexpected error, check server logs.' + content: *ref_1 + NotAuthorizedOrNotAdmin: + description: 'Authentication failed, not logged in or not an admin.' + content: *ref_0 + InvalidInputParameters: + description: Input parameters are missing/invalid. + content: *ref_6 + MismatchedEtag: + description: Given etag did not match the most updated stored one. + content: *ref_57 + Success: + description: Whether the operation succeeded or failed. + content: *ref_7 + NotAuthorized: + description: > + Authentication failed: not logged in or user doesn't have the + permissions for this operation. + content: *ref_11 + DocumentNotFound: + description: Document with given ID was not found. + content: *ref_12 + CollectionNotFound: + description: Collection with given ID was not found. + content: *ref_23 + PipelineNotFound: + description: Pipeline with given ID was not found. + content: *ref_36 + ClassifierNotFound: + description: Classifier with given ID was not found. + content: *ref_34 + parameters: + userIdParam: + name: user_id + in: path + required: true + description: ID of the user on which to operate. + schema: *ref_3 + docIdParam: + name: doc_id + in: path + required: true + description: The id of the document on which to operate. + schema: *ref_10 + collectionIdParam: + name: collection_id + in: path + required: true + description: The id of the collection on which to operate. + schema: *ref_21 + pipelineIdParam: + name: pipeline_id + in: path + required: true + description: The id of the pipeline on which to operate. + schema: *ref_35 + classifierIdParam: + name: classifier_id + in: path + required: true + description: The id of the classifier on which to operate. + schema: *ref_33 +tags: + - name: admin + description: > + Operations in the "admin" blueprint. These operations are generally only + available when the "eve" auth module is running and are only accessible to + logged-in users that are administrators. + x-displayName: admin + - name: annotations + description: Operations in the "annotations" blueprint. + x-displayName: annotations + - name: auth + description: Operations in the "auth" blueprint. + x-displayName: auth + - name: auth_eve + description: These operations are only available if using "eve" auth module. + x-displayName: auth_eve + - name: auth_vegas + description: These operations are only available if using "vegas" auth module. + x-displayName: auth_vegas + - name: collections + description: Operations in the "collections" blueprint. + x-displayName: collections + - name: documents + description: Operations in the "documents" blueprint. + x-displayName: documents + - name: iaa_reports + description: Operations in the "iaa_reports" blueprint. + x-displayName: iaa_reports + - name: pipelines + description: Operations in the "pipelines" blueprint. + x-displayName: pipelines +x-tagGroups: + - name: openapi + tags: + - admin + - annotations + - auth + - auth_eve + - auth_vegas + - collections + - documents + - iaa_reports + - pipelines diff --git a/backend/pine/backend/api/swagger-ui/VERSION b/backend/pine/backend/api/swagger-ui/VERSION new file mode 100644 index 0000000..ca25ff6 --- /dev/null +++ b/backend/pine/backend/api/swagger-ui/VERSION @@ -0,0 +1 @@ +3.50.0 diff --git a/backend/pine/backend/api/swagger-ui/favicon-16x16.png b/backend/pine/backend/api/swagger-ui/favicon-16x16.png new file mode 100644 index 0000000..8b194e6 Binary files /dev/null and b/backend/pine/backend/api/swagger-ui/favicon-16x16.png differ diff --git a/backend/pine/backend/api/swagger-ui/favicon-32x32.png b/backend/pine/backend/api/swagger-ui/favicon-32x32.png new file mode 100644 index 0000000..249737f Binary files /dev/null and b/backend/pine/backend/api/swagger-ui/favicon-32x32.png differ diff --git a/backend/pine/backend/api/swagger-ui/index.html b/backend/pine/backend/api/swagger-ui/index.html new file mode 100644 index 0000000..5bb4812 --- /dev/null +++ b/backend/pine/backend/api/swagger-ui/index.html @@ -0,0 +1,60 @@ + + + + + + Swagger UI + + + + + + + +
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+
+
+
+ +
+

pine.backend.api.bp

+
+

Module Contents

+
+

Functions

+ ++++ + + + + + + + + + + + + + + +

openapi_spec()

swagger_ui_index()

swagger_ui(file: str)

init_app(app)

+
+
+pine.backend.api.bp.bp
+
+ +
+
+pine.backend.api.bp.LOGGER
+
+ +
+
+pine.backend.api.bp.openapi_spec()
+
+ +
+
+pine.backend.api.bp.swagger_ui_index()
+
+ +
+
+pine.backend.api.bp.swagger_ui(file: str)
+
+ +
+
+pine.backend.api.bp.init_app(app)
+
+ +
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/docs/build/html/autoapi/pine/backend/api/index.html b/docs/build/html/autoapi/pine/backend/api/index.html new file mode 100644 index 0000000..341babc --- /dev/null +++ b/docs/build/html/autoapi/pine/backend/api/index.html @@ -0,0 +1,139 @@ + + + + + + + + + pine.backend.api — pine documentation + + + + + + + + + + + + + + + + + + +
+
+
+
+ +
+

pine.backend.api

+

This module implements all methods required for SwaggerUI to run on the +backend of PINE.

+
+

Submodules

+
+ +
+
+
+ + +
+
+
+
+ +
+
+ + + + \ No newline at end of file diff --git a/docs/build/html/autoapi/pine/backend/auth/index.html b/docs/build/html/autoapi/pine/backend/auth/index.html index 20afaff..1ae7a53 100644 --- a/docs/build/html/autoapi/pine/backend/auth/index.html +++ b/docs/build/html/autoapi/pine/backend/auth/index.html @@ -19,7 +19,7 @@ - +