From b7c62d0ac8e55ab3f23eb00402c4eead7b0343e4 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sat, 3 Dec 2022 12:03:10 +0100 Subject: [PATCH 01/12] Add script that can dump openapi schema without a running galaxy --- lib/galaxy/webapps/galaxy/fast_app.py | 28 ++++++++++++++++++++++++-- scripts/dump_openapi_schema.py | 29 +++++++++++++++++++++++++++ 2 files changed, 55 insertions(+), 2 deletions(-) create mode 100644 scripts/dump_openapi_schema.py diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py index 648c9d7412c..6ad0a5517c6 100644 --- a/lib/galaxy/webapps/galaxy/fast_app.py +++ b/lib/galaxy/webapps/galaxy/fast_app.py @@ -1,3 +1,8 @@ +from typing import ( + Any, + Dict, +) + from a2wsgi import WSGIMiddleware from fastapi import ( FastAPI, @@ -142,12 +147,31 @@ def include_legacy_openapi(app, gx_app): return app.openapi_schema -def initialize_fast_app(gx_wsgi_webapp, gx_app): - app = FastAPI( +def get_fastapi_instance() -> FastAPI: + return FastAPI( title="Galaxy API", docs_url="/api/docs", openapi_tags=api_tags_metadata, ) + + +def get_openapi_schema() -> Dict[str, Any]: + """ + Dumps openAPI schema without starting a full app and webserver. + """ + app = get_fastapi_instance() + include_all_package_routers(app, "galaxy.webapps.galaxy.api") + return get_openapi( + title=app.title, + version=app.version, + openapi_version=app.openapi_version, + description=app.description, + routes=app.routes, + ) + + +def initialize_fast_app(gx_wsgi_webapp, gx_app): + app = get_fastapi_instance() add_exception_handler(app) add_galaxy_middleware(app, gx_app) add_request_id_middleware(app) diff --git a/scripts/dump_openapi_schema.py b/scripts/dump_openapi_schema.py new file mode 100644 index 00000000000..fc7ff469742 --- /dev/null +++ b/scripts/dump_openapi_schema.py @@ -0,0 +1,29 @@ +import json +import os +import sys + +sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib"))) + +import click +import yaml + +from galaxy.webapps.galaxy.fast_app import get_openapi_schema + + +@click.command("Write openapi schema to path") +@click.argument("schema_path", type=click.Path(dir_okay=False, writable=True), required=False) +def write_open_api_schema(schema_path): + openapi_schema = get_openapi_schema() + if schema_path: + if schema_path.endswith((".yml", ".yml")): + with open(schema_path, "w") as f: + yaml.safe_dump(openapi_schema, f) + else: + with open(schema_path, "w") as f: + json.dump(openapi_schema, f, sort_keys=True) + else: + print(json.dumps(openapi_schema, sort_keys=True)) + + +if __name__ == "__main__": + write_open_api_schema() From 7b864a8c458362d162ced06a37cf1c106b68af06 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 4 Dec 2022 21:06:41 +0100 Subject: [PATCH 02/12] Add makefile target to update autogenerated client --- Makefile | 5 +++- client/package.json | 2 ++ client/yarn.lock | 59 ++++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 64 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index ca88e90de8a..62972721db6 100644 --- a/Makefile +++ b/Makefile @@ -168,7 +168,10 @@ ifndef YARN else cd client && yarn install $(YARN_INSTALL_OPTS) endif - + + +update-client-api-schema: node-deps + $(IN_VENV) cd client && python ../scripts/dump_openapi_schema.py | yarn run openapi-typescript --output src/schema/schema.ts && npx prettier --write src/schema/schema.ts client: node-deps ## Rebuild client-side artifacts for local development. cd client && yarn run build diff --git a/client/package.json b/client/package.json index 2d275fa459c..9f493a09502 100644 --- a/client/package.json +++ b/client/package.json @@ -67,6 +67,8 @@ "markdown-it": "^12.3.2", "markdown-it-regexp": "^0.4.0", "object-hash": "^3.0.0", + "openapi-typescript": "^6.1.0", + "openapi-typescript-fetch": "^1.1.3", "pinia": "^2.0.23", "pinia-plugin-persistedstate": "^2.4.0", "popper.js": "^1.16.1", diff --git a/client/yarn.lock b/client/yarn.lock index 3cb54acb123..238cb3c8dc8 100644 --- a/client/yarn.lock +++ b/client/yarn.lock @@ -2495,6 +2495,11 @@ ansi-colors@^1.0.1: dependencies: ansi-wrap "^0.1.0" +ansi-colors@^4.1.3: + version "4.1.3" + resolved "https://registry.yarnpkg.com/ansi-colors/-/ansi-colors-4.1.3.tgz#37611340eb2243e70cc604cad35d63270d48781b" + integrity sha512-/6w/C21Pm1A7aZitlI5Ni/2J6FFQN8i1Cvz3kHABAAbw93v/NlvKdVOqz7CCWz/3iv/JplRSEEZ83XION15ovw== + ansi-escapes@^4.2.1: version "4.3.2" resolved "https://registry.yarnpkg.com/ansi-escapes/-/ansi-escapes-4.3.2.tgz#6b2291d1db7d98b6521d5f1efa42d0f3a9feb65e" @@ -3154,6 +3159,13 @@ buffer@^6.0.3: base64-js "^1.3.1" ieee754 "^1.2.1" +busboy@^1.6.0: + version "1.6.0" + resolved "https://registry.yarnpkg.com/busboy/-/busboy-1.6.0.tgz#966ea36a9502e43cdb9146962523b92f531f6893" + integrity sha512-8SFQbg/0hQ9xy3UNTB0YEnsNBbWfhf7RtnzpL7TkBiTBRfrQ9Fxcnz7VJsleJpyp6rVLvXiuORqjlHi5q+PYuA== + dependencies: + streamsearch "^1.1.0" + bytes@3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/bytes/-/bytes-3.0.0.tgz#d32815404d689699f85a4ea4fa8755dd13a96048" @@ -4820,6 +4832,17 @@ fast-deep-equal@^3.1.1, fast-deep-equal@^3.1.3: resolved "https://registry.yarnpkg.com/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz#3a7d56b559d6cbc3eb512325244e619a65c6c525" integrity sha512-f3qQ9oQy9j2AhBe/H9VC91wLmKBCCU/gDOnKNAYG5hswO7BLKj09Hc5HYNz9cGI++xlpDCIgDaitVs03ATR84Q== +fast-glob@^3.2.12: + version "3.2.12" + resolved "https://registry.yarnpkg.com/fast-glob/-/fast-glob-3.2.12.tgz#7f39ec99c2e6ab030337142da9e0c18f37afae80" + integrity sha512-DVj4CQIYYow0BlaelwK1pHl5n5cRSJfM60UA0zK891sVInoPri2Ekj7+e1CT3/3qxXenpI+nBBmQAcJPJgaj4w== + dependencies: + "@nodelib/fs.stat" "^2.0.2" + "@nodelib/fs.walk" "^1.2.3" + glob-parent "^5.1.2" + merge2 "^1.3.0" + micromatch "^4.0.4" + fast-glob@^3.2.9: version "3.2.11" resolved "https://registry.yarnpkg.com/fast-glob/-/fast-glob-3.2.11.tgz#a1172ad95ceb8a16e20caa5c5e56480e5129c1d9" @@ -7850,6 +7873,23 @@ open@^8.0.9: is-docker "^2.1.1" is-wsl "^2.2.0" +openapi-typescript-fetch@^1.1.3: + version "1.1.3" + resolved "https://registry.yarnpkg.com/openapi-typescript-fetch/-/openapi-typescript-fetch-1.1.3.tgz#354e6803b7885c7142ae11adc1b758afafd8aa2e" + integrity sha512-smLZPck4OkKMNExcw8jMgrMOGgVGx2N/s6DbKL2ftNl77g5HfoGpZGFy79RBzU/EkaO0OZpwBnslfdBfh7ZcWg== + +openapi-typescript@^6.1.0: + version "6.1.0" + resolved "https://registry.yarnpkg.com/openapi-typescript/-/openapi-typescript-6.1.0.tgz#404d94ea8598f757c526f9a414e66ba96c050dad" + integrity sha512-4G0hQu9zXHESZe4fZouucmA+6J5oKSBNYzG0gPbV9V4aKBNIwfUY86ur/cxyTMzuN9vQuAiMe//q4ZMXgMvGtQ== + dependencies: + ansi-colors "^4.1.3" + fast-glob "^3.2.12" + js-yaml "^4.1.0" + supports-color "^9.2.3" + undici "^5.12.0" + yargs-parser "^21.1.1" + optionator@^0.8.1: version "0.8.3" resolved "https://registry.yarnpkg.com/optionator/-/optionator-0.8.3.tgz#84fa1d036fe9d3c7e21d99884b601167ec8fb495" @@ -9553,6 +9593,11 @@ streamroller@^3.1.2: debug "^4.3.4" fs-extra "^8.1.0" +streamsearch@^1.1.0: + version "1.1.0" + resolved "https://registry.yarnpkg.com/streamsearch/-/streamsearch-1.1.0.tgz#404dd1e2247ca94af554e841a8ef0eaa238da764" + integrity sha512-Mcc5wHehp9aXz1ax6bZUyY5afg9u2rv5cqQI3mRrYkGC8rW2hM02jWuwjtL++LS5qinSyhj2QfLyNsuc+VsExg== + string-length@^4.0.1: version "4.0.2" resolved "https://registry.yarnpkg.com/string-length/-/string-length-4.0.2.tgz#a8a8dc7bd5c1a82b9b3c8b87e125f66871b6e57a" @@ -9703,6 +9748,11 @@ supports-color@^8.0.0: dependencies: has-flag "^4.0.0" +supports-color@^9.2.3: + version "9.2.3" + resolved "https://registry.yarnpkg.com/supports-color/-/supports-color-9.2.3.tgz#a6e2c97fc20c80abecd69e50aebe4783ff77d45a" + integrity sha512-aszYUX/DVK/ed5rFLb/dDinVJrQjG/vmU433wtqVSD800rYsJNWxh2R3USV90aLSU+UsyQkbNeffVLzc6B6foA== + supports-hyperlinks@^2.0.0: version "2.2.0" resolved "https://registry.yarnpkg.com/supports-hyperlinks/-/supports-hyperlinks-2.2.0.tgz#4f77b42488765891774b70c79babd87f9bd594bb" @@ -10137,6 +10187,13 @@ undertaker@^1.2.1: object.reduce "^1.0.0" undertaker-registry "^1.0.0" +undici@^5.12.0: + version "5.13.0" + resolved "https://registry.yarnpkg.com/undici/-/undici-5.13.0.tgz#56772fba89d8b25e39bddc8c26a438bd73ea69bb" + integrity sha512-UDZKtwb2k7KRsK4SdXWG7ErXiL7yTGgLWvk2AXO1JMjgjh404nFo6tWSCM2xMpJwMPx3J8i/vfqEh1zOqvj82Q== + dependencies: + busboy "^1.6.0" + unicode-canonical-property-names-ecmascript@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/unicode-canonical-property-names-ecmascript/-/unicode-canonical-property-names-ecmascript-2.0.0.tgz#301acdc525631670d39f6146e0e77ff6bbdebddc" @@ -10912,7 +10969,7 @@ yargs-parser@^20.2.2: resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== -yargs-parser@^21.0.1: +yargs-parser@^21.0.1, yargs-parser@^21.1.1: version "21.1.1" resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== From 1192bb542871a47bb65beb73019c2ea90a0ca8db Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 6 Dec 2022 13:14:37 +0100 Subject: [PATCH 03/12] Add generated schema --- client/src/schema/fetcher.ts | 6 + client/src/schema/index.ts | 2 + client/src/schema/schema.ts | 14045 +++++++++++++++++++++++++++++++++ 3 files changed, 14053 insertions(+) create mode 100644 client/src/schema/fetcher.ts create mode 100644 client/src/schema/index.ts create mode 100644 client/src/schema/schema.ts diff --git a/client/src/schema/fetcher.ts b/client/src/schema/fetcher.ts new file mode 100644 index 00000000000..b6fc3819fb4 --- /dev/null +++ b/client/src/schema/fetcher.ts @@ -0,0 +1,6 @@ +import { paths } from "./schema"; +import { Fetcher } from "openapi-typescript-fetch"; +import { getAppRoot } from "onload/loadConfig"; + +export const fetcher = Fetcher.for(); +fetcher.configure({ baseUrl: getAppRoot() }); diff --git a/client/src/schema/index.ts b/client/src/schema/index.ts new file mode 100644 index 00000000000..b0301ae534a --- /dev/null +++ b/client/src/schema/index.ts @@ -0,0 +1,2 @@ +export type { components, operations, paths } from "./schema"; +export { fetcher } from "./fetcher"; diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts new file mode 100644 index 00000000000..8aba6eee8da --- /dev/null +++ b/client/src/schema/schema.ts @@ -0,0 +1,14045 @@ +/** + * This file was auto-generated by openapi-typescript. + * Do not make direct changes to the file. + */ + +export interface paths { + "/api/configuration": { + /** + * Return an object containing exposable configuration settings + * @description Return an object containing exposable configuration settings. + * + * A more complete list is returned if the user is an admin. + * Pass in `view` and a comma-seperated list of keys to control which + * configuration settings are returned. + */ + get: operations["index_api_configuration_get"]; + }; + "/api/configuration/decode/{encoded_id}": { + /** + * Decode a given id + * @description Decode a given id. + */ + get: operations["decode_id_api_configuration_decode__encoded_id__get"]; + }; + "/api/configuration/dynamic_tool_confs": { + /** + * Return dynamic tool configuration files + * @description Return dynamic tool configuration files. + */ + get: operations["dynamic_tool_confs_api_configuration_dynamic_tool_confs_get"]; + }; + "/api/configuration/tool_lineages": { + /** + * Return tool lineages for tools that have them + * @description Return tool lineages for tools that have them. + */ + get: operations["tool_lineages_api_configuration_tool_lineages_get"]; + }; + "/api/configuration/toolbox": { + /** + * Reload the Galaxy toolbox (but not individual tools) + * @description Reload the Galaxy toolbox (but not individual tools). + */ + put: operations["reload_toolbox_api_configuration_toolbox_put"]; + }; + "/api/dataset_collections": { + /** Create a new dataset collection instance. */ + post: operations["create_api_dataset_collections_post"]; + }; + "/api/dataset_collections/{hdca_id}/contents/{parent_id}": { + /** Returns direct child contents of indicated dataset collection parent ID. */ + get: operations["contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get"]; + }; + "/api/dataset_collections/{id}": { + /** Returns detailed information about the given collection. */ + get: operations["show_api_dataset_collections__id__get"]; + }; + "/api/dataset_collections/{id}/attributes": { + /** Returns `dbkey`/`extension` attributes for all the collection elements. */ + get: operations["attributes_api_dataset_collections__id__attributes_get"]; + }; + "/api/dataset_collections/{id}/copy": { + /** Copy the given collection datasets to a new collection using a new `dbkey` attribute. */ + post: operations["copy_api_dataset_collections__id__copy_post"]; + }; + "/api/dataset_collections/{id}/download": { + /** + * Download the content of a dataset collection as a `zip` archive. + * @description Download the content of a history dataset collection as a `zip` archive + * while maintaining approximate collection structure. + */ + get: operations["download_dataset_collection_api_dataset_collections__id__download_get"]; + }; + "/api/dataset_collections/{id}/prepare_download": { + /** + * Prepare an short term storage object that the collection will be downloaded to. + * @description The history dataset collection will be written as a `zip` archive to the + * returned short term storage object. Progress tracking this file's creation + * can be tracked with the short_term_storage API. + */ + post: operations["prepare_collection_download_api_dataset_collections__id__prepare_download_post"]; + }; + "/api/dataset_collections/{id}/suitable_converters": { + /** Returns a list of applicable converters for all datatypes in the given collection. */ + get: operations["suitable_converters_api_dataset_collections__id__suitable_converters_get"]; + }; + "/api/datasets": { + /** Search datasets or collections using a query system. */ + get: operations["index_api_datasets_get"]; + /** + * Deletes or purges a batch of datasets. + * @description Deletes or purges a batch of datasets. + * **Warning**: only the ownership of the datasets (and upload state for HDAs) is checked, + * no other checks or restrictions are made. + */ + delete: operations["delete_batch_api_datasets_delete"]; + }; + "/api/datasets/{dataset_id}": { + /** + * Displays information about and/or content of a dataset. + * @description **Note**: Due to the multipurpose nature of this endpoint, which can receive a wild variety of parameters + * and return different kinds of responses, the documentation here will be limited. + * To get more information please check the source code. + */ + get: operations["show_api_datasets__dataset_id__get"]; + }; + "/api/datasets/{dataset_id}/converted": { + /** + * Return a a map with all the existing converted datasets associated with this instance. + * @description Return a map of ` : ` containing all the *existing* converted datasets. + */ + get: operations["converted_api_datasets__dataset_id__converted_get"]; + }; + "/api/datasets/{dataset_id}/converted/{ext}": { + /** + * Return information about datasets made by converting this dataset to a new format. + * @description Return information about datasets made by converting this dataset to a new format. + * + * If there is no existing converted dataset for the format in `ext`, one will be created. + * + * **Note**: `view` and `keys` are also available to control the serialization of the dataset. + */ + get: operations["converted_ext_api_datasets__dataset_id__converted__ext__get"]; + }; + "/api/datasets/{dataset_id}/get_content_as_text": { + /** Returns dataset content as Text. */ + get: operations["get_content_as_text_api_datasets__dataset_id__get_content_as_text_get"]; + }; + "/api/datasets/{dataset_id}/hash": { + /** Compute dataset hash for dataset and update model */ + put: operations["compute_hash_api_datasets__dataset_id__hash_put"]; + }; + "/api/datasets/{dataset_id}/inheritance_chain": { + /** For internal use, this endpoint may change without warning. */ + get: operations["show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get"]; + }; + "/api/datasets/{dataset_id}/permissions": { + /** + * Set permissions of the given history dataset to the given role ids. + * @description Set permissions of the given history dataset to the given role ids. + */ + put: operations["update_permissions_api_datasets__dataset_id__permissions_put"]; + }; + "/api/datasets/{dataset_id}/storage": { + /** Display user-facing storage details related to the objectstore a dataset resides in. */ + get: operations["show_storage_api_datasets__dataset_id__storage_get"]; + }; + "/api/datasets/{history_content_id}/display": { + /** + * Displays (preview) or downloads dataset content. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + get: operations["display_api_datasets__history_content_id__display_get"]; + /** + * Check if dataset content can be previewed or downloaded. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + head: operations["display_api_datasets__history_content_id__display_head"]; + }; + "/api/datasets/{history_content_id}/metadata_file": { + /** Returns the metadata file associated with this history item. */ + get: operations["get_metadata_file_api_datasets__history_content_id__metadata_file_get"]; + }; + "/api/datatypes": { + /** + * Lists all available data types + * @description Gets the list of all available data types. + */ + get: operations["index_api_datatypes_get"]; + }; + "/api/datatypes/converters": { + /** + * Returns the list of all installed converters + * @description Gets the list of all installed converters. + */ + get: operations["converters_api_datatypes_converters_get"]; + }; + "/api/datatypes/edam_data": { + /** + * Returns a dictionary/map of datatypes and EDAM data + * @description Gets a map of datatypes and their corresponding EDAM data. + */ + get: operations["edam_data_api_datatypes_edam_data_get"]; + }; + "/api/datatypes/edam_data/detailed": { + /** + * Returns a dictionary of datatypes and EDAM data details + * @description Gets a map of datatypes and their corresponding EDAM data. + * EDAM data contains the EDAM iri, label, and definition. + */ + get: operations["edam_data_detailed_api_datatypes_edam_data_detailed_get"]; + }; + "/api/datatypes/edam_formats": { + /** + * Returns a dictionary/map of datatypes and EDAM formats + * @description Gets a map of datatypes and their corresponding EDAM formats. + */ + get: operations["edam_formats_api_datatypes_edam_formats_get"]; + }; + "/api/datatypes/edam_formats/detailed": { + /** + * Returns a dictionary of datatypes and EDAM format details + * @description Gets a map of datatypes and their corresponding EDAM formats. + * EDAM formats contain the EDAM iri, label, and definition. + */ + get: operations["edam_formats_detailed_api_datatypes_edam_formats_detailed_get"]; + }; + "/api/datatypes/mapping": { + /** + * Returns mappings for data types and their implementing classes + * @description Gets mappings for data types. + */ + get: operations["mapping_api_datatypes_mapping_get"]; + }; + "/api/datatypes/sniffers": { + /** + * Returns the list of all installed sniffers + * @description Gets the list of all installed data type sniffers. + */ + get: operations["sniffers_api_datatypes_sniffers_get"]; + }; + "/api/datatypes/types_and_mapping": { + /** + * Returns all the data types extensions and their mappings + * @description Combines the datatype information from (/api/datatypes) and the + * mapping information from (/api/datatypes/mapping) into a single + * response. + */ + get: operations["types_and_mapping_api_datatypes_types_and_mapping_get"]; + }; + "/api/folders/{folder_id}/contents": { + /** + * Returns a list of a folder's contents (files and sub-folders) with additional metadata about the folder. + * @description Returns a list of a folder's contents (files and sub-folders). + * + * Additional metadata for the folder is provided in the response as a separate object containing data + * for breadcrumb path building, permissions and other folder's details. + * + * *Note*: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting). + * + * **Security note**: + * - Accessing a library folder or sub-folder requires only access to the parent library. + * - Deleted folders can only be accessed by admins or users with `MODIFY` permission. + * - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders. + */ + get: operations["index_api_folders__folder_id__contents_get"]; + /** Creates a new library file from an existing HDA/HDCA. */ + post: operations["add_history_datasets_to_library_api_folders__folder_id__contents_post"]; + }; + "/api/folders/{id}": { + /** + * Displays information about a particular library folder. + * @description Returns detailed information about the library folder with the given ID. + */ + get: operations["show_api_folders__id__get"]; + /** + * Updates the information of an existing library folder. + * @description Updates the information of an existing library folder. + */ + put: operations["update_api_folders__id__put"]; + /** + * Create a new library folder underneath the one specified by the ID. + * @description Returns detailed information about the newly created library folder. + */ + post: operations["create_api_folders__id__post"]; + /** + * Marks the specified library folder as deleted (or undeleted). + * @description Marks the specified library folder as deleted (or undeleted). + */ + delete: operations["delete_api_folders__id__delete"]; + /** + * Update + * @description Updates the information of an existing library folder. + */ + patch: operations["update_api_folders__id__patch"]; + }; + "/api/folders/{id}/permissions": { + /** + * Gets the current or available permissions of a particular library folder. + * @description Gets the current or available permissions of a particular library. + * The results can be paginated and additionally filtered by a query. + */ + get: operations["get_permissions_api_folders__id__permissions_get"]; + /** + * Sets the permissions to manage a library folder. + * @description Sets the permissions to manage a library folder. + */ + post: operations["set_permissions_api_folders__id__permissions_post"]; + }; + "/api/ftp_files": { + /** + * Displays remote files available to the user. Please use /api/remote_files instead. + * @deprecated + * @description Lists all remote files available to the user from different sources. + */ + get: operations["index_api_ftp_files_get"]; + }; + "/api/genomes": { + /** Return a list of installed genomes */ + get: operations["index_api_genomes_get"]; + }; + "/api/genomes/{id}": { + /** Return information about build */ + get: operations["show_api_genomes__id__get"]; + }; + "/api/genomes/{id}/indexes": { + /** Return all available indexes for a genome id for provided type */ + get: operations["indexes_api_genomes__id__indexes_get"]; + }; + "/api/genomes/{id}/sequences": { + /** Return raw sequence data */ + get: operations["sequences_api_genomes__id__sequences_get"]; + }; + "/api/groups/{group_id}/roles": { + /** Displays a collection (list) of groups. */ + get: operations["index_api_groups__group_id__roles_get"]; + }; + "/api/groups/{group_id}/roles/{id}": { + /** Displays information about a group role. */ + get: operations["group_role_api_groups__group_id__roles__id__get"]; + }; + "/api/groups/{group_id}/roles/{role_id}": { + /** Adds a role to a group */ + put: operations["update_api_groups__group_id__roles__role_id__put"]; + /** Removes a role from a group */ + delete: operations["delete_api_groups__group_id__roles__role_id__delete"]; + }; + "/api/groups/{group_id}/user/{id}": { + /** + * Displays information about a group user. + * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Displays information about a group user. + */ + get: operations["group_user_api_groups__group_id__user__id__get"]; + }; + "/api/groups/{group_id}/user/{user_id}": { + /** + * Adds a user to a group + * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Adds a user to a group + */ + put: operations["update_api_groups__group_id__user__user_id__put"]; + /** + * Removes a user from a group + * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Removes a user from a group + */ + delete: operations["delete_api_groups__group_id__user__user_id__delete"]; + }; + "/api/groups/{group_id}/users": { + /** + * Displays a collection (list) of groups. + * @description GET /api/groups/{encoded_group_id}/users + * Displays a collection (list) of groups. + */ + get: operations["index_api_groups__group_id__users_get"]; + }; + "/api/groups/{group_id}/users/{id}": { + /** + * Displays information about a group user. + * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Displays information about a group user. + */ + get: operations["group_user_api_groups__group_id__users__id__get"]; + }; + "/api/groups/{group_id}/users/{user_id}": { + /** + * Adds a user to a group + * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Adds a user to a group + */ + put: operations["update_api_groups__group_id__users__user_id__put"]; + /** + * Removes a user from a group + * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Removes a user from a group + */ + delete: operations["delete_api_groups__group_id__users__user_id__delete"]; + }; + "/api/histories": { + /** Returns histories for the current user. */ + get: operations["index_api_histories_get"]; + /** + * Creates a new history. + * @description The new history can also be copied form a existing history or imported from an archive or URL. + */ + post: operations["create_api_histories_post"]; + }; + "/api/histories/deleted": { + /** Returns deleted histories for the current user. */ + get: operations["index_deleted_api_histories_deleted_get"]; + }; + "/api/histories/deleted/{id}/undelete": { + /** Restores a deleted history with the given ID (that hasn't been purged). */ + post: operations["undelete_api_histories_deleted__id__undelete_post"]; + }; + "/api/histories/from_store": { + /** Create histories from a model store. */ + post: operations["create_from_store_api_histories_from_store_post"]; + }; + "/api/histories/from_store_async": { + /** Launch a task to create histories from a model store. */ + post: operations["create_from_store_async_api_histories_from_store_async_post"]; + }; + "/api/histories/most_recently_used": { + /** Returns the most recently used history of the user. */ + get: operations["show_recent_api_histories_most_recently_used_get"]; + }; + "/api/histories/published": { + /** Return all histories that are published. */ + get: operations["published_api_histories_published_get"]; + }; + "/api/histories/shared_with_me": { + /** Return all histories that are shared with the current user. */ + get: operations["shared_with_me_api_histories_shared_with_me_get"]; + }; + "/api/histories/{history_id}/contents": { + /** + * Returns the contents of the given history. + * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``. + * + * - The contents can be filtered and queried using the appropriate parameters. + * - The amount of information returned for each item can be customized. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + get: operations["history_contents_api_histories__history_id__contents_get"]; + /** + * Batch update specific properties of a set items contained in the given History. + * @description Batch update specific properties of a set items contained in the given History. + * + * If you provide an invalid/unknown property key the request will not fail, but no changes + * will be made to the items. + */ + put: operations["update_batch_api_histories__history_id__contents_put"]; + /** + * Create a new `HDA` or `HDCA` in the given History. + * @deprecated + * @description Create a new `HDA` or `HDCA` in the given History. + */ + post: operations["create_api_histories__history_id__contents_post"]; + }; + "/api/histories/{history_id}/contents/archive/{filename}.{format}": { + /** + * Build and return a compressed archive of the selected history contents. + * @description Build and return a compressed archive of the selected history contents. + * + * **Note**: this is a volatile endpoint and settings and behavior may change. + */ + get: operations["archive_api_histories__history_id__contents_archive__filename___format__get"]; + }; + "/api/histories/{history_id}/contents/archive/{id}": { + /** + * Build and return a compressed archive of the selected history contents. + * @description Build and return a compressed archive of the selected history contents. + * + * **Note**: this is a volatile endpoint and settings and behavior may change. + */ + get: operations["archive_api_histories__history_id__contents_archive__id__get"]; + }; + "/api/histories/{history_id}/contents/bulk": { + /** + * Executes an operation on a set of items contained in the given History. + * @description Executes an operation on a set of items contained in the given History. + * + * The items to be processed can be explicitly set or determined by a dynamic query. + */ + put: operations["bulk_operation_api_histories__history_id__contents_bulk_put"]; + }; + "/api/histories/{history_id}/contents/dataset_collections/{id}/download": { + /** + * Download the content of a dataset collection as a `zip` archive. + * @description Download the content of a history dataset collection as a `zip` archive + * while maintaining approximate collection structure. + */ + get: operations["download_dataset_collection_api_histories__history_id__contents_dataset_collections__id__download_get"]; + }; + "/api/histories/{history_id}/contents/dataset_collections/{id}/prepare_download": { + /** + * Prepare an short term storage object that the collection will be downloaded to. + * @description The history dataset collection will be written as a `zip` archive to the + * returned short term storage object. Progress tracking this file's creation + * can be tracked with the short_term_storage API. + */ + post: operations["prepare_collection_download_api_histories__history_id__contents_dataset_collections__id__prepare_download_post"]; + }; + "/api/histories/{history_id}/contents/datasets/{id}/materialize": { + /** Materialize a deferred dataset into real, usable dataset. */ + post: operations["materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post"]; + }; + "/api/histories/{history_id}/contents/{dataset_id}/permissions": { + /** + * Set permissions of the given history dataset to the given role ids. + * @description Set permissions of the given history dataset to the given role ids. + */ + put: operations["update_permissions_api_histories__history_id__contents__dataset_id__permissions_put"]; + }; + "/api/histories/{history_id}/contents/{direction}/{hid}/{limit}": { + /** + * Get content items around a particular `HID`. + * @description .. warning:: For internal use to support the scroller functionality. + * + * This endpoint provides random access to a large history without having + * to know exactly how many pages are in the final query. Pick a target HID + * and filters, and the endpoint will get a maximum of `limit` history items "around" the `hid`. + * + * Additional counts are provided in the HTTP headers. + * + * The `direction` determines what items are selected: + * + * a) item counts: + * + * - total matches-up: hid < {hid} + * - total matches-down: hid > {hid} + * - total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid}) + * - displayed matches-up: hid <= {hid} (hid == {hid} is included) + * - displayed matches-down: hid > {hid} + * - displayed matches: displayed matches-up + displayed matches-down + * + * b) {limit} history items: + * + * - if direction == "before": hid <= {hid} + * - if direction == "after": hid > {hid} + * - if direction == "near": "near" {hid}, so that + * n. items before <= limit // 2, + * n. items after <= limit // 2 + 1. + * + * .. note:: This endpoint uses slightly different filter params syntax. Instead of using `q`/`qv` parameters, + * it uses the following syntax for query parameters:: + * + * ?[field]-[operator]=[value] + * + * Example:: + * + * ?update_time-gt=2015-01-29 + */ + get: operations["contents_near_api_histories__history_id__contents__direction___hid___limit__get"]; + }; + "/api/histories/{history_id}/contents/{history_content_id}/display": { + /** + * Displays (preview) or downloads dataset content. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + get: operations["history_contents_display_api_histories__history_id__contents__history_content_id__display_get"]; + /** + * Check if dataset content can be previewed or downloaded. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + head: operations["history_contents_display_api_histories__history_id__contents__history_content_id__display_head"]; + }; + "/api/histories/{history_id}/contents/{history_content_id}/extra_files": { + /** Generate list of extra files. */ + get: operations["extra_files_api_histories__history_id__contents__history_content_id__extra_files_get"]; + }; + "/api/histories/{history_id}/contents/{history_content_id}/metadata_file": { + /** Returns the metadata file associated with this history item. */ + get: operations["get_metadata_file_api_histories__history_id__contents__history_content_id__metadata_file_get"]; + }; + "/api/histories/{history_id}/contents/{id}": { + /** + * Return detailed information about an HDA within a history. + * @deprecated + * @description Return detailed information about an `HDA` or `HDCA` within a history. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + get: operations["history_content_api_histories__history_id__contents__id__get"]; + /** + * Updates the values for the history content item with the given ``ID``. + * @deprecated + * @description Updates the values for the history content item with the given ``ID``. + */ + put: operations["update_api_histories__history_id__contents__id__put"]; + /** + * Delete the history dataset with the given ``ID``. + * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset). + * + * **Note**: Currently does not stop any active jobs for which this dataset is an output. + */ + delete: operations["delete_api_histories__history_id__contents__id__delete"]; + }; + "/api/histories/{history_id}/contents/{id}/validate": { + /** + * Validates the metadata associated with a dataset within a History. + * @description Validates the metadata associated with a dataset within a History. + */ + put: operations["validate_api_histories__history_id__contents__id__validate_put"]; + }; + "/api/histories/{history_id}/contents/{type}s": { + /** + * Returns the contents of the given history filtered by type. + * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``. + * + * - The contents can be filtered and queried using the appropriate parameters. + * - The amount of information returned for each item can be customized. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + get: operations["index_api_histories__history_id__contents__type_s_get"]; + /** + * Create a new `HDA` or `HDCA` in the given History. + * @description Create a new `HDA` or `HDCA` in the given History. + */ + post: operations["create_api_histories__history_id__contents__type_s_post"]; + }; + "/api/histories/{history_id}/contents/{type}s/{id}": { + /** + * Return detailed information about a specific HDA or HDCA with the given `ID` within a history. + * @description Return detailed information about an `HDA` or `HDCA` within a history. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + get: operations["history_content_typed_api_histories__history_id__contents__type_s__id__get"]; + /** + * Updates the values for the history content item with the given ``ID``. + * @description Updates the values for the history content item with the given ``ID``. + */ + put: operations["update_api_histories__history_id__contents__type_s__id__put"]; + /** + * Delete the history content with the given ``ID`` and specified type. + * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset). + * + * **Note**: Currently does not stop any active jobs for which this dataset is an output. + */ + delete: operations["delete_api_histories__history_id__contents__type_s__id__delete"]; + }; + "/api/histories/{history_id}/contents/{type}s/{id}/jobs_summary": { + /** + * Return detailed information about an `HDA` or `HDCAs` jobs. + * @description Return detailed information about an `HDA` or `HDCAs` jobs. + * + * **Warning**: We allow anyone to fetch job state information about any object they + * can guess an encoded ID for - it isn't considered protected data. This keeps + * polling IDs as part of state calculation for large histories and collections as + * efficient as possible. + */ + get: operations["show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get"]; + }; + "/api/histories/{history_id}/contents/{type}s/{id}/prepare_store_download": { + /** Prepare a dataset or dataset collection for export-style download. */ + post: operations["prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post"]; + }; + "/api/histories/{history_id}/contents/{type}s/{id}/write_store": { + /** Prepare a dataset or dataset collection for export-style download and write to supplied URI. */ + post: operations["write_store_api_histories__history_id__contents__type_s__id__write_store_post"]; + }; + "/api/histories/{history_id}/contents_from_store": { + /** + * Create contents from store. + * @description Create history contents from model store. + * Input can be a tarfile created with build_objects script distributed + * with galaxy-data, from an exported history with files stripped out, + * or hand-crafted JSON dictionary. + */ + post: operations["create_from_store_api_histories__history_id__contents_from_store_post"]; + }; + "/api/histories/{history_id}/jobs_summary": { + /** + * Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations. + * @description Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations. + * + * **Warning**: We allow anyone to fetch job state information about any object they + * can guess an encoded ID for - it isn't considered protected data. This keeps + * polling IDs as part of state calculation for large histories and collections as + * efficient as possible. + */ + get: operations["index_jobs_summary_api_histories__history_id__jobs_summary_get"]; + }; + "/api/histories/{history_id}/materialize": { + /** Materialize a deferred library or HDA dataset into real, usable dataset in specified history. */ + post: operations["materialize_to_history_api_histories__history_id__materialize_post"]; + }; + "/api/histories/{id}": { + /** Returns the history with the given ID. */ + get: operations["history_api_histories__id__get"]; + /** Updates the values for the history with the given ID. */ + put: operations["update_api_histories__id__put"]; + /** Marks the history with the given ID as deleted. */ + delete: operations["delete_api_histories__id__delete"]; + }; + "/api/histories/{id}/citations": { + /** Return all the citations for the tools used to produce the datasets in the history. */ + get: operations["citations_api_histories__id__citations_get"]; + }; + "/api/histories/{id}/custom_builds_metadata": { + /** Returns meta data for custom builds. */ + get: operations["get_custom_builds_metadata_api_histories__id__custom_builds_metadata_get"]; + }; + "/api/histories/{id}/disable_link_access": { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + put: operations["disable_link_access_api_histories__id__disable_link_access_put"]; + }; + "/api/histories/{id}/enable_link_access": { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + put: operations["enable_link_access_api_histories__id__enable_link_access_put"]; + }; + "/api/histories/{id}/exports": { + /** Get previous history exports (to links). Effectively returns serialized JEHA objects. */ + get: operations["index_exports_api_histories__id__exports_get"]; + /** + * Start job (if needed) to create history export for corresponding history. + * @description This will start a job to create a history export archive. + * + * Calling this endpoint multiple times will return the 202 status code until the archive + * has been completely generated and is ready to download. When ready, it will return + * the 200 status code along with the download link information. + * + * If the history will be exported to a `directory_uri`, instead of returning the download + * link information, the Job ID will be returned so it can be queried to determine when + * the file has been written. + */ + put: operations["archive_export_api_histories__id__exports_put"]; + }; + "/api/histories/{id}/exports/{jeha_id}": { + /** + * If ready and available, return raw contents of exported history as a downloadable archive. + * @description See ``PUT /api/histories/{id}/exports`` to initiate the creation + * of the history export - when ready, that route will return 200 status + * code (instead of 202) and this route can be used to download the archive. + */ + get: operations["history_archive_download_api_histories__id__exports__jeha_id__get"]; + }; + "/api/histories/{id}/prepare_store_download": { + /** Return a short term storage token to monitor download of the history. */ + post: operations["prepare_store_download_api_histories__id__prepare_store_download_post"]; + }; + "/api/histories/{id}/publish": { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + put: operations["publish_api_histories__id__publish_put"]; + }; + "/api/histories/{id}/share_with_users": { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + put: operations["share_with_users_api_histories__id__share_with_users_put"]; + }; + "/api/histories/{id}/sharing": { + /** + * Get the current sharing status of the given item. + * @description Return the sharing status of the item. + */ + get: operations["sharing_api_histories__id__sharing_get"]; + }; + "/api/histories/{id}/slug": { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + put: operations["set_slug_api_histories__id__slug_put"]; + }; + "/api/histories/{id}/unpublish": { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + put: operations["unpublish_api_histories__id__unpublish_put"]; + }; + "/api/histories/{id}/write_store": { + /** Prepare history for export-style download and write to supplied URI. */ + post: operations["write_store_api_histories__id__write_store_post"]; + }; + "/api/invocations/{invocation_id}/biocompute": { + /** + * Return a BioCompute Object for the workflow invocation. + * @deprecated + * @description The BioCompute Object endpoints are in beta - important details such + * as how inputs and outputs are represented, how the workflow is encoded, + * and how author and version information is encoded, and how URLs are + * generated will very likely change in important ways over time. + * + * **Deprecation Notice**: please use the asynchronous short_term_storage export system instead. + * + * 1. call POST `api/invocations/{id}/prepare_store_download` with payload: + * ``` + * { + * model_store_format: bco.json + * } + * ``` + * 2. Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready` until `SUCCESS` + * + * 3. Get the resulting file with `api/short_term_storage/${storageRequestId}` + */ + get: operations["export_invocation_bco_api_invocations__invocation_id__biocompute_get"]; + }; + "/api/invocations/{invocation_id}/biocompute/download": { + /** + * Return a BioCompute Object for the workflow invocation as a file for download. + * @deprecated + * @description The BioCompute Object endpoints are in beta - important details such + * as how inputs and outputs are represented, how the workflow is encoded, + * and how author and version information is encoded, and how URLs are + * generated will very likely change in important ways over time. + * + * **Deprecation Notice**: please use the asynchronous short_term_storage export system instead. + * + * 1. call POST `api/invocations/{id}/prepare_store_download` with payload: + * ``` + * { + * model_store_format: bco.json + * } + * ``` + * 2. Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready` until `SUCCESS` + * + * 3. Get the resulting file with `api/short_term_storage/${storageRequestId}` + */ + get: operations["download_invocation_bco_api_invocations__invocation_id__biocompute_download_get"]; + }; + "/api/invocations/{invocation_id}/prepare_store_download": { + /** Prepare a workflow invocation export-style download. */ + post: operations["prepare_store_download_api_invocations__invocation_id__prepare_store_download_post"]; + }; + "/api/invocations/{invocation_id}/write_store": { + /** Prepare a workflow invocation export-style download and write to supplied URI. */ + post: operations["write_store_api_invocations__invocation_id__write_store_post"]; + }; + "/api/job_lock": { + /** + * Job Lock Status + * @description Get job lock status. + */ + get: operations["job_lock_status_api_job_lock_get"]; + /** + * Update Job Lock + * @description Set job lock status. + */ + put: operations["update_job_lock_api_job_lock_put"]; + }; + "/api/jobs": { + /** Index */ + get: operations["index_api_jobs_get"]; + }; + "/api/jobs/{id}": { + /** + * Show + * @description Return dictionary containing description of job data + * + * Parameters + * - id: ID of job to return + * - full: Return extra information ? + */ + get: operations["show_api_jobs__id__get"]; + }; + "/api/libraries": { + /** + * Returns a list of summary data for all libraries. + * @description Returns a list of summary data for all libraries. + */ + get: operations["index_api_libraries_get"]; + /** + * Creates a new library and returns its summary information. + * @description Creates a new library and returns its summary information. Currently, only admin users can create libraries. + */ + post: operations["create_api_libraries_post"]; + }; + "/api/libraries/deleted": { + /** + * Returns a list of summary data for all libraries marked as deleted. + * @description Returns a list of summary data for all libraries marked as deleted. + */ + get: operations["index_deleted_api_libraries_deleted_get"]; + }; + "/api/libraries/from_store": { + /** Create libraries from a model store. */ + post: operations["create_from_store_api_libraries_from_store_post"]; + }; + "/api/libraries/{id}": { + /** + * Returns summary information about a particular library. + * @description Returns summary information about a particular library. + */ + get: operations["show_api_libraries__id__get"]; + /** + * Marks the specified library as deleted (or undeleted). + * @description Marks the specified library as deleted (or undeleted). + * Currently, only admin users can delete or restore libraries. + */ + delete: operations["delete_api_libraries__id__delete"]; + /** + * Updates the information of an existing library. + * @description Updates the information of an existing library. + */ + patch: operations["update_api_libraries__id__patch"]; + }; + "/api/libraries/{id}/permissions": { + /** + * Gets the current or available permissions of a particular library. + * @description Gets the current or available permissions of a particular library. + * The results can be paginated and additionally filtered by a query. + */ + get: operations["get_permissions_api_libraries__id__permissions_get"]; + /** + * Sets the permissions to access and manipulate a library. + * @description Sets the permissions to access and manipulate a library. + */ + post: operations["set_permissions_api_libraries__id__permissions_post"]; + }; + "/api/licenses": { + /** + * Lists all available SPDX licenses + * @description Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/). + */ + get: operations["index_api_licenses_get"]; + }; + "/api/licenses/{id}": { + /** + * Gets the SPDX license metadata associated with the short identifier + * @description Returns the license metadata associated with the given + * [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/). + */ + get: operations["get_api_licenses__id__get"]; + }; + "/api/metrics": { + /** + * Records a collection of metrics. + * @description Record any metrics sent and return some status object. + */ + post: operations["create_api_metrics_post"]; + }; + "/api/pages": { + /** + * Lists all Pages viewable by the user. + * @description Get a list with summary information of all Pages available to the user. + */ + get: operations["index_api_pages_get"]; + /** + * Create a page and return summary information. + * @description Get a list with details of all Pages available to the user. + */ + post: operations["create_api_pages_post"]; + }; + "/api/pages/{id}": { + /** + * Return a page summary and the content of the last revision. + * @description Return summary information about a specific Page and the content of the last revision. + */ + get: operations["show_api_pages__id__get"]; + /** + * Marks the specific Page as deleted. + * @description Marks the Page with the given ID as deleted. + */ + delete: operations["delete_api_pages__id__delete"]; + }; + "/api/pages/{id}.pdf": { + /** + * Return a PDF document of the last revision of the Page. + * @description Return a PDF document of the last revision of the Page. + * + * This feature may not be available in this Galaxy. + */ + get: operations["show_pdf_api_pages__id__pdf_get"]; + }; + "/api/pages/{id}/disable_link_access": { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + put: operations["disable_link_access_api_pages__id__disable_link_access_put"]; + }; + "/api/pages/{id}/enable_link_access": { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + put: operations["enable_link_access_api_pages__id__enable_link_access_put"]; + }; + "/api/pages/{id}/prepare_download": { + /** + * Return a PDF document of the last revision of the Page. + * @description Return a STS download link for this page to be downloaded as a PDF. + * + * This feature may not be available in this Galaxy. + */ + post: operations["prepare_pdf_api_pages__id__prepare_download_post"]; + }; + "/api/pages/{id}/publish": { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + put: operations["publish_api_pages__id__publish_put"]; + }; + "/api/pages/{id}/share_with_users": { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + put: operations["share_with_users_api_pages__id__share_with_users_put"]; + }; + "/api/pages/{id}/sharing": { + /** + * Get the current sharing status of the given Page. + * @description Return the sharing status of the item. + */ + get: operations["sharing_api_pages__id__sharing_get"]; + }; + "/api/pages/{id}/slug": { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + put: operations["set_slug_api_pages__id__slug_put"]; + }; + "/api/pages/{id}/unpublish": { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + put: operations["unpublish_api_pages__id__unpublish_put"]; + }; + "/api/quotas": { + /** + * Displays a list with information of quotas that are currently active. + * @description Displays a list with information of quotas that are currently active. + */ + get: operations["index_api_quotas_get"]; + /** + * Creates a new quota. + * @description Creates a new quota. + */ + post: operations["create_api_quotas_post"]; + }; + "/api/quotas/deleted": { + /** + * Displays a list with information of quotas that have been deleted. + * @description Displays a list with information of quotas that have been deleted. + */ + get: operations["index_deleted_api_quotas_deleted_get"]; + }; + "/api/quotas/deleted/{id}": { + /** + * Displays details on a particular quota that has been deleted. + * @description Displays details on a particular quota that has been deleted. + */ + get: operations["deleted_quota_api_quotas_deleted__id__get"]; + }; + "/api/quotas/deleted/{id}/undelete": { + /** + * Restores a previously deleted quota. + * @description Restores a previously deleted quota. + */ + post: operations["undelete_api_quotas_deleted__id__undelete_post"]; + }; + "/api/quotas/{id}": { + /** + * Displays details on a particular active quota. + * @description Displays details on a particular active quota. + */ + get: operations["quota_api_quotas__id__get"]; + /** + * Updates an existing quota. + * @description Updates an existing quota. + */ + put: operations["update_api_quotas__id__put"]; + /** + * Deletes an existing quota. + * @description Deletes an existing quota. + */ + delete: operations["delete_api_quotas__id__delete"]; + }; + "/api/remote_files": { + /** + * Displays remote files available to the user. + * @description Lists all remote files available to the user from different sources. + */ + get: operations["index_api_remote_files_get"]; + }; + "/api/remote_files/plugins": { + /** + * Display plugin information for each of the gxfiles:// URI targets available. + * @description Display plugin information for each of the gxfiles:// URI targets available. + */ + get: operations["plugins_api_remote_files_plugins_get"]; + }; + "/api/roles": { + /** Index */ + get: operations["index_api_roles_get"]; + /** Create */ + post: operations["create_api_roles_post"]; + }; + "/api/roles/{id}": { + /** Show */ + get: operations["show_api_roles__id__get"]; + }; + "/api/short_term_storage/{storage_request_id}": { + /** Serve the staged download specified by request ID. */ + get: operations["serve_api_short_term_storage__storage_request_id__get"]; + }; + "/api/short_term_storage/{storage_request_id}/ready": { + /** Determine if specified storage request ID is ready for download. */ + get: operations["is_ready_api_short_term_storage__storage_request_id__ready_get"]; + }; + "/api/tags": { + /** + * Apply a new set of tags to an item. + * @description Replaces the tags associated with an item with the new ones specified in the payload. + * + * - The previous tags will be __deleted__. + * - If no tags are provided in the request body, the currently associated tags will also be __deleted__. + */ + put: operations["update_api_tags_put"]; + }; + "/api/tasks/{task_id}/state": { + /** Determine state of task ID */ + get: operations["state_api_tasks__task_id__state_get"]; + }; + "/api/tool_data": { + /** + * Lists all available data tables + * @description Get the list of all available data tables. + */ + get: operations["index_api_tool_data_get"]; + }; + "/api/tool_data/{table_name}": { + /** + * Get details of a given data table + * @description Get details of a given tool data table. + */ + get: operations["show_api_tool_data__table_name__get"]; + /** + * Removes an item from a data table + * @description Removes an item from a data table and reloads it to return its updated details. + */ + delete: operations["delete_api_tool_data__table_name__delete"]; + }; + "/api/tool_data/{table_name}/fields/{field_name}": { + /** + * Get information about a particular field in a tool data table + * @description Reloads a data table and return its details. + */ + get: operations["show_field_api_tool_data__table_name__fields__field_name__get"]; + }; + "/api/tool_data/{table_name}/fields/{field_name}/files/{file_name}": { + /** + * Get information about a particular field in a tool data table + * @description Download a file associated with the data table field. + */ + get: operations["download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get"]; + }; + "/api/tool_data/{table_name}/reload": { + /** + * Reloads a tool data table + * @description Reloads a data table and return its details. + */ + get: operations["reload_api_tool_data__table_name__reload_get"]; + }; + "/api/tool_shed_repositories": { + /** Lists installed tool shed repositories. */ + get: operations["index_api_tool_shed_repositories_get"]; + }; + "/api/tool_shed_repositories/check_for_updates": { + /** Check for updates to the specified repository, or all installed repositories. */ + get: operations["check_for_updates_api_tool_shed_repositories_check_for_updates_get"]; + }; + "/api/tool_shed_repositories/{id}": { + /** Show installed tool shed repository. */ + get: operations["show_api_tool_shed_repositories__id__get"]; + }; + "/api/tools/fetch": { + /** Upload files to Galaxy */ + post: operations["fetch_json_api_tools_fetch_post+fetch_form_api_tools_fetch_post"]; + }; + "/api/tours": { + /** + * Index + * @description Return list of available tours. + */ + get: operations["index_api_tours_get"]; + }; + "/api/tours/{tour_id}": { + /** + * Show + * @description Return a tour definition. + */ + get: operations["show_api_tours__tour_id__get"]; + /** + * Update Tour + * @description Return a tour definition. + */ + post: operations["update_tour_api_tours__tour_id__post"]; + }; + "/api/users/recalculate_disk_usage": { + /** Triggers a recalculation of the current user disk usage. */ + put: operations["recalculate_disk_usage_api_users_recalculate_disk_usage_put"]; + }; + "/api/users/{user_id}/api_key": { + /** Return the user's API key */ + get: operations["get_or_create_api_key_api_users__user_id__api_key_get"]; + /** Creates a new API key for the user */ + post: operations["create_api_key_api_users__user_id__api_key_post"]; + /** Delete the current API key of the user */ + delete: operations["delete_api_key_api_users__user_id__api_key_delete"]; + }; + "/api/users/{user_id}/api_key/detailed": { + /** Return the user's API key with extra information. */ + get: operations["get_api_key_detailed_api_users__user_id__api_key_detailed_get"]; + }; + "/api/version": { + /** + * Return Galaxy version information: major/minor version, optional extra info + * @description Return Galaxy version information: major/minor version, optional extra info. + */ + get: operations["version_api_version_get"]; + }; + "/api/visualizations/{id}/disable_link_access": { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + put: operations["disable_link_access_api_visualizations__id__disable_link_access_put"]; + }; + "/api/visualizations/{id}/enable_link_access": { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + put: operations["enable_link_access_api_visualizations__id__enable_link_access_put"]; + }; + "/api/visualizations/{id}/publish": { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + put: operations["publish_api_visualizations__id__publish_put"]; + }; + "/api/visualizations/{id}/share_with_users": { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + put: operations["share_with_users_api_visualizations__id__share_with_users_put"]; + }; + "/api/visualizations/{id}/sharing": { + /** + * Get the current sharing status of the given Page. + * @description Return the sharing status of the item. + */ + get: operations["sharing_api_visualizations__id__sharing_get"]; + }; + "/api/visualizations/{id}/slug": { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + put: operations["set_slug_api_visualizations__id__slug_put"]; + }; + "/api/visualizations/{id}/unpublish": { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + put: operations["unpublish_api_visualizations__id__unpublish_put"]; + }; + "/api/whoami": { + /** + * Return information about the current authenticated user + * @description Return information about the current authenticated user. + */ + get: operations["whoami_api_whoami_get"]; + }; + "/api/workflows": { + /** + * Lists stored workflows viewable by the user. + * @description Lists stored workflows viewable by the user. + */ + get: operations["index_api_workflows_get"]; + }; + "/api/workflows/{id}/disable_link_access": { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + put: operations["disable_link_access_api_workflows__id__disable_link_access_put"]; + }; + "/api/workflows/{id}/enable_link_access": { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + put: operations["enable_link_access_api_workflows__id__enable_link_access_put"]; + }; + "/api/workflows/{id}/publish": { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + put: operations["publish_api_workflows__id__publish_put"]; + }; + "/api/workflows/{id}/share_with_users": { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + put: operations["share_with_users_api_workflows__id__share_with_users_put"]; + }; + "/api/workflows/{id}/sharing": { + /** + * Get the current sharing status of the given item. + * @description Return the sharing status of the item. + */ + get: operations["sharing_api_workflows__id__sharing_get"]; + }; + "/api/workflows/{id}/slug": { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + put: operations["set_slug_api_workflows__id__slug_put"]; + }; + "/api/workflows/{id}/unpublish": { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + put: operations["unpublish_api_workflows__id__unpublish_put"]; + }; + "/api/workflows/{workflow_id}": { + /** Add the deleted flag to a workflow. */ + delete: operations["delete_workflow_api_workflows__workflow_id__delete"]; + }; + "/api/workflows/{workflow_id}/undelete": { + /** Remove the deleted flag from a workflow. */ + post: operations["undelete_workflow_api_workflows__workflow_id__undelete_post"]; + }; +} + +export type webhooks = Record; + +export interface components { + schemas: { + /** APIKeyModel */ + APIKeyModel: { + /** + * Create Time + * Format: date-time + * @description The time and date this API key was created. + */ + create_time: string; + /** + * Key + * @description API key to interact with the Galaxy API + */ + key: string; + }; + /** + * AsyncFile + * @description Base model definition with common configuration used by all derived models. + */ + AsyncFile: { + /** + * Storage Request Id + * Format: uuid + */ + storage_request_id: string; + task: components["schemas"]["AsyncTaskResultSummary"]; + }; + /** + * AsyncTaskResultSummary + * @description Base model definition with common configuration used by all derived models. + */ + AsyncTaskResultSummary: { + /** + * ID + * @description Celery AsyncResult ID for this task + */ + id: string; + /** + * Ignored + * @description Indicated whether the Celery AsyncResult will be available for retrieval + */ + ignored: boolean; + /** Name of task being done derived from Celery AsyncResult */ + name?: string; + /** Queue of task being done derived from Celery AsyncResult */ + queue?: string; + }; + /** + * BasicRoleModel + * @description Base model definition with common configuration used by all derived models. + */ + BasicRoleModel: { + /** + * ID + * @description Encoded ID of the role + */ + id: string; + /** + * Name + * @description Name of the role + */ + name: string; + /** + * Type + * @description Type or category of the role + */ + type: string; + }; + /** Body_create_api_histories_post */ + Body_create_api_histories_post: { + /** + * All Datasets + * @default true + */ + all_datasets?: Record; + /** Archive File */ + archive_file?: Record; + /** Archive Source */ + archive_source?: Record; + /** + * Archive Type + * @default url + */ + archive_type?: Record; + /** History Id */ + history_id?: Record; + /** Name */ + name?: Record; + }; + /** Body_fetch_form_api_tools_fetch_post */ + Body_fetch_form_api_tools_fetch_post: { + /** Files */ + files?: string[]; + /** History Id */ + history_id: Record; + /** Targets */ + targets: Record; + }; + /** + * BulkOperationItemError + * @description Base model definition with common configuration used by all derived models. + */ + BulkOperationItemError: { + /** Error */ + error: string; + item: components["schemas"]["HistoryContentItem"]; + }; + /** + * ChangeDatatypeOperationParams + * @description Base model definition with common configuration used by all derived models. + */ + ChangeDatatypeOperationParams: { + /** Datatype */ + datatype: string; + /** + * Type + * @enum {string} + */ + type: "change_datatype"; + }; + /** + * ChangeDbkeyOperationParams + * @description Base model definition with common configuration used by all derived models. + */ + ChangeDbkeyOperationParams: { + /** Dbkey */ + dbkey: string; + /** + * Type + * @enum {string} + */ + type: "change_dbkey"; + }; + /** + * CheckForUpdatesResponse + * @description Base model definition with common configuration used by all derived models. + */ + CheckForUpdatesResponse: { + /** + * Message + * @description Unstructured description of tool shed updates discovered or failure + */ + message: string; + /** + * Status + * @description 'ok' or 'error' + * @enum {string} + */ + status: "ok" | "error"; + }; + /** + * CollectionElementIdentifier + * @description Base model definition with common configuration used by all derived models. + */ + CollectionElementIdentifier: { + /** + * Collection Type + * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`. + */ + collection_type?: string; + /** + * Element Identifiers + * @description List of elements that should be in the new sub-collection. + */ + element_identifiers?: components["schemas"]["CollectionElementIdentifier"][]; + /** + * ID + * @description The encoded ID of the element. + */ + id?: string; + /** + * Name + * @description The name of the element. + */ + name?: string; + /** + * Source + * @description The source of the element. + */ + src: components["schemas"]["ColletionSourceType"]; + /** + * Tags + * @description The list of tags associated with the element. + */ + tags?: string[]; + }; + /** + * ColletionSourceType + * @description An enumeration. + * @enum {string} + */ + ColletionSourceType: "hda" | "ldda" | "hdca" | "new_collection"; + /** + * CompositeDataElement + * @description Base model definition with common configuration used by all derived models. + */ + CompositeDataElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + composite: components["schemas"]["CompositeItems"]; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Name */ + name?: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "composite"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** CompositeFileInfo */ + CompositeFileInfo: { + /** + * Description + * @description Summary description of the purpouse of this file + */ + description?: string; + /** + * Is binary + * @description Whether this file is a binary file + */ + is_binary: boolean; + /** + * MIME type + * @description The MIME type of this file + */ + mimetype?: string; + /** + * Name + * @description The name of this composite file + */ + name: string; + /** Optional */ + optional: boolean; + /** Spaces to tabulation */ + space_to_tab: boolean; + /** Substitute name with metadata */ + substitute_name_with_metadata?: string; + /** To posix lines */ + to_posix_lines: boolean; + }; + /** + * CompositeItems + * @description Base model definition with common configuration used by all derived models. + */ + CompositeItems: { + /** Elements */ + elements: ( + | components["schemas"]["FileDataElement"] + | components["schemas"]["PastedDataElement"] + | components["schemas"]["UrlDataElement"] + | components["schemas"]["PathDataElement"] + | components["schemas"]["ServerDirElement"] + | components["schemas"]["FtpImportElement"] + )[]; + }; + /** + * ComputeDatasetHashPayload + * @description Base model definition with common configuration used by all derived models. + */ + ComputeDatasetHashPayload: { + /** + * Extra Files Path + * @description If set, extra files path to compute a hash for. + */ + extra_files_path?: string; + /** + * @description Hash function name to use to compute dataset hashes. + * @default MD5 + */ + hash_function?: components["schemas"]["HashFunctionNameEnum"]; + }; + /** + * ConvertedDatasetsMap + * @description Map of `file extension` -> `converted dataset encoded id` + * @example { + * "csv": "dataset_id" + * } + */ + ConvertedDatasetsMap: { + [key: string]: string | undefined; + }; + /** + * CreateHistoryContentFromStore + * @description Base model definition with common configuration used by all derived models. + */ + CreateHistoryContentFromStore: { + model_store_format?: components["schemas"]["ModelStoreFormat"]; + /** Store Content Uri */ + store_content_uri?: string; + /** Store Dict */ + store_dict?: Record; + }; + /** + * CreateHistoryContentPayload + * @description Base model definition with common configuration used by all derived models. + */ + CreateHistoryContentPayload: { + /** + * Collection Type + * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`. + */ + collection_type?: string; + /** + * Content + * @description Depending on the `source` it can be: + * - The encoded id from the library dataset + * - The encoded id from the library folder + * - The encoded id from the HDA + * - The encoded id from the HDCA + */ + content?: string | string; + /** + * Copy Elements + * @description If the source is a collection, whether to copy child HDAs into the target history as well, defaults to False but this is less than ideal and may be changed in future releases. + * @default false + */ + copy_elements?: boolean; + /** + * DBKey + * @description TODO + */ + dbkey?: string; + /** + * Element Identifiers + * @description List of elements that should be in the new collection. + */ + element_identifiers?: components["schemas"]["CollectionElementIdentifier"][]; + /** + * Folder Id + * @description The ID of the library folder that will contain the collection. Required if `instance_type=library`. + */ + folder_id?: string; + /** + * Hide Source Items + * @description Whether to mark the original HDAs as hidden. + * @default false + */ + hide_source_items?: boolean; + /** + * History Id + * @description The ID of the history that will contain the collection. Required if `instance_type=history`. + */ + history_id?: string; + /** + * Instance Type + * @description The type of the instance, either `history` (default) or `library`. + * @default history + * @enum {string} + */ + instance_type?: "history" | "library"; + /** + * Name + * @description The name of the new collection. + */ + name?: string; + /** + * Source + * @description The source of the content. Can be other history element to be copied or library elements. + */ + source?: components["schemas"]["HistoryContentSource"]; + /** + * Type + * @description The type of content to be created in the history. + * @default dataset + */ + type?: components["schemas"]["HistoryContentType"]; + }; + /** + * CreateHistoryFromStore + * @description Base model definition with common configuration used by all derived models. + */ + CreateHistoryFromStore: { + model_store_format?: components["schemas"]["ModelStoreFormat"]; + /** Store Content Uri */ + store_content_uri?: string; + /** Store Dict */ + store_dict?: Record; + }; + /** + * CreateLibrariesFromStore + * @description Base model definition with common configuration used by all derived models. + */ + CreateLibrariesFromStore: { + model_store_format?: components["schemas"]["ModelStoreFormat"]; + /** Store Content Uri */ + store_content_uri?: string; + /** Store Dict */ + store_dict?: Record; + }; + /** + * CreateLibraryFilePayload + * @description Base model definition with common configuration used by all derived models. + */ + CreateLibraryFilePayload: { + /** + * From HDA ID + * @description The ID of an accessible HDA to copy into the library. + */ + from_hda_id?: string; + /** + * From HDCA ID + * @description The ID of an accessible HDCA to copy into the library. Nested collections are not allowed, you must flatten the collection first. + */ + from_hdca_id?: string; + /** + * LDDA Message + * @description The new message attribute of the LDDA created. + * @default + */ + ldda_message?: string; + }; + /** + * CreateLibraryFolderPayload + * @description Base model definition with common configuration used by all derived models. + */ + CreateLibraryFolderPayload: { + /** + * Description + * @description A detailed description of the library folder. + * @default + */ + description?: string; + /** + * Name + * @description The name of the library folder. + */ + name: string; + }; + /** + * CreateLibraryPayload + * @description Base model definition with common configuration used by all derived models. + */ + CreateLibraryPayload: { + /** + * Description + * @description A detailed description of the Library. + * @default + */ + description?: string; + /** + * Name + * @description The name of the Library. + */ + name: string; + /** + * Synopsis + * @description A short text describing the contents of the Library. + * @default + */ + synopsis?: string; + }; + /** CreateMetricsPayload */ + CreateMetricsPayload: { + /** + * List of metrics to be recorded. + * @default [] + * @example [ + * { + * "args": "{\"test\":\"value\"}", + * "level": 0, + * "namespace": "test-source", + * "time": "2021-01-23T18:25:43.511Z" + * } + * ] + */ + metrics?: components["schemas"]["Metric"][]; + }; + /** + * CreateNewCollectionPayload + * @description Base model definition with common configuration used by all derived models. + */ + CreateNewCollectionPayload: { + /** + * Collection Type + * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`. + */ + collection_type?: string; + /** + * Copy Elements + * @description Whether to create a copy of the source HDAs for the new collection. + * @default false + */ + copy_elements?: boolean; + /** + * Element Identifiers + * @description List of elements that should be in the new collection. + */ + element_identifiers?: components["schemas"]["CollectionElementIdentifier"][]; + /** + * Folder Id + * @description The ID of the library folder that will contain the collection. Required if `instance_type=library`. + */ + folder_id?: string; + /** + * Hide Source Items + * @description Whether to mark the original HDAs as hidden. + * @default false + */ + hide_source_items?: boolean; + /** + * History Id + * @description The ID of the history that will contain the collection. Required if `instance_type=history`. + */ + history_id?: string; + /** + * Instance Type + * @description The type of the instance, either `history` (default) or `library`. + * @default history + * @enum {string} + */ + instance_type?: "history" | "library"; + /** + * Name + * @description The name of the new collection. + */ + name?: string; + }; + /** + * CreatePagePayload + * @description Base model definition with common configuration used by all derived models. + */ + CreatePagePayload: { + /** + * Annotation + * @description Annotation that will be attached to the page. + */ + annotation?: string; + /** + * Content + * @description Raw text contents of the first page revision (type dependent on content_format). + * @default + */ + content?: string; + /** + * Content format + * @description Either `markdown` or `html`. + * @default html + */ + content_format?: components["schemas"]["PageContentFormat"]; + /** + * Workflow invocation ID + * @description Encoded ID used by workflow generated reports. + */ + invocation_id?: string; + /** + * Identifier + * @description The title slug for the page URL, must be unique. + */ + slug: string; + /** + * Title + * @description The name of the page + */ + title: string; + }; + /** + * CreateQuotaParams + * @description Base model definition with common configuration used by all derived models. + */ + CreateQuotaParams: { + /** + * Amount + * @description Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``) + */ + amount: string; + /** + * Default + * @description Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. None is equivalent to ``no``. + * @default no + */ + default?: components["schemas"]["DefaultQuotaValues"]; + /** + * Description + * @description Detailed text description for this Quota. + */ + description: string; + /** + * Groups + * @description A list of group IDs or names to associate with this quota. + * @default [] + */ + in_groups?: string[]; + /** + * Users + * @description A list of user IDs or user emails to associate with this quota. + * @default [] + */ + in_users?: string[]; + /** + * Name + * @description The name of the quota. This must be unique within a Galaxy instance. + */ + name: string; + /** + * Operation + * @description Quotas can have one of three `operations`:- `=` : The quota is exactly the amount specified- `+` : The amount specified will be added to the amounts of the user's other associated quota definitions- `-` : The amount specified will be subtracted from the amounts of the user's other associated quota definitions + * @default = + */ + operation?: components["schemas"]["QuotaOperation"]; + }; + /** + * CreateQuotaResult + * @description Contains basic information about a Quota + */ + CreateQuotaResult: { + /** + * ID + * @description The `encoded identifier` of the quota. + */ + id: string; + /** + * Message + * @description Text message describing the result of the operation. + */ + message: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Quota"; + /** + * Name + * @description The name of the quota. This must be unique within a Galaxy instance. + */ + name: string; + /** + * URL + * @deprecated + * @description The relative URL to get this particular Quota details from the rest API. + */ + url: string; + }; + /** + * CustomBuildsMetadataResponse + * @description Base model definition with common configuration used by all derived models. + */ + CustomBuildsMetadataResponse: { + /** + * Fasta HDAs + * @description A list of label/value pairs with all the datasets of type `FASTA` contained in the History. + * - `label` is item position followed by the name of the dataset. + * - `value` is the encoded database ID of the dataset. + */ + fasta_hdas: components["schemas"]["LabelValuePair"][]; + /** + * Installed Builds + * @description TODO + */ + installed_builds: components["schemas"]["LabelValuePair"][]; + }; + /** + * CustomHistoryItem + * @description Can contain any serializable property of the item. + * + * Allows arbitrary custom keys to be specified in the serialization + * parameters without a particular view (predefined set of keys). + */ + CustomHistoryItem: Record; + /** + * DCESummary + * @description Dataset Collection Element summary information. + */ + DCESummary: { + /** + * Element Identifier + * @description The actual name of this element. + */ + element_identifier: string; + /** + * Element Index + * @description The position index of this element inside the collection. + */ + element_index: number; + /** + * Element Type + * @description The type of the element. Used to interpret the `object` field. + */ + element_type: components["schemas"]["DCEType"]; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "DatasetCollectionElement"; + /** + * Object + * @description The element's specific data depending on the value of `element_type`. + */ + object: + | components["schemas"]["HDAObject"] + | components["schemas"]["HDADetailed"] + | components["schemas"]["DCObject"]; + }; + /** + * DCEType + * @description Available types of dataset collection elements. + * @enum {string} + */ + DCEType: "hda" | "dataset_collection"; + /** + * DCObject + * @description Dataset Collection Object + */ + DCObject: { + /** + * Collection Type + * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`. + */ + collection_type?: string; + /** + * Contents URL + * @description The relative URL to access the contents of this History. + */ + contents_url?: string; + /** + * Element Count + * @description The number of elements contained in the dataset collection. It may be None or undefined if the collection could not be populated. + */ + element_count?: number; + /** + * Elements + * @description The summary information of each of the elements inside the dataset collection. + * @default [] + */ + elements?: components["schemas"]["DCESummary"][]; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "DatasetCollection"; + /** + * Populated + * @description Whether the dataset collection elements (and any subcollections elements) were successfully populated. + */ + populated?: boolean; + }; + /** + * DataElementsFromTarget + * @description Base model definition with common configuration used by all derived models. + */ + DataElementsFromTarget: { + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Destination */ + destination: + | components["schemas"]["HdaDestination"] + | components["schemas"]["LibraryFolderDestination"] + | components["schemas"]["LibraryDestination"]; + elements_from: components["schemas"]["ElementsFromType"]; + /** Ftp Path */ + ftp_path?: string; + /** Path */ + path?: string; + /** Server Dir */ + server_dir?: string; + src: components["schemas"]["ItemsFromSrc"]; + /** Url */ + url?: string; + }; + /** + * DataElementsTarget + * @description Base model definition with common configuration used by all derived models. + */ + DataElementsTarget: { + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Destination */ + destination: + | components["schemas"]["HdaDestination"] + | components["schemas"]["LibraryFolderDestination"] + | components["schemas"]["LibraryDestination"]; + /** Elements */ + elements: ( + | ( + | components["schemas"]["FileDataElement"] + | components["schemas"]["PastedDataElement"] + | components["schemas"]["UrlDataElement"] + | components["schemas"]["PathDataElement"] + | components["schemas"]["ServerDirElement"] + | components["schemas"]["FtpImportElement"] + | components["schemas"]["CompositeDataElement"] + ) + | components["schemas"]["NestedElement"] + )[]; + }; + /** + * DatasetAssociationRoles + * @description Base model definition with common configuration used by all derived models. + */ + DatasetAssociationRoles: { + /** + * Access Roles + * @description A list of roles that can access the dataset. The user has to **have all these roles** in order to access this dataset. Users without access permission **cannot** have other permissions on this dataset. If there are no access roles set on the dataset it is considered **unrestricted**. + * @default [] + */ + access_dataset_roles?: string[][]; + /** + * Manage Roles + * @description A list of roles that can manage permissions on the dataset. Users with **any** of these roles can manage permissions of this dataset. If you remove yourself you will lose the ability to manage this dataset unless you are an admin. + * @default [] + */ + manage_dataset_roles?: string[][]; + /** + * Modify Roles + * @description A list of roles that can modify the library item. This is a library related permission. User with **any** of these roles can modify name, metadata, and other information about this library item. + * @default [] + */ + modify_item_roles?: string[][]; + }; + /** + * DatasetCollectionAttributesResult + * @description Base model definition with common configuration used by all derived models. + */ + DatasetCollectionAttributesResult: { + /** + * Dbkey + * @description TODO + */ + dbkey: string; + /** Dbkeys */ + dbkeys?: string[]; + /** + * Extension + * @description The dataset file extension. + * @example txt + */ + extension: string; + /** Extensions */ + extensions?: string[]; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "HistoryDatasetCollectionAssociation"; + tags: components["schemas"]["TagCollection"]; + }; + /** + * DatasetCollectionContentElements + * @description Represents a collection of elements contained in the dataset collection. + */ + DatasetCollectionContentElements: components["schemas"]["DCESummary"][]; + /** + * DatasetErrorMessage + * @description Base model definition with common configuration used by all derived models. + */ + DatasetErrorMessage: { + /** + * Dataset + * @description The encoded ID of the dataset and its source. + */ + dataset: components["schemas"]["DatasetSourceId"]; + /** + * Error Message + * @description The error message returned while processing this dataset. + */ + error_message: string; + }; + /** + * DatasetInheritanceChain + * @description Base model definition with common configuration used by all derived models. + * @default [] + */ + DatasetInheritanceChain: components["schemas"]["DatasetInheritanceChainEntry"][]; + /** + * DatasetInheritanceChainEntry + * @description Base model definition with common configuration used by all derived models. + */ + DatasetInheritanceChainEntry: { + /** + * Dep + * @description Name of the source of the referenced dataset at this point of the inheritance chain. + */ + dep: string; + /** + * Name + * @description Name of the referenced dataset + */ + name: string; + }; + /** + * DatasetPermissions + * @description Role-based permissions for accessing and managing a dataset. + */ + DatasetPermissions: { + /** + * Access + * @description The set of roles (encoded IDs) that can access this dataset. + * @default [] + */ + access?: string[]; + /** + * Management + * @description The set of roles (encoded IDs) that can manage this dataset. + * @default [] + */ + manage?: string[]; + }; + /** + * DatasetSourceId + * @description Base model definition with common configuration used by all derived models. + */ + DatasetSourceId: { + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Source + * @description The source of this dataset, either `hda` or `ldda` depending of its origin. + */ + src: components["schemas"]["DatasetSourceType"]; + }; + /** + * DatasetSourceType + * @description An enumeration. + * @enum {string} + */ + DatasetSourceType: "hda" | "ldda"; + /** + * DatasetStorageDetails + * @description Base model definition with common configuration used by all derived models. + */ + DatasetStorageDetails: { + /** + * Dataset State + * @description The model state of the supplied dataset instance. + */ + dataset_state: string; + /** + * Description + * @description A description of how this dataset is stored. + */ + description?: string; + /** + * Hashes + * @description The file contents hashes associated with the supplied dataset instance. + */ + hashes: Record[]; + /** + * Name + * @description The display name of the destination ObjectStore for this dataset. + */ + name?: string; + /** + * Object Store Id + * @description The identifier of the destination ObjectStore for this dataset. + */ + object_store_id?: string; + /** + * Percent Used + * @description The percentage indicating how full the store is. + */ + percent_used?: number; + /** + * Sources + * @description The file sources associated with the supplied dataset instance. + */ + sources: Record[]; + }; + /** + * DatasetTextContentDetails + * @description Base model definition with common configuration used by all derived models. + */ + DatasetTextContentDetails: { + /** + * Item Data + * @description First chunk of text content (maximum 1MB) of the dataset. + */ + item_data?: string; + /** + * Item Url + * @description URL to access this dataset. + */ + item_url: string; + /** + * Truncated + * @description Whether the text in `item_data` has been truncated or contains the whole contents. + */ + truncated: boolean; + }; + /** DatatypeConverter */ + DatatypeConverter: { + /** + * Source + * @description Source type for conversion + * @example bam + */ + source: string; + /** + * Target + * @description Target type for conversion + * @example bai + */ + target: string; + /** + * Tool identifier + * @description The converter tool identifier + * @example CONVERTER_Bam_Bai_0 + */ + tool_id: string; + }; + /** + * DatatypeConverterList + * @default [] + */ + DatatypeConverterList: components["schemas"]["DatatypeConverter"][]; + /** DatatypeDetails */ + DatatypeDetails: { + /** + * Composite files + * @description A collection of files composing this data type + */ + composite_files?: components["schemas"]["CompositeFileInfo"][]; + /** + * Description + * @description A summary description for this data type + */ + description?: string; + /** + * Description URL + * Format: uri + * @description The URL to a detailed description for this datatype + * @example https://wiki.galaxyproject.org/Learn/Datatypes#Bed + */ + description_url?: string; + /** + * Display in upload + * @description If True, the associated file extension will be displayed in the `File Format` select list in the `Upload File from your computer` tool in the `Get Data` tool section of the tool panel + * @default false + */ + display_in_upload?: boolean; + /** + * Extension + * @description The data type’s Dataset file extension + * @example bed + */ + extension: string; + }; + /** DatatypeEDAMDetails */ + DatatypeEDAMDetails: { + /** + * Definition + * @description The EDAM definition + * @example Entry (gene) format of the NCBI database. + */ + definition?: string; + /** + * Label + * @description The EDAM label + * @example NCBI gene report format + */ + label?: string; + /** + * Prefix IRI + * @description The EDAM prefixed Resource Identifier + * @example format_1782 + */ + prefix_IRI: string; + }; + /** DatatypesCombinedMap */ + DatatypesCombinedMap: { + /** + * Datatypes + * @description List of datatypes extensions + */ + datatypes: string[]; + /** + * Datatypes Mapping + * @description Dictionaries for mapping datatype's extensions/classes with their implementation classes + */ + datatypes_mapping: components["schemas"]["DatatypesMap"]; + }; + /** + * DatatypesEDAMDetailsDict + * @default {} + */ + DatatypesEDAMDetailsDict: { + [key: string]: components["schemas"]["DatatypeEDAMDetails"] | undefined; + }; + /** DatatypesMap */ + DatatypesMap: { + /** + * Classes Map + * @description Dictionary mapping datatype's classes with their base classes + */ + class_to_classes: { + [key: string]: + | { + [key: string]: boolean | undefined; + } + | undefined; + }; + /** + * Extension Map + * @description Dictionary mapping datatype's extensions with implementation classes + */ + ext_to_class_name: { + [key: string]: string | undefined; + }; + }; + /** + * DefaultQuota + * @description Base model definition with common configuration used by all derived models. + */ + DefaultQuota: { + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "DefaultQuotaAssociation"; + /** + * Type + * @description The type of the default quota. Either one of: + * - `registered`: the associated quota will affect registered users. + * - `unregistered`: the associated quota will affect unregistered users. + */ + type: components["schemas"]["DefaultQuotaTypes"]; + }; + /** + * DefaultQuotaTypes + * @description An enumeration. + * @enum {string} + */ + DefaultQuotaTypes: "unregistered" | "registered"; + /** + * DefaultQuotaValues + * @description An enumeration. + * @enum {string} + */ + DefaultQuotaValues: "unregistered" | "registered" | "no"; + /** + * DeleteDatasetBatchPayload + * @description Base model definition with common configuration used by all derived models. + */ + DeleteDatasetBatchPayload: { + /** + * Datasets + * @description The list of datasets IDs with their sources to be deleted/purged. + */ + datasets: components["schemas"]["DatasetSourceId"][]; + /** + * Purge + * @description Whether to permanently delete from disk the specified datasets. *Warning*: this is a destructive operation. + * @default false + */ + purge?: boolean; + }; + /** + * DeleteDatasetBatchResult + * @description Base model definition with common configuration used by all derived models. + */ + DeleteDatasetBatchResult: { + /** + * Errors + * @description A list of dataset IDs and the corresponding error message if something went wrong while processing the dataset. + */ + errors?: components["schemas"]["DatasetErrorMessage"][]; + /** + * Success Count + * @description The number of datasets successfully processed. + */ + success_count: number; + }; + /** + * DeleteHistoryContentPayload + * @description Base model definition with common configuration used by all derived models. + */ + DeleteHistoryContentPayload: { + /** + * Purge + * @description Whether to remove the dataset from storage. Datasets will only be removed from storage once all HDAs or LDDAs that refer to this datasets are deleted. + * @default false + */ + purge?: boolean; + /** + * Recursive + * @description When deleting a dataset collection, whether to also delete containing datasets. + * @default false + */ + recursive?: boolean; + /** + * Stop Job + * @description Whether to stop the creating job if all the job's outputs are deleted. + * @default false + */ + stop_job?: boolean; + }; + /** + * DeleteHistoryContentResult + * @description Contains minimum information about the deletion state of a history item. + * + * Can also contain any other properties of the item. + */ + DeleteHistoryContentResult: { + /** + * Deleted + * @description True if the item was successfully deleted. + */ + deleted: boolean; + /** + * ID + * @description The encoded ID of the history item. + */ + id: string; + /** + * Purged + * @description True if the item was successfully removed from disk. + */ + purged?: boolean; + }; + /** DeleteHistoryPayload */ + DeleteHistoryPayload: { + /** + * Purge + * @description Whether to definitely remove this history from disk. + * @default false + */ + purge?: boolean; + }; + /** + * DeleteLibraryPayload + * @description Base model definition with common configuration used by all derived models. + */ + DeleteLibraryPayload: { + /** + * Undelete + * @description Whether to restore this previously deleted library. + */ + undelete: boolean; + }; + /** + * DeleteQuotaPayload + * @description Base model definition with common configuration used by all derived models. + */ + DeleteQuotaPayload: { + /** + * Purge + * @description Whether to also purge the Quota after deleting it. + * @default false + */ + purge?: boolean; + }; + /** + * DirectionOptions + * @description An enumeration. + * @enum {string} + */ + DirectionOptions: "near" | "before" | "after"; + /** + * DisplayApp + * @description Basic linked information about an application that can display certain datatypes. + */ + DisplayApp: { + /** + * Label + * @description The label or title of the Display Application. + */ + label: string; + /** + * Links + * @description The collection of link details for this Display Application. + */ + links: components["schemas"]["Hyperlink"][]; + }; + /** + * ElementsFromType + * @description An enumeration. + * @enum {string} + */ + ElementsFromType: "archive" | "bagit" | "bagit_archive" | "directory"; + /** + * ExportHistoryArchivePayload + * @description Base model definition with common configuration used by all derived models. + */ + ExportHistoryArchivePayload: { + /** + * Directory URI + * @description A writable directory destination where the history will be exported using the `galaxy.files` URI infrastructure. + */ + directory_uri?: string; + /** + * File Name + * @description The name of the file containing the exported history. + */ + file_name?: string; + /** + * Force Rebuild + * @description Whether to force a rebuild of the history archive. + */ + force?: boolean; + /** + * GZip + * @description Whether to export as gzip archive. + * @default true + */ + gzip?: boolean; + /** + * Include Deleted + * @description Whether to include deleted datasets in the exported archive. + * @default false + */ + include_deleted?: boolean; + /** + * Include Hidden + * @description Whether to include hidden datasets in the exported archive. + * @default false + */ + include_hidden?: boolean; + }; + /** + * ExtraFiles + * @description Base model definition with common configuration used by all derived models. + */ + ExtraFiles: { + /** + * Fuzzy Root + * @description Prevent Galaxy from checking for a single file in a directory and re-interpreting the archive + * @default true + */ + fuzzy_root?: boolean; + /** Items From */ + items_from?: string; + src: components["schemas"]["Src"]; + }; + /** + * FetchDataPayload + * @description Base model definition with common configuration used by all derived models. + */ + FetchDataPayload: { + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id: string; + /** Targets */ + targets: ( + | components["schemas"]["DataElementsTarget"] + | components["schemas"]["HdcaDataItemsTarget"] + | components["schemas"]["DataElementsFromTarget"] + | components["schemas"]["HdcaDataItemsFromTarget"] + | components["schemas"]["FtpImportTarget"] + )[]; + }; + /** + * FileDataElement + * @description Base model definition with common configuration used by all derived models. + */ + FileDataElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Name */ + name?: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "files"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** + * FileLibraryFolderItem + * @description Base model definition with common configuration used by all derived models. + */ + FileLibraryFolderItem: { + /** Can Manage */ + can_manage: boolean; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** + * Date Uploaded + * Format: date-time + */ + date_uploaded: string; + /** Deleted */ + deleted: boolean; + /** File Ext */ + file_ext: string; + /** File Size */ + file_size: string; + /** Id */ + id: string; + /** Is Private */ + is_private: boolean; + /** Is Unrestricted */ + is_unrestricted: boolean; + /** Ldda Id */ + ldda_id: string; + /** Message */ + message?: string; + /** Name */ + name: string; + /** Raw Size */ + raw_size: number; + /** + * State + * @description The current state of this dataset. + */ + state: components["schemas"]["galaxy__model__Dataset__states"]; + /** Tags */ + tags: string; + /** + * Type + * @enum {string} + */ + type: "file"; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time: string; + }; + /** + * FilesSourcePlugin + * @description Base model definition with common configuration used by all derived models. + */ + FilesSourcePlugin: { + /** + * Documentation + * @description Documentation or extended description for this plugin. + * @example Galaxy's library import directory + */ + doc: string; + /** + * ID + * @description The `FilesSource` plugin identifier + * @example _import + */ + id: string; + /** + * Label + * @description The display label for this plugin. + * @example Library Import Directory + */ + label: string; + /** + * Requires groups + * @description Only users belonging to the groups specified here can access this files source. + */ + requires_groups?: string; + /** + * Requires roles + * @description Only users with the roles specified here can access this files source. + */ + requires_roles?: string; + /** + * Type + * @description The type of the plugin. + * @example gximport + */ + type: string; + /** + * URI root + * @description The URI root used by this type of plugin. + * @example gximport:// + */ + uri_root: string; + /** + * Writeable + * @description Whether this files source plugin allows write access. + * @example false + */ + writable: boolean; + }; + /** + * FilesSourcePluginList + * @description Base model definition with common configuration used by all derived models. + * @default [] + * @example [ + * { + * "doc": "Galaxy's library import directory", + * "id": "_import", + * "label": "Library Import Directory", + * "type": "gximport", + * "uri_root": "gximport://", + * "writable": false + * } + * ] + */ + FilesSourcePluginList: components["schemas"]["FilesSourcePlugin"][]; + /** + * FolderLibraryFolderItem + * @description Base model definition with common configuration used by all derived models. + */ + FolderLibraryFolderItem: { + /** Can Manage */ + can_manage: boolean; + /** Can Modify */ + can_modify: boolean; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** Deleted */ + deleted: boolean; + /** + * Description + * @description A detailed description of the library folder. + * @default + */ + description?: string; + /** Id */ + id: string; + /** Name */ + name: string; + /** + * Type + * @enum {string} + */ + type: "folder"; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time: string; + }; + /** + * FtpImportElement + * @description Base model definition with common configuration used by all derived models. + */ + FtpImportElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Ftp Path */ + ftp_path: string; + /** Info */ + info?: string; + /** Name */ + name?: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "ftp_import"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** + * FtpImportTarget + * @description Base model definition with common configuration used by all derived models. + */ + FtpImportTarget: { + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + destination: components["schemas"]["HdcaDestination"]; + elements_from?: components["schemas"]["ElementsFromType"]; + /** Ftp Path */ + ftp_path: string; + /** Name */ + name?: string; + /** + * Src + * @enum {string} + */ + src: "ftp_import"; + /** Tags */ + tags?: string[]; + }; + /** + * GroupModel + * @description User group model + */ + GroupModel: { + /** + * ID + * @description Encoded group ID + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Group"; + /** + * Name + * @description The name of the group. + */ + name: string; + }; + /** + * GroupQuota + * @description Base model definition with common configuration used by all derived models. + */ + GroupQuota: { + /** + * Group + * @description Information about a user group associated with a quota. + */ + group: components["schemas"]["GroupModel"]; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "GroupQuotaAssociation"; + }; + /** + * GroupRoleListModel + * @description Base model definition with common configuration used by all derived models. + */ + GroupRoleListModel: components["schemas"]["GroupRoleModel"][]; + /** + * GroupRoleModel + * @description Base model definition with common configuration used by all derived models. + */ + GroupRoleModel: { + /** + * ID + * @description Encoded ID of the role + */ + id: string; + /** + * Name + * @description Name of the role + */ + name: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + }; + /** + * GroupUserListModel + * @description Base model definition with common configuration used by all derived models. + */ + GroupUserListModel: components["schemas"]["GroupUserModel"][]; + /** + * GroupUserModel + * @description Base model definition with common configuration used by all derived models. + */ + GroupUserModel: { + /** + * Email + * @description Email of the user + */ + email: string; + /** + * ID + * @description Encoded ID of the user + */ + id: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + }; + /** + * HDADetailed + * @description History Dataset Association detailed information. + */ + HDADetailed: { + /** + * Accessible + * @description Whether this item is accessible to the current user due to permissions. + */ + accessible: boolean; + /** + * Annotation + * @description An annotation to provide details or to help understand the purpose and usage of this item. + */ + annotation: string; + /** + * API Type + * @description TODO + * @default file + * @enum {string} + */ + api_type?: "file"; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time?: string; + /** + * Created from basename + * @description The basename of the output that produced this dataset. + */ + created_from_basename?: string; + /** + * Creating Job ID + * @description The encoded ID of the job that created this dataset. + */ + creating_job: string; + /** + * Data Type + * @description The fully qualified name of the class implementing the data type of this dataset. + * @example galaxy.datatypes.data.Text + */ + data_type: string; + /** + * Dataset ID + * @description The encoded ID of the dataset associated with this item. + */ + dataset_id: string; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * Display Applications + * @description Contains new-style display app urls. + */ + display_apps: components["schemas"]["DisplayApp"][]; + /** + * Legacy Display Applications + * @description Contains old-style display app urls. + */ + display_types: components["schemas"]["DisplayApp"][]; + /** + * Download URL + * @description The URL to download this item from the server. + */ + download_url: string; + /** + * Extension + * @description The extension of the dataset. + * @example txt + */ + extension: string; + /** + * File extension + * @description The extension of the file. + */ + file_ext: string; + /** + * File Name + * @description The full path to the dataset file. + */ + file_name?: string; + /** + * File Size + * @description The file size in bytes. + */ + file_size: number; + /** + * Genome Build + * @description TODO + * @default ? + */ + genome_build?: string; + /** + * HDA or LDDA + * @description Whether this dataset belongs to a history (HDA) or a library (LDDA). + * @default hda + */ + hda_ldda?: components["schemas"]["DatasetSourceType"]; + /** + * HID + * @description The index position of this item in the History. + */ + hid: number; + /** + * Content Type + * @description The type of this item. + */ + history_content_type: components["schemas"]["HistoryContentType"]; + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Metadata Files + * @description Collection of metadata files associated with this dataset. + */ + meta_files: components["schemas"]["MetadataFile"][]; + /** + * Metadata + * @description The metadata associated with this dataset. + */ + metadata?: Record; + /** + * Metadata Data Lines + * @description TODO + * @default 0 + */ + metadata_data_lines?: number; + /** + * Metadata DBKey + * @description TODO + * @default ? + */ + metadata_dbkey?: string; + /** + * Miscellaneous Blurb + * @description TODO + */ + misc_blurb?: string; + /** + * Miscellaneous Information + * @description TODO + */ + misc_info?: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "HistoryDatasetAssociation"; + /** + * Name + * @description The name of the item. + */ + name?: string; + /** + * Peek + * @description A few lines of contents from the start of the file. + */ + peek?: string; + /** + * Permissions + * @description Role-based access and manage control permissions for the dataset. + */ + permissions: components["schemas"]["DatasetPermissions"]; + /** + * Purged + * @description Whether this dataset has been removed from disk. + */ + purged: boolean; + /** + * Rerunnable + * @description Whether the job creating this dataset can be run again. + */ + rerunnable: boolean; + /** + * Resubmitted + * @description Whether the job creating this dataset has been resubmitted. + */ + resubmitted: boolean; + /** + * State + * @description The current state of this dataset. + */ + state: components["schemas"]["galaxy__model__Dataset__states"]; + tags: components["schemas"]["TagCollection"]; + /** + * Type + * @description This is always `file` for datasets. + * @default file + * @enum {string} + */ + type?: "file"; + /** + * Type - ID + * @description The type and the encoded ID of this item. Used for caching. + * @example dataset-616e371b2cc6c62e + */ + type_id?: string; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time?: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + /** + * UUID + * Format: uuid4 + * @description Universal unique identifier for this dataset. + */ + uuid: string; + /** + * Validated State + * @description The state of the datatype validation for this dataset. + */ + validated_state: components["schemas"]["validated_states"]; + /** + * Validated State Message + * @description The message with details about the datatype validation result for this dataset. + */ + validated_state_message: string; + /** + * Visible + * @description Whether this item is visible or hidden to the user by default. + */ + visible: boolean; + /** + * Visualizations + * @description The collection of visualizations that can be applied to this dataset. + */ + visualizations: components["schemas"]["Visualization"][]; + }; + /** + * HDAObject + * @description History Dataset Association Object + */ + HDAObject: { + /** + * HDA or LDDA + * @description Whether this dataset belongs to a history (HDA) or a library (LDDA). + * @default hda + */ + hda_ldda?: components["schemas"]["DatasetSourceType"]; + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "HistoryDatasetAssociation"; + /** + * State + * @description The current state of this dataset. + */ + state: components["schemas"]["galaxy__model__Dataset__states"]; + }; + /** + * HDASummary + * @description History Dataset Association summary information. + */ + HDASummary: { + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time?: string; + /** + * Dataset ID + * @description The encoded ID of the dataset associated with this item. + */ + dataset_id: string; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * Extension + * @description The extension of the dataset. + * @example txt + */ + extension: string; + /** + * HID + * @description The index position of this item in the History. + */ + hid: number; + /** + * Content Type + * @description The type of this item. + */ + history_content_type: components["schemas"]["HistoryContentType"]; + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Name + * @description The name of the item. + */ + name?: string; + /** + * Purged + * @description Whether this dataset has been removed from disk. + */ + purged: boolean; + /** + * State + * @description The current state of this dataset. + */ + state: components["schemas"]["galaxy__model__Dataset__states"]; + tags: components["schemas"]["TagCollection"]; + /** + * Type + * @description The type of this item. + */ + type: string; + /** + * Type - ID + * @description The type and the encoded ID of this item. Used for caching. + * @example dataset-616e371b2cc6c62e + */ + type_id?: string; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time?: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + /** + * Visible + * @description Whether this item is visible or hidden to the user by default. + */ + visible: boolean; + }; + /** + * HDCADetailed + * @description History Dataset Collection Association detailed information. + */ + HDCADetailed: { + /** + * Collection ID + * @description The encoded ID of the dataset collection associated with this HDCA. + */ + collection_id: string; + /** + * Collection Type + * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`. + */ + collection_type?: string; + /** + * Contents URL + * @description The relative URL to access the contents of this History. + */ + contents_url: string; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time?: string; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * Element Count + * @description The number of elements contained in the dataset collection. It may be None or undefined if the collection could not be populated. + */ + element_count?: number; + /** + * Elements + * @description The summary information of each of the elements inside the dataset collection. + * @default [] + */ + elements?: components["schemas"]["DCESummary"][]; + /** + * Elements Datatypes + * @description A set containing all the different element datatypes in the collection. + */ + elements_datatypes: string[]; + /** + * HID + * @description The index position of this item in the History. + */ + hid: number; + /** + * Content Type + * @description The type of this item. + */ + history_content_type: components["schemas"]["HistoryContentType"]; + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Job Source ID + * @description The encoded ID of the Job that produced this dataset collection. Used to track the state of the job. + */ + job_source_id?: string; + /** + * Job Source Type + * @description The type of job (model class) that produced this dataset collection. Used to track the state of the job. + */ + job_source_type?: components["schemas"]["JobSourceType"]; + /** + * Job State Summary + * @description Overview of the job states working inside the dataset collection. + */ + job_state_summary?: components["schemas"]["HDCJobStateSummary"]; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "HistoryDatasetCollectionAssociation"; + /** + * Name + * @description The name of the item. + */ + name?: string; + /** + * Populated + * @description Whether the dataset collection elements (and any subcollections elements) were successfully populated. + */ + populated: boolean; + /** + * Populated State + * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated. + */ + populated_state: components["schemas"]["populated_states"]; + /** + * Populated State Message + * @description Optional message with further information in case the population of the dataset collection failed. + */ + populated_state_message?: string; + tags: components["schemas"]["TagCollection"]; + /** + * Type + * @description This is always `collection` for dataset collections. + * @default collection + * @enum {string} + */ + type?: "collection"; + /** + * Type - ID + * @description The type and the encoded ID of this item. Used for caching. + * @example dataset-616e371b2cc6c62e + */ + type_id?: string; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time?: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + /** + * Visible + * @description Whether this item is visible or hidden to the user by default. + */ + visible: boolean; + }; + /** + * HDCASummary + * @description History Dataset Collection Association summary information. + */ + HDCASummary: { + /** + * Collection ID + * @description The encoded ID of the dataset collection associated with this HDCA. + */ + collection_id: string; + /** + * Collection Type + * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`. + */ + collection_type?: string; + /** + * Contents URL + * @description The relative URL to access the contents of this History. + */ + contents_url: string; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time?: string; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * Element Count + * @description The number of elements contained in the dataset collection. It may be None or undefined if the collection could not be populated. + */ + element_count?: number; + /** + * HID + * @description The index position of this item in the History. + */ + hid: number; + /** + * Content Type + * @description The type of this item. + */ + history_content_type: components["schemas"]["HistoryContentType"]; + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Job Source ID + * @description The encoded ID of the Job that produced this dataset collection. Used to track the state of the job. + */ + job_source_id?: string; + /** + * Job Source Type + * @description The type of job (model class) that produced this dataset collection. Used to track the state of the job. + */ + job_source_type?: components["schemas"]["JobSourceType"]; + /** + * Job State Summary + * @description Overview of the job states working inside the dataset collection. + */ + job_state_summary?: components["schemas"]["HDCJobStateSummary"]; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "HistoryDatasetCollectionAssociation"; + /** + * Name + * @description The name of the item. + */ + name?: string; + /** + * Populated State + * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated. + */ + populated_state: components["schemas"]["populated_states"]; + /** + * Populated State Message + * @description Optional message with further information in case the population of the dataset collection failed. + */ + populated_state_message?: string; + tags: components["schemas"]["TagCollection"]; + /** + * Type + * @description This is always `collection` for dataset collections. + * @default collection + * @enum {string} + */ + type?: "collection"; + /** + * Type - ID + * @description The type and the encoded ID of this item. Used for caching. + * @example dataset-616e371b2cc6c62e + */ + type_id?: string; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time?: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + /** + * Visible + * @description Whether this item is visible or hidden to the user by default. + */ + visible: boolean; + }; + /** + * HDCJobStateSummary + * @description Overview of the job states working inside a dataset collection. + */ + HDCJobStateSummary: { + /** + * All jobs + * @description Total number of jobs associated with a dataset collection. + * @default 0 + */ + all_jobs?: number; + /** + * Deleted jobs + * @description Number of jobs in the `deleted` state. + * @default 0 + */ + deleted?: number; + /** + * Deleted new jobs + * @description Number of jobs in the `deleted_new` state. + * @default 0 + */ + deleted_new?: number; + /** + * Jobs with errors + * @description Number of jobs in the `error` state. + * @default 0 + */ + error?: number; + /** + * Failed jobs + * @description Number of jobs in the `failed` state. + * @default 0 + */ + failed?: number; + /** + * New jobs + * @description Number of jobs in the `new` state. + * @default 0 + */ + new?: number; + /** + * OK jobs + * @description Number of jobs in the `ok` state. + * @default 0 + */ + ok?: number; + /** + * Paused jobs + * @description Number of jobs in the `paused` state. + * @default 0 + */ + paused?: number; + /** + * Queued jobs + * @description Number of jobs in the `queued` state. + * @default 0 + */ + queued?: number; + /** + * Resubmitted jobs + * @description Number of jobs in the `resubmitted` state. + * @default 0 + */ + resubmitted?: number; + /** + * Running jobs + * @description Number of jobs in the `running` state. + * @default 0 + */ + running?: number; + /** + * Upload jobs + * @description Number of jobs in the `upload` state. + * @default 0 + */ + upload?: number; + /** + * Waiting jobs + * @description Number of jobs in the `waiting` state. + * @default 0 + */ + waiting?: number; + }; + /** HTTPValidationError */ + HTTPValidationError: { + /** Detail */ + detail?: components["schemas"]["ValidationError"][]; + }; + /** + * HashFunctionNameEnum + * @description Particular pieces of information that can be requested for a dataset. + * @enum {string} + */ + HashFunctionNameEnum: "MD5" | "SHA-1" | "SHA-256" | "SHA-512"; + /** + * HdaDestination + * @description Base model definition with common configuration used by all derived models. + */ + HdaDestination: { + /** + * Type + * @enum {string} + */ + type: "hdas"; + }; + /** + * HdcaDataItemsFromTarget + * @description Base model definition with common configuration used by all derived models. + */ + HdcaDataItemsFromTarget: { + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + destination: components["schemas"]["HdcaDestination"]; + elements_from: components["schemas"]["ElementsFromType"]; + /** Ftp Path */ + ftp_path?: string; + /** Name */ + name?: string; + /** Path */ + path?: string; + /** Server Dir */ + server_dir?: string; + src: components["schemas"]["ItemsFromSrc"]; + /** Tags */ + tags?: string[]; + /** Url */ + url?: string; + }; + /** + * HdcaDataItemsTarget + * @description Base model definition with common configuration used by all derived models. + */ + HdcaDataItemsTarget: { + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + destination: components["schemas"]["HdcaDestination"]; + /** Elements */ + elements: ( + | ( + | components["schemas"]["FileDataElement"] + | components["schemas"]["PastedDataElement"] + | components["schemas"]["UrlDataElement"] + | components["schemas"]["PathDataElement"] + | components["schemas"]["ServerDirElement"] + | components["schemas"]["FtpImportElement"] + | components["schemas"]["CompositeDataElement"] + ) + | components["schemas"]["NestedElement"] + )[]; + /** Name */ + name?: string; + /** Tags */ + tags?: string[]; + }; + /** + * HdcaDestination + * @description Base model definition with common configuration used by all derived models. + */ + HdcaDestination: { + /** + * Type + * @enum {string} + */ + type: "hdca"; + }; + /** + * HistoryActiveContentCounts + * @description Contains the number of active, deleted or hidden items in a History. + */ + HistoryActiveContentCounts: { + /** + * Active + * @description Number of active datasets. + */ + active: number; + /** + * Deleted + * @description Number of deleted datasets. + */ + deleted: number; + /** + * Hidden + * @description Number of hidden datasets. + */ + hidden: number; + }; + /** + * HistoryBeta + * @description History detailed information used in the new Beta History. + */ + HistoryBeta: { + /** + * Annotation + * @description An annotation to provide details or to help understand the purpose and usage of this item. + */ + annotation: string; + /** + * Active Contents + * @description Contains the number of active, deleted or hidden items in the History. + */ + contents_active: components["schemas"]["HistoryActiveContentCounts"]; + /** + * Contents URL + * @description The relative URL to access the contents of this History. + */ + contents_url: string; + /** + * Count + * @description The number of items in the history. + */ + count: number; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * Empty + * @description Whether this History has any content. + */ + empty: boolean; + /** + * Genome Build + * @description TODO + * @default ? + */ + genome_build?: string; + /** + * HID Counter + * @description TODO + */ + hid_counter: number; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Importable + * @description Whether this History can be imported by other users with a shared link. + */ + importable: boolean; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "History"; + /** + * Name + * @description The name of the history. + */ + name: string; + /** + * Nice Size + * @description Human-readable size of the contents of this history. + * @example 95.4 MB + */ + nice_size: string; + /** + * Published + * @description Whether this resource is currently publicly available to all users. + */ + published: boolean; + /** + * Purged + * @description Whether this History has been permanently removed. + */ + purged: boolean; + /** + * Size + * @description The total size of the contents of this history in bytes. + */ + size: number; + /** + * Slug + * @description Part of the URL to uniquely identify this History by link in a readable way. + */ + slug?: string; + /** + * State + * @description The current state of the History based on the states of the datasets it contains. + */ + state: components["schemas"]["galaxy__model__Dataset__states"]; + /** + * State Counts + * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states. + */ + state_details: { + [key: string]: number | undefined; + }; + /** + * State IDs + * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state. + */ + state_ids: { + [key: string]: string[] | undefined; + }; + tags: components["schemas"]["TagCollection"]; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + /** + * User ID + * @description The encoded ID of the user that owns this History. + */ + user_id: string; + /** + * Username and slug + * @description The relative URL in the form of /u/{username}/h/{slug} + */ + username_and_slug?: string; + }; + /** + * HistoryContentBulkOperationPayload + * @description Base model definition with common configuration used by all derived models. + */ + HistoryContentBulkOperationPayload: { + /** Items */ + items?: components["schemas"]["HistoryContentItem"][]; + operation: components["schemas"]["HistoryContentItemOperation"]; + /** Params */ + params?: + | components["schemas"]["ChangeDatatypeOperationParams"] + | components["schemas"]["ChangeDbkeyOperationParams"] + | components["schemas"]["TagOperationParams"]; + }; + /** + * HistoryContentBulkOperationResult + * @description Base model definition with common configuration used by all derived models. + */ + HistoryContentBulkOperationResult: { + /** Errors */ + errors: components["schemas"]["BulkOperationItemError"][]; + /** Success Count */ + success_count: number; + }; + /** + * HistoryContentItem + * @description Identifies a dataset or collection contained in a History. + */ + HistoryContentItem: { + /** + * Content Type + * @description The type of this item. + */ + history_content_type: components["schemas"]["HistoryContentType"]; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + }; + /** + * HistoryContentItemOperation + * @description An enumeration. + * @enum {string} + */ + HistoryContentItemOperation: + | "hide" + | "unhide" + | "delete" + | "undelete" + | "purge" + | "change_datatype" + | "change_dbkey" + | "add_tags" + | "remove_tags"; + /** + * HistoryContentSource + * @description An enumeration. + * @enum {string} + */ + HistoryContentSource: "hda" | "hdca" | "library" | "library_folder" | "new_collection"; + /** + * HistoryContentStats + * @description Base model definition with common configuration used by all derived models. + */ + HistoryContentStats: { + /** + * Total Matches + * @description The total number of items that match the search query without any pagination + */ + total_matches: number; + }; + /** + * HistoryContentType + * @description Available types of History contents. + * @enum {string} + */ + HistoryContentType: "dataset" | "dataset_collection"; + /** + * HistoryContentsResult + * @description List of history content items. + * Can contain different views and kinds of items. + */ + HistoryContentsResult: ( + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + )[]; + /** + * HistoryContentsWithStatsResult + * @description Includes stats with items counting + */ + HistoryContentsWithStatsResult: { + /** + * Contents + * @description The items matching the search query. Only the items fitting in the current page limit will be returned. + */ + contents: ( + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + )[]; + /** + * Stats + * @description Contains counting stats for the query. + */ + stats: components["schemas"]["HistoryContentStats"]; + }; + /** + * HistoryDetailed + * @description History detailed information. + */ + HistoryDetailed: { + /** + * Annotation + * @description An annotation to provide details or to help understand the purpose and usage of this item. + */ + annotation: string; + /** + * Contents URL + * @description The relative URL to access the contents of this History. + */ + contents_url: string; + /** + * Count + * @description The number of items in the history. + */ + count: number; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * Genome Build + * @description TODO + * @default ? + */ + genome_build?: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Importable + * @description Whether this History can be imported by other users with a shared link. + */ + importable: boolean; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "History"; + /** + * Name + * @description The name of the history. + */ + name: string; + /** + * Published + * @description Whether this resource is currently publicly available to all users. + */ + published: boolean; + /** + * Purged + * @description Whether this item has been permanently removed. + */ + purged: boolean; + /** + * Size + * @description The total size of the contents of this history in bytes. + */ + size: number; + /** + * Slug + * @description Part of the URL to uniquely identify this History by link in a readable way. + */ + slug?: string; + /** + * State + * @description The current state of the History based on the states of the datasets it contains. + */ + state: components["schemas"]["galaxy__model__Dataset__states"]; + /** + * State Counts + * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states. + */ + state_details: { + [key: string]: number | undefined; + }; + /** + * State IDs + * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state. + */ + state_ids: { + [key: string]: string[] | undefined; + }; + tags: components["schemas"]["TagCollection"]; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + /** + * User ID + * @description The encoded ID of the user that owns this History. + */ + user_id: string; + /** + * Username and slug + * @description The relative URL in the form of /u/{username}/h/{slug} + */ + username_and_slug?: string; + }; + /** + * HistorySummary + * @description History summary information. + */ + HistorySummary: { + /** + * Annotation + * @description An annotation to provide details or to help understand the purpose and usage of this item. + */ + annotation: string; + /** + * Count + * @description The number of items in the history. + */ + count: number; + /** + * Deleted + * @description Whether this item is marked as deleted. + */ + deleted: boolean; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "History"; + /** + * Name + * @description The name of the history. + */ + name: string; + /** + * Published + * @description Whether this resource is currently publicly available to all users. + */ + published: boolean; + /** + * Purged + * @description Whether this item has been permanently removed. + */ + purged: boolean; + tags: components["schemas"]["TagCollection"]; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + }; + /** + * Hyperlink + * @description Represents some text with an Hyperlink. + */ + Hyperlink: { + /** + * HRef + * Format: uri + * @description Specifies the linked document, resource, or location. + */ + href: string; + /** + * Target + * @description Specifies where to open the linked document. + * @example _blank + */ + target: string; + /** + * Text + * @description The text placeholder for the link. + */ + text: string; + }; + /** + * ImplicitCollectionJobsStateSummary + * @description Base model definition with common configuration used by all derived models. + */ + ImplicitCollectionJobsStateSummary: { + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model: "ImplicitCollectionJobs"; + /** + * Populated State + * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated. + */ + populated_state: components["schemas"]["populated_states"]; + /** + * States + * @description A dictionary of job states and the number of jobs in that state. + * @default {} + */ + states?: { + [key: string]: number | undefined; + }; + }; + /** + * InstalledRepositoryToolShedStatus + * @description Base model definition with common configuration used by all derived models. + */ + InstalledRepositoryToolShedStatus: { + /** + * Latest Installable Revision + * @description Most recent version avialable on the tool shed + */ + latest_installable_revision: string; + /** + * Repository Deprecated + * @description Repository has been depreciated on the tool shed + */ + repository_deprecated: string; + /** Revision Update */ + revision_update: string; + /** Revision Upgrade */ + revision_upgrade?: string; + }; + /** + * InstalledToolShedRepository + * @description Base model definition with common configuration used by all derived models. + */ + InstalledToolShedRepository: { + /** + * Changeset Revision + * @description Changeset revision of the repository - a mercurial commit hash + */ + changeset_revision: string; + /** + * Ctx Rev + * @description The linearized 0-based index of the changeset on the tool shed (0, 1, 2,...) + */ + ctx_rev: string; + /** Deleted */ + deleted: boolean; + /** Dist To Shed */ + dist_to_shed: boolean; + /** + * Error Message + * @default Installation error message, the empty string means no error was recorded + */ + error_message?: string; + /** + * ID + * @description Encoded ID of the install tool shed repository. + */ + id: string; + /** + * Installed Changeset Revision + * @description Initially installed changeset revision. Used to construct path to repository within Galaxies filesystem. Does not change if a repository is updated. + */ + installed_changeset_revision: string; + /** + * Model class + * @description The name of the database model class. + * @default ToolShedRepository + * @enum {string} + */ + model_class?: "ToolShedRepository"; + /** + * Name + * @description Name of repository + */ + name: string; + /** + * Owner + * @description Owner of repository + */ + owner: string; + /** Status */ + status: string; + /** + * Tool Shed + * @description Hostname of the tool shed this was installed from + */ + tool_shed: string; + /** Tool Shed Status */ + tool_shed_status?: components["schemas"]["InstalledRepositoryToolShedStatus"]; + /** Uninstalled */ + uninstalled: boolean; + }; + /** + * ItemTagsPayload + * @description Base model definition with common configuration used by all derived models. + */ + ItemTagsPayload: { + /** + * Item class + * @description The name of the class of the item that will be tagged. + */ + item_class: components["schemas"]["TaggableItemClass"]; + /** + * Item ID + * @description The `encoded identifier` of the item whose tags will be updated. + */ + item_id: string; + /** + * Item tags + * @description The list of tags that will replace the current tags associated with the item. + */ + item_tags?: components["schemas"]["TagCollection"]; + }; + /** + * ItemsFromSrc + * @description An enumeration. + * @enum {string} + */ + ItemsFromSrc: "url" | "files" | "path" | "ftp_import" | "server_dir"; + /** + * JobExportHistoryArchiveCollection + * @description Base model definition with common configuration used by all derived models. + */ + JobExportHistoryArchiveCollection: components["schemas"]["JobExportHistoryArchiveModel"][]; + /** + * JobExportHistoryArchiveModel + * @description Base model definition with common configuration used by all derived models. + */ + JobExportHistoryArchiveModel: { + /** + * Download URL + * @description Relative API URL to download the exported history archive. + */ + download_url: string; + /** + * External Download Latest URL + * Format: uri + * @description Fully qualified URL to download the latests version of the exported history archive. + */ + external_download_latest_url: string; + /** + * External Download Permanent URL + * Format: uri + * @description Fully qualified URL to download this particular version of the exported history archive. + */ + external_download_permanent_url: string; + /** + * ID + * @description The encoded database ID of the job that is currently processing a particular request. + */ + id: string; + /** + * Job ID + * @description The encoded database ID of the job that generated this history export archive. + */ + job_id: string; + /** + * Preparing + * @description Whether the history archive is currently being built or in preparation. + */ + preparing: boolean; + /** + * Ready + * @description Whether the export history job has completed successfully and the archive is ready to download + */ + ready: boolean; + /** + * Up to Date + * @description False, if a new export archive should be generated for the corresponding history. + */ + up_to_date: boolean; + }; + /** + * JobIdResponse + * @description Contains the ID of the job associated with a particular request. + */ + JobIdResponse: { + /** + * Job ID + * @description The encoded database ID of the job that is currently processing a particular request. + */ + job_id: string; + }; + /** + * JobImportHistoryResponse + * @description Base model definition with common configuration used by all derived models. + */ + JobImportHistoryResponse: { + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** + * Exit Code + * @description The exit code returned by the tool. Can be unset if the job is not completed yet. + */ + exit_code?: number; + /** + * Galaxy Version + * @description The (major) version of Galaxy used to create this job. + * @example 21.05 + */ + galaxy_version: string; + /** + * History ID + * @description The encoded ID of the history associated with this item. + */ + history_id?: string; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Message + * @description Text message containing information about the history import. + */ + message: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Job"; + /** + * State + * @description Current state of the job. + */ + state: components["schemas"]["galaxy__model__Job__states"]; + /** + * Tool ID + * @description Identifier of the tool that generated this job. + */ + tool_id: string; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time: string; + }; + /** + * JobIndexSortByEnum + * @description An enumeration. + * @enum {string} + */ + JobIndexSortByEnum: "create_time" | "update_time"; + /** + * JobIndexViewEnum + * @description An enumeration. + * @enum {string} + */ + JobIndexViewEnum: "collection" | "admin_job_list"; + /** JobLock */ + JobLock: { + /** + * Job lock status + * @description If active, jobs will not dispatch + */ + active: boolean; + }; + /** + * JobSourceType + * @description Available types of job sources (model classes) that produce dataset collections. + * @enum {string} + */ + JobSourceType: "Job" | "ImplicitCollectionJobs" | "WorkflowInvocation"; + /** + * JobStateSummary + * @description Base model definition with common configuration used by all derived models. + */ + JobStateSummary: { + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model: "Job"; + /** + * Populated State + * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated. + */ + populated_state: components["schemas"]["populated_states"]; + /** + * States + * @description A dictionary of job states and the number of jobs in that state. + * @default {} + */ + states?: { + [key: string]: number | undefined; + }; + }; + /** + * LabelValuePair + * @description Generic Label/Value pair model. + */ + LabelValuePair: { + /** + * Label + * @description The label of the item. + */ + label: string; + /** + * Value + * @description The value of the item. + */ + value: string; + }; + /** + * LegacyLibraryPermissionsPayload + * @description Base model definition with common configuration used by all derived models. + */ + LegacyLibraryPermissionsPayload: { + /** + * Access IDs + * @description A list of role encoded IDs defining roles that should have access permission on the library. + * @default [] + */ + LIBRARY_ACCESS_in?: string[] | string; + /** + * Manage IDs + * @description A list of role encoded IDs defining roles that should have manage permission on the library. + * @default [] + */ + LIBRARY_ADD_in?: string[] | string; + /** + * Modify IDs + * @description A list of role encoded IDs defining roles that should have modify permission on the library. + * @default [] + */ + LIBRARY_MANAGE_in?: string[] | string; + /** + * Add IDs + * @description A list of role encoded IDs defining roles that should be able to add items to the library. + * @default [] + */ + LIBRARY_MODIFY_in?: string[] | string; + }; + /** + * LibraryAvailablePermissions + * @description Base model definition with common configuration used by all derived models. + */ + LibraryAvailablePermissions: { + /** + * Page + * @description Current page . + */ + page: number; + /** + * Page Limit + * @description Maximum number of items per page. + */ + page_limit: number; + /** + * Roles + * @description A list available roles that can be assigned to a particular permission. + */ + roles: components["schemas"]["BasicRoleModel"][]; + /** + * Total + * @description Total number of items + */ + total: number; + }; + /** + * LibraryCurrentPermissions + * @description Base model definition with common configuration used by all derived models. + */ + LibraryCurrentPermissions: { + /** + * Access Role List + * @description A list containing pairs of role names and corresponding encoded IDs which have access to the Library. + */ + access_library_role_list: string[][]; + /** + * Add Role List + * @description A list containing pairs of role names and corresponding encoded IDs which can add items to the Library. + */ + add_library_item_role_list: string[][]; + /** + * Manage Role List + * @description A list containing pairs of role names and corresponding encoded IDs which can manage the Library. + */ + manage_library_role_list: string[][]; + /** + * Modify Role List + * @description A list containing pairs of role names and corresponding encoded IDs which can modify the Library. + */ + modify_library_role_list: string[][]; + }; + /** + * LibraryDestination + * @description Base model definition with common configuration used by all derived models. + */ + LibraryDestination: { + /** + * Description + * @description Description for library to create + */ + description?: string; + /** + * Name + * @description Must specify a library name + */ + name: string; + /** + * Synopsis + * @description Description for library to create + */ + synopsis?: string; + /** + * Type + * @enum {string} + */ + type: "library"; + }; + /** + * LibraryFolderContentsIndexResult + * @description Base model definition with common configuration used by all derived models. + */ + LibraryFolderContentsIndexResult: { + /** Folder Contents */ + folder_contents: ( + | components["schemas"]["FileLibraryFolderItem"] + | components["schemas"]["FolderLibraryFolderItem"] + )[]; + metadata: components["schemas"]["LibraryFolderMetadata"]; + }; + /** + * LibraryFolderContentsIndexSortByEnum + * @description An enumeration. + * @enum {string} + */ + LibraryFolderContentsIndexSortByEnum: "name" | "description" | "type" | "size" | "update_time"; + /** + * LibraryFolderCurrentPermissions + * @description Base model definition with common configuration used by all derived models. + */ + LibraryFolderCurrentPermissions: { + /** + * Add Role List + * @description A list containing pairs of role names and corresponding encoded IDs which can add items to the Library folder. + */ + add_library_item_role_list: string[][]; + /** + * Manage Role List + * @description A list containing pairs of role names and corresponding encoded IDs which can manage the Library folder. + */ + manage_folder_role_list: string[][]; + /** + * Modify Role List + * @description A list containing pairs of role names and corresponding encoded IDs which can modify the Library folder. + */ + modify_folder_role_list: string[][]; + }; + /** + * LibraryFolderDestination + * @description Base model definition with common configuration used by all derived models. + */ + LibraryFolderDestination: { + /** Library Folder Id */ + library_folder_id: string; + /** + * Type + * @enum {string} + */ + type: "library_folder"; + }; + /** + * LibraryFolderDetails + * @description Base model definition with common configuration used by all derived models. + */ + LibraryFolderDetails: { + /** + * Deleted + * @description Whether this folder is marked as deleted. + */ + deleted: boolean; + /** + * Description + * @description A detailed description of the library folder. + * @default + */ + description?: string; + /** + * Genome Build + * @description TODO + * @default ? + */ + genome_build?: string; + /** + * ID + * @description Encoded ID of the library folder. + */ + id: string; + /** + * Item Count + * @description A detailed description of the library folder. + */ + item_count: number; + /** + * Path + * @description The list of folder names composing the path to this folder. + * @default [] + */ + library_path?: string[]; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "LibraryFolder"; + /** + * Name + * @description The name of the library folder. + */ + name: string; + /** + * Parent Folder ID + * @description Encoded ID of the parent folder. Empty if it's the root folder. + */ + parent_id?: string; + /** + * Parent Library ID + * @description Encoded ID of the Library this folder belongs to. + */ + parent_library_id: string; + /** + * Update Time + * Format: date-time + * @description The last time and date this item was updated. + */ + update_time: string; + }; + /** + * LibraryFolderMetadata + * @description Base model definition with common configuration used by all derived models. + */ + LibraryFolderMetadata: { + /** Can Add Library Item */ + can_add_library_item: boolean; + /** Can Modify Folder */ + can_modify_folder: boolean; + /** Folder Description */ + folder_description: string; + /** Folder Name */ + folder_name: string; + /** Full Path */ + full_path: string[][]; + /** Parent Library Id */ + parent_library_id: string; + /** Total Rows */ + total_rows: number; + }; + /** + * LibraryFolderPermissionAction + * @description An enumeration. + * @enum {string} + */ + LibraryFolderPermissionAction: "set_permissions"; + /** + * LibraryFolderPermissionsPayload + * @description Base model definition with common configuration used by all derived models. + */ + LibraryFolderPermissionsPayload: { + /** + * Action + * @description Indicates what action should be performed on the library folder. + */ + action?: components["schemas"]["LibraryFolderPermissionAction"]; + /** + * Add IDs + * @description A list of role encoded IDs defining roles that should be able to add items to the library. + * @default [] + */ + "add_ids[]"?: string[] | string; + /** + * Manage IDs + * @description A list of role encoded IDs defining roles that should have manage permission on the library. + * @default [] + */ + "manage_ids[]"?: string[] | string; + /** + * Modify IDs + * @description A list of role encoded IDs defining roles that should have modify permission on the library. + * @default [] + */ + "modify_ids[]"?: string[] | string; + }; + /** + * LibraryLegacySummary + * @description Base model definition with common configuration used by all derived models. + */ + LibraryLegacySummary: { + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** + * Deleted + * @description Whether this Library has been deleted. + */ + deleted: boolean; + /** + * Description + * @description A detailed description of the Library. + * @default + */ + description?: string; + /** + * ID + * @description Encoded ID of the Library. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Library"; + /** + * Name + * @description The name of the Library. + */ + name: string; + /** + * Root Folder ID + * @description Encoded ID of the Library's base folder. + */ + root_folder_id: string; + /** + * Description + * @description A short text describing the contents of the Library. + */ + synopsis?: string; + }; + /** + * LibraryPermissionAction + * @description An enumeration. + * @enum {string} + */ + LibraryPermissionAction: "set_permissions" | "remove_restrictions"; + /** + * LibraryPermissionScope + * @description An enumeration. + * @enum {string} + */ + LibraryPermissionScope: "current" | "available"; + /** + * LibraryPermissionsPayload + * @description Base model definition with common configuration used by all derived models. + */ + LibraryPermissionsPayload: { + /** + * Access IDs + * @description A list of role encoded IDs defining roles that should have access permission on the library. + * @default [] + */ + "access_ids[]"?: string[] | string; + /** + * Action + * @description Indicates what action should be performed on the Library. + */ + action: components["schemas"]["LibraryPermissionAction"]; + /** + * Add IDs + * @description A list of role encoded IDs defining roles that should be able to add items to the library. + * @default [] + */ + "add_ids[]"?: string[] | string; + /** + * Manage IDs + * @description A list of role encoded IDs defining roles that should have manage permission on the library. + * @default [] + */ + "manage_ids[]"?: string[] | string; + /** + * Modify IDs + * @description A list of role encoded IDs defining roles that should have modify permission on the library. + * @default [] + */ + "modify_ids[]"?: string[] | string; + }; + /** + * LibrarySummary + * @description Base model definition with common configuration used by all derived models. + */ + LibrarySummary: { + /** + * Can User Add + * @description Whether the current user can add contents to this Library. + */ + can_user_add: boolean; + /** + * Can User Manage + * @description Whether the current user can manage the Library and its contents. + */ + can_user_manage: boolean; + /** + * Can User Modify + * @description Whether the current user can modify this Library. + */ + can_user_modify: boolean; + /** + * Create Time + * Format: date-time + * @description The time and date this item was created. + */ + create_time: string; + /** + * Create Time Pretty + * @description Nice time representation of the creation date. + * @example 2 months ago + */ + create_time_pretty: string; + /** + * Deleted + * @description Whether this Library has been deleted. + */ + deleted: boolean; + /** + * Description + * @description A detailed description of the Library. + * @default + */ + description?: string; + /** + * ID + * @description Encoded ID of the Library. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Library"; + /** + * Name + * @description The name of the Library. + */ + name: string; + /** + * Public + * @description Whether this Library has been deleted. + */ + public: boolean; + /** + * Root Folder ID + * @description Encoded ID of the Library's base folder. + */ + root_folder_id: string; + /** + * Description + * @description A short text describing the contents of the Library. + */ + synopsis?: string; + }; + /** + * LibrarySummaryList + * @description Base model definition with common configuration used by all derived models. + * @default [] + */ + LibrarySummaryList: components["schemas"]["LibrarySummary"][]; + /** LicenseMetadataModel */ + LicenseMetadataModel: { + /** + * Details URL + * Format: uri + * @description URL to the SPDX json details for this license + * @example http://spdx.org/licenses/Apache-2.0.json + */ + detailsUrl: string; + /** + * Deprecated License + * @description True if the entire license is deprecated + * @example false + */ + isDeprecatedLicenseId: boolean; + /** + * OSI approved + * @description Indicates if the [OSI](https://opensource.org/) has approved the license + * @example true + */ + isOsiApproved: boolean; + /** + * Identifier + * @description SPDX Identifier + * @example Apache-2.0 + */ + licenseId: string; + /** + * Name + * @description Full name of the license + * @example Apache License 2.0 + */ + name: string; + /** + * Recommended + * @description True if this license is recommended to be used + */ + recommended: boolean; + /** + * Reference + * @description Reference to the HTML format for the license file + * @example ./Apache-2.0.html + */ + reference: string; + /** + * Reference number + * @description *Deprecated* - this field is generated and is no longer in use + */ + referenceNumber: number; + /** + * Reference URLs + * @description Cross reference URL pointing to additional copies of the license + */ + seeAlso: string[]; + /** + * SPDX URL + * Format: uri + * @example https://spdx.org/licenses/Apache-2.0.html + */ + spdxUrl: string; + /** + * URL + * Format: uri + * @description License URL + * @example http://www.apache.org/licenses/LICENSE-2.0 + */ + url: string; + }; + /** + * MaterializeDatasetInstanceAPIRequest + * @description Base model definition with common configuration used by all derived models. + */ + MaterializeDatasetInstanceAPIRequest: { + /** + * Content + * @description Depending on the `source` it can be: + * - The encoded id of the source library dataset + * - The encoded id of the the HDA + */ + content?: string; + /** + * Source + * @description The source of the content. Can be other history element to be copied or library elements. + */ + source?: components["schemas"]["DatasetSourceType"]; + }; + /** + * MetadataFile + * @description Metadata file associated with a dataset. + */ + MetadataFile: { + /** + * Download URL + * @description The URL to download this item from the server. + */ + download_url: string; + /** + * File Type + * @description TODO + */ + file_type: string; + }; + /** Metric */ + Metric: { + /** + * Arguments + * @description A JSON string containing an array of extra data. + */ + args: string; + /** + * Level + * @description An integer representing the metric's log level. + */ + level: number; + /** + * Namespace + * @description Label indicating the source of the metric. + */ + namespace: string; + /** + * Timestamp + * @description The timestamp in ISO format. + * @example 2021-01-23T18:25:43.511Z + */ + time: string; + }; + /** + * ModelStoreFormat + * @description Available types of model stores for export. + * @enum {string} + */ + ModelStoreFormat: "tgz" | "tar" | "tar.gz" | "bag.zip" | "bag.tar" | "bag.tgz" | "rocrate.zip" | "bco.json"; + /** + * NestedElement + * @description Base model definition with common configuration used by all derived models. + */ + NestedElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + /** Elements */ + elements: ( + | ( + | components["schemas"]["FileDataElement"] + | components["schemas"]["PastedDataElement"] + | components["schemas"]["UrlDataElement"] + | components["schemas"]["PathDataElement"] + | components["schemas"]["ServerDirElement"] + | components["schemas"]["FtpImportElement"] + | components["schemas"]["CompositeDataElement"] + ) + | components["schemas"]["NestedElement"] + )[]; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Name */ + name?: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** + * PageContentFormat + * @description An enumeration. + * @enum {string} + */ + PageContentFormat: "markdown" | "html"; + /** + * PageDetails + * @description Base model definition with common configuration used by all derived models. + */ + PageDetails: { + /** + * Content + * @description Raw text contents of the first page revision (type dependent on content_format). + * @default + */ + content?: string; + /** + * Content format + * @description Either `markdown` or `html`. + * @default html + */ + content_format?: components["schemas"]["PageContentFormat"]; + /** + * Deleted + * @description Whether this Page has been deleted. + */ + deleted: boolean; + /** + * Encoded email + * @description The encoded email of the user + */ + email_hash: string; + /** + * Generate Date + * @description The date this page was generated. + */ + generate_time?: string; + /** + * Galaxy Version + * @description The version of Galaxy this page was generated with. + */ + generate_version?: string; + /** + * ID + * @description Encoded ID of the Page. + */ + id: string; + /** + * Importable + * @description Whether this Page can be imported. + */ + importable: boolean; + /** + * Latest revision ID + * @description The encoded ID of the last revision of this Page. + */ + latest_revision_id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Page"; + /** + * Published + * @description Whether this Page has been published. + */ + published: boolean; + /** + * List of revisions + * @description The history with the encoded ID of each revision of the Page. + */ + revision_ids: string[]; + /** + * Identifier + * @description The title slug for the page URL, must be unique. + */ + slug: string; + /** + * Title + * @description The name of the page + */ + title: string; + /** + * Username + * @description The name of the user owning this Page. + */ + username: string; + }; + /** + * PageSortByEnum + * @description An enumeration. + * @enum {string} + */ + PageSortByEnum: "create_time" | "update_time"; + /** + * PageSummary + * @description Base model definition with common configuration used by all derived models. + */ + PageSummary: { + /** + * Deleted + * @description Whether this Page has been deleted. + */ + deleted: boolean; + /** + * Encoded email + * @description The encoded email of the user + */ + email_hash: string; + /** + * ID + * @description Encoded ID of the Page. + */ + id: string; + /** + * Importable + * @description Whether this Page can be imported. + */ + importable: boolean; + /** + * Latest revision ID + * @description The encoded ID of the last revision of this Page. + */ + latest_revision_id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Page"; + /** + * Published + * @description Whether this Page has been published. + */ + published: boolean; + /** + * List of revisions + * @description The history with the encoded ID of each revision of the Page. + */ + revision_ids: string[]; + /** + * Identifier + * @description The title slug for the page URL, must be unique. + */ + slug: string; + /** + * Title + * @description The name of the page + */ + title: string; + /** + * Username + * @description The name of the user owning this Page. + */ + username: string; + }; + /** + * PageSummaryList + * @description Base model definition with common configuration used by all derived models. + * @default [] + */ + PageSummaryList: components["schemas"]["PageSummary"][]; + /** + * PastedDataElement + * @description Base model definition with common configuration used by all derived models. + */ + PastedDataElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Name */ + name?: string; + /** + * Paste Content + * @description Content to upload + */ + paste_content: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "pasted"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** + * PathDataElement + * @description Base model definition with common configuration used by all derived models. + */ + PathDataElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Link Data Only */ + link_data_only?: boolean; + /** Name */ + name?: string; + /** Path */ + path: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "path"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** + * PrepareStoreDownloadPayload + * @description Base model definition with common configuration used by all derived models. + */ + PrepareStoreDownloadPayload: { + /** + * Bco Merge History Metadata + * @description When reading tags/annotations to generate BCO object include history metadata. + * @default false + */ + bco_merge_history_metadata?: boolean; + /** + * Bco Override Algorithmic Error + * @description Override algorithmic error for 'error domain' when generating BioCompute object. + */ + bco_override_algorithmic_error?: { + [key: string]: string | undefined; + }; + /** + * Bco Override Empirical Error + * @description Override empirical error for 'error domain' when generating BioCompute object. + */ + bco_override_empirical_error?: { + [key: string]: string | undefined; + }; + /** + * Bco Override Environment Variables + * @description Override environment variables for 'execution_domain' when generating BioCompute object. + */ + bco_override_environment_variables?: { + [key: string]: string | undefined; + }; + /** + * Bco Override Xref + * @description Override xref for 'description domain' when generating BioCompute object. + */ + bco_override_xref?: components["schemas"]["XrefItem"][]; + /** + * Include deleted + * @description Include file contents for deleted datasets (if include_files is True). + * @default false + */ + include_deleted?: boolean; + /** + * Include Files + * @description include materialized files in export when available + * @default true + */ + include_files?: boolean; + /** + * Include hidden + * @description Include file contents for hidden datasets (if include_files is True). + * @default false + */ + include_hidden?: boolean; + /** + * @description format of model store to export + * @default tar.gz + */ + model_store_format?: components["schemas"]["ModelStoreFormat"]; + }; + /** + * QuotaDetails + * @description Base model containing common fields for Quotas. + */ + QuotaDetails: { + /** + * Bytes + * @description The amount, expressed in bytes, of this Quota. + */ + bytes: number; + /** + * Default + * @description A list indicating which types of default user quotas, if any, are associated with this quota. + * @default [] + */ + default?: components["schemas"]["DefaultQuota"][]; + /** + * Description + * @description Detailed text description for this Quota. + */ + description: string; + /** + * Display Amount + * @description Human-readable representation of the `amount` field. + */ + display_amount: string; + /** + * Groups + * @description A list of specific groups of users associated with this quota. + * @default [] + */ + groups?: components["schemas"]["GroupQuota"][]; + /** + * ID + * @description The `encoded identifier` of the quota. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Quota"; + /** + * Name + * @description The name of the quota. This must be unique within a Galaxy instance. + */ + name: string; + /** + * Operation + * @description Quotas can have one of three `operations`:- `=` : The quota is exactly the amount specified- `+` : The amount specified will be added to the amounts of the user's other associated quota definitions- `-` : The amount specified will be subtracted from the amounts of the user's other associated quota definitions + * @default = + */ + operation?: components["schemas"]["QuotaOperation"]; + /** + * Users + * @description A list of specific users associated with this quota. + * @default [] + */ + users?: components["schemas"]["UserQuota"][]; + }; + /** + * QuotaOperation + * @description An enumeration. + * @enum {string} + */ + QuotaOperation: "=" | "+" | "-"; + /** + * QuotaSummary + * @description Contains basic information about a Quota + */ + QuotaSummary: { + /** + * ID + * @description The `encoded identifier` of the quota. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Quota"; + /** + * Name + * @description The name of the quota. This must be unique within a Galaxy instance. + */ + name: string; + /** + * URL + * @deprecated + * @description The relative URL to get this particular Quota details from the rest API. + */ + url: string; + }; + /** + * QuotaSummaryList + * @description Base model definition with common configuration used by all derived models. + * @default [] + */ + QuotaSummaryList: components["schemas"]["QuotaSummary"][]; + /** + * RemoteFilesDisableMode + * @description An enumeration. + * @enum {string} + */ + RemoteFilesDisableMode: "folders" | "files"; + /** + * RemoteFilesFormat + * @description An enumeration. + * @enum {string} + */ + RemoteFilesFormat: "flat" | "jstree" | "uri"; + /** + * RequestDataType + * @description Particular pieces of information that can be requested for a dataset. + * @enum {string} + */ + RequestDataType: + | "state" + | "converted_datasets_state" + | "data" + | "features" + | "raw_data" + | "track_config" + | "genome_data" + | "in_use_state"; + /** + * Requirement + * @description Available types of job sources (model classes) that produce dataset collections. + * @enum {string} + */ + Requirement: "logged_in" | "new_history" | "admin"; + /** + * RoleDefinitionModel + * @description Base model definition with common configuration used by all derived models. + */ + RoleDefinitionModel: { + /** + * Description + * @description Description of the role + */ + description: string; + /** + * Group IDs + * @default [] + */ + group_ids?: string[]; + /** + * Name + * @description Name of the role + */ + name: string; + /** + * User IDs + * @default [] + */ + user_ids?: string[]; + }; + /** + * RoleListModel + * @description Base model definition with common configuration used by all derived models. + */ + RoleListModel: components["schemas"]["RoleModel"][]; + /** + * RoleModel + * @description Base model definition with common configuration used by all derived models. + */ + RoleModel: { + /** + * Description + * @description Description of the role + */ + description?: string; + /** + * ID + * @description Encoded ID of the role + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "Role"; + /** + * Name + * @description Name of the role + */ + name: string; + /** + * Type + * @description Type or category of the role + */ + type: string; + /** + * URL + * @deprecated + * @description The relative URL to access this item. + */ + url: string; + }; + /** + * ServerDirElement + * @description Base model definition with common configuration used by all derived models. + */ + ServerDirElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Link Data Only */ + link_data_only?: boolean; + /** Name */ + name?: string; + /** Server Dir */ + server_dir: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "server_dir"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + }; + /** + * SetSlugPayload + * @description Base model definition with common configuration used by all derived models. + */ + SetSlugPayload: { + /** + * New Slug + * @description The slug that will be used to access this shared item. + */ + new_slug: string; + }; + /** + * ShareWithExtra + * @description Base model definition with common configuration used by all derived models. + */ + ShareWithExtra: { + /** + * Can Share + * @description Indicates whether the resource can be directly shared or requires further actions. + * @default false + */ + can_share?: boolean; + }; + /** + * ShareWithPayload + * @description Base model definition with common configuration used by all derived models. + */ + ShareWithPayload: { + /** + * Share Option + * @description User choice for sharing resources which its contents may be restricted: + * - None: The user did not choose anything yet or no option is needed. + * - make_public: The contents of the resource will be made publicly accessible. + * - make_accessible_to_shared: This will automatically create a new `sharing role` allowing protected contents to be accessed only by the desired users. + * - no_changes: This won't change the current permissions for the contents. The user which this resource will be shared may not be able to access all its contents. + */ + share_option?: components["schemas"]["SharingOptions"]; + /** + * User Identifiers + * @description A collection of encoded IDs (or email addresses) of users that this resource will be shared with. + */ + user_ids: (string | string)[]; + }; + /** + * ShareWithStatus + * @description Base model definition with common configuration used by all derived models. + */ + ShareWithStatus: { + /** + * Encoded Email + * @description Encoded owner email. + */ + email_hash?: string; + /** + * Errors + * @description Collection of messages indicating that the resource was not shared with some (or all users) due to an error. + * @default [] + */ + errors?: string[]; + /** + * Extra + * @description Optional extra information about this shareable resource that may be of interest. The contents of this field depend on the particular resource. + */ + extra?: components["schemas"]["ShareWithExtra"]; + /** + * ID + * @description The encoded ID of the resource to be shared. + */ + id: string; + /** + * Importable + * @description Whether this resource can be published using a link. + */ + importable: boolean; + /** + * Published + * @description Whether this resource is currently published. + */ + published: boolean; + /** + * Title + * @description The title or name of the resource. + */ + title: string; + /** + * Username + * @description The owner's username. + */ + username?: string; + /** + * Username and slug + * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug} + */ + username_and_slug?: string; + /** + * Users shared with + * @description The list of encoded ids for users the resource has been shared. + * @default [] + */ + users_shared_with?: components["schemas"]["UserEmail"][]; + }; + /** + * SharingOptions + * @description Options for sharing resources that may have restricted access to all or part of their contents. + * @enum {string} + */ + SharingOptions: "make_public" | "make_accessible_to_shared" | "no_changes"; + /** + * SharingStatus + * @description Base model definition with common configuration used by all derived models. + */ + SharingStatus: { + /** + * Encoded Email + * @description Encoded owner email. + */ + email_hash?: string; + /** + * ID + * @description The encoded ID of the resource to be shared. + */ + id: string; + /** + * Importable + * @description Whether this resource can be published using a link. + */ + importable: boolean; + /** + * Published + * @description Whether this resource is currently published. + */ + published: boolean; + /** + * Title + * @description The title or name of the resource. + */ + title: string; + /** + * Username + * @description The owner's username. + */ + username?: string; + /** + * Username and slug + * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug} + */ + username_and_slug?: string; + /** + * Users shared with + * @description The list of encoded ids for users the resource has been shared. + * @default [] + */ + users_shared_with?: components["schemas"]["UserEmail"][]; + }; + /** + * Src + * @description An enumeration. + * @enum {string} + */ + Src: "url" | "pasted" | "files" | "path" | "composite" | "ftp_import" | "server_dir"; + /** + * StoreExportPayload + * @description Base model definition with common configuration used by all derived models. + */ + StoreExportPayload: { + /** + * Include deleted + * @description Include file contents for deleted datasets (if include_files is True). + * @default false + */ + include_deleted?: boolean; + /** + * Include Files + * @description include materialized files in export when available + * @default true + */ + include_files?: boolean; + /** + * Include hidden + * @description Include file contents for hidden datasets (if include_files is True). + * @default false + */ + include_hidden?: boolean; + /** + * @description format of model store to export + * @default tar.gz + */ + model_store_format?: components["schemas"]["ModelStoreFormat"]; + }; + /** + * SuitableConverter + * @description Base model definition with common configuration used by all derived models. + */ + SuitableConverter: { + /** + * Name + * @description The name of the converter. + */ + name: string; + /** + * Original Type + * @description The type to convert from. + */ + original_type: string; + /** + * Target Type + * @description The type to convert to. + */ + target_type: string; + /** + * Tool Id + * @description The ID of the tool that can perform the type conversion. + */ + tool_id: string; + }; + /** + * SuitableConverters + * @description Collection of converters that can be used on a particular dataset collection. + */ + SuitableConverters: components["schemas"]["SuitableConverter"][]; + /** + * TagCollection + * @description The collection of tags associated with an item. + */ + TagCollection: string[]; + /** + * TagOperationParams + * @description Base model definition with common configuration used by all derived models. + */ + TagOperationParams: { + /** Tags */ + tags: string[]; + /** Type */ + type: "add_tags" | "remove_tags"; + }; + /** + * TaggableItemClass + * @description An enumeration. + * @enum {unknown} + */ + TaggableItemClass: + | "History" + | "HistoryDatasetAssociation" + | "LibraryDatasetDatasetAssociation" + | "Page" + | "WorkflowStep" + | "StoredWorkflow" + | "Visualization" + | "HistoryDatasetCollection" + | "LibraryDatasetCollection" + | "Tool"; + /** ToolDataDetails */ + ToolDataDetails: { + /** + * Columns + * @description A list of column names + * @example [ + * "value", + * "dbkey", + * "name", + * "path" + * ] + */ + columns: string[]; + /** + * Fields + * @default [] + */ + fields?: string[][]; + /** + * Model class + * @description The name of class modelling this tool data + * @example TabularToolDataTable + */ + model_class: string; + /** + * Name + * @description The name of this tool data entry + * @example all_fasta + */ + name: string; + }; + /** ToolDataEntry */ + ToolDataEntry: { + /** + * Model class + * @description The name of class modelling this tool data + * @example TabularToolDataTable + */ + model_class: string; + /** + * Name + * @description The name of this tool data entry + * @example all_fasta + */ + name: string; + }; + /** ToolDataEntryList */ + ToolDataEntryList: components["schemas"]["ToolDataEntry"][]; + /** ToolDataField */ + ToolDataField: { + /** + * Base directories + * @description A list of directories where the data files are stored + */ + base_dir: string[]; + /** Fields */ + fields: { + [key: string]: string | undefined; + }; + /** + * Files + * @description A dictionary of file names and their size in bytes + * @example { + * "file.txt": 136 + * } + */ + files: { + [key: string]: number | undefined; + }; + /** + * Fingerprint + * @description SHA1 Hash + * @example 22b45237a85c2b3f474bf66888c534387ffe0ced + */ + fingerprint: string; + /** + * Model class + * @description The name of class modelling this tool data field + * @example TabularToolDataField + */ + model_class: string; + /** + * Name + * @description The name of the field + */ + name: string; + }; + /** ToolDataItem */ + ToolDataItem: { + /** + * Values + * @description A `\t` (TAB) separated list of column __contents__. You must specify a value for each of the columns of the data table. + * @example value dbkey name path + */ + values: string; + }; + /** Tour */ + Tour: { + /** + * Description + * @description Tour description + */ + description: string; + /** + * Identifier + * @description Tour identifier + */ + id: string; + /** + * Name + * @description Name of tour + */ + name: string; + /** + * Requirements + * @description Requirements to run the tour. + */ + requirements: components["schemas"]["Requirement"][]; + /** + * Tags + * @description Topic topic tags + */ + tags: string[]; + }; + /** TourDetails */ + TourDetails: { + /** + * Description + * @description Tour description + */ + description: string; + /** + * Name + * @description Name of tour + */ + name: string; + /** + * Requirements + * @description Requirements to run the tour. + */ + requirements: components["schemas"]["Requirement"][]; + /** + * Steps + * @description Tour steps + */ + steps: components["schemas"]["TourStep"][]; + /** + * Tags + * @description Topic topic tags + */ + tags: string[]; + /** + * Default title + * @description Default title for each step + */ + title_default?: string; + }; + /** + * TourList + * @default [] + */ + TourList: components["schemas"]["Tour"][]; + /** TourStep */ + TourStep: { + /** + * Content + * @description Text shown to the user + */ + content?: string; + /** + * Element + * @description CSS selector for the element to be described/clicked + */ + element?: string; + /** + * Placement + * @description Placement of the text box relative to the selected element + */ + placement?: string; + /** + * Post-click + * @description Elements that receive a click() event after the step is shown + */ + postclick?: boolean | string[]; + /** + * Pre-click + * @description Elements that receive a click() event before the step is shown + */ + preclick?: boolean | string[]; + /** + * Text-insert + * @description Text to insert if element is a text box (e.g. tool search or upload) + */ + textinsert?: string; + /** + * Title + * @description Title displayed in the header of the step container + */ + title?: string; + }; + /** + * UpdateCollectionAttributePayload + * @description Contains attributes that can be updated for all elements in a dataset collection. + */ + UpdateCollectionAttributePayload: { + /** + * Dbkey + * @description TODO + */ + dbkey: string; + }; + /** + * UpdateContentItem + * @description Used for updating a particular history item. All fields are optional. + */ + UpdateContentItem: { + /** + * Content Type + * @description The type of this item. + */ + history_content_type: components["schemas"]["HistoryContentType"]; + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + }; + /** + * UpdateHistoryContentsBatchPayload + * @description Contains property values that will be updated for all the history `items` provided. + * @example { + * "items": [ + * { + * "history_content_type": "dataset", + * "id": "string" + * } + * ], + * "visible": false + * } + */ + UpdateHistoryContentsBatchPayload: { + /** + * Items + * @description A list of content items to update with the changes. + */ + items: components["schemas"]["UpdateContentItem"][]; + }; + /** + * UpdateHistoryContentsPayload + * @description Contains arbitrary property values that will be updated for a particular history item. + * @example { + * "annotation": "Test", + * "visible": false + * } + */ + UpdateHistoryContentsPayload: Record; + /** + * UpdateLibraryFolderPayload + * @description Base model definition with common configuration used by all derived models. + */ + UpdateLibraryFolderPayload: { + /** + * Description + * @description The new description of the library folder. + */ + description?: string; + /** + * Name + * @description The new name of the library folder. + */ + name?: string; + }; + /** + * UpdateLibraryPayload + * @description Base model definition with common configuration used by all derived models. + */ + UpdateLibraryPayload: { + /** + * Description + * @description A detailed description of the Library. Leave unset to keep the existing. + */ + description?: string; + /** + * Name + * @description The new name of the Library. Leave unset to keep the existing. + */ + name?: string; + /** + * Synopsis + * @description A short text describing the contents of the Library. Leave unset to keep the existing. + */ + synopsis?: string; + }; + /** + * UpdateQuotaParams + * @description Base model definition with common configuration used by all derived models. + */ + UpdateQuotaParams: { + /** + * Amount + * @description Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``) + */ + amount?: string; + /** + * Default + * @description Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. Calling this method with ``default="no"`` on a non-default quota will throw an error. Not passing this parameter is equivalent to passing ``no``. + */ + default?: components["schemas"]["DefaultQuotaValues"]; + /** + * Description + * @description Detailed text description for this Quota. + */ + description?: string; + /** + * Groups + * @description A list of group IDs or names to associate with this quota. + */ + in_groups?: string[]; + /** + * Users + * @description A list of user IDs or user emails to associate with this quota. + */ + in_users?: string[]; + /** + * Name + * @description The new name of the quota. This must be unique within a Galaxy instance. + */ + name?: string; + /** + * Operation + * @description One of (``+``, ``-``, ``=``). If you wish to change this value, you must also provide the ``amount``, otherwise it will not take effect. + * @default = + */ + operation?: components["schemas"]["QuotaOperation"]; + }; + /** + * UrlDataElement + * @description Base model definition with common configuration used by all derived models. + */ + UrlDataElement: { + /** Md5 */ + MD5?: string; + /** + * Auto Decompress + * @description Decompress compressed data before sniffing? + * @default false + */ + auto_decompress?: boolean; + /** Collection Type */ + collection_type?: string; + /** Created From Basename */ + created_from_basename?: string; + /** + * Dbkey + * @default ? + */ + dbkey?: string; + /** + * Deferred + * @default false + */ + deferred?: boolean; + elements_from?: components["schemas"]["ElementsFromType"]; + /** + * Ext + * @default auto + */ + ext?: string; + extra_files?: components["schemas"]["ExtraFiles"]; + /** Info */ + info?: string; + /** Name */ + name?: string; + /** + * Space To Tab + * @default false + */ + space_to_tab?: boolean; + /** + * Src + * @enum {string} + */ + src: "url"; + /** Tags */ + tags?: string[]; + /** + * To Posix Lines + * @default false + */ + to_posix_lines?: boolean; + /** + * Url + * @description URL to upload + */ + url: string; + }; + /** + * UserEmail + * @description Base model definition with common configuration used by all derived models. + */ + UserEmail: { + /** + * Email + * @description The email of the user. + */ + email: string; + /** + * User ID + * @description The encoded ID of the user. + */ + id: string; + }; + /** + * UserModel + * @description User in a transaction context. + */ + UserModel: { + /** + * Active + * @description User is active + */ + active: boolean; + /** + * Deleted + * @description User is deleted + */ + deleted: boolean; + /** + * Email + * @description User email + */ + email: string; + /** + * ID + * @description User ID + */ + id: string; + /** + * Last password change + * Format: date-time + */ + last_password_change?: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "User"; + /** + * Username + * @description User username + */ + username: string; + }; + /** + * UserQuota + * @description Base model definition with common configuration used by all derived models. + */ + UserQuota: { + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model_class: "UserQuotaAssociation"; + /** + * User + * @description Information about a user associated with a quota. + */ + user: components["schemas"]["UserModel"]; + }; + /** ValidationError */ + ValidationError: { + /** Location */ + loc: string[]; + /** Message */ + msg: string; + /** Error Type */ + type: string; + }; + /** + * Visualization + * @description Base model definition with common configuration used by all derived models. + */ + Visualization: Record; + /** + * WorkflowInvocationStateSummary + * @description Base model definition with common configuration used by all derived models. + */ + WorkflowInvocationStateSummary: { + /** + * ID + * @description The encoded ID of this entity. + */ + id: string; + /** + * Model class + * @description The name of the database model class. + * @enum {string} + */ + model: "WorkflowInvocation"; + /** + * Populated State + * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated. + */ + populated_state: components["schemas"]["populated_states"]; + /** + * States + * @description A dictionary of job states and the number of jobs in that state. + * @default {} + */ + states?: { + [key: string]: number | undefined; + }; + }; + /** + * WorkflowSortByEnum + * @description An enumeration. + * @enum {string} + */ + WorkflowSortByEnum: "create_time" | "update_time" | "name" | "None"; + /** + * WriteInvocationStoreToPayload + * @description Base model definition with common configuration used by all derived models. + */ + WriteInvocationStoreToPayload: { + /** + * Bco Merge History Metadata + * @description When reading tags/annotations to generate BCO object include history metadata. + * @default false + */ + bco_merge_history_metadata?: boolean; + /** + * Bco Override Algorithmic Error + * @description Override algorithmic error for 'error domain' when generating BioCompute object. + */ + bco_override_algorithmic_error?: { + [key: string]: string | undefined; + }; + /** + * Bco Override Empirical Error + * @description Override empirical error for 'error domain' when generating BioCompute object. + */ + bco_override_empirical_error?: { + [key: string]: string | undefined; + }; + /** + * Bco Override Environment Variables + * @description Override environment variables for 'execution_domain' when generating BioCompute object. + */ + bco_override_environment_variables?: { + [key: string]: string | undefined; + }; + /** + * Bco Override Xref + * @description Override xref for 'description domain' when generating BioCompute object. + */ + bco_override_xref?: components["schemas"]["XrefItem"][]; + /** + * Include deleted + * @description Include file contents for deleted datasets (if include_files is True). + * @default false + */ + include_deleted?: boolean; + /** + * Include Files + * @description include materialized files in export when available + * @default true + */ + include_files?: boolean; + /** + * Include hidden + * @description Include file contents for hidden datasets (if include_files is True). + * @default false + */ + include_hidden?: boolean; + /** + * @description format of model store to export + * @default tar.gz + */ + model_store_format?: components["schemas"]["ModelStoreFormat"]; + /** + * Target URI + * @description Galaxy Files URI to write mode store content to. + */ + target_uri: string; + }; + /** + * WriteStoreToPayload + * @description Base model definition with common configuration used by all derived models. + */ + WriteStoreToPayload: { + /** + * Include deleted + * @description Include file contents for deleted datasets (if include_files is True). + * @default false + */ + include_deleted?: boolean; + /** + * Include Files + * @description include materialized files in export when available + * @default true + */ + include_files?: boolean; + /** + * Include hidden + * @description Include file contents for hidden datasets (if include_files is True). + * @default false + */ + include_hidden?: boolean; + /** + * @description format of model store to export + * @default tar.gz + */ + model_store_format?: components["schemas"]["ModelStoreFormat"]; + /** + * Target URI + * @description Galaxy Files URI to write mode store content to. + */ + target_uri: string; + }; + /** XrefItem */ + XrefItem: { + /** + * Access Time + * Format: date-time + * @description Date and time the external reference was accessed + */ + access_time: string; + /** + * Ids + * @description List of reference identifiers + */ + ids: string[]; + /** + * Name + * @description Name of external reference + */ + name: string; + /** + * Namespace + * @description External resource vendor prefix + */ + namespace: string; + }; + /** + * states + * @description An enumeration. + * @enum {string} + */ + galaxy__model__Dataset__states: + | "new" + | "upload" + | "queued" + | "running" + | "ok" + | "empty" + | "error" + | "paused" + | "setting_metadata" + | "failed_metadata" + | "deferred" + | "discarded"; + /** + * states + * @description An enumeration. + * @enum {string} + */ + galaxy__model__Job__states: + | "new" + | "resubmitted" + | "upload" + | "waiting" + | "queued" + | "running" + | "ok" + | "error" + | "failed" + | "paused" + | "deleting" + | "deleted" + | "deleted_new" + | "stop" + | "stopped"; + /** + * populated_states + * @description An enumeration. + * @enum {string} + */ + populated_states: "new" | "ok" | "failed"; + /** + * validated_states + * @description An enumeration. + * @enum {string} + */ + validated_states: "unknown" | "invalid" | "ok"; + }; + responses: never; + parameters: never; + requestBodies: never; + headers: never; + pathItems: never; +} + +export type external = Record; + +export interface operations { + index_api_configuration_get: { + /** + * Return an object containing exposable configuration settings + * @description Return an object containing exposable configuration settings. + * + * A more complete list is returned if the user is an admin. + * Pass in `view` and a comma-seperated list of keys to control which + * configuration settings are returned. + */ + parameters?: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Object containing exposable configuration settings */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + decode_id_api_configuration_decode__encoded_id__get: { + /** + * Decode a given id + * @description Decode a given id. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description Encoded id to be decoded */ + path: { + encoded_id: string; + }; + }; + responses: { + /** @description Decoded id */ + 200: { + content: { + "application/json": { + [key: string]: number | undefined; + }; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + dynamic_tool_confs_api_configuration_dynamic_tool_confs_get: { + /** + * Return dynamic tool configuration files + * @description Return dynamic tool configuration files. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Dynamic tool configuration files */ + 200: { + content: { + "application/json": { + [key: string]: string | undefined; + }[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + tool_lineages_api_configuration_tool_lineages_get: { + /** + * Return tool lineages for tools that have them + * @description Return tool lineages for tools that have them. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Tool lineages for tools that have them */ + 200: { + content: { + "application/json": { + [key: string]: Record | undefined; + }[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + reload_toolbox_api_configuration_toolbox_put: { + /** + * Reload the Galaxy toolbox (but not individual tools) + * @description Reload the Galaxy toolbox (but not individual tools). + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_dataset_collections_post: { + /** Create a new dataset collection instance. */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateNewCollectionPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["HDCADetailed"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get: { + /** Returns direct child contents of indicated dataset collection parent ID. */ + parameters: { + /** @description The type of collection instance. Either `history` (default) or `library`. */ + /** @description The maximum number of content elements to return. */ + /** @description The number of content elements that will be skipped before returning. */ + query?: { + instance_type?: "history" | "library"; + limit?: number; + offset?: number; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the dataset collection. */ + /** @description Parent collection ID describing what collection the contents belongs to. */ + path: { + hdca_id: string; + parent_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetCollectionContentElements"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_dataset_collections__id__get: { + /** Returns detailed information about the given collection. */ + parameters: { + /** @description The type of collection instance. Either `history` (default) or `library`. */ + query?: { + instance_type?: "history" | "library"; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the dataset collection. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["HDCADetailed"] | components["schemas"]["HDCASummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + attributes_api_dataset_collections__id__attributes_get: { + /** Returns `dbkey`/`extension` attributes for all the collection elements. */ + parameters: { + /** @description The type of collection instance. Either `history` (default) or `library`. */ + query?: { + instance_type?: "history" | "library"; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the dataset collection. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetCollectionAttributesResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + copy_api_dataset_collections__id__copy_post: { + /** Copy the given collection datasets to a new collection using a new `dbkey` attribute. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the dataset collection to copy. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateCollectionAttributePayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + download_dataset_collection_api_dataset_collections__id__download_get: { + /** + * Download the content of a dataset collection as a `zip` archive. + * @description Download the content of a history dataset collection as a `zip` archive + * while maintaining approximate collection structure. + */ + parameters: { + /** @description The encoded database identifier of the History. */ + query?: { + history_id?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the `HDCA` contained in the history. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + prepare_collection_download_api_dataset_collections__id__prepare_download_post: { + /** + * Prepare an short term storage object that the collection will be downloaded to. + * @description The history dataset collection will be written as a `zip` archive to the + * returned short term storage object. Progress tracking this file's creation + * can be tracked with the short_term_storage API. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the `HDCA` contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncFile"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + suitable_converters_api_dataset_collections__id__suitable_converters_get: { + /** Returns a list of applicable converters for all datatypes in the given collection. */ + parameters: { + /** @description The type of collection instance. Either `history` (default) or `library`. */ + query?: { + instance_type?: "history" | "library"; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the dataset collection. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SuitableConverters"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_datasets_get: { + /** Search datasets or collections using a query system. */ + parameters?: { + /** @description Optional identifier of a History. Use it to restrict the search whithin a particular History. */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + query?: { + history_id?: string; + view?: string; + keys?: string; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_batch_api_datasets_delete: { + /** + * Deletes or purges a batch of datasets. + * @description Deletes or purges a batch of datasets. + * **Warning**: only the ownership of the datasets (and upload state for HDAs) is checked, + * no other checks or restrictions are made. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["DeleteDatasetBatchPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DeleteDatasetBatchResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_datasets__dataset_id__get: { + /** + * Displays information about and/or content of a dataset. + * @description **Note**: Due to the multipurpose nature of this endpoint, which can receive a wild variety of parameters + * and return different kinds of responses, the documentation here will be limited. + * To get more information please check the source code. + */ + parameters: { + /** @description The type of information about the dataset to be requested. */ + /** @description The type of information about the dataset to be requested. Each of these values may require additional parameters in the request and may return different responses. */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + hda_ldda?: components["schemas"]["DatasetSourceType"]; + data_type?: components["schemas"]["RequestDataType"]; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + converted_api_datasets__dataset_id__converted_get: { + /** + * Return a a map with all the existing converted datasets associated with this instance. + * @description Return a map of ` : ` containing all the *existing* converted datasets. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["ConvertedDatasetsMap"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + converted_ext_api_datasets__dataset_id__converted__ext__get: { + /** + * Return information about datasets made by converting this dataset to a new format. + * @description Return information about datasets made by converting this dataset to a new format. + * + * If there is no existing converted dataset for the format in `ext`, one will be created. + * + * **Note**: `view` and `keys` are also available to control the serialization of the dataset. + */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + /** @description File extension of the new format to convert this dataset to. */ + path: { + dataset_id: string; + ext: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["HDADetailed"] | components["schemas"]["HDASummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_content_as_text_api_datasets__dataset_id__get_content_as_text_get: { + /** Returns dataset content as Text. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetTextContentDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + compute_hash_api_datasets__dataset_id__hash_put: { + /** Compute dataset hash for dataset and update model */ + parameters: { + /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */ + query?: { + hda_ldda?: components["schemas"]["DatasetSourceType"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ComputeDatasetHashPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncTaskResultSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get: { + /** For internal use, this endpoint may change without warning. */ + parameters: { + /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */ + query?: { + hda_ldda?: components["schemas"]["DatasetSourceType"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetInheritanceChain"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_permissions_api_datasets__dataset_id__permissions_put: { + /** + * Set permissions of the given history dataset to the given role ids. + * @description Set permissions of the given history dataset to the given role ids. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + requestBody: { + content: { + /** + * @example { + * "access_ids[]": [], + * "action": "set_permissions", + * "manage_ids[]": [], + * "modify_ids[]": [] + * } + */ + "application/json": Record; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetAssociationRoles"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_storage_api_datasets__dataset_id__storage_get: { + /** Display user-facing storage details related to the objectstore a dataset resides in. */ + parameters: { + /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */ + query?: { + hda_ldda?: components["schemas"]["DatasetSourceType"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + dataset_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetStorageDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + display_api_datasets__history_content_id__display_get: { + /** + * Displays (preview) or downloads dataset content. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + parameters: { + /** @description The encoded database identifier of the History. */ + /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */ + /** @description TODO */ + /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */ + /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */ + query?: { + history_id?: string; + preview?: boolean; + filename?: string; + to_ext?: string; + raw?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + display_api_datasets__history_content_id__display_head: { + /** + * Check if dataset content can be previewed or downloaded. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + parameters: { + /** @description The encoded database identifier of the History. */ + /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */ + /** @description TODO */ + /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */ + /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */ + query?: { + history_id?: string; + preview?: boolean; + filename?: string; + to_ext?: string; + raw?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_metadata_file_api_datasets__history_content_id__metadata_file_get: { + /** Returns the metadata file associated with this history item. */ + parameters: { + /** @description The encoded database identifier of the History. */ + /** @description The name of the metadata file to retrieve. */ + query: { + history_id?: string; + metadata_file: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_datatypes_get: { + /** + * Lists all available data types + * @description Gets the list of all available data types. + */ + parameters?: { + /** @description Whether to return only the datatype's extension rather than the datatype's details */ + /** @description Whether to return only datatypes which can be uploaded */ + query?: { + extension_only?: boolean; + upload_only?: boolean; + }; + }; + responses: { + /** @description List of data types */ + 200: { + content: { + "application/json": components["schemas"]["DatatypeDetails"][] | string[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + converters_api_datatypes_converters_get: { + /** + * Returns the list of all installed converters + * @description Gets the list of all installed converters. + */ + responses: { + /** @description List of all datatype converters */ + 200: { + content: { + "application/json": components["schemas"]["DatatypeConverterList"]; + }; + }; + }; + }; + edam_data_api_datatypes_edam_data_get: { + /** + * Returns a dictionary/map of datatypes and EDAM data + * @description Gets a map of datatypes and their corresponding EDAM data. + */ + responses: { + /** @description Dictionary/map of datatypes and EDAM data */ + 200: { + content: { + "application/json": { + [key: string]: string | undefined; + }; + }; + }; + }; + }; + edam_data_detailed_api_datatypes_edam_data_detailed_get: { + /** + * Returns a dictionary of datatypes and EDAM data details + * @description Gets a map of datatypes and their corresponding EDAM data. + * EDAM data contains the EDAM iri, label, and definition. + */ + responses: { + /** @description Dictionary of EDAM data details containing the EDAM iri, label, and definition */ + 200: { + content: { + "application/json": components["schemas"]["DatatypesEDAMDetailsDict"]; + }; + }; + }; + }; + edam_formats_api_datatypes_edam_formats_get: { + /** + * Returns a dictionary/map of datatypes and EDAM formats + * @description Gets a map of datatypes and their corresponding EDAM formats. + */ + responses: { + /** @description Dictionary/map of datatypes and EDAM formats */ + 200: { + content: { + "application/json": { + [key: string]: string | undefined; + }; + }; + }; + }; + }; + edam_formats_detailed_api_datatypes_edam_formats_detailed_get: { + /** + * Returns a dictionary of datatypes and EDAM format details + * @description Gets a map of datatypes and their corresponding EDAM formats. + * EDAM formats contain the EDAM iri, label, and definition. + */ + responses: { + /** @description Dictionary of EDAM format details containing the EDAM iri, label, and definition */ + 200: { + content: { + "application/json": components["schemas"]["DatatypesEDAMDetailsDict"]; + }; + }; + }; + }; + mapping_api_datatypes_mapping_get: { + /** + * Returns mappings for data types and their implementing classes + * @description Gets mappings for data types. + */ + responses: { + /** @description Dictionary to map data types with their classes */ + 200: { + content: { + "application/json": components["schemas"]["DatatypesMap"]; + }; + }; + }; + }; + sniffers_api_datatypes_sniffers_get: { + /** + * Returns the list of all installed sniffers + * @description Gets the list of all installed data type sniffers. + */ + responses: { + /** @description List of datatype sniffers */ + 200: { + content: { + "application/json": string[]; + }; + }; + }; + }; + types_and_mapping_api_datatypes_types_and_mapping_get: { + /** + * Returns all the data types extensions and their mappings + * @description Combines the datatype information from (/api/datatypes) and the + * mapping information from (/api/datatypes/mapping) into a single + * response. + */ + parameters?: { + /** @description Whether to return only the datatype's extension rather than the datatype's details */ + /** @description Whether to return only datatypes which can be uploaded */ + query?: { + extension_only?: boolean; + upload_only?: boolean; + }; + }; + responses: { + /** @description Dictionary to map data types with their classes */ + 200: { + content: { + "application/json": components["schemas"]["DatatypesCombinedMap"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_folders__folder_id__contents_get: { + /** + * Returns a list of a folder's contents (files and sub-folders) with additional metadata about the folder. + * @description Returns a list of a folder's contents (files and sub-folders). + * + * Additional metadata for the folder is provided in the response as a separate object containing data + * for breadcrumb path building, permissions and other folder's details. + * + * *Note*: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting). + * + * **Security note**: + * - Accessing a library folder or sub-folder requires only access to the parent library. + * - Deleted folders can only be accessed by admins or users with `MODIFY` permission. + * - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders. + */ + parameters: { + /** @description Maximum number of contents to return. */ + /** @description Return contents from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, contents between position 200-299 will be returned. */ + /** @description Used to filter the contents. Only the folders and files which name contains this text will be returned. */ + /** @description Returns also deleted contents. Deleted contents can only be retrieved by Administrators or users with */ + /** @description Sort results by specified field. */ + /** @description Sort results in descending order. */ + query?: { + limit?: number; + offset?: number; + search_text?: string; + include_deleted?: boolean; + order_by?: components["schemas"]["LibraryFolderContentsIndexSortByEnum"]; + sort_desc?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + folder_id: string; + }; + }; + responses: { + /** @description The contents of the folder that match the query parameters. */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderContentsIndexResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + add_history_datasets_to_library_api_folders__folder_id__contents_post: { + /** Creates a new library file from an existing HDA/HDCA. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + folder_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateLibraryFilePayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_folders__id__get: { + /** + * Displays information about a particular library folder. + * @description Returns detailed information about the library folder with the given ID. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_folders__id__put: { + /** + * Updates the information of an existing library folder. + * @description Updates the information of an existing library folder. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateLibraryFolderPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_folders__id__post: { + /** + * Create a new library folder underneath the one specified by the ID. + * @description Returns detailed information about the newly created library folder. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateLibraryFolderPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_folders__id__delete: { + /** + * Marks the specified library folder as deleted (or undeleted). + * @description Marks the specified library folder as deleted (or undeleted). + */ + parameters: { + /** @description Whether to restore a deleted library folder. */ + query?: { + undelete?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_folders__id__patch: { + /** + * Update + * @description Updates the information of an existing library folder. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateLibraryFolderPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_permissions_api_folders__id__permissions_get: { + /** + * Gets the current or available permissions of a particular library folder. + * @description Gets the current or available permissions of a particular library. + * The results can be paginated and additionally filtered by a query. + */ + parameters: { + /** @description The scope of the permissions to retrieve. Either the `current` permissions or the `available`. */ + /** @description The page number to retrieve when paginating the available roles. */ + /** @description The maximum number of permissions per page when paginating. */ + /** @description Optional search text to retrieve only the roles matching this query. */ + query?: { + scope?: components["schemas"]["LibraryPermissionScope"]; + page?: number; + page_limit?: number; + q?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["LibraryFolderCurrentPermissions"] + | components["schemas"]["LibraryAvailablePermissions"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + set_permissions_api_folders__id__permissions_post: { + /** + * Sets the permissions to manage a library folder. + * @description Sets the permissions to manage a library folder. + */ + parameters: { + /** @description Indicates what action should be performed on the Library. Currently only `set_permissions` is supported. */ + query?: { + action?: components["schemas"]["LibraryFolderPermissionAction"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the library folder. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["LibraryFolderPermissionsPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibraryFolderCurrentPermissions"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_ftp_files_get: { + /** + * Displays remote files available to the user. Please use /api/remote_files instead. + * @deprecated + * @description Lists all remote files available to the user from different sources. + */ + parameters?: { + /** @description The source to load datasets from. Possible values: ftpdir, userdir, importdir */ + /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */ + /** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */ + /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */ + query?: { + target?: string; + format?: components["schemas"]["RemoteFilesFormat"]; + recursive?: boolean; + disable?: components["schemas"]["RemoteFilesDisableMode"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_genomes_get: { + /** Return a list of installed genomes */ + parameters?: { + /** @description If true, return genome keys with chromosome lengths */ + query?: { + chrom_info?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Installed genomes */ + 200: { + content: { + "application/json": string[][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_genomes__id__get: { + /** Return information about build */ + parameters: { + /** @description If true, return reference data */ + /** @description Limits size of returned data */ + /** @description Limits size of returned data */ + /** @description Limits size of returned data */ + /** @description Limits size of returned data */ + /** @description Format */ + query?: { + reference?: boolean; + num?: number; + chrom?: string; + low?: number; + high?: number; + format?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description Genome ID */ + path: { + id: string; + }; + }; + responses: { + /** @description Information about genome build */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + indexes_api_genomes__id__indexes_get: { + /** Return all available indexes for a genome id for provided type */ + parameters: { + /** @description Index type */ + /** @description Format */ + query?: { + type?: string; + format?: string; + }; + /** @description Genome ID */ + path: { + id: string; + }; + }; + responses: { + /** @description Indexes for a genome id for provided type */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + sequences_api_genomes__id__sequences_get: { + /** Return raw sequence data */ + parameters: { + /** @description If true, return reference data */ + /** @description Limits size of returned data */ + /** @description Limits size of returned data */ + /** @description Limits size of returned data */ + /** @description Format */ + query?: { + reference?: boolean; + chrom?: string; + low?: number; + high?: number; + format?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description Genome ID */ + path: { + id: string; + }; + }; + responses: { + /** @description Raw sequence data */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_groups__group_id__roles_get: { + /** Displays a collection (list) of groups. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + path: { + group_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupRoleListModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + group_role_api_groups__group_id__roles__id__get: { + /** Displays information about a group role. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the role */ + path: { + group_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupRoleModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_groups__group_id__roles__role_id__put: { + /** Adds a role to a group */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the role */ + path: { + group_id: string; + role_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupRoleModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_groups__group_id__roles__role_id__delete: { + /** Removes a role from a group */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the role */ + path: { + group_id: string; + role_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupRoleModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + group_user_api_groups__group_id__user__id__get: { + /** + * Displays information about a group user. + * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Displays information about a group user. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the user */ + path: { + group_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_groups__group_id__user__user_id__put: { + /** + * Adds a user to a group + * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Adds a user to a group + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the user */ + path: { + group_id: string; + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_groups__group_id__user__user_id__delete: { + /** + * Removes a user from a group + * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Removes a user from a group + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the user */ + path: { + group_id: string; + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_groups__group_id__users_get: { + /** + * Displays a collection (list) of groups. + * @description GET /api/groups/{encoded_group_id}/users + * Displays a collection (list) of groups. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + path: { + group_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserListModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + group_user_api_groups__group_id__users__id__get: { + /** + * Displays information about a group user. + * @description GET /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Displays information about a group user. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the user */ + path: { + group_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_groups__group_id__users__user_id__put: { + /** + * Adds a user to a group + * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Adds a user to a group + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the user */ + path: { + group_id: string; + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_groups__group_id__users__user_id__delete: { + /** + * Removes a user from a group + * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + * Removes a user from a group + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the group */ + /** @description The ID of the user */ + path: { + group_id: string; + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GroupUserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_histories_get: { + /** Returns histories for the current user. */ + parameters?: { + /** @description Whether all histories from other users in this Galaxy should be included. Only admins are allowed to query all histories. */ + /** + * @deprecated + * @description Whether to return only deleted items. + */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + all?: boolean; + deleted?: boolean; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_histories_post: { + /** + * Creates a new history. + * @description The new history can also be copied form a existing history or imported from an archive or URL. + */ + parameters?: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody?: { + content: { + "application/x-www-form-urlencoded": components["schemas"]["Body_create_api_histories_post"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["JobImportHistoryResponse"] + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_deleted_api_histories_deleted_get: { + /** Returns deleted histories for the current user. */ + parameters?: { + /** @description Whether all histories from other users in this Galaxy should be included. Only admins are allowed to query all histories. */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + all?: boolean; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + undelete_api_histories_deleted__id__undelete_post: { + /** Restores a deleted history with the given ID (that hasn't been purged). */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_from_store_api_histories_from_store_post: { + /** Create histories from a model store. */ + parameters?: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateHistoryFromStore"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_from_store_async_api_histories_from_store_async_post: { + /** Launch a task to create histories from a model store. */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateHistoryFromStore"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_recent_api_histories_most_recently_used_get: { + /** Returns the most recently used history of the user. */ + parameters?: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + published_api_histories_published_get: { + /** Return all histories that are published. */ + parameters?: { + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + shared_with_me_api_histories_shared_with_me_get: { + /** Return all histories that are shared with the current user. */ + parameters?: { + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_contents_api_histories__history_id__contents_get: { + /** + * Returns the contents of the given history. + * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``. + * + * - The contents can be filtered and queried using the appropriate parameters. + * - The amount of information returned for each item can be customized. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + parameters: { + /** + * @description Only `dev` value is allowed. Set it to use the latest version of this endpoint. **All parameters marked as `deprecated` will be ignored when this parameter is set.** + * @example dev + */ + /** + * @deprecated + * @description Legacy name for the `dataset_details` parameter. + */ + /** + * @deprecated + * @description A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the specific datasets will be returned. Also, setting this value will return `all` details of the content item. + */ + /** + * @deprecated + * @description A list or comma-separated list of kinds of contents to return (currently just `dataset` and `dataset_collection` are available). If unset, all types will be returned. + */ + /** + * @deprecated + * @description Whether to return deleted or undeleted datasets only. Leave unset for both. + */ + /** + * @deprecated + * @description Whether to return visible or hidden datasets only. Leave unset for both. + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + query?: { + v?: string; + details?: string; + ids?: string; + types?: string[]; + deleted?: boolean; + visible?: boolean; + view?: string; + keys?: string; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + responses: { + /** @description The contents of the history that match the query. */ + 200: { + content: { + "application/json": components["schemas"]["HistoryContentsResult"]; + "application/vnd.galaxy.history.contents.stats+json": components["schemas"]["HistoryContentsWithStatsResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_batch_api_histories__history_id__contents_put: { + /** + * Batch update specific properties of a set items contained in the given History. + * @description Batch update specific properties of a set items contained in the given History. + * + * If you provide an invalid/unknown property key the request will not fail, but no changes + * will be made to the items. + */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateHistoryContentsBatchPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["HistoryContentsResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_histories__history_id__contents_post: { + /** + * Create a new `HDA` or `HDCA` in the given History. + * @deprecated + * @description Create a new `HDA` or `HDCA` in the given History. + */ + parameters: { + /** + * @description The type of the history element to create. + * @example dataset + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + type?: components["schemas"]["HistoryContentType"]; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateHistoryContentPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + | ( + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + archive_api_histories__history_id__contents_archive__filename___format__get: { + /** + * Build and return a compressed archive of the selected history contents. + * @description Build and return a compressed archive of the selected history contents. + * + * **Note**: this is a volatile endpoint and settings and behavior may change. + */ + parameters: { + /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + query?: { + dry_run?: boolean; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + filename: string; + format: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + archive_api_histories__history_id__contents_archive__id__get: { + /** + * Build and return a compressed archive of the selected history contents. + * @description Build and return a compressed archive of the selected history contents. + * + * **Note**: this is a volatile endpoint and settings and behavior may change. + */ + parameters: { + /** @description The name that the Archive will have (defaults to history name). */ + /** + * @deprecated + * @description Output format of the archive. + */ + /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + query?: { + filename?: string; + format?: string; + dry_run?: boolean; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + bulk_operation_api_histories__history_id__contents_bulk_put: { + /** + * Executes an operation on a set of items contained in the given History. + * @description Executes an operation on a set of items contained in the given History. + * + * The items to be processed can be explicitly set or determined by a dynamic query. + */ + parameters: { + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + query?: { + q?: string[]; + qv?: string[]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["HistoryContentBulkOperationPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["HistoryContentBulkOperationResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + download_dataset_collection_api_histories__history_id__contents_dataset_collections__id__download_get: { + /** + * Download the content of a dataset collection as a `zip` archive. + * @description Download the content of a history dataset collection as a `zip` archive + * while maintaining approximate collection structure. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the `HDCA` contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + prepare_collection_download_api_histories__history_id__contents_dataset_collections__id__prepare_download_post: { + /** + * Prepare an short term storage object that the collection will be downloaded to. + * @description The history dataset collection will be written as a `zip` archive to the + * returned short term storage object. Progress tracking this file's creation + * can be tracked with the short_term_storage API. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the `HDCA` contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + responses: { + /** @description Short term storage reference for async monitoring of this download. */ + 200: { + content: { + "application/json": components["schemas"]["AsyncFile"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + /** @description Required asynchronous tasks required for this operation not available. */ + 501: never; + }; + }; + materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post: { + /** Materialize a deferred dataset into real, usable dataset. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncTaskResultSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_permissions_api_histories__history_id__contents__dataset_id__permissions_put: { + /** + * Set permissions of the given history dataset to the given role ids. + * @description Set permissions of the given history dataset to the given role ids. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + dataset_id: string; + }; + }; + requestBody: { + content: { + /** + * @example { + * "access_ids[]": [], + * "action": "set_permissions", + * "manage_ids[]": [], + * "modify_ids[]": [] + * } + */ + "application/json": Record; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DatasetAssociationRoles"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + contents_near_api_histories__history_id__contents__direction___hid___limit__get: { + /** + * Get content items around a particular `HID`. + * @description .. warning:: For internal use to support the scroller functionality. + * + * This endpoint provides random access to a large history without having + * to know exactly how many pages are in the final query. Pick a target HID + * and filters, and the endpoint will get a maximum of `limit` history items "around" the `hid`. + * + * Additional counts are provided in the HTTP headers. + * + * The `direction` determines what items are selected: + * + * a) item counts: + * + * - total matches-up: hid < {hid} + * - total matches-down: hid > {hid} + * - total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid}) + * - displayed matches-up: hid <= {hid} (hid == {hid} is included) + * - displayed matches-down: hid > {hid} + * - displayed matches: displayed matches-up + displayed matches-down + * + * b) {limit} history items: + * + * - if direction == "before": hid <= {hid} + * - if direction == "after": hid > {hid} + * - if direction == "near": "near" {hid}, so that + * n. items before <= limit // 2, + * n. items after <= limit // 2 + 1. + * + * .. note:: This endpoint uses slightly different filter params syntax. Instead of using `q`/`qv` parameters, + * it uses the following syntax for query parameters:: + * + * ?[field]-[operator]=[value] + * + * Example:: + * + * ?update_time-gt=2015-01-29 + */ + parameters: { + /** @description A timestamp in ISO format to check if the history has changed since this particular date/time. If it hasn't changed, no additional processing will be done and 204 status code will be returned. */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + since?: string; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The target `HID` to get content around it. */ + /** @description Determines what items are selected before, after or near the target `hid`. */ + /** @description The maximum number of content items to return above and below the target `HID`. */ + path: { + history_id: string; + hid: number; + direction: components["schemas"]["DirectionOptions"]; + limit: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["HistoryContentsResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_contents_display_api_histories__history_id__contents__history_content_id__display_get: { + /** + * Displays (preview) or downloads dataset content. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + parameters: { + /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */ + /** @description TODO */ + /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */ + /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */ + query?: { + preview?: boolean; + filename?: string; + to_ext?: string; + raw?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + history_id: string; + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_contents_display_api_histories__history_id__contents__history_content_id__display_head: { + /** + * Check if dataset content can be previewed or downloaded. + * @description Streams the dataset for download or the contents preview to be displayed in a browser. + */ + parameters: { + /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */ + /** @description TODO */ + /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */ + /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */ + query?: { + preview?: boolean; + filename?: string; + to_ext?: string; + raw?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + history_id: string; + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + extra_files_api_histories__history_id__contents__history_content_id__extra_files_get: { + /** Generate list of extra files. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + /** @description The encoded database identifier of the dataset. */ + path: { + history_id: string; + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_metadata_file_api_histories__history_id__contents__history_content_id__metadata_file_get: { + /** Returns the metadata file associated with this history item. */ + parameters: { + /** @description The name of the metadata file to retrieve. */ + query: { + metadata_file: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the dataset. */ + path: { + history_id: string; + history_content_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_content_api_histories__history_id__contents__id__get: { + /** + * Return detailed information about an HDA within a history. + * @deprecated + * @description Return detailed information about an `HDA` or `HDCA` within a history. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + parameters: { + /** + * @description The type of the history element to show. + * @example dataset + */ + /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + type?: components["schemas"]["HistoryContentType"]; + fuzzy_count?: number; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_histories__history_id__contents__id__put: { + /** + * Updates the values for the history content item with the given ``ID``. + * @deprecated + * @description Updates the values for the history content item with the given ``ID``. + */ + parameters: { + /** + * @description The type of the history element to show. + * @example dataset + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + type?: components["schemas"]["HistoryContentType"]; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateHistoryContentsPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_histories__history_id__contents__id__delete: { + /** + * Delete the history dataset with the given ``ID``. + * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset). + * + * **Note**: Currently does not stop any active jobs for which this dataset is an output. + */ + parameters: { + /** + * @description The type of the history element to show. + * @example dataset + */ + /** + * @deprecated + * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA. + */ + /** + * @deprecated + * @description When deleting a dataset collection, whether to also delete containing datasets. + */ + /** + * @deprecated + * @description Whether to stop the creating job if all outputs of the job have been deleted. + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + type?: components["schemas"]["HistoryContentType"]; + purge?: boolean; + recursive?: boolean; + stop_job?: boolean; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["DeleteHistoryContentPayload"]; + }; + }; + responses: { + /** @description Request has been executed. */ + 200: { + content: { + "application/json": components["schemas"]["DeleteHistoryContentResult"]; + }; + }; + /** @description Request accepted, processing will finish later. */ + 202: { + content: { + "application/json": components["schemas"]["DeleteHistoryContentResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + validate_api_histories__history_id__contents__id__validate_put: { + /** + * Validates the metadata associated with a dataset within a History. + * @description Validates the metadata associated with a dataset within a History. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_histories__history_id__contents__type_s_get: { + /** + * Returns the contents of the given history filtered by type. + * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``. + * + * - The contents can be filtered and queried using the appropriate parameters. + * - The amount of information returned for each item can be customized. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + parameters: { + /** + * @description Only `dev` value is allowed. Set it to use the latest version of this endpoint. **All parameters marked as `deprecated` will be ignored when this parameter is set.** + * @example dev + */ + /** + * @deprecated + * @description Legacy name for the `dataset_details` parameter. + */ + /** + * @deprecated + * @description A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the specific datasets will be returned. Also, setting this value will return `all` details of the content item. + */ + /** + * @deprecated + * @description A list or comma-separated list of kinds of contents to return (currently just `dataset` and `dataset_collection` are available). If unset, all types will be returned. + */ + /** + * @deprecated + * @description Whether to return deleted or undeleted datasets only. Leave unset for both. + */ + /** + * @deprecated + * @description Whether to return visible or hidden datasets only. Leave unset for both. + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + /** + * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. + * @example create_time-gt + */ + /** + * @description The value to filter by. + * @example 2015-01-29 + */ + /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */ + /** @description The maximum number of items to return. */ + /** + * @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. + * @example name-dsc,create_time + */ + query?: { + v?: string; + details?: string; + ids?: string; + types?: string[]; + deleted?: boolean; + visible?: boolean; + view?: string; + keys?: string; + q?: string[]; + qv?: string[]; + offset?: number; + limit?: number; + order?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + type: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryContentsResult"] + | components["schemas"]["HistoryContentsWithStatsResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_histories__history_id__contents__type_s_post: { + /** + * Create a new `HDA` or `HDCA` in the given History. + * @description Create a new `HDA` or `HDCA` in the given History. + */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateHistoryContentPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + | ( + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_content_typed_api_histories__history_id__contents__type_s__id__get: { + /** + * Return detailed information about a specific HDA or HDCA with the given `ID` within a history. + * @description Return detailed information about an `HDA` or `HDCA` within a history. + * + * **Note**: Anonymous users are allowed to get their current history contents. + */ + parameters: { + /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + fuzzy_count?: number; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_histories__history_id__contents__type_s__id__put: { + /** + * Updates the values for the history content item with the given ``ID``. + * @description Updates the values for the history content item with the given ``ID``. + */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateHistoryContentsPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_histories__history_id__contents__type_s__id__delete: { + /** + * Delete the history content with the given ``ID`` and specified type. + * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset). + * + * **Note**: Currently does not stop any active jobs for which this dataset is an output. + */ + parameters: { + /** + * @deprecated + * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA. + */ + /** + * @deprecated + * @description When deleting a dataset collection, whether to also delete containing datasets. + */ + /** + * @deprecated + * @description Whether to stop the creating job if all outputs of the job have been deleted. + */ + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + purge?: boolean; + recursive?: boolean; + stop_job?: boolean; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["DeleteHistoryContentPayload"]; + }; + }; + responses: { + /** @description Request has been executed. */ + 200: { + content: { + "application/json": components["schemas"]["DeleteHistoryContentResult"]; + }; + }; + /** @description Request accepted, processing will finish later. */ + 202: { + content: { + "application/json": components["schemas"]["DeleteHistoryContentResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get: { + /** + * Return detailed information about an `HDA` or `HDCAs` jobs. + * @description Return detailed information about an `HDA` or `HDCAs` jobs. + * + * **Warning**: We allow anyone to fetch job state information about any object they + * can guess an encoded ID for - it isn't considered protected data. This keeps + * polling IDs as part of state calculation for large histories and collections as + * efficient as possible. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["JobStateSummary"] + | components["schemas"]["ImplicitCollectionJobsStateSummary"] + | components["schemas"]["WorkflowInvocationStateSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post: { + /** Prepare a dataset or dataset collection for export-style download. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["StoreExportPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncFile"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + write_store_api_histories__history_id__contents__type_s__id__write_store_post: { + /** Prepare a dataset or dataset collection for export-style download and write to supplied URI. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */ + path: { + history_id: string; + id: string; + type: components["schemas"]["HistoryContentType"]; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["WriteStoreToPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncTaskResultSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_from_store_api_histories__history_id__contents_from_store_post: { + /** + * Create contents from store. + * @description Create history contents from model store. + * Input can be a tarfile created with build_objects script distributed + * with galaxy-data, from an exported history with files stripped out, + * or hand-crafted JSON dictionary. + */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateHistoryContentFromStore"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["HDADetailed"] + | components["schemas"]["HDASummary"] + | components["schemas"]["HDCADetailed"] + | components["schemas"]["HDCASummary"] + | components["schemas"]["CustomHistoryItem"] + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_jobs_summary_api_histories__history_id__jobs_summary_get: { + /** + * Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations. + * @description Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations. + * + * **Warning**: We allow anyone to fetch job state information about any object they + * can guess an encoded ID for - it isn't considered protected data. This keeps + * polling IDs as part of state calculation for large histories and collections as + * efficient as possible. + */ + parameters: { + /** @description A comma-separated list of encoded ids of job summary objects to return - if `ids` is specified types must also be specified and have same length. */ + /** @description A comma-separated list of type of object represented by elements in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. */ + query?: { + ids?: string; + types?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": ( + | components["schemas"]["JobStateSummary"] + | components["schemas"]["ImplicitCollectionJobsStateSummary"] + | components["schemas"]["WorkflowInvocationStateSummary"] + )[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + materialize_to_history_api_histories__history_id__materialize_post: { + /** Materialize a deferred library or HDA dataset into real, usable dataset in specified history. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the History. */ + path: { + history_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["MaterializeDatasetInstanceAPIRequest"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncTaskResultSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_api_histories__id__get: { + /** Returns the history with the given ID. */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_histories__id__put: { + /** Updates the values for the history with the given ID. */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": Record; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_histories__id__delete: { + /** Marks the history with the given ID as deleted. */ + parameters: { + /** @description View to be passed to the serializer */ + /** @description Comma-separated list of keys to be passed to the serializer */ + query?: { + purge?: boolean; + view?: string; + keys?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["DeleteHistoryPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["HistoryBeta"] + | components["schemas"]["HistoryDetailed"] + | components["schemas"]["HistorySummary"] + | Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + citations_api_histories__id__citations_get: { + /** Return all the citations for the tools used to produce the datasets in the history. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_custom_builds_metadata_api_histories__id__custom_builds_metadata_get: { + /** Returns meta data for custom builds. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["CustomBuildsMetadataResponse"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + disable_link_access_api_histories__id__disable_link_access_put: { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + enable_link_access_api_histories__id__enable_link_access_put: { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_exports_api_histories__id__exports_get: { + /** Get previous history exports (to links). Effectively returns serialized JEHA objects. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["JobExportHistoryArchiveCollection"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + archive_export_api_histories__id__exports_put: { + /** + * Start job (if needed) to create history export for corresponding history. + * @description This will start a job to create a history export archive. + * + * Calling this endpoint multiple times will return the 202 status code until the archive + * has been completely generated and is ready to download. When ready, it will return + * the 200 status code along with the download link information. + * + * If the history will be exported to a `directory_uri`, instead of returning the download + * link information, the Job ID will be returned so it can be queried to determine when + * the file has been written. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["ExportHistoryArchivePayload"]; + }; + }; + responses: { + /** @description Object containing url to fetch export from. */ + 200: { + content: { + "application/json": + | components["schemas"]["JobExportHistoryArchiveModel"] + | components["schemas"]["JobIdResponse"]; + }; + }; + /** @description The exported archive file is not ready yet. */ + 202: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + history_archive_download_api_histories__id__exports__jeha_id__get: { + /** + * If ready and available, return raw contents of exported history as a downloadable archive. + * @description See ``PUT /api/histories/{id}/exports`` to initiate the creation + * of the history export - when ready, that route will return 200 status + * code (instead of 202) and this route can be used to download the archive. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + /** + * @description The ID of the specific Job Export History Association or `latest` (default) to download the last generated archive. + * @example latest + */ + path: { + id: string; + jeha_id: string | "latest"; + }; + }; + responses: { + /** @description The archive file containing the History. */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + prepare_store_download_api_histories__id__prepare_store_download_post: { + /** Return a short term storage token to monitor download of the history. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["StoreExportPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncFile"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + publish_api_histories__id__publish_put: { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + share_with_users_api_histories__id__share_with_users_put: { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ShareWithPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["ShareWithStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + sharing_api_histories__id__sharing_get: { + /** + * Get the current sharing status of the given item. + * @description Return the sharing status of the item. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + set_slug_api_histories__id__slug_put: { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SetSlugPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + unpublish_api_histories__id__unpublish_put: { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + write_store_api_histories__id__write_store_post: { + /** Prepare history for export-style download and write to supplied URI. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the History. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["WriteStoreToPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncTaskResultSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + export_invocation_bco_api_invocations__invocation_id__biocompute_get: { + /** + * Return a BioCompute Object for the workflow invocation. + * @deprecated + * @description The BioCompute Object endpoints are in beta - important details such + * as how inputs and outputs are represented, how the workflow is encoded, + * and how author and version information is encoded, and how URLs are + * generated will very likely change in important ways over time. + * + * **Deprecation Notice**: please use the asynchronous short_term_storage export system instead. + * + * 1. call POST `api/invocations/{id}/prepare_store_download` with payload: + * ``` + * { + * model_store_format: bco.json + * } + * ``` + * 2. Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready` until `SUCCESS` + * + * 3. Get the resulting file with `api/short_term_storage/${storageRequestId}` + */ + parameters: { + query?: { + merge_history_metadata?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Invocation. */ + path: { + invocation_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + download_invocation_bco_api_invocations__invocation_id__biocompute_download_get: { + /** + * Return a BioCompute Object for the workflow invocation as a file for download. + * @deprecated + * @description The BioCompute Object endpoints are in beta - important details such + * as how inputs and outputs are represented, how the workflow is encoded, + * and how author and version information is encoded, and how URLs are + * generated will very likely change in important ways over time. + * + * **Deprecation Notice**: please use the asynchronous short_term_storage export system instead. + * + * 1. call POST `api/invocations/{id}/prepare_store_download` with payload: + * ``` + * { + * model_store_format: bco.json + * } + * ``` + * 2. Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready` until `SUCCESS` + * + * 3. Get the resulting file with `api/short_term_storage/${storageRequestId}` + */ + parameters: { + query?: { + merge_history_metadata?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Invocation. */ + path: { + invocation_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + prepare_store_download_api_invocations__invocation_id__prepare_store_download_post: { + /** Prepare a workflow invocation export-style download. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Invocation. */ + path: { + invocation_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["PrepareStoreDownloadPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncFile"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + write_store_api_invocations__invocation_id__write_store_post: { + /** Prepare a workflow invocation export-style download and write to supplied URI. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Invocation. */ + path: { + invocation_id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["WriteInvocationStoreToPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["AsyncTaskResultSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + job_lock_status_api_job_lock_get: { + /** + * Job Lock Status + * @description Get job lock status. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["JobLock"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_job_lock_api_job_lock_put: { + /** + * Update Job Lock + * @description Set job lock status. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["JobLock"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["JobLock"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_jobs_get: { + /** Index */ + parameters?: { + /** @description If true, and requestor is an admin, will return external job id and user email. This is only available to admins. */ + /** @description an encoded user id to restrict query to, must be own id if not admin user */ + /** @description Determines columns to return. Defaults to 'collection'. */ + /** @description Limit listing of jobs to those that are updated after specified date (e.g. '2014-01-01') */ + /** @description Limit listing of jobs to those that are updated before specified date (e.g. '2014-01-01') */ + /** @description Limit listing of jobs to those that match the history_id. If none, jobs from any history may be returned. */ + /** @description Limit listing of jobs to those that match the specified workflow ID. If none, jobs from any workflow (or from no workflows) may be returned. */ + /** @description Limit listing of jobs to those that match the specified workflow invocation ID. If none, jobs from any workflow invocation (or from no workflows) may be returned. */ + /** @description Sort results by specified field. */ + /** + * @description A mix of free text and GitHub-style tags used to filter the index operation. + * + * ## Query Structure + * + * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form + * `:` or `:''`. The tag name + * *generally* (but not exclusively) corresponds to the name of an attribute on the model + * being indexed (i.e. a column in the database). + * + * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted, + * generally a partial match will be used to filter the query (i.e. in terms of the implementation + * this means the database operation `ILIKE` will typically be used). + * + * Once the tagged filters are extracted from the search query, the remaing text is just + * used to search various documented attributes of the object. + * + * ## GitHub-style Tags Available + * + * `user` + * : The user email of the user that executed the Job. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.) + * + * `tool_id` + * : The tool ID corresponding to the job. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.) + * + * `runner` + * : The job runner name used to execte the job. (The tag `r` can be used a short hand alias for this tag to filter on this attribute.) This tag is only available for requests using admin keys and/or sessions. + * + * `handler` + * : The job handler name used to execute the job. (The tag `h` can be used a short hand alias for this tag to filter on this attribute.) This tag is only available for requests using admin keys and/or sessions. + * + * ## Free Text + * + * Free text search terms will be searched against the following attributes of the + * Jobs: `user`, `tool`, `handler`, `runner`. + */ + /** @description Maximum number of jobs to return. */ + /** @description Return jobs starting from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be returned. */ + /** @description A list or comma-separated list of states to filter job query on. If unspecified, jobs of any state may be returned. */ + /** @description Limit listing of jobs to those that match one of the included tool_ids. If none, all are returned */ + /** @description Limit listing of jobs to those that match one of the included tool ID sql-like patterns. If none, all are returned */ + query?: { + user_details?: boolean; + user_id?: string; + view?: components["schemas"]["JobIndexViewEnum"]; + date_range_min?: string | string; + date_range_max?: string | string; + history_id?: string; + workflow_id?: string; + invocation_id?: string; + order_by?: components["schemas"]["JobIndexSortByEnum"]; + search?: string; + limit?: number; + offset?: number; + state?: string[]; + tool_id?: string[]; + tool_id_like?: string[]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_jobs__id__get: { + /** + * Show + * @description Return dictionary containing description of job data + * + * Parameters + * - id: ID of job to return + * - full: Return extra information ? + */ + parameters: { + query?: { + full?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_libraries_get: { + /** + * Returns a list of summary data for all libraries. + * @description Returns a list of summary data for all libraries. + */ + parameters?: { + /** @description Whether to include deleted libraries in the result. */ + query?: { + deleted?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummaryList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_libraries_post: { + /** + * Creates a new library and returns its summary information. + * @description Creates a new library and returns its summary information. Currently, only admin users can create libraries. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateLibraryPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_deleted_api_libraries_deleted_get: { + /** + * Returns a list of summary data for all libraries marked as deleted. + * @description Returns a list of summary data for all libraries marked as deleted. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummaryList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_from_store_api_libraries_from_store_post: { + /** Create libraries from a model store. */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateLibrariesFromStore"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummary"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_libraries__id__get: { + /** + * Returns summary information about a particular library. + * @description Returns summary information about a particular library. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Library. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_libraries__id__delete: { + /** + * Marks the specified library as deleted (or undeleted). + * @description Marks the specified library as deleted (or undeleted). + * Currently, only admin users can delete or restore libraries. + */ + parameters: { + /** @description Whether to restore a deleted library. */ + query?: { + undelete?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Library. */ + path: { + id: string; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["DeleteLibraryPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_libraries__id__patch: { + /** + * Updates the information of an existing library. + * @description Updates the information of an existing library. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Library. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateLibraryPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["LibrarySummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_permissions_api_libraries__id__permissions_get: { + /** + * Gets the current or available permissions of a particular library. + * @description Gets the current or available permissions of a particular library. + * The results can be paginated and additionally filtered by a query. + */ + parameters: { + /** @description The scope of the permissions to retrieve. Either the `current` permissions or the `available`. */ + /** @description Indicates whether the roles available for the library access are requested. */ + /** @description The page number to retrieve when paginating the available roles. */ + /** @description The maximum number of permissions per page when paginating. */ + /** @description Optional search text to retrieve only the roles matching this query. */ + query?: { + scope?: components["schemas"]["LibraryPermissionScope"]; + is_library_access?: boolean; + page?: number; + page_limit?: number; + q?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Library. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["LibraryCurrentPermissions"] + | components["schemas"]["LibraryAvailablePermissions"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + set_permissions_api_libraries__id__permissions_post: { + /** + * Sets the permissions to access and manipulate a library. + * @description Sets the permissions to access and manipulate a library. + */ + parameters: { + /** @description Indicates what action should be performed on the Library. */ + query?: { + action?: components["schemas"]["LibraryPermissionAction"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Library. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": + | components["schemas"]["LibraryPermissionsPayload"] + | components["schemas"]["LegacyLibraryPermissionsPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": + | components["schemas"]["LibraryLegacySummary"] + | components["schemas"]["LibraryCurrentPermissions"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_licenses_get: { + /** + * Lists all available SPDX licenses + * @description Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/). + */ + responses: { + /** @description List of SPDX licenses */ + 200: { + content: { + "application/json": components["schemas"]["LicenseMetadataModel"][]; + }; + }; + }; + }; + get_api_licenses__id__get: { + /** + * Gets the SPDX license metadata associated with the short identifier + * @description Returns the license metadata associated with the given + * [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/). + */ + parameters: { + /** + * @description The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) + * @example Apache-2.0 + */ + path: { + id: Record; + }; + }; + responses: { + /** @description SPDX license metadata */ + 200: { + content: { + "application/json": components["schemas"]["LicenseMetadataModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_metrics_post: { + /** + * Records a collection of metrics. + * @description Record any metrics sent and return some status object. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateMetricsPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_pages_get: { + /** + * Lists all Pages viewable by the user. + * @description Get a list with summary information of all Pages available to the user. + */ + parameters?: { + /** @description Whether to include deleted pages in the result. */ + /** @description Sort page index by this specified attribute on the page model */ + /** @description Sort in descending order? */ + query?: { + deleted?: boolean; + user_id?: string; + show_published?: boolean; + show_shared?: boolean; + sort_by?: components["schemas"]["PageSortByEnum"]; + sort_desc?: boolean; + limit?: number; + offset?: number; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description A list with summary page information. */ + 200: { + content: { + "application/json": components["schemas"]["PageSummaryList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_pages_post: { + /** + * Create a page and return summary information. + * @description Get a list with details of all Pages available to the user. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreatePagePayload"]; + }; + }; + responses: { + /** @description The page summary information. */ + 200: { + content: { + "application/json": components["schemas"]["PageSummary"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_pages__id__get: { + /** + * Return a page summary and the content of the last revision. + * @description Return summary information about a specific Page and the content of the last revision. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description The page summary information. */ + 200: { + content: { + "application/json": components["schemas"]["PageDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_pages__id__delete: { + /** + * Marks the specific Page as deleted. + * @description Marks the Page with the given ID as deleted. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_pdf_api_pages__id__pdf_get: { + /** + * Return a PDF document of the last revision of the Page. + * @description Return a PDF document of the last revision of the Page. + * + * This feature may not be available in this Galaxy. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description PDF document with the last revision of the page. */ + 200: { + content: { + "application/pdf": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + /** @description PDF conversion service not available. */ + 501: never; + }; + }; + disable_link_access_api_pages__id__disable_link_access_put: { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + enable_link_access_api_pages__id__enable_link_access_put: { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + prepare_pdf_api_pages__id__prepare_download_post: { + /** + * Return a PDF document of the last revision of the Page. + * @description Return a STS download link for this page to be downloaded as a PDF. + * + * This feature may not be available in this Galaxy. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Short term storage reference for async monitoring of this download. */ + 200: { + content: { + "application/json": components["schemas"]["AsyncFile"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + /** @description PDF conversion service not available. */ + 501: never; + }; + }; + publish_api_pages__id__publish_put: { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + share_with_users_api_pages__id__share_with_users_put: { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ShareWithPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["ShareWithStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + sharing_api_pages__id__sharing_get: { + /** + * Get the current sharing status of the given Page. + * @description Return the sharing status of the item. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + set_slug_api_pages__id__slug_put: { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SetSlugPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + unpublish_api_pages__id__unpublish_put: { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Page. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_quotas_get: { + /** + * Displays a list with information of quotas that are currently active. + * @description Displays a list with information of quotas that are currently active. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["QuotaSummaryList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_quotas_post: { + /** + * Creates a new quota. + * @description Creates a new quota. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CreateQuotaParams"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["CreateQuotaResult"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_deleted_api_quotas_deleted_get: { + /** + * Displays a list with information of quotas that have been deleted. + * @description Displays a list with information of quotas that have been deleted. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["QuotaSummaryList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + deleted_quota_api_quotas_deleted__id__get: { + /** + * Displays details on a particular quota that has been deleted. + * @description Displays details on a particular quota that has been deleted. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Quota. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["QuotaDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + undelete_api_quotas_deleted__id__undelete_post: { + /** + * Restores a previously deleted quota. + * @description Restores a previously deleted quota. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Quota. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + quota_api_quotas__id__get: { + /** + * Displays details on a particular active quota. + * @description Displays details on a particular active quota. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Quota. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["QuotaDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_quotas__id__put: { + /** + * Updates an existing quota. + * @description Updates an existing quota. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Quota. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["UpdateQuotaParams"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_quotas__id__delete: { + /** + * Deletes an existing quota. + * @description Deletes an existing quota. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded identifier of the Quota. */ + path: { + id: string; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["DeleteQuotaPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_remote_files_get: { + /** + * Displays remote files available to the user. + * @description Lists all remote files available to the user from different sources. + */ + parameters?: { + /** @description The source to load datasets from. Possible values: ftpdir, userdir, importdir */ + /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */ + /** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */ + /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */ + query?: { + target?: string; + format?: components["schemas"]["RemoteFilesFormat"]; + recursive?: boolean; + disable?: components["schemas"]["RemoteFilesDisableMode"]; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description A list with details about the remote files available to the user. */ + 200: { + content: { + "application/json": Record[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + plugins_api_remote_files_plugins_get: { + /** + * Display plugin information for each of the gxfiles:// URI targets available. + * @description Display plugin information for each of the gxfiles:// URI targets available. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description A list with details about each plugin. */ + 200: { + content: { + "application/json": components["schemas"]["FilesSourcePluginList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_roles_get: { + /** Index */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["RoleListModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_roles_post: { + /** Create */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["RoleDefinitionModel"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["RoleModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_roles__id__get: { + /** Show */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["RoleModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + serve_api_short_term_storage__storage_request_id__get: { + /** Serve the staged download specified by request ID. */ + parameters: { + path: { + storage_request_id: string; + }; + }; + responses: { + /** @description The archive file containing the History. */ + 200: never; + /** @description Request was cancelled without an exception condition recorded. */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + is_ready_api_short_term_storage__storage_request_id__ready_get: { + /** Determine if specified storage request ID is ready for download. */ + parameters: { + path: { + storage_request_id: string; + }; + }; + responses: { + /** @description Boolean indicating if the storage is ready. */ + 200: { + content: { + "application/json": boolean; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_api_tags_put: { + /** + * Apply a new set of tags to an item. + * @description Replaces the tags associated with an item with the new ones specified in the payload. + * + * - The previous tags will be __deleted__. + * - If no tags are provided in the request body, the currently associated tags will also be __deleted__. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ItemTagsPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + state_api_tasks__task_id__state_get: { + /** Determine state of task ID */ + parameters: { + path: { + task_id: string; + }; + }; + responses: { + /** @description String indicating task state. */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_tool_data_get: { + /** + * Lists all available data tables + * @description Get the list of all available data tables. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description A list with details on individual data tables. */ + 200: { + content: { + "application/json": components["schemas"]["ToolDataEntryList"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_tool_data__table_name__get: { + /** + * Get details of a given data table + * @description Get details of a given tool data table. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** + * @description The name of the tool data table + * @example all_fasta + */ + path: { + table_name: string; + }; + }; + responses: { + /** @description A description of the given data table and its content */ + 200: { + content: { + "application/json": components["schemas"]["ToolDataDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_tool_data__table_name__delete: { + /** + * Removes an item from a data table + * @description Removes an item from a data table and reloads it to return its updated details. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** + * @description The name of the tool data table + * @example all_fasta + */ + path: { + table_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ToolDataItem"]; + }; + }; + responses: { + /** @description A description of the affected data table and its content */ + 200: { + content: { + "application/json": components["schemas"]["ToolDataDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_field_api_tool_data__table_name__fields__field_name__get: { + /** + * Get information about a particular field in a tool data table + * @description Reloads a data table and return its details. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** + * @description The name of the tool data table + * @example all_fasta + */ + /** @description The name of the tool data table field */ + path: { + table_name: string; + field_name: string; + }; + }; + responses: { + /** @description Information about a data table field */ + 200: { + content: { + "application/json": components["schemas"]["ToolDataField"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get: { + /** + * Get information about a particular field in a tool data table + * @description Download a file associated with the data table field. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** + * @description The name of the tool data table + * @example all_fasta + */ + /** @description The name of the tool data table field */ + /** @description The name of a file associated with this data table field */ + path: { + table_name: string; + field_name: string; + file_name: string; + }; + }; + responses: { + /** @description Information about a data table field */ + 200: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + reload_api_tool_data__table_name__reload_get: { + /** + * Reloads a tool data table + * @description Reloads a data table and return its details. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** + * @description The name of the tool data table + * @example all_fasta + */ + path: { + table_name: string; + }; + }; + responses: { + /** @description A description of the reloaded data table and its content */ + 200: { + content: { + "application/json": components["schemas"]["ToolDataDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_tool_shed_repositories_get: { + /** Lists installed tool shed repositories. */ + parameters?: { + /** @description Filter by repository name. */ + /** @description Filter by repository owner. */ + /** @description Filter by changeset revision. */ + /** @description Filter by whether the repository has been deleted. */ + /** @description Filter by whether the repository has been uninstalled. */ + query?: { + name?: string; + owner?: string; + changeset?: string; + deleted?: boolean; + uninstalled?: boolean; + }; + }; + responses: { + /** @description A list of installed tool shed repository objects. */ + 200: { + content: { + "application/json": components["schemas"]["InstalledToolShedRepository"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + check_for_updates_api_tool_shed_repositories_check_for_updates_get: { + /** Check for updates to the specified repository, or all installed repositories. */ + parameters?: { + query?: { + id?: string; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description A description of the state and updates message. */ + 200: { + content: { + "application/json": components["schemas"]["CheckForUpdatesResponse"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + show_api_tool_shed_repositories__id__get: { + /** Show installed tool shed repository. */ + parameters: { + /** @description The encoded database identifier of the installed Tool Shed Repository. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["InstalledToolShedRepository"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + "fetch_json_api_tools_fetch_post+fetch_form_api_tools_fetch_post": { + /** Upload files to Galaxy */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["FetchDataPayload"]; + "multipart/form-data": components["schemas"]["Body_fetch_form_api_tools_fetch_post"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_tours_get: { + /** + * Index + * @description Return list of available tours. + */ + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["TourList"]; + }; + }; + }; + }; + show_api_tours__tour_id__get: { + /** + * Show + * @description Return a tour definition. + */ + parameters: { + path: { + tour_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["TourDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + update_tour_api_tours__tour_id__post: { + /** + * Update Tour + * @description Return a tour definition. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + path: { + tour_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["TourDetails"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + recalculate_disk_usage_api_users_recalculate_disk_usage_put: { + /** Triggers a recalculation of the current user disk usage. */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_or_create_api_key_api_users__user_id__api_key_get: { + /** Return the user's API key */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the user to get. */ + path: { + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + create_api_key_api_users__user_id__api_key_post: { + /** Creates a new API key for the user */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the user to get. */ + path: { + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_api_key_api_users__user_id__api_key_delete: { + /** Delete the current API key of the user */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the user to get. */ + path: { + user_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + get_api_key_detailed_api_users__user_id__api_key_detailed_get: { + /** Return the user's API key with extra information. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The ID of the user to get. */ + path: { + user_id: string; + }; + }; + responses: { + /** @description The API key of the user. */ + 200: { + content: { + "application/json": components["schemas"]["APIKeyModel"]; + }; + }; + /** @description The user doesn't have an API key. */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + version_api_version_get: { + /** + * Return Galaxy version information: major/minor version, optional extra info + * @description Return Galaxy version information: major/minor version, optional extra info. + */ + responses: { + /** @description Galaxy version information: major/minor version, optional extra info */ + 200: { + content: { + "application/json": Record; + }; + }; + }; + }; + disable_link_access_api_visualizations__id__disable_link_access_put: { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + enable_link_access_api_visualizations__id__enable_link_access_put: { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + publish_api_visualizations__id__publish_put: { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + share_with_users_api_visualizations__id__share_with_users_put: { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ShareWithPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["ShareWithStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + sharing_api_visualizations__id__sharing_get: { + /** + * Get the current sharing status of the given Page. + * @description Return the sharing status of the item. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + set_slug_api_visualizations__id__slug_put: { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SetSlugPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + unpublish_api_visualizations__id__unpublish_put: { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Visualization. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + whoami_api_whoami_get: { + /** + * Return information about the current authenticated user + * @description Return information about the current authenticated user. + */ + parameters?: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description Information about the current authenticated user */ + 200: { + content: { + "application/json": components["schemas"]["UserModel"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + index_api_workflows_get: { + /** + * Lists stored workflows viewable by the user. + * @description Lists stored workflows viewable by the user. + */ + parameters?: { + /** @description Whether to restrict result to deleted workflows. */ + /** @description Whether to restrict result to hidden workflows. */ + /** @description Whether to include a list of missing tools per workflow entry */ + /** @description In unspecified, default ordering depends on other parameters but generally the user's own workflows appear first based on update time */ + /** @description Sort in descending order? */ + /** + * @description A mix of free text and GitHub-style tags used to filter the index operation. + * + * ## Query Structure + * + * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form + * `:` or `:''`. The tag name + * *generally* (but not exclusively) corresponds to the name of an attribute on the model + * being indexed (i.e. a column in the database). + * + * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted, + * generally a partial match will be used to filter the query (i.e. in terms of the implementation + * this means the database operation `ILIKE` will typically be used). + * + * Once the tagged filters are extracted from the search query, the remaing text is just + * used to search various documented attributes of the object. + * + * ## GitHub-style Tags Available + * + * `name` + * : The stored workflow's name. (The tag `n` can be used a short hand alias for this tag to filter on this attribute.) + * + * `tag` + * : The workflow's tag, if the tag contains a colon an approach will be made to match the key and value of the tag separately. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.) + * + * `user` + * : The stored workflow's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.) + * + * `is:published` + * : Include only published workflows in the final result. Be sure the the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's. + * + * `is:share_with_me` + * : Include only workflows shared with the requesting user. Be sure the the query parameter `show_shared` is set to `true` if to include shared workflows. + * + * ## Free Text + * + * Free text search terms will be searched against the following attributes of the + * Stored Workflows: `name`, `tag`, `user`. + */ + /** @description Set this to true to skip joining workflow step counts and optimize the resulting index query. Response objects will not contain step counts. */ + query?: { + show_deleted?: boolean; + show_hidden?: boolean; + missing_tools?: boolean; + show_published?: boolean; + show_shared?: boolean; + sort_by?: components["schemas"]["WorkflowSortByEnum"]; + sort_desc?: boolean; + limit?: number; + offset?: number; + search?: string; + skip_step_counts?: boolean; + }; + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + }; + responses: { + /** @description A list with summary stored workflow information per viewable entry. */ + 200: { + content: { + "application/json": Record[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + disable_link_access_api_workflows__id__disable_link_access_put: { + /** + * Makes this item inaccessible by a URL link. + * @description Makes this item inaccessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + enable_link_access_api_workflows__id__enable_link_access_put: { + /** + * Makes this item accessible by a URL link. + * @description Makes this item accessible by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + publish_api_workflows__id__publish_put: { + /** + * Makes this item public and accessible by a URL link. + * @description Makes this item publicly available by a URL link and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + share_with_users_api_workflows__id__share_with_users_put: { + /** + * Share this item with specific users. + * @description Shares this item with specific users and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ShareWithPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["ShareWithStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + sharing_api_workflows__id__sharing_get: { + /** + * Get the current sharing status of the given item. + * @description Return the sharing status of the item. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + set_slug_api_workflows__id__slug_put: { + /** + * Set a new slug for this shared item. + * @description Sets a new slug to access this item by URL. The new slug must be unique. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SetSlugPayload"]; + }; + }; + responses: { + /** @description Successful Response */ + 204: never; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + unpublish_api_workflows__id__unpublish_put: { + /** + * Removes this item from the published list. + * @description Removes this item from the published list and return the current sharing status. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SharingStatus"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + delete_workflow_api_workflows__workflow_id__delete: { + /** Add the deleted flag to a workflow. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + workflow_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + undelete_workflow_api_workflows__workflow_id__undelete_post: { + /** Remove the deleted flag from a workflow. */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string; + }; + /** @description The encoded database identifier of the Stored Workflow. */ + path: { + workflow_id: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; +} From d39dd525c98035f4da6defd1a4021ec73fb35599 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 4 Dec 2022 22:02:27 +0100 Subject: [PATCH 04/12] Use autogenerated client in datatypes service --- .../Datatypes/{factory.js => factory.ts} | 2 +- client/src/components/Datatypes/index.js | 2 +- client/src/components/Datatypes/index.test.js | 18 ++++-------------- .../Datatypes/{model.js => model.ts} | 13 ++++++++++--- client/src/components/Datatypes/services.js | 16 ---------------- client/src/components/Datatypes/services.ts | 13 +++++++++++++ .../Datatypes/test-data/datatypes.json | 1 + .../Datatypes/test-data/datatypes.mapping.json | 1 + .../src/components/Datatypes/test_fixtures.js | 11 ----------- .../src/components/Datatypes/test_fixtures.ts | 12 ++++++++++++ 10 files changed, 43 insertions(+), 46 deletions(-) rename client/src/components/Datatypes/{factory.js => factory.ts} (81%) rename client/src/components/Datatypes/{model.js => model.ts} (60%) delete mode 100644 client/src/components/Datatypes/services.js create mode 100644 client/src/components/Datatypes/services.ts create mode 120000 client/src/components/Datatypes/test-data/datatypes.json create mode 120000 client/src/components/Datatypes/test-data/datatypes.mapping.json delete mode 100644 client/src/components/Datatypes/test_fixtures.js create mode 100644 client/src/components/Datatypes/test_fixtures.ts diff --git a/client/src/components/Datatypes/factory.js b/client/src/components/Datatypes/factory.ts similarity index 81% rename from client/src/components/Datatypes/factory.js rename to client/src/components/Datatypes/factory.ts index b691f7af110..623fcd6c4ba 100644 --- a/client/src/components/Datatypes/factory.js +++ b/client/src/components/Datatypes/factory.ts @@ -1,4 +1,4 @@ -import { DatatypesMapperModel } from "./model.js"; +import { DatatypesMapperModel } from "./model"; import { getDatatypes } from "./services"; export async function getDatatypesMapper(upload_only = true) { diff --git a/client/src/components/Datatypes/index.js b/client/src/components/Datatypes/index.js index 3350500fd3b..950d4e4e699 100644 --- a/client/src/components/Datatypes/index.js +++ b/client/src/components/Datatypes/index.js @@ -1 +1 @@ -export { getDatatypesMapper } from "./factory.js"; +export { getDatatypesMapper } from "./factory"; diff --git a/client/src/components/Datatypes/index.test.js b/client/src/components/Datatypes/index.test.js index 07455a6c2cf..81abea7170c 100644 --- a/client/src/components/Datatypes/index.test.js +++ b/client/src/components/Datatypes/index.test.js @@ -1,23 +1,13 @@ -import axios from "axios"; -import MockAdapter from "axios-mock-adapter"; - import { getDatatypesMapper } from "./index"; +import { getDatatypes } from "./services"; import { typesAndMappingResponse } from "./test_fixtures"; +jest.mock("./services"); + describe("Datatypes/index.js", () => { - let axiosMock; - - beforeEach(() => { - axiosMock = new MockAdapter(axios); - }); - - afterEach(() => { - axiosMock.restore(); - }); - describe("getDatatypesMapper", () => { it("should fetch logic from API for comparing datatypes in a hierarchy", async () => { - axiosMock.onGet(`/api/datatypes/types_and_mapping`).reply(200, typesAndMappingResponse); + getDatatypes.mockResolvedValue(typesAndMappingResponse); await getDatatypesMapper().then((mapper) => { expect(mapper.isSubType("txt", "data")).toBe(true); expect(mapper.isSubType("txt", "txt")).toBe(true); diff --git a/client/src/components/Datatypes/model.js b/client/src/components/Datatypes/model.ts similarity index 60% rename from client/src/components/Datatypes/model.js rename to client/src/components/Datatypes/model.ts index 908f4e93118..ee00599d77c 100644 --- a/client/src/components/Datatypes/model.js +++ b/client/src/components/Datatypes/model.ts @@ -1,5 +1,12 @@ +import { components } from "schema"; + +export type DatatypesCombinedMap = components["schemas"]["DatatypesCombinedMap"]; + export class DatatypesMapperModel { - constructor(typesAndMapping) { + datatypes: DatatypesCombinedMap["datatypes"]; + datatypesMapping: DatatypesCombinedMap["datatypes_mapping"]; + + constructor(typesAndMapping: DatatypesCombinedMap) { // create a shallow copy of the datatypes, otherwise sort mutates in place // and causes a possible infinite render update loop. this.datatypes = [...typesAndMapping.datatypes]; @@ -7,14 +14,14 @@ export class DatatypesMapperModel { this.datatypesMapping = typesAndMapping.datatypes_mapping; } - isSubType(child, parent) { + isSubType(child: string, parent: string): boolean { const mapping = this.datatypesMapping; child = mapping.ext_to_class_name[child]; parent = mapping.ext_to_class_name[parent]; return mapping.class_to_classes[child] && parent in mapping.class_to_classes[child]; } - isSubTypeOfAny(child, parents) { + isSubTypeOfAny(child: string, parents: DatatypesCombinedMap["datatypes"]): boolean { return parents.some((parent) => this.isSubType(child, parent)); } } diff --git a/client/src/components/Datatypes/services.js b/client/src/components/Datatypes/services.js deleted file mode 100644 index c1f4c4ca228..00000000000 --- a/client/src/components/Datatypes/services.js +++ /dev/null @@ -1,16 +0,0 @@ -import axios from "axios"; -import { rethrowSimple } from "utils/simple-error"; -import { getAppRoot } from "onload/loadConfig"; - -export async function getDatatypes(upload_only = true) { - try { - const request = await axios.get(`${getAppRoot()}api/datatypes/types_and_mapping`, { - params: { - upload_only: upload_only, - }, - }); - return request.data; - } catch (e) { - rethrowSimple(e); - } -} diff --git a/client/src/components/Datatypes/services.ts b/client/src/components/Datatypes/services.ts new file mode 100644 index 00000000000..63e05ab94e6 --- /dev/null +++ b/client/src/components/Datatypes/services.ts @@ -0,0 +1,13 @@ +import { rethrowSimple } from "utils/simple-error"; +import { fetcher } from "schema/fetcher"; + +const getTypesAndMappings = fetcher.path("/api/datatypes/types_and_mapping").method("get").create(); + +export async function getDatatypes(upload_only = true) { + try { + const response = await getTypesAndMappings({ upload_only }); + return response.data; + } catch (e) { + rethrowSimple(e); + } +} diff --git a/client/src/components/Datatypes/test-data/datatypes.json b/client/src/components/Datatypes/test-data/datatypes.json new file mode 120000 index 00000000000..f32f2aee513 --- /dev/null +++ b/client/src/components/Datatypes/test-data/datatypes.json @@ -0,0 +1 @@ +../../../../tests/qunit/test-data/json/datatypes.json \ No newline at end of file diff --git a/client/src/components/Datatypes/test-data/datatypes.mapping.json b/client/src/components/Datatypes/test-data/datatypes.mapping.json new file mode 120000 index 00000000000..de79c06a39b --- /dev/null +++ b/client/src/components/Datatypes/test-data/datatypes.mapping.json @@ -0,0 +1 @@ +../../../../tests/qunit/test-data/json/datatypes.mapping.json \ No newline at end of file diff --git a/client/src/components/Datatypes/test_fixtures.js b/client/src/components/Datatypes/test_fixtures.js deleted file mode 100644 index 4dba51dd0e3..00000000000 --- a/client/src/components/Datatypes/test_fixtures.js +++ /dev/null @@ -1,11 +0,0 @@ -// TODO: Swap these awful relative paths to an alias -import DatatypesMappingJson from "qunit/test-data/json/datatypes.mapping.json"; -import DatatypesJson from "qunit/test-data/json/datatypes.json"; -import { DatatypesMapperModel } from "./model.js"; - -export const typesAndMappingResponse = { - datatypes: DatatypesJson, - datatypes_mapping: DatatypesMappingJson, -}; - -export const testDatatypesMapper = new DatatypesMapperModel(typesAndMappingResponse); diff --git a/client/src/components/Datatypes/test_fixtures.ts b/client/src/components/Datatypes/test_fixtures.ts new file mode 100644 index 00000000000..0e58ccb475c --- /dev/null +++ b/client/src/components/Datatypes/test_fixtures.ts @@ -0,0 +1,12 @@ +// TODO: Swap these awful relative paths to an alias +import DatatypesMappingJson from "./test-data/datatypes.mapping.json"; +import DatatypesJson from "./test-data/datatypes.json"; +import { DatatypesMapperModel } from "./model"; +import type { DatatypesCombinedMap } from "./model"; + +export const typesAndMappingResponse: DatatypesCombinedMap = { + datatypes: DatatypesJson, + datatypes_mapping: DatatypesMappingJson, +}; + +export const testDatatypesMapper = new DatatypesMapperModel(typesAndMappingResponse); From 2c8cf9846056e1674f8c56e655cd7e2312ce5cc4 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 4 Dec 2022 22:39:31 +0100 Subject: [PATCH 05/12] Strip trailing slash in getAppRoot --- client/src/onload/loadConfig.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/onload/loadConfig.js b/client/src/onload/loadConfig.js index e19504669f8..c35111ecb6f 100644 --- a/client/src/onload/loadConfig.js +++ b/client/src/onload/loadConfig.js @@ -80,5 +80,5 @@ export function getAppRoot(defaultRoot = "/") { console.warn("Unable to find index link in head", err); } } - return root; + return (root || "").replace(/\/$/, ""); } From ee083cde3f5eba4b43e061158f30dd3653f350a4 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 5 Dec 2022 10:59:45 +0100 Subject: [PATCH 06/12] Only strip trailing slash for fetcher --- client/src/onload/loadConfig.js | 7 +++++-- client/src/schema/fetcher.ts | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/client/src/onload/loadConfig.js b/client/src/onload/loadConfig.js index c35111ecb6f..724bcb53615 100644 --- a/client/src/onload/loadConfig.js +++ b/client/src/onload/loadConfig.js @@ -68,7 +68,7 @@ export function get() { * * @param {*} defaultRoot */ -export function getAppRoot(defaultRoot = "/") { +export function getAppRoot(defaultRoot = "/", stripTrailingSlash = false) { let root = defaultRoot; try { // try actual config @@ -80,5 +80,8 @@ export function getAppRoot(defaultRoot = "/") { console.warn("Unable to find index link in head", err); } } - return (root || "").replace(/\/$/, ""); + if (stripTrailingSlash) { + root = (root || "").replace(/\/$/, ""); + } + return root; } diff --git a/client/src/schema/fetcher.ts b/client/src/schema/fetcher.ts index b6fc3819fb4..87987a43e9e 100644 --- a/client/src/schema/fetcher.ts +++ b/client/src/schema/fetcher.ts @@ -3,4 +3,4 @@ import { Fetcher } from "openapi-typescript-fetch"; import { getAppRoot } from "onload/loadConfig"; export const fetcher = Fetcher.for(); -fetcher.configure({ baseUrl: getAppRoot() }); +fetcher.configure({ baseUrl: getAppRoot(undefined, true) }); From 87e68c24e4b3d406acea70c5665ef9640b2beb56 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 5 Dec 2022 12:56:52 +0100 Subject: [PATCH 07/12] Convert Dataset/services.js to typescript and use typed client --- .../Dataset/DatasetLink/DatasetLink.vue | 5 +- client/src/components/Dataset/DatasetList.vue | 23 +++--- .../Dataset/compositeDatasetUtils.js | 6 +- client/src/components/Dataset/services.js | 72 ----------------- client/src/components/Dataset/services.ts | 77 +++++++++++++++++++ .../History/CurrentHistory/HistoryPanel.vue | 8 +- 6 files changed, 93 insertions(+), 98 deletions(-) delete mode 100644 client/src/components/Dataset/services.js create mode 100644 client/src/components/Dataset/services.ts diff --git a/client/src/components/Dataset/DatasetLink/DatasetLink.vue b/client/src/components/Dataset/DatasetLink/DatasetLink.vue index d4dc2eb37bb..59d04c5bd8f 100644 --- a/client/src/components/Dataset/DatasetLink/DatasetLink.vue +++ b/client/src/components/Dataset/DatasetLink/DatasetLink.vue @@ -5,8 +5,8 @@