Class: Rafflesia::Maps

Inherits:
Object
  • Object
show all
Defined in:
lib/rafflesia/maps.rb

Instance Method Summary collapse

Constructor Details

#initialize(client) ⇒ Maps

Returns a new instance of Maps.



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# File 'lib/rafflesia/maps.rb', line 9

def initialize(client)
  @client = client
end

Instance Method Details

#metadataIngest(allow_network: nil, database: nil, emdb_ids: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapMetadataIngestData

POST /v1/maps/metadata/ingest

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil) —

    Allow remote EMDB metadata download when an entry is not already cached.

  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • emdb_ids (Array<String>, nil) (defaults to: nil) —

    EMDB accessions to ingest metadata for, for example EMD-14322.

  • output_format (Rafflesia::Types::MapMetadataIngestRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 26

def metadataIngest(
  allow_network: nil,
  database: nil,
  emdb_ids: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'database' => database,
    'emdb_ids' => emdb_ids,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/metadata/ingest',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapMetadataIngestData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsCandidatesExport(archive_artifact_manifest_object_id: nil, archive_artifact_manifest_path: nil, dataset_name: nil, dataset_version: nil, output_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelCandidateExportData

POST /v1/maps/models/candidates/export

Parameters:

  • archive_artifact_manifest_object_id (String, nil) (defaults to: nil)
  • archive_artifact_manifest_path (String, nil) (defaults to: nil)
  • dataset_name (String, nil) (defaults to: nil)
  • dataset_version (String, nil) (defaults to: nil)
  • output_dir (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 71

def modelsCandidatesExport(
  archive_artifact_manifest_object_id: nil,
  archive_artifact_manifest_path: nil,
  dataset_name: nil,
  dataset_version: nil,
  output_dir: nil,
  request_options: {}
)
  body = {
    'archive_artifact_manifest_object_id' => archive_artifact_manifest_object_id,
    'archive_artifact_manifest_path' => archive_artifact_manifest_path,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'output_dir' => output_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/candidates/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelCandidateExportData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsEvidenceExport(allow_network: nil, database: nil, map_ids: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelEvidenceData

POST /v1/maps/models/evidence/export

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil) —

    Allow remote EMDB metadata download when a referenced map is not already cached.

  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • map_ids (Array<String>, nil) (defaults to: nil) —

    Restrict to associations for these map ids; empty means every recorded association.

  • output_format (Rafflesia::Types::MapModelEvidenceExportRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 111

def modelsEvidenceExport(
  allow_network: nil,
  database: nil,
  map_ids: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'database' => database,
    'map_ids' => map_ids,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/evidence/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelEvidenceData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsFitApply(candidate:, map_id:, structure_id:, max_voxel_bytes: nil, target_id: nil, threshold: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelFitCandidateApplyData

POST /v1/maps/models/fit/apply

Parameters:

  • candidate (Rafflesia::MapModelFitCandidate)
  • map_id (String)
  • max_voxel_bytes (Integer, nil) (defaults to: nil)
  • structure_id (String)
  • target_id (String, nil) (defaults to: nil)
  • threshold (Float, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 157

def modelsFitApply(
  candidate:,
  map_id:,
  structure_id:,
  max_voxel_bytes: nil,
  target_id: nil,
  threshold: nil,
  request_options: {}
)
  body = {
    'candidate' => candidate,
    'map_id' => map_id,
    'max_voxel_bytes' => max_voxel_bytes,
    'structure_id' => structure_id,
    'target_id' => target_id,
    'threshold' => threshold
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/fit/apply',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelFitCandidateApplyData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsFitCandidates(cyclic_copy_count:, map_id:, seed:, structure_id:, candidate_count: nil, max_voxel_bytes: nil, maximum_radius_angstrom: nil, minimum_radius_angstrom: nil, restart_count: nil, threshold: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelFitCandidateSearchData

POST /v1/maps/models/fit/candidates

Parameters:

  • candidate_count (Integer, nil) (defaults to: nil)
  • cyclic_copy_count (Integer)
  • map_id (String)
  • max_voxel_bytes (Integer, nil) (defaults to: nil)
  • maximum_radius_angstrom (Float, nil) (defaults to: nil)
  • minimum_radius_angstrom (Float, nil) (defaults to: nil)
  • restart_count (Integer, nil) (defaults to: nil)
  • seed (Integer)
  • structure_id (String)
  • threshold (Float, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 199

def modelsFitCandidates(
  cyclic_copy_count:,
  map_id:,
  seed:,
  structure_id:,
  candidate_count: nil,
  max_voxel_bytes: nil,
  maximum_radius_angstrom: nil,
  minimum_radius_angstrom: nil,
  restart_count: nil,
  threshold: nil,
  request_options: {}
)
  body = {
    'candidate_count' => candidate_count,
    'cyclic_copy_count' => cyclic_copy_count,
    'map_id' => map_id,
    'max_voxel_bytes' => max_voxel_bytes,
    'maximum_radius_angstrom' => maximum_radius_angstrom,
    'minimum_radius_angstrom' => minimum_radius_angstrom,
    'restart_count' => restart_count,
    'seed' => seed,
    'structure_id' => structure_id,
    'threshold' => threshold
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/fit/candidates',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelFitCandidateSearchData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsFitExport(candidate_dataset_manifest_path: nil, candidate_table_path: nil, dataset_name: nil, dataset_version: nil, max_pairs: nil, max_voxel_bytes: nil, output_dir: nil, threshold: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelFitBatchExportData

POST /v1/maps/models/fit/export

Parameters:

  • candidate_dataset_manifest_path (String, nil) (defaults to: nil)
  • candidate_table_path (String, nil) (defaults to: nil)
  • dataset_name (String, nil) (defaults to: nil)
  • dataset_version (String, nil) (defaults to: nil)
  • max_pairs (Integer, nil) (defaults to: nil)
  • max_voxel_bytes (Integer, nil) (defaults to: nil)
  • output_dir (String, nil) (defaults to: nil)
  • threshold (Float, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 247

def modelsFitExport(
  candidate_dataset_manifest_path: nil,
  candidate_table_path: nil,
  dataset_name: nil,
  dataset_version: nil,
  max_pairs: nil,
  max_voxel_bytes: nil,
  output_dir: nil,
  threshold: nil,
  request_options: {}
)
  body = {
    'candidate_dataset_manifest_path' => candidate_dataset_manifest_path,
    'candidate_table_path' => candidate_table_path,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'max_pairs' => max_pairs,
    'max_voxel_bytes' => max_voxel_bytes,
    'output_dir' => output_dir,
    'threshold' => threshold
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/fit/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelFitBatchExportData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsFitScore(map_id:, structure_id:, max_voxel_bytes: nil, threshold: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelFitScoreData

POST /v1/maps/models/fit/score

Parameters:

  • map_id (String)
  • max_voxel_bytes (Integer, nil) (defaults to: nil)
  • structure_id (String)
  • threshold (Float, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 287

def modelsFitScore(
  map_id:,
  structure_id:,
  max_voxel_bytes: nil,
  threshold: nil,
  request_options: {}
)
  body = {
    'map_id' => map_id,
    'max_voxel_bytes' => max_voxel_bytes,
    'structure_id' => structure_id,
    'threshold' => threshold
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/fit/score',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelFitScoreData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsLinksCreate(map_id:, structure_id:, metadata: nil, method_: nil, model_id: nil, source: nil, source_url: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelAssociationData

POST /v1/maps/models/links/create

Parameters:

  • map_id (String)
  • metadata (Hash{String => String}, nil) (defaults to: nil)
  • method (String, nil)
  • model_id (String, nil) (defaults to: nil)
  • source (String, nil) (defaults to: nil)
  • source_url (String, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 322

def modelsLinksCreate(
  map_id:,
  structure_id:,
  metadata: nil,
  method_: nil,
  model_id: nil,
  source: nil,
  source_url: nil,
  request_options: {}
)
  body = {
    'map_id' => map_id,
    'metadata' => metadata,
    'method' => method_,
    'model_id' => model_id,
    'source' => source,
    'source_url' => source_url,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/links/create',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelAssociationData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#modelsList(database: nil, map_id: nil, model_id: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, structure_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMapModelAssociationsData

POST /v1/maps/models/list

Parameters:

  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • map_id (String, nil) (defaults to: nil)
  • model_id (String, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::MapModelListRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • structure_id (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 367

def modelsList(
  database: nil,
  map_id: nil,
  model_id: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  structure_id: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'map_id' => map_id,
    'model_id' => model_id,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/models/list',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMapModelAssociationsData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#recordsFetch(emdb_id:, allow_network: nil, include_volume: nil, max_download_bytes: nil, volume_source_url: nil, request_options: {}) ⇒ Rafflesia::EnvelopeCryoEmMapData

POST /v1/maps/records/fetch

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil)
  • emdb_id (String)
  • include_volume (Boolean, nil) (defaults to: nil) —

    When true, download and store the EMDB voxel map object instead of metadata JSON.

  • max_download_bytes (Integer, nil) (defaults to: nil) —

    Maximum EMDB volume download size in bytes; defaults to 500 MiB.

  • volume_source_url (String, nil) (defaults to: nil) —

    Optional explicit EMDB map volume URL; defaults to the canonical EMDB FTP map path.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 414

def recordsFetch(
  emdb_id:,
  allow_network: nil,
  include_volume: nil,
  max_download_bytes: nil,
  volume_source_url: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'emdb_id' => emdb_id,
    'include_volume' => include_volume,
    'max_download_bytes' => max_download_bytes,
    'volume_source_url' => volume_source_url
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/records/fetch',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeCryoEmMapData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#recordsImport(path:, emdb_id: nil, map_id: nil, source: nil, request_options: {}) ⇒ Rafflesia::EnvelopeCryoEmMapData

POST /v1/maps/records/import

Parameters:

  • emdb_id (String, nil) (defaults to: nil)
  • map_id (String, nil) (defaults to: nil)
  • path (String)
  • source (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 448

def recordsImport(
  path:,
  emdb_id: nil,
  map_id: nil,
  source: nil,
  request_options: {}
)
  body = {
    'emdb_id' => emdb_id,
    'map_id' => map_id,
    'path' => path,
    'source' => source
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/maps/records/import',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeCryoEmMapData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#recordsMetadata(map_id:, request_options: {}) ⇒ Rafflesia::EnvelopeCryoEmMapData

POST /v1/maps/records/metadata

Parameters:

  • map_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/maps.rb', line 477

def recordsMetadata(
  map_id:,
  request_options: {}
)
  body = {
    'map_id' => map_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/maps/records/metadata',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeCryoEmMapData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end