google_api_genomics

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Genomics API client library. Uploads, processes, queries, and searches Genomics data in the cloud.
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lib/google_api/genomics/v1/api/variantsets.ex

# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an &quot;AS IS&quot; BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

# NOTE: This class is auto generated by the swagger code generator program.
# https://github.com/swagger-api/swagger-codegen.git
# Do not edit the class manually.

defmodule GoogleApi.Genomics.V1.Api.Variantsets do
  @moduledoc """
  API calls for all endpoints tagged `Variantsets`.
  """

  alias GoogleApi.Genomics.V1.Connection
  alias GoogleApi.Gax.{Request, Response}

  @doc """
  Creates a new variant set.  The provided variant set must have a valid &#x60;datasetId&#x60; set - all other fields are optional. Note that the &#x60;id&#x60; field will be ignored, as this is assigned by the server.

  ## Parameters

  - connection (GoogleApi.Genomics.V1.Connection): Connection to server
  - optional_params (KeywordList): [optional] Optional parameters
    - :$.xgafv (String.t): V1 error format.
    - :access_token (String.t): OAuth access token.
    - :alt (String.t): Data format for response.
    - :callback (String.t): JSONP
    - :fields (String.t): Selector specifying which fields to include in a partial response.
    - :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    - :oauth_token (String.t): OAuth 2.0 token for the current user.
    - :prettyPrint (boolean()): Returns response with indentations and line breaks.
    - :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    - :upload_protocol (String.t): Upload protocol for media (e.g. \&quot;raw\&quot;, \&quot;multipart\&quot;).
    - :uploadType (String.t): Legacy upload protocol for media (e.g. \&quot;media\&quot;, \&quot;multipart\&quot;).
    - :body (VariantSet): 

  ## Returns

  {:ok, %GoogleApi.Genomics.V1.Model.VariantSet{}} on success
  {:error, info} on failure
  """
  @spec genomics_variantsets_create(Tesla.Env.client(), keyword()) ::
          {:ok, GoogleApi.Genomics.V1.Model.VariantSet.t()} | {:error, Tesla.Env.t()}
  def genomics_variantsets_create(connection, optional_params \\ [], opts \\ []) do
    optional_params_config = %{
      :"$.xgafv" => :query,
      :access_token => :query,
      :alt => :query,
      :callback => :query,
      :fields => :query,
      :key => :query,
      :oauth_token => :query,
      :prettyPrint => :query,
      :quotaUser => :query,
      :upload_protocol => :query,
      :uploadType => :query,
      :body => :body
    }

    request =
      Request.new()
      |> Request.method(:post)
      |> Request.url("/v1/variantsets")
      |> Request.add_optional_params(optional_params_config, optional_params)

    connection
    |> Connection.execute(request)
    |> Response.decode(opts ++ [struct: %GoogleApi.Genomics.V1.Model.VariantSet{}])
  end

  @doc """
  Deletes a variant set including all variants, call sets, and calls within. This is not reversible.

  ## Parameters

  - connection (GoogleApi.Genomics.V1.Connection): Connection to server
  - variant_set_id (String.t): The ID of the variant set to be deleted.
  - optional_params (KeywordList): [optional] Optional parameters
    - :$.xgafv (String.t): V1 error format.
    - :access_token (String.t): OAuth access token.
    - :alt (String.t): Data format for response.
    - :callback (String.t): JSONP
    - :fields (String.t): Selector specifying which fields to include in a partial response.
    - :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    - :oauth_token (String.t): OAuth 2.0 token for the current user.
    - :prettyPrint (boolean()): Returns response with indentations and line breaks.
    - :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    - :upload_protocol (String.t): Upload protocol for media (e.g. \&quot;raw\&quot;, \&quot;multipart\&quot;).
    - :uploadType (String.t): Legacy upload protocol for media (e.g. \&quot;media\&quot;, \&quot;multipart\&quot;).

  ## Returns

  {:ok, %GoogleApi.Genomics.V1.Model.Empty{}} on success
  {:error, info} on failure
  """
  @spec genomics_variantsets_delete(Tesla.Env.client(), String.t(), keyword()) ::
          {:ok, GoogleApi.Genomics.V1.Model.Empty.t()} | {:error, Tesla.Env.t()}
  def genomics_variantsets_delete(connection, variant_set_id, optional_params \\ [], opts \\ []) do
    optional_params_config = %{
      :"$.xgafv" => :query,
      :access_token => :query,
      :alt => :query,
      :callback => :query,
      :fields => :query,
      :key => :query,
      :oauth_token => :query,
      :prettyPrint => :query,
      :quotaUser => :query,
      :upload_protocol => :query,
      :uploadType => :query
    }

    request =
      Request.new()
      |> Request.method(:delete)
      |> Request.url("/v1/variantsets/{variantSetId}", %{
        "variantSetId" => URI.encode_www_form(variant_set_id)
      })
      |> Request.add_optional_params(optional_params_config, optional_params)

    connection
    |> Connection.execute(request)
    |> Response.decode(opts ++ [struct: %GoogleApi.Genomics.V1.Model.Empty{}])
  end

  @doc """
  Exports variant set data to an external destination.

  ## Parameters

  - connection (GoogleApi.Genomics.V1.Connection): Connection to server
  - variant_set_id (String.t): Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set.
  - optional_params (KeywordList): [optional] Optional parameters
    - :$.xgafv (String.t): V1 error format.
    - :access_token (String.t): OAuth access token.
    - :alt (String.t): Data format for response.
    - :callback (String.t): JSONP
    - :fields (String.t): Selector specifying which fields to include in a partial response.
    - :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    - :oauth_token (String.t): OAuth 2.0 token for the current user.
    - :prettyPrint (boolean()): Returns response with indentations and line breaks.
    - :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    - :upload_protocol (String.t): Upload protocol for media (e.g. \&quot;raw\&quot;, \&quot;multipart\&quot;).
    - :uploadType (String.t): Legacy upload protocol for media (e.g. \&quot;media\&quot;, \&quot;multipart\&quot;).
    - :body (ExportVariantSetRequest): 

  ## Returns

  {:ok, %GoogleApi.Genomics.V1.Model.Operation{}} on success
  {:error, info} on failure
  """
  @spec genomics_variantsets_export(Tesla.Env.client(), String.t(), keyword()) ::
          {:ok, GoogleApi.Genomics.V1.Model.Operation.t()} | {:error, Tesla.Env.t()}
  def genomics_variantsets_export(connection, variant_set_id, optional_params \\ [], opts \\ []) do
    optional_params_config = %{
      :"$.xgafv" => :query,
      :access_token => :query,
      :alt => :query,
      :callback => :query,
      :fields => :query,
      :key => :query,
      :oauth_token => :query,
      :prettyPrint => :query,
      :quotaUser => :query,
      :upload_protocol => :query,
      :uploadType => :query,
      :body => :body
    }

    request =
      Request.new()
      |> Request.method(:post)
      |> Request.url("/v1/variantsets/{variantSetId}:export", %{
        "variantSetId" => URI.encode_www_form(variant_set_id)
      })
      |> Request.add_optional_params(optional_params_config, optional_params)

    connection
    |> Connection.execute(request)
    |> Response.decode(opts ++ [struct: %GoogleApi.Genomics.V1.Model.Operation{}])
  end

  @doc """
  Gets a variant set by ID.

  ## Parameters

  - connection (GoogleApi.Genomics.V1.Connection): Connection to server
  - variant_set_id (String.t): Required. The ID of the variant set.
  - optional_params (KeywordList): [optional] Optional parameters
    - :$.xgafv (String.t): V1 error format.
    - :access_token (String.t): OAuth access token.
    - :alt (String.t): Data format for response.
    - :callback (String.t): JSONP
    - :fields (String.t): Selector specifying which fields to include in a partial response.
    - :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    - :oauth_token (String.t): OAuth 2.0 token for the current user.
    - :prettyPrint (boolean()): Returns response with indentations and line breaks.
    - :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    - :upload_protocol (String.t): Upload protocol for media (e.g. \&quot;raw\&quot;, \&quot;multipart\&quot;).
    - :uploadType (String.t): Legacy upload protocol for media (e.g. \&quot;media\&quot;, \&quot;multipart\&quot;).

  ## Returns

  {:ok, %GoogleApi.Genomics.V1.Model.VariantSet{}} on success
  {:error, info} on failure
  """
  @spec genomics_variantsets_get(Tesla.Env.client(), String.t(), keyword()) ::
          {:ok, GoogleApi.Genomics.V1.Model.VariantSet.t()} | {:error, Tesla.Env.t()}
  def genomics_variantsets_get(connection, variant_set_id, optional_params \\ [], opts \\ []) do
    optional_params_config = %{
      :"$.xgafv" => :query,
      :access_token => :query,
      :alt => :query,
      :callback => :query,
      :fields => :query,
      :key => :query,
      :oauth_token => :query,
      :prettyPrint => :query,
      :quotaUser => :query,
      :upload_protocol => :query,
      :uploadType => :query
    }

    request =
      Request.new()
      |> Request.method(:get)
      |> Request.url("/v1/variantsets/{variantSetId}", %{
        "variantSetId" => URI.encode_www_form(variant_set_id)
      })
      |> Request.add_optional_params(optional_params_config, optional_params)

    connection
    |> Connection.execute(request)
    |> Response.decode(opts ++ [struct: %GoogleApi.Genomics.V1.Model.VariantSet{}])
  end

  @doc """
  Updates a variant set using patch semantics.

  ## Parameters

  - connection (GoogleApi.Genomics.V1.Connection): Connection to server
  - variant_set_id (String.t): The ID of the variant to be updated (must already exist).
  - optional_params (KeywordList): [optional] Optional parameters
    - :$.xgafv (String.t): V1 error format.
    - :access_token (String.t): OAuth access token.
    - :alt (String.t): Data format for response.
    - :callback (String.t): JSONP
    - :fields (String.t): Selector specifying which fields to include in a partial response.
    - :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    - :oauth_token (String.t): OAuth 2.0 token for the current user.
    - :prettyPrint (boolean()): Returns response with indentations and line breaks.
    - :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    - :upload_protocol (String.t): Upload protocol for media (e.g. \&quot;raw\&quot;, \&quot;multipart\&quot;).
    - :uploadType (String.t): Legacy upload protocol for media (e.g. \&quot;media\&quot;, \&quot;multipart\&quot;).
    - :updateMask (String.t): An optional mask specifying which fields to update. Supported fields:  * metadata. * name. * description.  Leaving &#x60;updateMask&#x60; unset is equivalent to specifying all mutable fields.
    - :body (VariantSet): 

  ## Returns

  {:ok, %GoogleApi.Genomics.V1.Model.VariantSet{}} on success
  {:error, info} on failure
  """
  @spec genomics_variantsets_patch(Tesla.Env.client(), String.t(), keyword()) ::
          {:ok, GoogleApi.Genomics.V1.Model.VariantSet.t()} | {:error, Tesla.Env.t()}
  def genomics_variantsets_patch(connection, variant_set_id, optional_params \\ [], opts \\ []) do
    optional_params_config = %{
      :"$.xgafv" => :query,
      :access_token => :query,
      :alt => :query,
      :callback => :query,
      :fields => :query,
      :key => :query,
      :oauth_token => :query,
      :prettyPrint => :query,
      :quotaUser => :query,
      :upload_protocol => :query,
      :uploadType => :query,
      :updateMask => :query,
      :body => :body
    }

    request =
      Request.new()
      |> Request.method(:patch)
      |> Request.url("/v1/variantsets/{variantSetId}", %{
        "variantSetId" => URI.encode_www_form(variant_set_id)
      })
      |> Request.add_optional_params(optional_params_config, optional_params)

    connection
    |> Connection.execute(request)
    |> Response.decode(opts ++ [struct: %GoogleApi.Genomics.V1.Model.VariantSet{}])
  end

  @doc """
  Returns a list of all variant sets matching search criteria.  Implements [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).

  ## Parameters

  - connection (GoogleApi.Genomics.V1.Connection): Connection to server
  - optional_params (KeywordList): [optional] Optional parameters
    - :$.xgafv (String.t): V1 error format.
    - :access_token (String.t): OAuth access token.
    - :alt (String.t): Data format for response.
    - :callback (String.t): JSONP
    - :fields (String.t): Selector specifying which fields to include in a partial response.
    - :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    - :oauth_token (String.t): OAuth 2.0 token for the current user.
    - :prettyPrint (boolean()): Returns response with indentations and line breaks.
    - :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    - :upload_protocol (String.t): Upload protocol for media (e.g. \&quot;raw\&quot;, \&quot;multipart\&quot;).
    - :uploadType (String.t): Legacy upload protocol for media (e.g. \&quot;media\&quot;, \&quot;multipart\&quot;).
    - :body (SearchVariantSetsRequest): 

  ## Returns

  {:ok, %GoogleApi.Genomics.V1.Model.SearchVariantSetsResponse{}} on success
  {:error, info} on failure
  """
  @spec genomics_variantsets_search(Tesla.Env.client(), keyword()) ::
          {:ok, GoogleApi.Genomics.V1.Model.SearchVariantSetsResponse.t()}
          | {:error, Tesla.Env.t()}
  def genomics_variantsets_search(connection, optional_params \\ [], opts \\ []) do
    optional_params_config = %{
      :"$.xgafv" => :query,
      :access_token => :query,
      :alt => :query,
      :callback => :query,
      :fields => :query,
      :key => :query,
      :oauth_token => :query,
      :prettyPrint => :query,
      :quotaUser => :query,
      :upload_protocol => :query,
      :uploadType => :query,
      :body => :body
    }

    request =
      Request.new()
      |> Request.method(:post)
      |> Request.url("/v1/variantsets/search")
      |> Request.add_optional_params(optional_params_config, optional_params)

    connection
    |> Connection.execute(request)
    |> Response.decode(opts ++ [struct: %GoogleApi.Genomics.V1.Model.SearchVariantSetsResponse{}])
  end
end
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